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)
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 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 3.1.21.4). 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 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 3.1.21.4.
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 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 3.1.21.4). 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.
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)
The final phase of cell nucleus division following ANAPHASE, in which two daughter nuclei are formed, the CYTOPLASM completes division, and the CHROMOSOMES lose their distinctness and are transformed into CHROMATIN threads.
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.
A type of chromosomal aberration involving DNA BREAKS. Chromosome breakage can result in CHROMOSOMAL TRANSLOCATION; CHROMOSOME INVERSION; or SEQUENCE DELETION.
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.
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.
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.
A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.
A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.
The common chimpanzee, a species of the genus Pan, family HOMINIDAE. It lives in Africa, primarily in the tropical rainforests. There are a number of recognized subspecies.
A genetic process by which the adult organism is realized via mechanisms that lead to the restriction in the possible fates of cells, eventually leading to their differentiated state. Mechanisms involved cause heritable changes to cells without changes to DNA sequence such as DNA METHYLATION; HISTONE modification; DNA REPLICATION TIMING; NUCLEOSOME positioning; and heterochromatization which result in selective gene expression or repression.
A species of fruit fly much used in genetics because of the large size of its chromosomes.
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Partial cDNA (DNA, COMPLEMENTARY) sequences that are unique to the cDNAs from which they were derived.
The chromosomal constitution of a cell containing multiples of the normal number of CHROMOSOMES; includes triploidy (symbol: 3N), tetraploidy (symbol: 4N), etc.
The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.

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 ...
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
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 abc.com 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 - http://www.scopus.com/inward/record.url?scp=0029013276&partnerID=8YFLogxK. UR - http://www.scopus.com/inward/citedby.url?scp=0029013276&partnerID=8YFLogxK. 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 ...
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.
... 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 Ouyang, Shu; Buell C ...
Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research, 12, 4127-4138. Tautz, D. ( ... 1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17, 6463- ... Tribolium Sequencing Consortium (2008). The genome of the model beetle and pest Tribolium castaneum Nature 452, 949-955. ... His thesis dealt with the first generic description of simple sequences (now often called microsatellites). This work became ...
"Nucleic Acids Research. 13 (12): 4401-4410. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535.. ... De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and ... "Nucleic Acids Res. 36 (7): 2284-94. doi:10.1093/nar/gkn064. PMC 2367713. PMID 18287116.. ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ...
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 ...
... 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 ...
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 ...
... 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, ...
... 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 ...
Repeated sequences (also known as repetitive elements, repeating units or repeats) are patterns of nucleic acids (DNA or RNA) ... "The 3D folding of metazoan genomes correlates with the association of similar repetitive elements". Nucleic Acids Research. 44 ... with over two-thirds of the sequence consisting of repetitive elements in humans. Repetitive elements found in genomes fall ... The disposition of repetitive elements consists either in arrays of tandemly repeated sequences, or in repeats dispersed ...
"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 ...
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.. ... 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 ...
Nucleic Acids Research. 46 (11): 5504-5524. doi:10.1093/nar/gky263. ISSN 0305-1048. PMC 6009586. PMID 29912433. v t e. ... "Demethylation of repetitive DNA sequences in neuroblastoma". Genes, Chromosomes and Cancer. 17 (4): 234-244. doi:10.1002/(SICI) ...
... enzymatic methylation of nucleic acid binding proteins". Amino Acids. 15 (4): 291-306. doi:10.1007/BF01320895. PMID 9891755. ... Epplen C, Epplen JT (1994). "Expression of (cac)n/(gtg)n simple repetitive sequences in mRNA of human lymphocytes". Hum. Genet ... The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has two repeats of quasi-RRM ... HnRNPA1 also bound to terminal leader sequences and intergenic sequences that are crucial for efficient viral replication. ...
Strand DJ, McDonald JF (June 1985). "Copia is transcriptionally responsive to environmental stress". Nucleic Acids Research. 13 ... "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 ... Insertional mutagenesis uses the features of a TE to insert a sequence. In most cases this is used to remove a DNA sequence or ...
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot ... The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive ... Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16: 1-11. doi:10.1111/j.1432-1033.1970.tb01046.x.. ... Low-complexity regions are regions in the sequence with only a few amino acids, which in turn, causes redundancy within that ...
"Identification of a conserved sequence in the non-coding regions of many human genes". Nucleic Acids Research. 17 (2): 699-722 ... Jurka, Jerzy; Walichiewicz, Jolanta; Milosavljevic, Aleksandar (October 1992). "Prototypic sequences for human repetitive DNA ... Nucleic Acids Research. 23 (1): 98-102. doi:10.1093/nar/23.1.98. PMC 306635. PMID 7870595. Lander; et al. (2001). "Initial ... The MIR consensus sequence is 260 basepairs long and has an A/T-rich 3' end. Like other Short interspersed nuclear elements ( ...
Nucleic Acids Research. 8 (24): 6113-28. doi:10.1093/nar/8.24.6113. PMC 328076. PMID 6258162. Kapitonov VV, Tempel S, Jurka J ( ... The first description of an approximately 6.4 kb long LINE-derived sequence was published by J. Adams et al. in 1980. Based on ... Kapitonov VV, Pavlicek A, Jurka J (2006-01-01). Anthology of Human Repetitive DNA. Wiley-VCH Verlag GmbH & Co. KGaA. doi: ... Nucleic Acids Research. 42 (1): 396-416. doi:10.1093/nar/gkt898. PMC 3874205. PMID 24101588. Kazazian HH, Wong C, Youssoufian H ...
The effect of homogenizing DNA sequences is the same. Repetitive sequences play the role of uncoupling the gene conversion ... Nucleic Acids Res. 12 (3): 1641-55. doi:10.1093/nar/12.3.1641. PMC 318605. PMID 6322113. Hess JF, Fox M, Schmid C, Shen CK ( ... Interspersed+Repetitive+Sequences at the US National Library of Medicine Medical Subject Headings (MeSH). ... Some types of interspersed repetitive DNA elements allow new genes to evolve by uncoupling similar DNA sequences from gene ...
Nucleic Acids Research. 20 (5): 1083-5. doi:10.1093/nar/20.5.1083. PMC 312094. PMID 1549470. Bauman, Robert. Microbiology with ... Highly repetitive in nature, human DNA is well known for its extreme instability in multicopy vector systems. It has been found ... Fosmid clones were used to help assess the accuracy of the Public Human Genome Sequence. The fertility plasmid or F-plasmid was ... The first step in sequencing entire genomes is cloning the genome into manageable units of some 50-200 kilobases in length. It ...
One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot ... Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. ... a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16 (1): 1-11. doi:10.1111 ... Low-complexity regions are regions in the sequence with only a few amino acids, which in turn, causes redundancy within that ...
"Escherichia coli DNA topoisomerase I catalyzed linking of single-stranded rings of complementary base sequences". Nucleic Acids ... Dimri GP, Rudd KE, Morgan MK, Bayat H, Ames GF (July 1992). "Physical mapping of repetitive extragenic palindromic sequences in ... March 2011). "Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli". Nucleic Acids ... Besides preferential binding to a specific DNA sequence, IHF also binds to DNA in a non-sequence specific manner with the ...
Nucleic acids[edit]. The convention for a nucleic acid sequence is to list the nucleotides as they occur from the 5' end to the ... All polymers are made of repetitive units called monomers. Biopolymers often have a well-defined structure, though this is not ... Nucleic acid sequence can be determined using gel electrophoresis and capillary electrophoresis. Lastly, mechanical properties ... There are a number of biophysical techniques for determining sequence information. Protein sequence can be determined by Edman ...
Probes for northern blotting are composed of nucleic acids with a complementary sequence to all or part of the RNA of interest ... Gortner, G.; Pfenninger, M.; Kahl, G.; Weising, K. (1996). "Northern blot analysis of simple repetitive sequence transcription ... In this procedure, the substrate nucleic acid (that is affixed to the membrane) is a collection of isolated DNA fragments, and ... Nucleic Acids Research. 21 (14): 3337-3338. doi:10.1093/nar/21.14.3337. PMC 309787. PMID 8341618. Streit, S.; Michalski, C. W ...
KSHV has a genome which is approximately 165,000 nucleic acid bases in length. KSHV is a rhadinovirus, and is remarkable since ... Starting from these fragments, this research team was then able to sequence the entire genome of the virus less than two years ... C content and is oriented in a repetitive head-to-tail fashion. During latency, the virus genome depends on the host ... KSHV is a herpesvirus, and is a large double-stranded DNA virus with a protein covering that packages its nucleic acids, called ...
The piwi domain is a protein domain found in piwi proteins and a large number of related nucleic acid-binding proteins, ... In addition, Piwi associates with heterochromatin protein 1, an epigenetic modifier, and piRNA-complementary sequences. These ... genomic organization that may originate from repetitive regions of the genome such as retrotransposons or regions normally ... Argonautes, the most well-studied family of nucleic-acid binding proteins, are RNase H-like enzymes that carry out the ...
DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov 25;21(23):5408-17.y Brosius J. Plasmid ... He observed analogous trends in the field of repetitive or transposed genomic elements (TEs) including retroposed elements. ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ... Protein sequence analysis: automated microsequencing. Science. 1983 Feb 11;219(4585):650-9. Brosius J, Dull TJ, Sleeter DD, ...
... non-coding terminal DNA sequences known as telomeres on the ends of chromosomes. These repetitive, non-coding sequences are ... Heumann, John M. (November 1976). "A model for replication of the ends of linear chromosomes". Nucleic Acids Research. 3 (11): ... In order to mitigate the negative effects of this gradual loss of genetic material, eukaryotes have evolved repetitive, ...
... technique that uses fluorescent probes that bind to only those 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 ... RNA probes can be designed for any gene or any sequence within a gene for visualization of mRNA,[3][4][5] lncRNA[6][7][8] and ... The size of the human genome is so large, compared to the length that could be sequenced directly, that it was necessary to ...
Nucleic Acids Research. 40 (20): e159. doi:10.1093/nar/gks709. PMC 3488212. PMID 22844100.. CS1 maint: Multiple names: authors ... It (re)uses data from one or more earlier or later frames in a sequence to describe the current frame. Intra-frame coding, on ... Grammar-based codes like this can compress highly repetitive input extremely effectively, for instance, a biological data ... Individual frames of a video sequence are compared from one frame to the next, and the video compression codec sends only the ...
Deppenmeier, U. (2002). "The unique biochemistry of methanogenesis". Prog Nucleic Acid Res Mol Biol. Progress in Nucleic Acid ... Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the ... "Nucleic Acids Res. 27 (23): 4658-70. doi:10.1093/nar/27.23.4658. PMC 148756 . PMID 10556324.. ... In 1977, Carl Woese, a microbiologist studying the genetic sequencing of organisms, developed a new sequencing method that ...
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. ...
"Scalable Nucleic Acid Quality Assessments for Illumina Next-Generation Sequencing Library Prep" (PDF). Retrieved 2017-12-27.. ... Other challenges have to deal with repetitive sequences that often prevent complete genome assemblies because they occur in ... Shotgun sequencing[edit]. Main article: Shotgun sequencing. Shotgun sequencing is a sequencing method designed for analysis of ... RNA sequencing was one of the earliest forms of nucleotide sequencing. The major landmark of RNA sequencing is the sequence of ...
"siVirus: web-based antiviral siRNA design software for highly divergent viral sequences". Nucleic Acids Research. 34 (Web ... Such problems occur more frequently when the dsRNA contains repetitive sequences. It has been estimated from studying the ... "Nucleic Acids Research. 33 (Web Server issue): W589-91. doi:10.1093/nar/gki419. PMC 1160180. PMID 15980542.. ... "Nucleic Acids Research. 32 (Web Server issue): W113-20. doi:10.1093/nar/gkh408. PMC 441546. PMID 15215362.. ...
"SAGA: sequence alignment by genetic algorithm". Nucleic Acids Res. 24 (8): 1515-24. doi:10.1093/nar/24.8.1515. PMC 145823 ... Therefore it make sense to construct an algorithm to assist in repetitive calculations of multiple sequence alignments. ... sequences of S. {\displaystyle S}. until the modified sequences, S. i. ′. {\displaystyle S_{i}^{'}}. , all conform to length L ... A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or ...
The ability to quickly mediate global changes is also apparent in the rapid expression of non-coding repetitive sequences. The ... 2015). "LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs". Nucleic Acids ... Large-scale sequencing of cDNA libraries and more recently transcriptomic sequencing by next generation sequencing indicate ... The annealing of complementary sequences, such as antisense or repetitive regions between transcripts, forms an RNA duplex that ...
"Nucleic Acids Research. 13 (12): 4401-10. doi:10.1093/nar/13.12.4401. PMC 321795. PMID 2409535.. ... De novo repeat identification is an initial scan of sequence data that seeks to find the repetitive regions of the genome, and ... "Nucleic Acids Research. 36 (7): 2284-94. doi:10.1093/nar/gkn064. PMC 2367713. PMID 18287116.. ... A consensus sequence is a sequence that is created based on the repeats that comprise a TE family. A base pair in a consensus ...
Britten, RJ; Davidson, EH (1971 Jun). "Repetitive and non-repetitive DNA sequences and a speculation on the origins of ... Nucleic Acids Research 35 (Database): D332-D338. doi:10.1093/nar/gkl828.. *↑ Glass JI, Assad-Garcia N, Alperovich N, Yooseph S ... The C. elegans Sequencing Consortium (1998). "Genome sequence of the nematode C. elegans: a platform for investigating biology" ... "Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans". Journal of Molecular ...
"Nucleic Acids Research. 41 (7): 4336-43. doi:10.1093/nar/gkt135. PMC 3627607. PMID 23460208.. ... The PAM sequence appears to be important during spacer insertion in type I-E systems. That sequence contains a strongly ... Analysis of CRISPRs in metagenomic data is more challenging, as CRISPR loci do not typically assemble, due to their repetitive ... "Nucleic Acids Research. 41 (20): e188. doi:10.1093/nar/gkt780. PMC 3814374. PMID 23999092.. ...
During translation, ribosomes convert a sequence of mRNA (messenger RNA) to an amino acid sequence. Each 3-base-pair-long ... "Chemistry for Biologists: Nucleic acids". www.rsc.org. Retrieved 2019-02-20.. ... the ribosome enters the elongation period which follows a repetitive cycle. First a tRNA with the correct amino acid enters the ... Amino Acid SynthesisEdit. Pathways that form each amino acid[4]. Amino Acid R-group‡ Pathway* ...
Nucleic acid sequence - succession of nucleotides in a nucleic acid. *Pangenesis - former theory that inheritance was based on ... of human DNA consisting of non-coding repetitive sequences.[90] The reasons for the presence of so much noncoding DNA in ... In addition to RNA and DNA, many artificial nucleic acid analogues have been created to study the properties of nucleic acids, ... At the time, "yeast nucleic acid" (RNA) was thought to occur only in plants, while "thymus nucleic acid" (DNA) only in animals ...
"Nucleic Acids Research. 9 (12): 2871-2888. doi:10.1093/nar/9.12.2871. ISSN 0305-1048. PMC 326899 . PMID 6269062.. ... Assembly of complex genomes is additionally complicated by the great abundance of repetitive sequences, meaning similar short ... Whole genome shotgun sequencing[edit]. History[edit]. The first genome sequenced by shotgun sequencing was that of cauliflower ... Next-generation sequencing[edit]. The classical shotgun sequencing was based on the Sanger sequencing method: this was the most ...
Several introns contain Alu repetitive sequences. A TATA-like sequence (TTATAAAA) and a CAAT-like sequence (GTCATCAT) are ... "Nucleic Acids Res. 15 (7): 3179. doi:10.1093/nar/15.7.3179. PMC 340920. PMID 3562250.. ... Except for the signal NH2-terminal peptide, which is absent in the mature enzyme, the amino acid sequence deduced from the ... In native Japanese, this variant ALDH2 gene encodes lysine instead of glutamic acid at amino acid 487 and therefore encodes a ...
... and/or-cloning nucleic acid sequences" U.S. Patent 4,683,195 *^ a b "Kary B. Mullis - Nobel Lecture: The Polymerase Chain ... The human genome has many repetitive regions that can be found within gene sequences or in non-coding regions of the genome. ... "Nucleic Acids Res. 18 (21): 6409-6412. doi:10.1093/nar/18.21.6409. PMC 332522. PMID 2243783.. ... "Nucleic Acids Research. 17 (7): 2503-2516. doi:10.1093/nar/17.7.2503. PMC 317639. PMID 2785681.. ...
The type of nucleic acid is irrelevant to the shape of the genome. Among RNA viruses and certain DNA viruses, the genome is ... Defences against these viruses involve RNA interference from repetitive DNA sequences within archaean genomes that are related ... A viral genome, irrespective of nucleic acid type, is almost always either single-stranded or double-stranded. Single-stranded ... Proteins associated with nucleic acid are known as nucleoproteins, and the association of viral capsid proteins with viral ...
Both label the sequence with one-letter amino-acid code (see amino acid) at each Cα position, using different colors or symbols ... nucleic acids, and drug molecules - many of which featuring α-helices, such as subtilisin, human growth hormone, and ... with the rest being non-repetitive regions, or "loops" that connect the helices. In classifying proteins by their dominant fold ... Amino-acid propensitiesEdit. Different amino-acid sequences have different propensities for forming α-helical structure. ...
Nucleic Acids Research 33(3):1069-1076. 7. Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV (2003). PlantProm ... 8. Shahmuradov IA, Solovyev VV (2003) PromH: promoters identification using orthologous genomic sequences. Nucl. Acids. Res., ... Shakhmuradov IA, Kolchanov NA, Solovyev VV, Ratner VA (1986) Enhancer-like structures in middle repetitive DNA elements of ... a database of plant promoter sequences. Nucl. Acids. Res. 31: 114-117 ...
"Nucleic Acids Res. 31 (5): 1576-1583. doi:10.1093/nar/gkg208. PMC 149817. PMID 12595567.. ... On the ends of each chromosome are repetitive sequences of DNA, telomeres, that protect the chromosome from joining with other ...
Stable nucleic acid lipid particle (SNALP). Stable for systemic delivery, broad cell-tye delivery ... small RNA related controls involved in gene expression and the protection of the genome against mobile repetitive DNA sequences ... nucleic acids that induce RNAi) either via expression in viruses or synthesis of oligonucleotides.[51] Optimistically many ... As of 2014, the miRBase web site,[34] an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic ...
"Sequence logos: a new way to display consensus sequences". Nucleic Acids Res. 18 (20): 6097-6100. doi:10.1093/nar/18.20.6097 ... Repetitive sequences in the database or query can also distort both the search results and the assessment of statistical ... A sequence alignment, produced by ClustalO, of mammalian histone proteins. Sequences are the amino acids for residues 120-180 ... Sequenced RNA, such as expressed sequence tags and full-length mRNAs, can be aligned to a sequenced genome to find where there ...
Nucleic Acids Research, 45(10): e86".. *^ Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K (2017). „Universal Patterns ... Chistul reproductiv si ciclurile de viață repetitive în cancer[modificare , modificare sursă]. Sub titlul "Polyploid giant ... 2001). „Initial sequencing and analysis of the human genome. Nature 409 (6822): 860-921. doi:10.1038/35057062".. Mentenanță CS1 ... 2010). „The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465 (7297): 473-7. doi: ...
Nucleic Acids Res 40(4): e27. Tembe, W., J. Lowey, and E. Suh. 2010. G-SQZ: Compact encoding of genomic sequence and quality ... this approach has been criticized to be extravagant because genomic sequences often contain repetitive content (e.g., ... Choosing a consensus reference sequence over a more specific reference sequence (e.g., the revised Cambridge Reference Sequence ... microsatellite sequences) or many sequences exhibit high levels of similarity (e.g., multiple genome sequences from the same ...
Vassetzky NS, Kramerov DA (January 2013). "SINEBase: a database and tool for SINE analysis". Nucleic Acids Research. 41 ( ... For example, the 5' of the Alu sine is derived from 7SL RNA, a sequence transcribed by RNA Polymerase III which codes for the ... Jurka J (December 2004). "Evolutionary impact of human Alu repetitive elements". Current Opinion in Genetics & Development. 14 ... These dog-specific SINEs may code for a splice acceptor site, altering the sequences that appear as exons or introns in each ...
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 ...
The present invention provides methods and probe nucleic acids for detecting mutant forms of target nucleic acids that comprise ... repetitive nucleotide sequences. In certain embodiments, for example, these approaches and reagents can be used to detect ... The probe nucleic acids, target nucleic acids, and/or amplicons of the target nucleic acids (e.g., via primer nucleic acids ... nucleic acid when the probe nucleic acid is bound to the target nucleic acid and/or to the amplicon of the target nucleic acid ...
Associations of Repetitive Sequences, Nucleic Acid with chemical compounds. *Gene context of Repetitive Sequences, Nucleic Acid ... Biological context of Repetitive Sequences, Nucleic Acid. *The distribution of the middle repetitive sequences in the genome ... High impact information on Repetitive Sequences, Nucleic Acid. *Chemical compound and disease context of Repetitive Sequences, ... diagnostic and therapeutic context of Repetitive Sequences, Nucleic Acid. *The structure and evolution of a repetitive sequence ...
"Repetitive Sequences, Nucleic Acid" by people in this website by year, and whether "Repetitive Sequences, Nucleic Acid" was a ... Repetitive Sequences, Nucleic Acid*Repetitive Sequences, Nucleic Acid. *Nucleic Acid Repetitive Sequences ... "Repetitive Sequences, Nucleic Acid" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ... Below are the most recent publications written about "Repetitive Sequences, Nucleic Acid" by people in Profiles. ...
Nucleic Acids Res. 54087.Google Scholar. *. Manuelidis, L. (1976). Repeating restriction fragments of human DNA. Nucleic Acids ... Repetitive DNA sequences in methotrexate- and methasquin-sensitive and -resistant Chinese hamster cell lines. ... Manuelidis, L. (1978a). Complex and simple sequences in human repeated DNAs. Chromosoma (Berlin) 661.Google Scholar ... methotrexate resistance restriction endonuclease analysis repetitive DNA HSRs This work was supported in part by grants to the ...
Repetitive Sequences, Nucleic Acid / genetics* * Retroelements / genetics * Retroviridae / genetics * Sequence Analysis, DNA ... Background: Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and ... Defragmented output includes a map of repeats present in the query sequence, with the options to report masked query sequence(s ... Censor is a tool to rapidly identify repetitive elements by comparison to known repeats. It uses WU-BLAST for speed and ...
Nucleic Acids Res. 23: 1087-1088.. OpenUrlFREE Full Text. *↵. Spertini, D., C. Beliveau and G. Bellemare, 1999 Screening of ... subterminal sequences contain repeats of different sequences (Liu et al. 2001). Mutagenesis of these repetitive sequences, ... These studies led to identification of the minimal cis-sequence of Tol2 and the functional repetitive sequence in the ... Functional Dissection of the Tol2 Transposable Element Identified the Minimal cis-Sequence and a Highly Repetitive Sequence in ...
Repetitive Sequences, Nucleic Acid* Substances * DNA, Fungal * Nucleic Acid Heteroduplexes * Polydeoxyribonucleotides * ... Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair Nature. 1993 Sep 16;365( ...
The sequences flanking the Mov15 provirus were molecularly cloned and shown to consist of a tandemly repeated sequence of 31 ... Nucleic Acid Hybridization. Polymorphism, Genetic. Polymorphism, Restriction Fragment Length. Repetitive Sequences, Nucleic ... The repetitive sequence was also found at the subtelomeric region of three autosomes. A similar level of amplification as the ... 2575587 - Isolation of a novel mildly repetitive dna sequence that is predominantly located at th.... 15660977 - Resistance to ...
... cloning and sequencing. PGRS was present in at least 26... ... The polymorphic GC-rich repetitive sequence (PGRS) found on the ... Staden R (1987) Computer handling of sequence projects. In: Bishop MJ, Rawling CJ (eds) Nucleic acid and protein sequence ... Repetitive sequences Triplet repeats Strain typing Epidemiology Tuberculosis This is a preview of subscription content, log in ... The polymorphic GC-rich repetitive sequence (PGRS) found on the chromosome of Mycobacterium tuberculosis was characterized by ...
Repetitive DNA sequences in Mycoplasma pneumoniae.Nucleic Acids Res.16198883378350. ... A repetitive element sequence-based PCR (rep-PCR) has been described for the molecular genotyping of S. aureus (2). This high- ... Repetitive sequence-based (Rep)-PCR genotyping as described here is based on the presence of homologues of Mycoplasma ... Molecular Genotyping of Staphylococcus aureus Strains: Comparison of Repetitive Element Sequence-Based PCR with Various Typing ...
These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (te ... Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem ... Repetitive Sequences, Nucleic Acid*. Sex Chromosomes / genetics. From MEDLINE®/PubMed®, a database of the U.S. National Library ... These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres ...
Repetitive Sequences, Nucleic Acid*. RNA Polymerase II. Unique Identifier: 86302779. Chemical Identifiers (Names). EC 2.7.2.3 ( ... SEQUENCE CONSTRUCTION BUT ALSO HUMAN ENDEAVOR IN MUSICAL COMPOSITION.. Ohno S; Ohno M. Immunogenetics 24: 71-8 (1986). Abstract ... DNA sequences last week (As a comment about the relationship of music. to Alchemy), I did a little research and got the ... sequences can be transformed into musical scores using one set rule.. Conversely, musical scores can be transcribed to coding ...
Nucleic Acids Res, 34(20):5932-42, Jan 2006. *Repetitive elements *Reneker J, Shyu CR. (2005) Refined repetitive sequence ... Nucleic Acids Res, 33(Web Server issue):W535-9. *Hollenberg LC. (2000) Fast quantum search algorithms in protein sequence ... 2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. ... Rognes T. (2001) ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches. Nucleic Acids Res ...
This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome ... chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the ... Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and ... Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-3500 (2003). ...
Understanding and Editing of Genomic Repetitive Sequences within Nucleic Acid Strings Steve Chappell Mitchell, Technology & ... We have carried out an automated compilation of genetic patent data of both nucleic acid and amino acid sequence data from five ... We have carried out an automated compilation of genetic patent data of both nucleic acid and amino acid sequence data from five ... Understanding and Editing of Genomic Repetitive Sequences within Nucleic Acid Strings. Abstract ...
... 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 Ouyang, Shu; Buell C ...
Repetitive Sequences, Nucleic Acid. *Support, Non-U.S. Govt. Substances:. *DNA, Plant ... The clones containing 5S rDNA genes, 18S-25S rDNA sequences and the 180 bp paracentromeric repeated element account for 3.6%, ... Clones carrying chloroplast DNA and various nuclear repeated sequences have been identified. Twenty-one per cent of the clones ... The survey of the library for clones containing unlinked DNA sequences indicates that the proportion of chimeric clones is ...
Repetitive Sequences, Nucleic Acid. 1. 2007. 2007. December 2006. Chromosomal Proteins, Non-Histone. 6. 2007. 2012. August 2010 ... Repetitive Sequences, Nucleic Acid. Chromosomal Proteins, Non-Histone. Centromere. Nucleosomes. DNA-Binding Proteins. Cell ...
Repetitive Sequences, Nucleic Acid. *Retrotransposons*. *Sequence Homology, Amino Acid. *Support, Non-U.S. Govt ... The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences ... A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse ... these sequences over most of their evolutionary history. One sequence, Ta17, is located in the mitochondrial genome. The ...
The results provided a comprehensive view on the SSR sequence distribution and evolution for comparison among morphtypes B. ... The results provided a comprehensive view on the SSR sequence distribution and evolution for comparison among morphtypes B. ... Although thesis sequences have sparked great interest as a means of studying genetic variation, linkage mapping and evolution, ... Although thesis sequences have sparked great interest as a means of studying genetic variation, linkage mapping and evolution, ...
... targeting nucleic acids and compositions thereof. Nucleic acid sequences encoding the... US-9,745,561. Genetic test and genetic ... Methods of using engineered nucleic-acid targeting nucleic acids. The present disclosure provides engineered cross-type-nucleic ... The invention relates to the nucleotide and amino acid sequences, and to the activity and use, of the luciferases LuAL, Lu164, ... The present provides selection markers, methods, nucleic acids, and vectors of use in the preparation of recombinant ...
Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids ... Genome sequencing data has been deposited at the NCBI SRA (BioProject accession no. PRJNA613498) and 16S rRNA gene sequences at ... 4 was 2.11 μM and the Ki values were 62.5 μM and ,200 μM for 1-amino-2-naphthol and sulfanilic acid, respectively (Fig. 5D). ... S5) for sequencing: Firmicutes (one Clostridium ramosum and one Ruminococcus lactaris) and Bacteroidetes (two Bacteroides ...
Nucleosides Nucleotides Nucleic Acids. 2019 Oct 24:1-9. doi: 10.1080/15257770.2019.1669170. [Epub ahead of print] ... Cooperative recognition of a repetitive sequence through consecutive formation of triplex and duplex structures. ... Nucleosides Nucleotides Nucleic Acids. 2019 Oct 22:1-12. doi: 10.1080/15257770.2019.1679833. [Epub ahead of print] ... Effects of micro wet milling on bioaccessibility of phosphatidic acid and lysophosphatidic acid in komatsuna during in vitro ...
Whole-cell repetitive element sequence-based polymerase chain reaction allows rapid assessment of clonal relationships of ... Nucleic Acids Res. 1991 Dec 25;19(24):6823-31.. PMID:. 1762913. Free PMC Article ... Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. ... Analysis of relationships among isolates of Citrobacter diversus by using DNA fingerprints generated by repetitive sequence- ...
Tautz, D, Renz, M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127 ... Nucleic Acids Res 19:4008 Dornburg, V, van Vuuren, D, van de Ven, G, Langeveld, H, Meeusen, M, Banse, M, van Oorschot, M, Ros, ... Powell, W, Machray, GC, Provan, J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215-222 ...
Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the ... matrices using non-nucleotide probes which sequence specifically hybridize to one or more target sequences of the nucleic acid ... either before or after the nucleic acid is bound to the matrix, in order to ... identification and/or quantitation of nucleic acids which are electrostatically immobilized to ...
Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Research, 12, 4127-4138. Tautz, D. ( ... 1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17, 6463- ... Tribolium Sequencing Consortium (2008). The genome of the model beetle and pest Tribolium castaneum Nature 452, 949-955. ... His thesis dealt with the first generic description of simple sequences (now often called microsatellites). This work became ...
Nucleic Acids Research 22(7): 1315-1315.. *HOELZEL, AR, LOPEZ, JV, DOVER, GA & OBRIEN, SJ (1994). RAPID EVOLUTION OF A ... HETEROPLASMIC REPETITIVE SEQUENCE IN THE MITOCHONDRIAL-DNA CONTROL REGION OF CARNIVORES. Journal Of Molecular Evolution 39(2): ... Hoelzel, A.R., Hancock, J.M. & Dover, G.A. (1993). Generation of VNTRs and heteroplasmy by sequence turnover in the ... inferred from mitochondrial DNA sequences. Molecular Phylogenetics And Evolution 27(3): 398-409. ...
Base Sequence [G02.111.570.080]. *Repetitive Sequences, Nucleic Acid [G02.111.570.080.708]. *Tandem Repeat Sequences [G02.111. ... Sequence-Level Analysis of the Major European Huntington Disease Haplotype. Am J Hum Genet. 2015 Sep 03; 97(3):435-44. ... An increased number of contiguous trinucleotide repeats in the DNA sequence from one generation to the next. The presence of ... Base Sequence [G05.360.080]. *Repetitive Sequences, Nucleic Acid [G05.360.080.708]. *Tandem Repeat Sequences [G05.360.080.708. ...
Categories: Repetitive Sequences, Nucleic Acid Image Types: Photo, Illustrations, Video, Color, Black&White, PublicDomain, ...
  • Repetitive nucleotide sequences, such as direct or inverted repeats, are observed in many organisms. (google.com)
  • We demonstrated that Tol2 vectors with 200 bp from the left end and 150 bp from the right end were capable of transposition without reducing the transpositional efficiency and found that these sequences, including the terminal inverted repeats (TIRs) and the subterminal regions, are sufficient and required for transposition. (genetics.org)
  • Eukaryotic genomes contain a large proportion of repetitive DNA sequences, mostly transposable elements (TEs) and tandem repeats. (biomedsearch.com)
  • Simple sequences are ubiquitous repetitive components of eukaryotic genomes. (wikipedia.org)
  • Repetitive elements in genomes of parasitic protozoa. (semanticscholar.org)
  • Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. (semanticscholar.org)
  • Short-sequence DNA repeats in prokaryotic genomes. (semanticscholar.org)
  • Based on the sequenced genomes and gene annotations of 31 plant and algal species in Phytozome version 8.0 ( http://www.phytozome.net/ ), we examined TRs in a genome-wide scale, characterized their distributions and motif features, and explored their putative biological functions. (g3journal.org)
  • Seqping provides researchers a seamless pipeline to train species-specific HMMs and predict genes in newly sequenced or less-studied genomes. (biomedcentral.com)
  • These advances enabled the research community to sequence many plant genomes and transcriptomes. (biomedcentral.com)
  • After the assembly process, the next critical step is annotation of these newly sequenced genomes. (biomedcentral.com)
  • In British patent application no. 8525252 (publication no. 2166445) there are described various DNA sequences which may be used as probes to hybridize individually at a number of polymorphic sites within the human and animal genomes enabling the production of a "fingerprint" composed of marked bands of differing molecular weights. (google.com.au)
  • With the advent and new advances in sequencing technologies, it is possible to analyze whole plant genomes for SSR discovery. (thefreelibrary.com)
  • Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes [ PMID: 17442114 ]. (ebi.ac.uk)
  • Moreover, repetitive portions for instance enterobacterial repetitive intergenic consensus (ERIC) [ 19 - 21 ] and repetitive extragenic palindromic (REP) [ 22 ] are as well established in prokaryotic genomes. (biomedcentral.com)
  • In non-recombining regions of the Y chromosome repetitive DNA sequences are accumulated, representing a dominant and early process forming the Y chromosome, probably before genes start to degenerate. (biomedsearch.com)
  • All these efforts have brought about a significant enrichment of the in enriching chickpea genomic information, which are certainly useful for the marker-trait association, comparative sequence analyses of orthologous genes and improvement of chickpea by genetic transformation. (nature.com)
  • The clones containing 5S rDNA genes, 18S-25S rDNA sequences and the 180 bp paracentromeric repeated element account for 3.6%, 8.9% and 5.8%, respectively. (harvard.edu)
  • These nucleic acids range from oligonucleotides consisting of less than 20 nucleotides to artificial constructs thousands or millions of basepairs in length, typically containing a heterogeneous collection of genes from pathogenic bacteria, viruses and other genetic parasites belonging to practically every kingdom of living organisms. (i-sis.org.uk)
  • The constructs typically contain antibiotic resistance marker genes plus a heterogeneous array of genes from pathogenic bacteria, viruses and other genetic parasites belonging to practically every kingdom of living organisms on earth (2).Most of the naked nucleic acids and constructs have either never existed in nature, or if they have, not in such large amounts. (i-sis.org.uk)
  • With his move to the University of Cologne he started projects in comparative genomics, with a special focus on the evolution of new genes, which resulted in the discovery of de novo evolution of genes from non-coding sequences. (wikipedia.org)
  • In contrast, electrophoretic mobility patterns for multiple metabolic enzymes (multilocus enzyme electrophoresis [MLEE]), DNA sequence analysis of such housekeeping genes, and restriction fragment length polymorphisms in and around genomic ribosomal DNA loci (ribotyping) give largely concordant and reproducible assessments of the E. coli population structure ( 2 , 11 , 20 , 32 , 37 , 45 ). (asm.org)
  • By subcloning portions of the eibA and eibF genes, we have identified distinct sequence segments sufficient to cause Ig binding, multimerization, and discrimination between IgA and IgG. (asm.org)
  • Hence, there is a pressing need to develop accurate and fast tools to analyze genomic sequences, especially to identify genes and determine their functions. (biomedcentral.com)
  • Earlier studies using cells deficient in the Dnmt1 enzyme showed considerable decreases in the level of genomic DNA methylation at CpG-rich repetitive elements and imprinted genes ( 17 , 25 , 27 ). (pubmedcentralcanada.ca)
  • The rRNA genes ( rrn ) of chloroplasts resemble their prokaryotic ancestors not only in that they have similar primary coding sequences but also in that they typically exist in an operon. (plantcell.org)
  • Sequences of the 16S rRNA, hrpF and efP genes of five strains representing the races 1, 4 and 6 were used for multilocus sequence analysis. (omicsonline.org)
  • Based on sequence analysis of 16S rRNA and hrpF genes, the Indian strains were found to be very closely related to the strain Xcc ATCC 33913 (race 3, UK), whereas based on efP sequences, they were found to be closely related to strains race 1 Xcc B100 (Italy) and race 9 Xcc 8004 (UK). (omicsonline.org)
  • Genes encoding carbapenemases and extended-spectrum β-lactamases were detected by PCR and verified by DNA sequencing of representative samples. (dovepress.com)
  • This polycistronic mRNA contains the coding sequences for three different genes that have originated from a single transcription start site upstream of Gene 1. (els.net)
  • These sequence characteristics correlate with the frequent absence of these genes from genomic databases. (biomedcentral.com)
  • However, the fact is that these genes can, in many cases, be reconstructed from large amounts of "raw" next-generation sequence (NGS) data available from the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI). (biomedcentral.com)
  • The sequences of both these genes are in line with the GC-rich characteristics mentioned above. (biomedcentral.com)
  • The sequences of the chicken LPPR2 , MMP14 and MRPL2 genes (Additional file 1 ) were assembled from multiple pooled RNA-seq datasets from the SRA. (biomedcentral.com)
  • The newly identified chicken MMP14 and MRPL2 genes also showed the GC-rich sequence characteristics. (biomedcentral.com)
  • To show that this sequence pattern causes persistent problems for correct gene assembly, we analyzed the 89 genes (Supplemental Table 6A in [ 1 ]) reported as missing in chicken but present in some other bird species. (biomedcentral.com)
  • Therefore, there is no systematic bias in the sequence composition of the majority of P. humilis genes. (biomedcentral.com)
  • The Rps1 -k region was sequenced to understand the possible evolutionary steps that shaped the generation of Phytophthora resistance genes in soybean. (biomedcentral.com)
  • Sequence analysis predicted a few full-length genes including two Rps1 -k genes, Rps1 -k-1 and Rps1 -k-2. (biomedcentral.com)
  • TRANSPOSONS are genetic elements that move from one locus to another locus and reside in the genome as repetitive sequences. (genetics.org)
  • Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. (nature.com)
  • Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. (nature.com)
  • On the other hand, effective anchoring of sequence scaffolds to the genetic linkage groups based on genetic markers to have a chromosome-level genome assembly is essential to identify genetic loci governing traits followed by marker-assisted breeding and comparative mapping with other species. (nature.com)
  • Although these sequences are widely used for studying genetic variation, linkage mapping and evolution, little attention had been paid to the chromosomal distribution and cytogenetic diversity of these sequences. (frontiersin.org)
  • Recent investigations associated with gene therapy and vaccines leave little doubt that naked and free nucleic acids are readily taken up by the cells of all species including human beings, and may become integrated into the cell s genetic material. (i-sis.org.uk)
  • Naked nucleic acids are DNA/RNA produced in the laboratory and intended for use in, or as the result of genetic engineering (1). (i-sis.org.uk)
  • A transposable element ( TE or transposon ) is a DNA sequence that can change its position within a genome , sometimes creating or reversing mutations and altering the cell's genetic identity and genome size . (wikipedia.org)
  • Demographic history and biologically relevant genetic variation of Native Mexicans inferred from whole-genome sequencing Nature Communications, 8, 1005. (unam.mx)
  • The validation by UPGMA cluster analysis of 32 genotypes based on Nei's genetic distance, showed high quality and effectiveness of those novel SSR markers developed via next generation sequencing technology. (biomedcentral.com)
  • Various molecular techniques such as RFLP patterns, repetitive sequence based PCR (rep-PCR), 16S rRNA gene analysis, hrp (hypersensitive response and pathogenicity) gene and amplified fragment length polymorphism have been used to study the genetic variability among various bacteria [ 7 - 10 ]. (omicsonline.org)
  • Messenger ribonucleic acids (mRNAs) are molecules that represent the intermediate step in the conversion of genetic information carried in a cell's DNA (deoxyribonucleic acid) into functional proteins. (els.net)
  • We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. (plos.org)
  • In our study, we employed long read sequencing combined with genetic and optical mapping, and syntenic information to produce a chromosomal level assembly. (plos.org)
  • Enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) produced species- and strain-specific profiles for Lactobacillus crispatus , Lactobacillus gallinarum , Lactobacillus johnsonii , and Lactobacillus reuteri isolates. (asm.org)
  • Although the ERIC-PCR (Enterobacterial repetitive intergenic consensus-PCR) assay is fast and easy to perform, scarce studies have reported its use in epidemiological studies in TB outbreaks. (scielo.br)
  • The Enterobacterial Repetitive Intergenic Consensus sequence (ERIC) are repetitive elements of 126 bp and appear to be restricted to transcribed regions of the bacterial chromosome, either in intergenic regions of polycistronic operons or in untranslated regions upstream or downstream of open reading frames. (scielo.br)
  • Three families of repetitive sequences (Rep) including repetitive extragenic palindromic (REP) sequences, Enterobacterial Repetitive Intergenic Consensus (ERIC) sequences, and the BOX element have been identified [ 11 ]. (omicsonline.org)
  • Clonal relationships among the bla OXA-48 -harboring K. pneumoniae isolates were determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR and pulsed-field gel electrophoresis (PFGE). (dovepress.com)
  • The present invention provides methods and probe nucleic acids for detecting mutant forms of target nucleic acids that comprise repetitive nucleotide sequences. (google.com)
  • The present invention relates to the detection of target nucleic acids that include repetitive nucleotide sequences. (google.com)
  • 2007) Clustered sequence representation for fast homology search. (uottawa.ca)
  • Most mariner-type elements are known only from their sequences obtained through homology-based PCR screens or by sequence analysis (genomic or expressed sequence tag). (asmscience.org)
  • Binding of IgG Fc is associated with a sequence that is highly conserved among all Eib proteins but otherwise unique. (asm.org)
  • Consequently, the sizes of the Eib proteins appeared much greater than predicted from the gene sequences, implying stable multimerization. (asm.org)
  • 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. (embl-heidelberg.de)
  • The present status of erythrocyte spectrin structure: the 106-residue repetitive structure is a basic feature of an entire class of proteins. (embl-heidelberg.de)
  • Estimating the total mouse DNA methylation according to the B1 repetitive elements. (currentprotocols.com)
  • We discuss how synergy between adaptive and innate immune responses can lead to autoimmunity, including aspects such as colocalization between receptor and ligand, the impact that methylation and other modifications have on the receptors' sensitivity to nucleic acids, and gene dosage of these receptors. (jimmunol.org)
  • In contrast, both Dnmt1 and Dnmt3a and/or Dnmt3b were required for methylation of a select class of sequences which included abundant murine LINE-1 promoters. (pubmedcentralcanada.ca)
  • We used a novel hemimethylation assay to show that even in wild-type cells these sequences contain high levels of hemimethylated DNA, suggestive of poor maintenance methylation. (pubmedcentralcanada.ca)
  • We showed that Dnmt3a and/or -3b could restore methylation of these sequences to pretreatment levels following transient exposure of cells to 5-aza-CdR, whereas Dnmt1 by itself could not. (pubmedcentralcanada.ca)
  • We conclude that ongoing de novo methylation by Dnmt3a and/or Dnmt3b compensates for inefficient maintenance methylation by Dnmt1 of these endogenous repetitive sequences. (pubmedcentralcanada.ca)
  • The mammalian DNA methyltransferases (DNA methyltransferase 1 [Dnmt1], Dnmt3a, and Dnmt3b) establish and maintain genomic methylation patterns which are of critical importance in various biological processes, including development, genomic imprinting, silencing of parasitic sequence elements, and tumorigenesis ( 3 , 14 , 17 , 31 ). (pubmedcentralcanada.ca)
  • Recent studies using cells deficient in both the Dnmt3a and -3b enzymes showed that CpG-rich retroviral and intracisternal A particle (IAP) elements became slightly demethylated, and Igf-2 and Xist became extensively demethylated, in the absence of these enzymes, implying that Dnmt1 by itself had sequence specificity in maintaining the methylation of these sequences ( 20 ). (pubmedcentralcanada.ca)
  • These previous studies all focused on the methylation of CpG-rich sequences in knockout cells. (pubmedcentralcanada.ca)
  • We found that methylation levels of CpG-poor sequences were, in general, uniformly reduced in Dnmt1-deficient cells. (pubmedcentralcanada.ca)
  • However, there was considerable variability among different regions in the efficiency with which DNA methylation was retained in Dnmt3a- and/or Dnmt3b-deficient cells indicating a sequence preference for the Dnmt1 enzyme. (pubmedcentralcanada.ca)
  • We further investigated one of the sequences that was poorly maintained by Dnmt1 alone and showed that it had a surprisingly high level of hemimethylation, even in wild-type cells, suggesting poor maintenance methylation balanced by a continuing high rate of de novo methylation mediated by Dnmt3a and/or Dnmt3b. (pubmedcentralcanada.ca)
  • PGRS was present in at least 26 loci and consisted of many tandem repeats of the consensus sequence CGGCGGCAA. (springer.com)
  • 1. A synthetic oligonucleotide comprising: a chromosome-specific sequence consisting of 25-35 contiguous nucleotides perfectly complementary to a repeat sequence on a specific human chromosome, wherein the chromosome-specific sequence is less than 84% identical to a consensus repeat sequence of all human chromosomes. (freepatentsonline.com)
  • 3. The oligonucleotide of claim 1, wherein the consensus repeat sequence is selected from the group consisting of an alpha satellite, beta satellite, gamma satellite, satellite 1, satellite 2 and a satellite 3 repeat. (freepatentsonline.com)
  • Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. (mdpi.com)
  • Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. (biomedcentral.com)
  • NtcA is known to bind to DNA sites with the consensus sequence GTA-N 8 -TAC ( 8 ), of which GT-N 10 -AC is an important subset ( 9 ). (asm.org)
  • 8. The composition of claim 1 , wherein the one or more nucleic acid molecules have been degraded except for that portion of the molecule or molecules that are protected from degradation by hybridization to the non-nucleotide probe. (google.com)
  • While molecular methods, such as DNA-DNA hybridization ( 22 ), ribotyping ( 71 ), sodium dodecyl sulfate-polyacrylamide gel electrophoresis ( 19 ), randomly amplified polymorphic DNA PCR ( 19 ), and 16S rRNA gene sequencing ( 41 ), have been used with some success, many of these techniques are not readily adaptable to high-throughput applications required for large-scale ecological studies. (asm.org)
  • These labeled probes are used primarily for hybridization to nucleic acid fragments of interest in a variety of applications. (currentprotocols.com)
  • Chemiluminescent detection of nucleic acid hybridization. (currentprotocols.com)
  • Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. (nih.gov)
  • 500 eukaryotic genome sequences are available in public repositories, the majority are highly fragmented with incomplete assemblies, which explains why considerable effort and resources are often spent to improve their quality after publication. (plos.org)
  • There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. (umassmed.edu)
  • Mobile elements (MEs) or transposable elements are DNA sequences that can be autonomously copied or moved through the genome, yet their highly repetitive sequence structure makes them difficult to detect. (biomedcentral.com)
  • Also, our study established a basis for further biochemical and molecular biological studies for understanding roles of the repetitive sequence in the subterminal region in transposition. (genetics.org)
  • Repetitive-element PCR (rep-PCR) fingerprinting is a promising molecular typing tool for Escherichia coli , including for discriminating between pathogenic and nonpathogenic clones, but is plagued by irreproducibility. (asm.org)
  • Target antigen production, sequencing sample preparation, and antibody humanization involve a great deal of repetitive molecular biology handling steps. (eppendorf.com)
  • All the strains were identified on the basis of 16S rRNA gene sequencing, and the phylogenetic diversity of the strains was analyzed. (frontiersin.org)
  • Two different B. henselae types based on partial 16S rRNA gene sequences have been described ( 3 ), with multiple DNA fingerprint patterns identified for each type ( 29 ). (asm.org)
  • In the green alga Chlamydomonas reinhardtii , the 4.5S rRNA is absent, but the ribosomal LSU contains two other small RNAs, 7S and 3S, which are similar in sequence to the 5′ end of E. coli 23S. (plantcell.org)
  • 2003) GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations. (uottawa.ca)
  • Aligning multiple genomic sequences with the threaded blockset aligner. (repeatmasker.org)
  • Pederson T. Repeated TALEs: visualizing DNA sequence localization and chromosome dynamics in live cells. (umassmed.edu)
  • The polymorphic GC-rich repetitive sequence (PGRS) found on the chromosome of Mycobacterium tuberculosis was characterized by means of mapping, cloning and sequencing. (springer.com)
  • Here we review the occurrence and role of repetitive DNA in Y chromosome evolution in various species with a focus on dioecious plants. (biomedsearch.com)
  • 4. The oligonucleotide of claim 1, wherein the chromosome-specific sequence is less than 84% identical to all other contiguous nucleic acid sequences within the human genome. (freepatentsonline.com)
  • 5. The oligonucleotide of claim 1, wherein the chromosome-specific sequence is specific for an alpha monomer repeat sequence from a chromosome selected from the group consisting of the Y chromosome, chromosome 2, and chromosome 4. (freepatentsonline.com)
  • The organisation of repetitive sequences in the pericentromeric region of human chromosome 10. (cam.ac.uk)
  • These data provide both physical information on sequences which may be involved in centromere function and a map across the centromere which has the potential to link yeast artificial chromosome (YAC) contigs currently being developed on both arms of this chromosome. (cam.ac.uk)
  • In this study, we measured the nuclear DNA content of Vallisneria spinulosa by flow cytometry, performed a de novo assembly, and annotated repetitive sequences by using a combination of next-generation sequencing (NGS) and bioinformatics tools. (peerj.com)
  • Rapid and cost-effective next-generation sequencing (NGS) technologies produce large volumes of DNA sequencing data in large-scale genome projects. (biomedcentral.com)
  • Large scale SSR marker development was successfully achieved using next generation sequencing of the V. faba genome. (biomedcentral.com)
  • Recent advances in next generation sequencing (NGS) technologies enable the generation of large volumes of sequence efficiently and cost-effectively [ 5 , 6 ]. (biomedcentral.com)
  • We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. (biomedcentral.com)
  • To identify polymorphic MEIs (pMEIs), both targeted and next-generation sequencing (NGS) analysis have been developed. (biomedcentral.com)
  • Since its introduction in 2005 next-generation sequencing (NGS) has fundamentally altered genomics research. (smi-online.co.uk)
  • An alternative approach to PCR-based fingerprinting, repetitive-element PCR (rep-PCR), uses as primers oligonucleotides homologous to defined sequences which are present in multiple copies in the bacterial genome ( 35 , 52 , 53 ). (asm.org)
  • For example, human centromeres consist of large blocks (200 kb to several megabases) of tandemly repeated 171-bp α-satellite ( Willard, 1998 ), but the sequences can differ from those of apes on homologous chromosomes ( Haaf and Willard, 1997 ). (plantcell.org)
  • The ability to multimerize is associated with a sequence close to the C terminus that is homologous to other family members such as YadA. (asm.org)
  • 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. (embl-heidelberg.de)
  • Structure and chromosomal mapping of a highly polymorphic repetitive DNA sequence from the pseudoautosomal region of the mouse sex chromosomes. (biomedsearch.com)
  • Hypervariability of simple sequences as a general source for polymorphic DNA markers. (wikipedia.org)
  • The sequences of these plasmids were analyzed by using whole-genome sequencing with Illumina Hiseq platform. (dovepress.com)
  • hypothesized that the relative frequency of microsatellites is higher in the single- or low-copy regions of the genome than in the repetitive regions. (frontiersin.org)
  • In the 29 land plants, including 22 dicots, 5 monocots, and 2 bryophytes, 5′-UTR and upstream intergenic 200-nt (UI200) regions had the first and second highest TR densities, whereas in the two green algae ( C. reinhardtii and Volvox carteri ) the first and second highest densities were found in intron and coding sequence (CDS) regions, respectively. (g3journal.org)
  • Comparative analyses of multi-species sequences from targeted genomic regions. (repeatmasker.org)
  • Another outcome is the ability to accurately identify sequences flanking simple sequence repeat (SSR) regions for use as locus-specific markers for downstream genotyping. (biomedcentral.com)
  • Synthetic repeat DNA sequences were then employed to identify the length, sequence, and directionality of repeat regions required for this activity. (elsevier.com)
  • The population structure of L . calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. (plos.org)
  • Pearson W, Lipman D (1988) Improved tools for biological sequence comparisons. (springer.com)
  • The effective, and accurate, retrieval of biological sequence information is crucial to users of patent databases. (piug.org)
  • There is also abundant evidence that the extraneous nucleic acids taken up can have significant and harmful biological effects including cancers in mammals. (i-sis.org.uk)
  • Despite sharing a common biological function, B2 RNA and Alu RNA share little similarity in sequence or secondary structure ( 7 , 24 ). (asm.org)
  • Ma H, Reyes-Gutierrez P, Pederson T. Visualization of repetitive DNA sequences in human chromosomes with transcription activator-like effectors. (umassmed.edu)
  • The distribution of moderately repeated DNA sequences among Chinese hamster chromosomes. (springer.com)
  • The role of repetitive DNA in structure and evolution of sex chromosomes in plants. (biomedsearch.com)
  • These repetitive sequences often colonize specific chromosomal (Y or W chromosomes, B chromosomes) or subchromosomal (telomeres, centromeres) niches. (biomedsearch.com)
  • PGRS was used as the target sequence for the polymerase chain reaction in an attempt to develop a new typing technique. (springer.com)
  • A polymerase chain reaction assay was developed based on conserved amino acid sequences shared between the Ta11-1 reverse transcriptase and those of non-LTR retrotransposons from other species. (harvard.edu)
  • A simple PCR reaction consists of a set of synthetic oligonucleotide primers that flank the target DNA sequence, target DNA, a thermostable DNA polymerase and dNTPs. (sigmaaldrich.com)
  • They are synthesised by the enzyme RNA polymerase, which recognises specific sequences in the DNA (promoters) to initiate the process called transcription. (els.net)
  • 2. The oligonucleotide of claim 1, wherein the repeat sequence is a member selected from the group consisting of a centromeric repeat, a pericentromeric repeat, a heterochromatin repeat, and a telomeric repeat. (freepatentsonline.com)
  • The library was screened by PCR amplification using pairs of primers corresponding to sequences dispersed in the genome. (harvard.edu)
  • A repetitive series of cycles involving template denaturation, primer annealing, followed by extension of the annealed primers, yields tremendous amounts of DNA. (sigmaaldrich.com)
  • The present provides selection markers, methods, nucleic acids, and vectors of use in the preparation of recombinant Clostridium spp. (patents.com)
  • This invention pertains to methods, kits and compositions suitable for the detection, identification and/or quantitation of nucleic acids which are electrostatically immobilized to matrices using non-nucleotide probes which sequence specifically hybridize to one or more target sequences of the nucleic. (google.com)
  • 2005), Supplementary Methods for the article Genome Sequencing in Microfabricated High-Density Picolitre Reactors, Nature, vol. 437:1-34. (freepatentsonline.com)
  • In this study, we aimed to genotype Mycobacterium tuberculosis and M. bovis isolates by ERIC-PCR and compare its discriminatory power with two other classically used methods: 12 loci-MIRU (Mycobacterial Interspersed Repetitive Units) and Spoligotyping. (scielo.br)
  • Extensive knowledge of the enzymology involved in biosynthesis and degradation of nucleic acids has permitted the development of simple methods for labeling RNA and DNA with radioisotopes or biotin. (currentprotocols.com)
  • Methods: Two hundred seventy-five non-repetitive stool samples were collected from Mozambican university students of both sexes. (deepdyve.com)
  • Because paraffin-embedded specimens are widely available, rapid and reliable methods are needed for obtaining nucleic acids, particularly RNA, from such specimens. (google.com)
  • Nucleic Acids Res , 27(11):2369-76, Jun 1999. (uottawa.ca)
  • 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). (embl-heidelberg.de)
  • The predominant structural feature elucidated from sequencing this large molecule is the nearly universal occurrence in both subunits of a single type of repetitive structure. (embl-heidelberg.de)
  • Transcriptome analysis of polar bear ( Ursus maritimus ) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). (mdpi.com)
  • Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. (mdpi.com)
  • Because these types of nucleic acids can also be found endogenous in a mammalian cell, the question of why these nucleic acids are not normally recognized by the innate immune system to promote autoimmunity remains unresolved. (jimmunol.org)
  • The DNA and RNA sequence data were obtained using Illumina HiSeq 2000 sequencing technology, from which we performed de novo genome assembly and gene annotation. (biomedcentral.com)
  • CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. (ebi.ac.uk)
  • The identification of the minimal cis -sequence of the Tol2 element and the construction of mini- Tol2 vectors will facilitate development of useful transposon tools in vertebrates. (genetics.org)
  • The Role That Sequence Searches Play in Patent Prosecution and FTO Analysis Mario Cloutier, Millennium Pharmaceuticals, Inc. (piug.org)
  • Patent Analysis of Short Sequence Dr. Kamalakar Gulukota, Gene-IT, Inc. (piug.org)
  • DNA sequence analysis near the Arabidopsis thaliana ABI3 gene revealed the presence of a non-LTR retrotransposon insertion that we have designated Ta11-1. (harvard.edu)
  • Closely related sequences were identified by PCR analysis of brown bear ( Ursus arctos ) and black bear ( Ursus americanus ) but were absent in non-Ursinae bear species. (mdpi.com)
  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. (repeatmasker.org)
  • MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. (repeatmasker.org)
  • Initial sequencing and comparative analysis of the mouse genome. (repeatmasker.org)
  • Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) analysis were also performed. (dovepress.com)
  • In silico genome comparison and distribution analysis of simple sequences repeats in cassava. (thefreelibrary.com)
  • Identifying potential therapeutic drug targets and validating their suitability is a complex process involving numerous experimental platforms, including DNA sequence analysis . (smi-online.co.uk)
  • High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum," Nucleic Acids Research , vol. 37, no. 13, pp. 4331-4340, 2009. (hindawi.com)
  • Other available techniques allow analysis of nucleic acids from such specimens. (google.com)
  • Cytogenetic Diversity of Simple Sequences Repeats in Morphotypes of Brassica rapa ssp. (frontiersin.org)
  • Although the amount of sequencing data used in this study was not sufficient for a whole-genome assembly, it could generate an overview of representative elements in the genome. (peerj.com)
  • The paucity of retrotransposons and the small genome size of A. thaliana support the hypothesis that most repetitive sequences have been lost from the genome and that mechanisms may exist to prevent amplification of extant element families. (harvard.edu)
  • The majority of the repetitive sequences are LTR-retrotransposons comprising 43% of the genome. (peerj.com)
  • It is an efficient and rapid in vitro method for enzymatic amplification of specific DNA or RNA sequences from nucleic acids of various sources. (sigmaaldrich.com)
  • The basic principle of PCR is amplification (up to a million times) of the specific DNA sequence of interest within a few hours. (aasv.org)
  • The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. (biomedcentral.com)
  • Detection of specific DNA sequences has become an important technology in health care, bioterrorism prevention, and genotyping. (omicsonline.org)
  • De novo quantitative bisulfite sequencing using the pyrosequencing technology. (currentprotocols.com)
  • SSRs have the advantage of being PCR-based markers because the flanking sequences are suitable for primer design [25]. (thefreelibrary.com)
  • These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl-heidelberg.de)
  • The genome size of Vallisneria spinulosa is approximately 3,595 Mbp, in which nearly 60% of the genome consists of repetitive sequences. (peerj.com)
  • Phylogenetic analyses indicated that the A. thaliana sequences are more closely related to each other than to elements from other organisms, consistent with the vertical evolution of these sequences over most of their evolutionary history. (harvard.edu)
  • GENESEQ, provided by Thomson Scientific, is one such database covering nucleotide and amino acid sequences disclosed in patents from 41 patent issuing authorities with coverage back to 1981. (piug.org)
  • Copy number variation of this repeat most likely accounts for the polymorphism in the mouse pseudoautosomal region detected with a probe from the flanking sequences. (biomedsearch.com)
  • Once the nucleic acid is immobilized, the detectable non-nucleotide probe/target sequence complex, formed before or after the immobilization of the nucleic acid, can be detected, identified or quantitated under a wide range of assay conditions as a means to detect, identify or quantitate the target sequence in the sample. (google.com)
  • Because it is reversibly bound, the non-nucleotide probe/target sequence can optionally be removed from the matrix for detecting, identifying or quantitating the target sequence in the sample. (google.com)
  • c) at least one non-nucleotide probe comprising a probing nucleobase sequence that is sequence specifically hybridized to at least a portion of the one or more target sequences to thereby form a non-nucleotide probe/target sequence complex and wherein the backbone of the non-nucleotide probe or probes is sufficiently neutral or positively charged, under electrostatic binding conditions that it exhibits little or no affinity for the matrix. (google.com)
  • 5. The composition of claim 4 , wherein to the non-nucleotide probe/target sequence complex is directly or indirectly linked a detectable antibody. (google.com)
  • 6. The composition of claim 5 , wherein the non-nucleotide probe or probes are peptide nucleic acid. (google.com)
  • The repetitive DNA provides an additional way to distinguish between different strains of parasite by hybridisation to genomic blots and may serve as a species-specific probe for diagnosis. (semanticscholar.org)
  • 5. The method as claimed in claim 1 wherein the repeat unit sequence of the polynucleotide probe consists of one of sequences 3-9. (google.com.au)
  • Based on the work on segmentation processes in Drosophila, he developed a general interest in studying the evolution of segmentation processes, especially in the model system Tribolium and he was involved in generating the first full genome sequencing for this beetle species. (wikipedia.org)
  • Three repetitive-element PCR techniques were evaluated for the ability to type strains of Lactobacillus species commonly identified in the chicken gastrointestinal tract. (asm.org)
  • ERIC sequence was initially well-characterized in Gram negative bacillus belonging to the family Enterobacteriaceae and has been used to characterize clonal difference in species from this family. (scielo.br)
  • The pipeline processes the genome and transcriptome sequences of the target species using GlimmerHMM, SNAP, and AUGUSTUS pipelines, followed by MAKER2 program to combine predictions from the three tools in association with the transcriptomic evidence. (biomedcentral.com)
  • These include metagenomics to compare different disease states or patient variablility , genome sequencing of model and pathogenic species or ELT compound library screening techniques. (smi-online.co.uk)
  • In addition, population structure of the species was analysed based on low-coverage genome sequence information from 61 individuals representing diverse geographic locations stretching from North-Western India across South-East Asia and Australia to Papua New Guinea. (plos.org)
  • Before PCR may be used for diagnostic purposes, it is essential to have prior knowledge of a unique DNA sequence in the target (suspect) organism, which might be specific to a genus, species, or strain. (aasv.org)
  • Polymorphism in Brucella strains detected by studying distribution of two short repetitive DNA elements. (semanticscholar.org)
  • A subset of NDM-1-positive E. coli isolates was identified as dominant sequence type 101 (ST101) while two strains belonging to ST167 and ST405 harbored NDM-5. (asm.org)
  • TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES). (umassmed.edu)
  • Alu RNA is related to B1 RNA in sequence and secondary structure: it is a tandem repeat of two B1-like RNAs connected by an A-rich linker ( 22 , 23 ). (asm.org)
  • Sixteen simple repeat and 63 tandem repeat sequences were identified from the locus. (biomedcentral.com)
  • The sequences flanking the Mov15 provirus were molecularly cloned and shown to consist of a tandemly repeated sequence of 31 nucleotides. (biomedsearch.com)
  • Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (embl-heidelberg.de)
  • Here the analyses of sequences of three overlapping BAC clones containing the 184,111 bp Rps1 -k region are reported. (biomedcentral.com)
  • Evolutionary conservation of sequence and secondary structures in CRISPR repeats. (ebi.ac.uk)
  • A suit of 28,503 primer pair sequences were designed and 150 were randomly selected for validation. (biomedcentral.com)