The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.
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 sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
The relationships of groups of organisms as reflected by their genetic makeup.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
RNA which does not code for protein but has some enzymatic, structural or regulatory function. Although ribosomal RNA (RNA, RIBOSOMAL) and transfer RNA (RNA, TRANSFER) are also untranslated RNAs they are not included in this scope.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
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.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.
The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.
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 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)
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).
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).
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.
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.
A class of untranslated RNA molecules that are typically greater than 200 nucleotides in length and do not code for proteins. Members of this class have been found to play roles in transcriptional regulation, post-transcriptional processing, CHROMATIN REMODELING, and in the epigenetic control of chromatin.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
Genotypic differences observed among individuals in a population.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
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.
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.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
The functional hereditary units of BACTERIA.
In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.
Proteins found in any species of bacterium.
The genetic complement of a BACTERIA as represented in its DNA.
Any method used for determining the location of and relative distances between genes on a chromosome.
A genus of gram-negative, chemoorganotrophic bacteria in the family CYTOPHAGACEAE. In some species there is a cyclic change in cell morphology.
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.
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 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 chromosomal constitution of cells, in which each type of CHROMOSOME is represented once. Symbol: N.
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.
The asymmetrical segregation of genes during replication which leads to the production of non-reciprocal recombinant strands and the apparent conversion of one allele into another. Thus, e.g., the meiotic products of an Aa individual may be AAAa or aaaA instead of AAaa, i.e., the A allele has been converted into the a allele or vice versa.
A plant genus of the family Cruciferae. It contains many species and cultivars used as food including cabbage, cauliflower, broccoli, Brussel sprouts, kale, collard greens, MUSTARD PLANT; (B. alba, B. junica, and B. nigra), turnips (BRASSICA NAPUS) and rapeseed (BRASSICA RAPA).
Plants whose roots, leaves, seeds, bark, or other constituent parts possess therapeutic, tonic, purgative, curative or other pharmacologic attributes, when administered to man or animals.
Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".
A plant family of the order Capparales, subclass Dilleniidae, class Magnoliopsida. They are mostly herbaceous plants with peppery-flavored leaves, due to gluconapin (GLUCOSINOLATES) and its hydrolysis product butenylisotrhiocyanate. The family includes many plants of economic importance that have been extensively altered and domesticated by humans. Flowers have 4 petals. Podlike fruits contain a number of seeds. Cress is a general term used for many in the Brassicacea family. Rockcress is usually ARABIS; Bittercress is usually CARDAMINE; Yellowcress is usually RORIPPA; Pennycress is usually THLASPI; Watercress refers to NASTURTIUM; or RORIPPA or TROPAEOLUM; Gardencress refers to LEPIDIUM; Indiancress refers to TROPAEOLUM.
The traditional Hindu system of medicine which is based on customs, beliefs, and practices of the Hindu culture. Ayurveda means "the science of Life": veda - science, ayur - life.
A plant genus of the family POACEAE.
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.
Critical and exhaustive investigation or experimentation, having for its aim the discovery of new facts and their correct interpretation, the revision of accepted conclusions, theories, or laws in the light of newly discovered facts, or the practical application of such new or revised conclusions, theories, or laws. (Webster, 3d ed)
Those individuals engaged in research.
Financial support of research activities.
Research that involves the application of the natural sciences, especially biology and physiology, to medicine.
The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.

A skeletal muscle-specific mouse Igf2 repressor lies 40 kb downstream of the gene. (1/1289)

Igf2 and H19 are closely linked and reciprocally expressed genes on distal chromosome 7 in the mouse. We have previously shown that a 130 kb YAC transgene contains multiple tissue-specific enhancers for expression of both genes during embryogenesis. The YAC also contains all the crucial elements responsible for initiating and maintaining appropriate parent-of-origin-specific expression of these genes at ectopic sites, with expression of Igf2 after paternal inheritance and of H19 after maternal inheritance. Located centrally between Igf2 and H19 are two prominent DNaseI hypersensitive sites, and two stretches of sequence that are conserved between mouse and human. In this study, we have deleted, from the transgene, a one kb part of the intergenic region that contains the hypersensitive sites and one of the homologous stretches. We demonstrate that this deletion results in loss of maternal Igf2 repression in skeletal muscle cells, most strikingly in the tongue, late in embryogenesis. We propose that the intergenic region functions as a tissue-specific repressor element, forming an integral part of the complex regulatory mechanism that controls monoallelic gene expression in this domain.  (+info)

Genotypic characterization of Bradyrhizobium strains nodulating small Senegalese legumes by 16S-23S rRNA intergenic gene spacers and amplified fragment length polymorphism fingerprint analyses. (2/1289)

We examined the genotypic diversity of 64 Bradyrhizobium strains isolated from nodules from 27 native leguminous plant species in Senegal (West Africa) belonging to the genera Abrus, Alysicarpus, Bryaspis, Chamaecrista, Cassia, Crotalaria, Desmodium, Eriosema, Indigofera, Moghania, Rhynchosia, Sesbania, Tephrosia, and Zornia, which play an ecological role and have agronomic potential in arid regions. The strains were characterized by intergenic spacer (between 16S and 23S rRNA genes) PCR and restriction fragment length polymorphism (IGS PCR-RFLP) and amplified fragment length polymorphism (AFLP) fingerprinting analyses. Fifty-three reference strains of the different Bradyrhizobium species and described groups were included for comparison. The strains were diverse and formed 27 groups by AFLP and 16 groups by IGS PCR-RFLP. The sizes of the IGS PCR products from the Bradyrhizobium strains that were studied varied from 780 to 1,038 bp and were correlated with the IGS PCR-RFLP results. The grouping of strains was consistent by the three methods AFLP, IGS PCR-RFLP, and previously reported 16S amplified ribosomal DNA restriction analysis. For investigating the whole genome, AFLP was the most discriminative technique, thus being of particular interest for future taxonomic studies in Bradyrhizobium, for which DNA is difficult to obtain in quantity and quality to perform extensive DNA:DNA hybridizations.  (+info)

Developmentally regulated excision of a 28-base-pair sequence from the Paramecium genome requires flanking DNA. (3/1289)

The micronuclear DNA of Paramecium tetraurelia is estimated to contain over 50,000 short DNA elements that are precisely removed during the formation of the transcriptionally active macronucleus. Each internal eliminated sequence (IES) is bounded by 5'-TA-3' dinucleotide repeats, a feature common to some classes of DNA transposons. We have developed an in vivo assay to analyze these highly efficient and precise DNA excision events. The microinjection of a cloned IES into mating cells results in accurately spliced products, and the transformed cells maintain the injected DNA as extrachromosomal molecules. A series of deletions flanking one side of a 28-bp IES were constructed and analyzed with the in vivo assay. Whereas 72 bp of DNA flanking the eliminated region is sufficient for excision, lengths of 31 and 18 bp result in reduced excision and removal of all wild-type sequences adjacent to the TA results in complete failure of excision. In contrast, nucleotide mutations within the middle of the 28-bp IES do not prevent excision. The results are consistent with a functional role for perfect inverted repeats flanking the IES.  (+info)

Application of tRNA intergenic spacer PCR for identification of Enterococcus species. (4/1289)

tRNA intergenic spacer PCR (tDNA-PCR) was evaluated for its usefulness in the differentiation of enterococcal species of human and animal origin. This technique was carried out for 124 strains belonging to 17 enterococcal species and generated DNA fragments, which were separated by capillary electrophoresis. tDNA-PCR enabled us to discriminate for all species tested. Enterococcus faecium showed minor but reproducible differences with Enterococcus durans, while Enterococcus hirae was easily distinguishable. Enterococcus avium, Enterococcus malodoratus, and Enterococcus raffinosus generated highly similar though distinctive patterns.  (+info)

Histone H2A.Z regulats transcription and is partially redundant with nucleosome remodeling complexes. (5/1289)

Nucleosomes impose a block to transcription that can be overcome in vivo by remodeling complexes such as SNF/SWI and histone modification complexes such as SAGA. Mutations in the major core histones relieve transcriptional repression and bypass the requirement for SNF/SWI and SAGA. We have found that the variant histone H2A.Z regulates gene transcription, and deletion of the gene encoding H2A.Z strongly increases the requirement for SNF/SWI and SAGA. This synthetic genetic interaction is seen at the level of single genes and acts downstream of promoter nucleosome reorganization. H2A.Z is preferentially crosslinked in vivo to intergenic DNA at the PH05 and GAL1 loci, and this association changes with transcriptional activation. These results describe a novel pathway for regulating transcription using variant histones to modulate chromatin structure.  (+info)

Biogeography of two species of Symbiodinium (Freudenthal) inhabiting the intertidal sea anemone Anthopleura elegantissima (Brandt). (6/1289)

We have analyzed the genetic profiles of dinoflagellate populations obtained from the Pacific coast sea anemone Anthopleura elegantissima (Brandt) at collection sites from Washington to California. Genetic differences within the symbiont populations of California anemones have been uncovered by restriction length polymorphism (RFLP) analysis of the small subunit (SSU) and large subunit (LSU) ribosomal RNA genes, and by denaturing gradient gel electrophoresis (DGGE) of the internal transcribed spacer region 2 (ITS 2). The existence of two Symbiodinium species is substantiated by sequence analysis of the variable regions V1, V2, and V3 of the SSUrDNA, which also establishes their phylogenetic relatedness to other members of the genus Symbiodinium. Anemones from Washington and Oregon harbor a single dinoflagellate species, for which we propose the name S. muscatinei sp. nov. At these northern locations, S. muscatinei either exists alone or co-occurs with the Chlorella-like green algal symbiont. Our results indicate that S. muscatinei co-occurs with a second dinoflagellate, S. californium, in mixed populations in central and southern California. We suggest that the geographic distribution of these dinoflagellates is related to the temperature cline created by latitude.  (+info)

Sequencing bands of ribosomal intergenic spacer analysis fingerprints for characterization and microscale distribution of soil bacterium populations responding to mercury spiking. (7/1289)

Two major emerging bands (a 350-bp band and a 650-bp band) within the RISA (ribosomal intergenic spacer analysis) profile of a soil bacterial community spiked with Hg(II) were selected for further identification of the populations involved in the response of the community to the added metal. The bands were cut out from polyacrylamide gels, cloned, characterized by restriction analysis, and sequenced for phylogenetic affiliation of dominant clones. The sequences were the intergenic spacer between the rrs and rrl genes and the first 130 nucleotides of the rrl gene. Comparison of sequences derived from the 350-bp band to The GenBank database permitted us to identify the bacteria as being mostly close relatives to low G+C firmicutes (Clostridium-like genera), while the 650-bp band permitted us to identify the bacteria as being mostly close relatives to beta-proteobacteria (Ralstonia-like genera). Oligonucleotide probes specific for the identified dominant bacteria were designed and hybridized with the RISA profiles derived from the control and spiked communities. These studies confirmed the contribution of these populations to the community response to the metal. Hybridization of the RISA profiles from subcommunities (bacterial pools associated with different soil microenvironments) also permitted to characterize the distribution and the dynamics of these populations at a microscale level following mercury spiking.  (+info)

Homoduplex and heteroduplex polymorphisms of the amplified ribosomal 16S-23S internal transcribed spacers describe genetic relationships in the "Bacillus cereus group". (8/1289)

Bacillus anthracis, Bacillus cereus, Bacillus mycoides, Bacillus pseudomycoides, Bacillus thuringiensis, and Bacillus weihenstephanensis are closely related in phenotype and genotype, and their genetic relationship is still open to debate. The present work uses amplified 16S-23S internal transcribed spacers (ITS) to discriminate between the strains and species and to describe the genetic relationships within the "B. cereus group," advantage being taken of homoduplex-heteroduplex polymorphisms (HHP) resolved by polyacrylamide gel electrophoresis and silver staining. One hundred forty-one strains belonging to the six species were investigated, and 73 ITS-HHP pattern types were distinguished by MDE, a polyacrylamide matrix specifically designed to resolve heteroduplex and single-strand conformation polymorphisms. The discriminating bands were confirmed as ITS by Southern hybridization, and the homoduplex or heteroduplex nature was identified by single-stranded DNA mung bean nuclease digestion. Several of the ITS-HHP types corresponded to specific phenotypes such as B. anthracis or serotypes of B. thuringiensis. Unweighted pair group method arithmetic average cluster analysis revealed two main groups. One included B. mycoides, B. weihenstephanensis, and B. pseudomycoides. The second included B. cereus and B. thuringiensis, B. anthracis appeared as a lineage of B. cereus.  (+info)

In contrast to bacteria which have no introns, eukaryotes (cells with a nucleus) have introns which are intervening sequences within genes which get spliced out when genes are transcribed and are not expressed in the protein. In contrast, exons are the sequences within a gene which do get expressed and translated into protein. Intergenic DNA, as the name suggests, is DNA between genes which does not code for proteins. Hope this helps gabriel vargas md/phd References Genes VII by Benjamin Lewin ...
Andolfatto took a different approach toward identifying functional non-coding sequences. He looked at coding and non-coding sequences from twelve D. melanogaster individuals and one D. simulans individual from the X-chromosome. He divided the non-coding sequences into 5 classes: 5 UTRs, 3 UTRs, introns, intergenic sequences within 2kb of a gene, and intergenic sequences more than 4kb from a gene. He then calculated a variety of population genetics statistics based on these sequences to determine if any of the non-coding DNA displays signatures of natural selection. I would expect that the UTRs (sequences that are transcribed, but not translated) are under more functional constraint than the intergenic regions and probably also display more signatures of positive selection. I also would expect that the introns would be constrained and have more evidence of positive selection (due to regulatory elements located within), and that the intergenic sequences located closer to genes are under more ...
Lytic herpes simplex virus 1 (HSV-1) infection triggers disruption of transcription termination (DoTT) of most cellular genes, resulting in extensive intergenic transcription. Similarly, cellular stress responses lead to gene-specific transcription downstream of genes (DoG). In this study, we performed a detailed comparison of DoTT/DoG transcription between HSV-1 infection, salt and heat stress in primary human fibroblasts using 4sU-seq and ATAC-seq. Although DoTT at late times of HSV-1 infection was substantially more prominent than DoG transcription in salt and heat stress, poly(A) read-through due to DoTT/DoG transcription and affected genes were significantly correlated between all three conditions, in particular at earlier times of infection. We speculate that HSV-1 either directly usurps a cellular stress response or disrupts the transcription termination machinery in other ways but with similar consequences. In contrast to previous reports, we found that inhibition of Ca\(^{2+}\) ...
From the nomenclature guidelines: Newly generated Transposon insertions, especially those located in apparently intergenic regions, may also be given Ti (transposon insertion) names. These consist of the designation identifying the laboratory of origin, the two letters Ti, and a number, all italicized. Example: eTi13 is an insertion of a Mos transposon into an intergenic region on LGIII ...
These reference sequences exist independently of genome builds. Explain. These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above. ...
These reference sequences exist independently of genome builds. Explain. These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above. ...
Up until relatively recently, researchers believed that the non-coding DNA sequences in the genomes of living things, including the human genome, had little, if any, function at all. Indeed, this non-coding DNA was often referred to as
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Over the years, many (though not all) Darwinists have stated that non-coding DNA is not worth exploring because it is thought to be mere evolutionary junk.
Hopkins researchers report that non-coding DNA, that contributes to inherited diseases like Parkinsons or mental disorders, may be more abundant than we realize.
Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive.. Here researchers from the Washington University School of Medicine characterized the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium they identified over three thousand unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls they discovered 111 differentially expressed lncRNAs, which they termed lung cancer associated lncRNAs (LCALs). A pan-cancer analysis of 324 ...
A central problem in the bioinformatics of gene regulation is to find the binding sites for regulatory proteins. One of the most promising approaches toward identifying these short and fuzzy sequence patterns is the comparative analysis of orthologous intergenic regions of related species. This analysis is complicated by various factors. First, one needs to take the phylogenetic relationship between the species into account in order to distinguish conservation that is due to the occurrence of functional sites from spurious conservation that is due to evolutionary proximity. Second, one has to deal with the complexities of multiple alignments of orthologous intergenic regions, and one has to consider the possibility that functional sites may occur outside of conserved segments. Here we present a new motif sampling algorithm, PhyloGibbs, that runs on arbitrary collections of multiple local sequence alignments of orthologous sequences. The algorithm searches over all ways in which an arbitrary number of
Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of Pseudomonas putida KT2440 to oxidative, osmotic, and membrane stress conditions at two time points was investigated via identification of differentially expressed mRNAs and sRNAs. A total of 440 small RNA transcripts were detected, where 10% correspond to previously annotated sRNAs, 40% are novel intergenic transcripts and 50% are novel transcripts antisense to annotated genes. Each stress elicits a unique response as far as the extent and dynamics of the transcriptional changes. Nearly 200 protein-encoding genes exhibited significant changes in all stress types, implicating their participation in a general stress response. Almost half of the sRNA transcripts were differentially expressed in at least one condition, suggesting possible functional roles in the cellular response to stress conditions. The data show a higher fraction of differentially
Polymorphisms in the oxyR-ahpC intergenic region One low level INH-resistant isolate displayed a G → A https://www.selleckchem.com/products/MK-1775.html substitution at position 32 upstream of the transcriptional start site of ahpC in the oxyR-ahpC intergenic region, which has previously. been shown to be involved in INH -resistance [15]. Combined sensitivity and specificity of katG and inhA promoter region for INH resistance Mutations in katG315 and -15C → T in inhA ACP-196 promoter region accounted together for 73% (33/44) INH -resistance. Since none of these mutations was observed in susceptible isolates, the combined specificity is 100%. Analysis of the rpoB gene responsible for RIF-resistance In this study, 7 RIFR isolates, and 100 RIF-sensitive (RIFs) clinical isolates were examined for mutations in a 158-bp fragment of rpoB gene. Of 7 RIFR isolates, resistance-associated. mutations in the core region of rpoB were found in all 7 (100.0%) isolates (Table 3). The nucleotide and amino ...
The genetic distances among primate lineages estimated from orthologous noncoding nucleotide sequences of β-type globin loci and their flanking and intergenic DNA agree closely with the distances (del
Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...
Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...
Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation ...
DNA (20 pmoles) was incubated in the presence (+) or in the absence (-) of 20 pmoles of OhrR. C-Binding of OhrR. to Motif 1 buy BMS202 and Motif 2 sequences. Gel shift assay of the intergenic region and the 60 bp double strand sequences containing at their centre the genuine 17 nt corresponding to Motif 1 and Motif 2, or mutated Motif 1 with AA in place of GC (Mut1 fragment) and CCC in place of AAA (Mut2 fragment). DNA (20 pmoles) was incubated with the indicated amount of OhrR in the presence of 1 mM DTT. We took advantage of restriction sites located within the ohr-ohrR intergenic region to define further OhrR binding site. ApoI cleaved once this fragment giving a 17 bp and a 96 bp fragment. In the presence of OhrR protein the longer fragment produced two shifted bands (Figure. 3). Two HpaII sites are located within ohr-ohrR intergenic region; HpaII cleavage produced three fragments of 26, 29 and 58 bp. In the presence of OhrR, the intensity of the 58 bp fragment decreased and two retarded ...
Hello , I m confused by the plethora of information about Humane Genes online, Some say there is a difference between Non-Coding DNA and Junk DNA, some say there is NOT. I read it in rationalwiki Non-coding DNA refers to portions of the genome that dont code for proteins, the Rest are Junk. As it...
On the Perl simulations front, Ive got the program running and used it to do the control simulations. The first controls use random sequences the same lengths and base compositions as the concatenated H. influenzae or N. meningitidis intergenic sequences, run with matrices specifying the corresponding USS or DUS core but with no recombination. These controls tell us what the baseline USS or DUS score is for a genome that hasnt experienced any accumulation. The second controls use the real H. influenzae or N. meningitidis intergenic sequences instead of random sequences, and run for a long time to see how long the sequences take to degenerate to the predetermined baselines (i.e. to become randomized with respect to USS or DUS). The score isnt a very sensitive indicator for this degeneration, as the genome may still contain an excess of the imperfectly matched cores, but Ill be able to tell this from the final analysis done at the end of the run ...
Not quite. What youre leaving out of this is the possibility of multiple levels of selection. In the original edition of The Selfish Gene (1976, p.76), Dawkins argued that the simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA. Cavalier-Smith (1977) drew a similar conclusion (before he had read Dawkins), and Doolittle and Sapienza (1980) and Orgel and Crick (1980) [yes, that Crick] independently developed the concept of selfish DNA a few years later. This is an explicitly multi-level selection approach because it specifies that non-coding DNA can be present due to selection within the genome rather than exclusively on the organism (or gene, in Dawkinss case) (see, e.g., Gregory 2004, 2005). (Incidentally, this idea of parasitic DNA dates back at least to 1945, when Gunnar Östergren characterized B chromosomes in this fashion). Of course, they tended to ...
Principal Investigator:GOTO Yuji, Project Period (FY):2010 - 2012, Research Category:Grant-in-Aid for Young Scientists (B), Research Field:Genetics/Genome dynamics
It is the relationship between the gene and the endo-environment of the organism, which it participates in the creation of, that mediates the activity of the gene. The study of the gene must also include the study of all that might happen the gene, which is a set of possibilities constrained and shaped by the organisms internal environment, which in turn is mediated by its external environment. Furthermore, the expression of the gene is moderated by the non-coding DNA in the chromosomes of the organisms (which may act as an analogue for the systems of organisation between people if we continue to stretch the metaphor) thus we can imagine contrasting mutations in the non-coding DNA with cultural adaptations, and imagine them also diffusing across the boundaries of societies, regulating the activities of people, who are akin to individual genes, in the Neo-Darwinian frame ...
The existence of functional, non-protein-coding DNA is all too frequently portrayed as a great surprise uncovered by genome sequencing projects, both in large media outlets and in scientific publications that should have better quality control in place.
Complete information for LINC00868 gene (RNA Gene), Long Intergenic Non-Protein Coding RNA 868, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
Complete information for LINC02003 gene (RNA Gene), Long Intergenic Non-Protein Coding RNA 2003, including: function, proteins, disorders, pathways, orthologs, and expression. GeneCards - The Human Gene Compendium
SecureSeal™ imaging spacers are ultrathin adhesive spacers which peel and stick to coverglass or microscope slides to confine specimens without the need for compression.Layer multiple spacers to custom build a chamber to any desired depthFor high resolution microscopy, sandwich specimen and spacer between two No. 0 coverglass
Conserved Fragments of Transposable Elements In Intergenic Regions: Evidence for Widespread Recruitment of MIR- and L2-derived Sequences Within the Mouse and Human ...
This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ.. ...
This track shows predictions from the Genscan program written by Chris Burge. The predictions are based on transcriptional, translational and donor/acceptor splicing signals as well as the length and compositional distributions of exons, introns and intergenic regions. For more information on the different gene tracks, see our Genes FAQ.. ...
A new study shows that there are regions of non-coding DNA that may have a connection to cancer growth and progression if altered.
Washington, DC - As members of Congress return to Capitol Hill today, 85 farm and farmer support organizations sent letters to the U.S. Environmental Protection Agency (EPA) and U.S. Department of Agriculture (USDA) urging them to better protect farm families from an unprecedented… Read More. ...
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important.
We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available,
It is thought that virtually all protein-coding genes in the human genome have already been discovered, yet a significant fraction of genetic variants associated with human disease map to the intergenic space. Furthermore, genome-wide studies of transcription have found that these intergenic regions are pervasively transcribed into different classes of RNA molecules. These include long intervening noncoding RNAs (lincRNAs), which contain at least 200 bases, and similarly to mRNAs, begin with a 5 cap and end with a poly(A) tail. Thousands of lincRNA genes were recently reported in human and mouse and several lines of evidence suggest that many of them are functionally important. For example, lincRNA expression varies across tissues and is commonly dysregulated in human disease, including cancer. Furthermore, the sequences of lincRNA exons were significantly conserved during vertebrate evolution. Accumulating evidence shows that lincRNAs play pivotal regulatory roles in diverse biological ...
It has been quite some time since the last update to the Quotes of interest series on junk DNA. Most of the posts have sought to demonstrate that the exhausting cliché that scientists dismissed possible functions for non-coding DNA until recently is false. Therefore, I have provided many quotes indicating that many (if not most) biologists continued to consider possible functions for various non-coding elements throughout the mythical period of neglect. This time, I want to discuss an example in which a particular kind of non-coding sequence was considered as probably non-functional - but because of knowledge about its biology, not because no function could be imagined.. The elements under discussion are endogenous retroviruses (ERVs) which, as the name suggests, are viral-like sequences that exist within the genome. Depending on who you ask, they are either very similar to or are interchangeable with long terminal repeat (LTR) retrotransposons. ERVs make up approximately 8% of the human ...
Title Minute Intergenic Rearrangement as a Cause of Apparent Gene Mutation Author Muller, H.J; Prokofyeva, A.; and Raffel, D. Binding PAPERBACK Publisher Nature, Vol. 135, p. 253, Feb. Publisher Year 1935 Condition Very Good Description Very good condition. First edition. Offprint. Original wrappers. * Genetics. Scie
Are you proposing a thought experiment in which we subtract all the repeat derived sequences (minus the small proportion of bases that regulate gene expression), and most of the the non regulatory intergenic sequences, reducing intron and intergenic sizes by, say 90%, such that we end up with a small number of short chromosomes (say 50 Mb in size - since we know the current division processes can cope with such a size) but keeping the necessary telomeric and centromeric repeats. This would be done with all members of the human species such that all the current copy number polymorphisms and regulatory snps are maintained and all genes are allowed up to 2000bp of regulatory sequences (although we will allow a proportion of genes to have larger regulatory regions). The ultimate result is a human genome that is say, 90% smaller than the current one. You suggest that the current cellular machinery would be able to cope with this change, such that there would be no viability or evolutionary ...
Daily News Thousands of Mutations Accumulate in the Human Brain Over a Lifetime Single-cell genome analyses reveal the amount of mutations a human brain cell will collect from its fetal beginnings until death.. ...
Daily News How Gaining and Losing Weight Affects the Body Millions of measurements from 23 people who consumed extra calories every day for a month reveal changes in proteins, metabolites, and gut microbiota that accompany shifts in body mass.. ...
Ian Musgrave has a good summary of genes appearing from non-coding DNA (ORFans) on the Pandas Thumb. I have written about ORFans here and here (dudes gotta link to himself sometimes). Ians post is targeted at some claims made by the creationist Paul Nelson, but he focuses more on the science that on the ignorant blowhard.. ...
CNES CNES - CNRS/INSU JOINT PRESS RELEASE: The Swedish Odin science mission, in which France is participating, is operating a 250-kg satellite launche
The specific name is without the a I.e. cespitosa not caespitosa . It applies to the other photo of C. cespitosa as well. (Sent: [email protected]) ...
Just talking with my family and they say Im crazy....anyone else do a cleanse. I do the master cleanse for 10 to 15 days to get the junk out.
TY - JOUR. T1 - The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. AU - Ranzani, Valeria. AU - Rossetti, Grazisa. AU - Panzeri, Ilaria. AU - Arrigoni, Alberto. AU - Bonnal, Raoul J P. AU - Curti, Serena. AU - Gruarin, Paola. AU - Provasi, Elena. AU - Sugliano, Elisa. AU - Marconi, Maurizio. AU - De Francesco, Raffaele. AU - Geginat, Jens. AU - Bodega, Beatrice. AU - Abrignani, Sergio. AU - Pagani, Massimiliano. PY - 2015/2/17. Y1 - 2015/2/17. N2 - Long noncoding RNAs are emerging as important regulators of cellular functions, but little is known of their role in the human immune system. Here we investigated long intergenic noncoding RNAs (lincRNAs) in 13 subsets of T lymphocytes and B lymphocytes by next-generation sequencing-based RNA sequencing (RNA-seq analysis) and de novo transcriptome reconstruction. We identified over 500 previously unknown lincRNAs and described lincRNA signatures. Expression of linc-MAF-4, ...
Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were
Although unicellular eukaryotes such as yeast have either no introns or very few, metazoans and especially vertebrate genomes have a large fraction of non-coding DNA. For instance, in the human genome only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA.[5] This can provide a practical advantage in omics-aided health care (such as precision medicine) because it makes commercialized whole exome sequencing a smaller and less expensive challenge than commercialized whole genome sequencing. The large variation in genome size and C-value across life forms has posed an interesting challenge called the C-value enigma. Across all eukaryotic genes in GenBank there were (in 2002), on average, 5.48 exons per gene. The average exon encoded 30-36 amino acids.[6] While the longest exon in the human genome is 11555 bp long, several exons have been found to be only 2 bp long.[7] A single-nucleotide exon has been reported from the Arabidopsis ...
BACKGROUND Long non-coding RNAs (lncRNAs) have a role in physiological and pathological processes, including cancer. The aim of this study was to investigate the expression of the long intergenic non-protein coding RNA 665 (LINC00665) gene and the cell cycle in hepatocellular carcinoma (HCC) using d …
Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052836],Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052836],See cases [RCV000052836 ...
from Zone in With Zon. A Short Walk in the Wondrous, Wacky World of Long-and now Circular-Noncoding RNAs. Im pleased by how much I learn when researching topics for new content, and this was certainly the case for long noncoding RNA (lncRNA), which was briefly mentioned in my last blog post, Ripples from the 2013 TIDES Conference. The topic piqued my interest so I set out to find out more. Plowing through lncRNA (aka lincRNA = large intergenic non-coding RNA) literature I quickly realized that there was an enormous amount of information, and the big challenge would be to capture some intriguing aspects without getting bogged down in technical weeds or being overly simplistic. In what follows there is a super brief introduction to what lncRNAs are and what they do-the latter is controversial-along with an appreciation for why lncRNAs are indeed a structurally and functionally wondrous class of nucleic acids that now encompass circular molecules. Maybe-to borrow from Forrest Gump-lncRNAs are ...
Wind two strands of elastic, eventually it will knot, ultimately it will double up on itself. Separate the strands. From the point of unwinding forces will be directed to different regions and the separation will naturally return to the wound state of the band. Do the same with each of 10 different bands or strings of any type, they will all behave in much the same way. For a given section of DNA being transcribed, the effect of separation will be much the same. For a given gene, there will be sequences that can tolerate force to greater or lesser degrees. For different transcripts, of a gene variation at those sequences may be crucial to the integrity of transcription machinery that separates DNA strands to initiate replication to RNA and for the outcome.. Cellular biology is enormously complex in all regards. The physics of molecular interaction, fluid dynamics, and chemistry combine in a system where cause and effect is near impossible to predict. At the most elementary level we hypothesize ...
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save-buffer) (vc-revert-buffer yes)) These did not work but instead I got an error message about the wrong number of arguments and other junk. How fix ...
All of these genes are encoded on the same DNA strand. For this reason, it was proposed that DUF1874 motif examples likely ... DUF1874 are frequently present in consecutive intergenic regions between consecutive genes. ... The DUF1874 motif has not (as of 2018) been detected in any classified organism, but rather is known only in metagenomic DNA ... attC sites are singled-stranded DNA elements that are used by integrons to enabling the rearrangement and integration of new ...
May 2010). "The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA". BMC Plant ... Funk HT, Berg S, Krupinska K, Maier UG, Krause K (August 2007). "Complete DNA sequences of the plastid genomes of two parasitic ... Dinoflagellate plastid genomes are not organised into a single circular DNA molecule like other plastid genomes, but into an ... Sugiura C, Kobayashi Y, Aoki S, Sugita C, Sugita M (September 2003). "Complete chloroplast DNA sequence of the moss ...
Microarrays use complementary DNA probes to bind to possible sRNA loci in intergenic regions. Northern blotting can reveal ... June 2001). "Novel small RNA-encoding genes in the intergenic regions of Escherichia coli". Curr. Biol. 11 (12): 941-950. doi: ... It is now known that most bacterial sRNAs are encoded by free-standing genes located in the intergenic regions (IGR) between ...
Single-stranded DNA can occur during plasmid replication. Weinberg Z, Lünse CE, Corbino KA, Ames TD, Nelson JW, Roth A, Perkins ... "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids ... In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. ... its potential relationship to plasmid replication leaves open the possibility that it functions as a single-stranded DNA. ...
"Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences". Genome ... "On the 30th Anniversary of DNA Sequencing in Population Genetics , I wish you'd made me angry earlier". Archived from the ...
Gonzalez IL, Sylvester JE (1995). "Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer ... McCallum FS, Maden BE (1986). "Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and ... Sylvester JE, Petersen R, Schmickel RD (1990). "Human ribosomal DNA: novel sequence organization in a 4.5-kb region upstream ... 1991). "Identification of p53 as a sequence-specific DNA-binding protein". Science. 252 (5013): 1708-1711. Bibcode:1991Sci... ...
Gonzalez IL, Sylvester JE (1995). "Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer ... regulated by DNA replication and DNA damage checkpoint pathways via localization of small subunits; RNR3 has a paralog, RNR1, ... McCallum FS, Maden BE (1986). "Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and ... Sylvester JE, Petersen R, Schmickel RD (1990). "Human ribosomal DNA: novel sequence organization in a 4.5-kb region upstream ...
SSLPs are repeated sequences over varying base lengths in intergenic regions of deoxyribonucleic acid (DNA). Variance in the ... a difference in DNA sequence amongst individuals. ...
Gonzalez IL, Sylvester JE (1995). "Complete sequence of the 43-kb human ribosomal DNA repeat: analysis of the intergenic spacer ... 2000). "The DNA sequence of human chromosome 21". Nature. 405 (6784): 311-319. Bibcode:2000Natur.405..311H. doi:10.1038/ ... McCallum FS, Maden BE (1986). "Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and ... Sylvester JE, Petersen R, Schmickel RD (1990). "Human ribosomal DNA: novel sequence organization in a 4.5-kb region upstream ...
Most ARRPOF motif examples are found in environmental DNA samples, and the host organism is unknown. The only classified ... "Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions". Nucleic Acids ... In terms of secondary structure, RNA and DNA are difficult to distinguish when only sequence information is available. Weinberg ... Because plasmid replication involves DNA molecules that are transiently single-stranded, it was also suggested that it is ...
Lundwall A (1996). "The structure of the semenogelin gene locus--nucleotide sequence of the intergenic and the flanking DNA". ... 2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ...
This unusual stretch is hypothesized to be important for DNA binding. The two intergenic noncoding portions of the genome are ... The genome of CaCV is made up of a single circular strand of DNA 2,063 nucleotides in length. DNA in general is made up of four ... Rep cleaves a location of the DNA exposing a free 3' OH for viral or cellular polymerase to act on. DNA replication occurs in ... PCR analysis and sequencing of the treated organ tissues revealed large amounts of CaCV DNA and canine parvovirus-2 DNA and ...
DNA-A typically encodes products for DNA replication, controls gene expression, and controls insect transmission. This suggests ... They are separated by an intergenic region (IR) which contains a conserved stem-loop sequence motif. Virus particles enter the ... Many mechanisms of (-) DNA replication initiation in the SPLCV have been identified but this first step in the replication ... The presence of DNA primase along with polymerase activity has been noted as one method of replication initiation. During ...
It was based on 2 regions of chloroplast DNA. These were the rbcL gene and the intergenic spacer between the transfer RNA genes ... Only a sampling of more species and more DNA from each will determine whether these groups are monophyletic or not. ... Stellera, for example, is nested within Wikstroemia, at least (see the phylogenetic tree below). A recent comparison of DNA ... nuclear ribosomal DNA) were used. All of the clades that were strongly supported in the previous study were recovered with even ...
Intergenic (also known as extragenic) suppression relieves the effects of a mutation in one gene by a mutation somewhere else ... Examples of such pathways include receptor-ligand interactions as well as the interaction of components involved in DNA ... Intergenic suppression is useful for identifying and studying interactions between molecules, such as proteins. For example, a ... These Intergenic suppressions are also likely to persist in the population. When these compensatory mutations are established ...
... of DNA Extraction Methods for Microbial Community Analysis in Indonesian Tempe Employing Amplified Ribosomal Intergenic Spacer ... Isolated from Tempe based on Enterobacterial Repetitive Intergenic Consensus-Polymerase Chain Reaction (ERIC-PCR)". HAYATI ... DNA sequence and mechanism of transfer". Journal of Bacteriology. 182 (1): 81-90. doi:10.1128/jb.182.1.81-90.2000. PMC 94243. ...
"Discrimination of Streptomyces albidoflavus strains based on the size and number of 16S-23S ribosomal DNA intergenic spacers". ...
hnRNPs also play a role in DNA damage response in coordination with p53. hnRNP K is rapidly induced after DNA damage by ... p53 regulates a large group of RNAs that are not translated into protein, called large intergenic noncoding RNAs (lincRNAs). ... BRCA1 in particular causes G2/M cell cycle arrest in response to DNA damage via the CHEK1 signaling cascade. hnRNP C is ... Through these genes, hnRNP is necessary to induce cell-cycle arrest in response to DNA damage by ionizing radiation. HER2 is ...
Many recurring DNA sequences were recognized for newt Hox clusters, counting an enrichment of DNA transposon-like sequences ... Furthermore, it was found that the length of introns and intergenic regions varied. In particular, the distance between HoxD13 ... and non-random accumulations of DNA transposons in newts and lizards. Researchers found that the non-random accretion of DNA- ... The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding DNA ...
The difference of mitochondrial DNA between fungal species is due to the variations in intergenic region, intron, and gene ... Genome size of mitochondrial DNA in M. nanum is 24,105 basepairs. The DNA is AT-rich and the GC content is only 24.47%. M. ... Mitochondrial DNA sequences have been used for phylogenetic studies in the dermatophytes. A typical fungal mitochondrial DNA ...
The guide RNA are mainly transcribed from the intergenic region of DNA maxicircle and these are complementary to mature mRNA. ... which is a short DNA sequence usually 2-6 base pairs in length that follows the DNA region targeted for cleavage by the CRISPR ... They have a large segment of highly organized DNA segments in their mitochondria. This mitochondrial DNA is circular and is ... Guide RNA (gRNA) is a piece of RNAs that function as guides for RNA- or DNA-targeting enzymes, which they form complexes with. ...
Studies to find their evolutionary relationship using chloroplast (RuBisCO gene) or mitochondrial DNA (intergenic spacer) ... Genetic analysis using microsatellite markers (short DNA sequences) suggests that a divergence between the two species occurred ...
"Increased levels of the long intergenic non-protein coding RNA POU3F3 promote DNA methylation in esophageal squamous cell ... The encoded protein recognizes an octamer sequence in the DNA of target genes. This protein may play a role in development of ...
... using sequence variations of an intron and two intergenic spacers of chloroplast DNA. Australian Systematic Botany 13, 745-754 ... based on chloroplast DNA sequence data. In B. Klitgaard and A. Bruneau (eds), Advances in Legume Systematics,part 10, pp. 197- ...
Intergenic regions account for ~ 30% of the genome and contain clusters of tandem repeats whose unit length is ~20 bp. ... Transcribed genes are found on both DNA strands. The standard genetic code is used for translation. Encoded genes include those ...
If DNA repair is deficient, DNA damage tends to accumulate. Such excess DNA damage can increase mutational errors during DNA ... In healthy cells, CpG dinucleotides of lower densities are found within coding and non-coding intergenic regions. Expression of ... Reduced DNA repair likely allows accumulation of DNA damages. Error prone translesion synthesis past some of these DNA damages ... a DNA repair gene; APC, a cell cycle regulator; MLH1, a DNA-repair gene; and BRCA1, another DNA-repair gene. Indeed, cancer ...
The DNA sequences for TUFs reside in the intergenic or intronic regions of the genome, which is often called junk DNA. This ... Transcripts of unknown function (TUFs) is the name that has been suggested for known RNA transcripts of DNA whose function is ... pseudogenes TUFs that reside on the same strand as protein-coding genes in the intronic region or entirely in the intergenic ...
... intergenic splicing may be a common phenomenon". DNA Res. 12 (5): 365-72. doi:10.1093/dnares/dsi017. PMID 16769693. Hills R, ... 2007). "MATN and LAPTM are parts of larger transcription units produced by intergenic splicing: ...
... intergenic splicing may be a common phenomenon". DNA Res. 12 (5): 365-72. doi:10.1093/dnares/dsi017. PMID 16769693. Liu Y, ... Hartley JL, Temple GF, Brasch MA (2001). "DNA cloning using in vitro site-specific recombination". Genome Res. 10 (11): 1788-95 ... 2007). "MATN and LAPTM are parts of larger transcription units produced by intergenic splicing: ... DNA Res. 12 (2): 117-26. doi:10.1093/dnares/12.2.117. PMID 16303743. Mehrle A, Rosenfelder H, Schupp I, et al. (2006). "The ...
Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of ... Phylogeny and biogeography of Panax L.(the ginseng genus, Araliaceae): inferences from ITS sequences of nuclear ribosomal DNA. ... The evolution of Araliaceae: a phylogenetic analysis based on ITS sequences of nuclear ribosomal DNA. Systematic Botany, 144- ... A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA. American ...
... spans about 90 million base pairs (the building material of DNA) and represents just under 3% of the total DNA in ... LINC00273 encoding protein Long intergenic non-protein coding RNA 273. *LOC124220: encoding protein Zymogen granule protein 16 ...
Fitting population genetics models (either forward time[15] or backward time) to DNA data to make inferences about demographic ... An untouched project in the development of computational genomics is the analysis of intergenic regions. Studies show that ... This data is collected from DNA, RNA, and other biological structures. Areas of focus include determining the characteristics ... Using DNA data to reconstruct the tree of life with computational phylogenetics ...
From the Dolan DNA Learning Center of Cold Spring Harbor Laboratory.. *RNAi screens in C. elegans in a 96-well liquid format ... Endogenously expressed miRNAs, including both intronic and intergenic miRNAs, are most important in translational repression[67 ... so it does not modify or change DNA in a deleterious effect.[166] SiRNA can also be used to produce a specific response in a ... nine miRNAs have been identified as epigenetically altered and effective in down regulating DNA repair enzymes.[32] ...
... spans almost 200 million base pairs (the building material of DNA) and represents about 6.5 percent of the total ... LINC00312: Long intergenic non-protein-coding RNA 312. *MITF: microphthalmia-associated transcription factor ... C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.. *C3orf23: encoding protein Uncharacterized protein ...
... of the genome being intergenic DNA.[5] This can provide a practical advantage in omics-aided health care (such as precision ... The term exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts. In RNA ... gene splices into the exon that is contained in the insertional DNA. This new exon contains the ORF for a reporter gene that ... metazoans and especially vertebrate genomes have a large fraction of non-coding DNA. For instance, in the human genome only 1.1 ...
... inflated with intronic and intergenic DNA." BMA Plant Biology, 2010. DOI: 10.1186/1471-2229-10-83 Zhao, R., Cao, Y., Xu, H., Lv ...
The host's DNA polymerase converts the single-stranded DNA into double-stranded DNA. 6. Late genes are now transcribed by the ... Size variability within the groups occurs mainly as a result of insertions and deletions of the intergenic regions. Viruses are ... Protein A* inhibits host DNA replication. Unlike protein A it is capable of cleaving the phi X viral DNA in the presence of ... a small DNA-binding protein J (25 - 40 amino acids in length) and DNA pilot protein H. Assembly of the viron uses two ...
It is caused by mutations in the gene WRN that encodes a protein with essential roles in repair of DNA damage. Mutations in the ... Sherald AF (September 1981). "Intergenic suppression of the black mutation of Drosophila melanogaster". Molecular & General ... The under-replication of rDNA occurs resulting in only 20% of DNA compared to the brain. Compare to the 47%, less rDNA in ... More than 60% of the genome appears to be functional non-protein-coding DNA[72] involved in gene expression control. ...
"Intergenic" refers to long non-coding RNAs that are transcribed from non-coding DNA sequences between protein-coding genes, ... Additionally, it was proposed to classify intergenic RNA domains of at least 50 kb in length as "very long intergenic non- ... DNA and Cell Biology. 25 (3): 135-41. doi:10.1089/dna.2006.25.135. PMID 16569192. Lin R, Maeda S, Liu C, Karin M, Edgington TS ... For example, the induction of an antisense transcript by a genetic mutation led to DNA methylation and silencing of sense genes ...
The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon ... November 1996). "Nested retrotransposons in the intergenic regions of the maize genome". Science. 274 (5288): 765-8. Bibcode: ... DNA transposons[edit]. A. Structure of DNA transposons (Mariner type). Two inverted tandem repeats (TIR) flank the transposase ... A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This ...
Papaver and Related Genera Based on DNA Sequences from ITS Nuclear Ribosomal DNA and Plastid trnL Intron and trnL-F Intergenic ...
DNA templated transcription, with some alternative splicing mechanism is the method of transcription. The virus exits the host ... A stem loop structure with a conserved nonanucleotide motif is located at the 5' intergenic region of circovirus genomes and is ...
Bidirectional promoters are short (,1 kbp) intergenic regions of DNA between the 5' ends of the genes in a bidirectional gene ... a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA ... which in turn are often brought to the promoter DNA by an activator protein's binding to its own DNA binding site nearby.. In ... This process of promoter location has been attributed to the structure of the holoenzyme to DNA and sigma 4 to DNA complexes.[ ...
DNA (red)/ Kinetochores (green). Holocentric organisms, including C. elegans, assemble diffuse kinetochores along the entire ... Introns make up 26% and intergenic regions 47% of the genome. Many genes are arranged in clusters and how many of these are ... Most changes are minor, adding or removing only a few base pairs of DNA. For example, the WS202 release of WormBase (April 2009 ... "C. elegans mre-11 is required for meiotic recombination and DNA repair but is dispensable for the meiotic G(2) DNA damage ...
... while important genes participating in the DNA-to-RNA transcription, protein translation and DNA/RNA replication are retained. ... The decrease in genome size is due to loss of protein coding genes and not due to lessening of inter-genic regions or open ... There is a drastic reduction in its genome size, as many genes are lost during the process of metabolism, and DNA repair and ...
LINC00511: encoding protein Long intergenic non-protein coding RNA 511. *LINC00674 encoding protein Long intergenic non-protein ... Chromosome 17 spans more than 83 million base pairs (the building material of DNA) and represents between 2.5 and 3% of the ...
Y-chromosome DNA. Kayser et al. (2006) found four members of O-M95, four members of O-M122(xM134), one member of C-M217, and ... 1999) said that the mtDNA 9‐bp deletion frequencies in the intergenic COII/tRNALys region for Vietnamese (23.2%) and ... a b Schurr, Theodore G. & Wallace, Douglas C. (2002). Mitochondrial DNA Diversity in Southeast Asian Populations. Human Biology ... 2000). Y chromosomal DNA variation in East Asian populations and its potential for inferring the peopling of Korea. Journal of ...
Bidirectional promoters are short (,1 kbp) intergenic regions of DNA between the 5' ends of the genes in a bidirectional gene ... a large proportion of carcinogenic gene silencing is a result of altered DNA methylation (see DNA methylation in cancer). DNA ... In genetics, a promoter is a sequence of DNA to which proteins bind that initiate transcription of a single RNA from the DNA ... which in turn are often brought to the promoter DNA by an activator protein's binding to its own DNA binding site nearby.. In ...
In somatic tissues, only 10% of CpG islands are methylated, the majority of them being located in intergenic and intragenic ... DNA methylation is a process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA ... Abbreviations: S-Adenosyl-L-homocysteine (SAH), S-adenosyl-L-methionine (SAM), DNA methyltransferase (DNA MTase), Uracil-DNA ... Ancient DNA methylation reconstruction, a method to reconstruct high-resolution DNA methylation from ancient DNA samples. The ...
... refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series ... Additional studies have demonstrated that codon biases can be statistically predicted in prokaryotes using only intergenic ... Fox JM, Erill I (June 2010). "Relative codon adaptation: a generic codon bias index for prediction of gene expression". DNA Res ... Codon usage in noncoding DNA regions can therefore play a major role in RNA secondary structure and downstream protein ...
1h15: X-RAY CRYSTAL STRUCTURE OF HLA-DRA1*0101/DRB5*0101 COMPLEXED WITH A PEPTIDE FROM EPSTEIN BARR VIRUS DNA POLYMERASE ... Wu S, Saunders TL, Bach FH (1987). "Polymorphism of human Ia antigens generated by reciprocal intergenic exchange between two ...
The DNA-transposase complex then inserts its DNA cargo at specific DNA motifs elsewhere in the genome, creating short TSDs upon ... "Nested retrotransposons in the intergenic regions of the maize genome". Science. 274 (5288): 765-8. Bibcode:1996Sci...274.. ... A DNA polymerase fills in the resulting gaps from the sticky ends and DNA ligase closes the sugar-phosphate backbone. This ... In bacteria, transposons can jump from chromosomal DNA to plasmid DNA and back, allowing for the transfer and permanent ...
The choanoflagellates have a circular mitochondrial DNA genome with long intergenic regions. This is four times as large as ...
Ancient DNA evidenceEdit. DNA evidence indicates Y. pestis infected humans 5,000 years ago in Bronze Age Eurasia,[47] but ... Intergenic RNA thermometer. Pathogenesis and immunityEdit. Oriental rat flea (Xenopsylla cheopis) infected with the Y. pestis ... 2013). "Yersinia pestis DNA from skeletal remains from the 6th century AD reveals insights into Justinianic Plague". PLoS ... In 2012, researchers in Germany collected samples of Yersinia pestis from gravesites with a view to reconstructing the DNA of ...
Attenuation involves a provisional stop signal (attenuator), located in the DNA segment that corresponds to the leader sequence ... M. Ballarino, "Coupled RNA Processing and Transcription of Intergenic Primary MicroRNAs", MOLECULAR AND CELLULAR BIOLOGY, Oct. ... once it forms RNA polymerase will disassociate from the DNA and transcription of the structural genes of the operon will not ... the ribosomes begin translating the mRNA while RNA polymerase is still transcribing the DNA sequence. This allows the process ...
DNA damage response, detection of DNA damage. • nucleotide-excision repair, DNA incision, 5'-to lesion. • DNA ligation. • DNA ... Audas TE, Jacob MD, Lee S (January 2012). "Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding ... nucleotide-excision repair, DNA gap filling. • DNA synthesis involved in DNA repair. • cellular response to UV. • DNA ... DNA-directed DNA polymerase activity. • nuclease activity. • exonuclease activity. • hydrolase activity. Cellular component. • ...
Additional support for two subgenera of Anemia (Schizaeaceae) from data for the chloroplast intergenic spacer region trnL-F and ... Molecular studies of representative species in the fern genus Elaphoglossum (Dryopteridaceae) based on cp DNA sequences rbcL, ...
About 10% of Angelman syndrome cases are caused by a mutation in the UBE3A gene, and another 3% result from a defect in the DNA ... LINC00926 encoding protein Long intergenic non-protein coding RNA 926. *MESDC2: encoding protein LDLR chaperone MESD ... Chromosome 15 spans about 101 million base pairs (the building material of DNA) and represents between 3% and 3.5% of the total ... Rarely, the condition is caused by an abnormality in the DNA region that controls the activity of genes on the paternal ...
Intergenic DNA, as the name suggests, is DNA between genes which does not code for proteins. Hope this helps gabriel vargas md/ ... Re: What is intergenic DNA compared to introns and exons?. Date: Fri May 5 16:40:29 2000. Posted By: Gabriel Vargas M.D.,Ph.D ...
A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast. J A Nickoloff, E Y Chen, and F ... A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast ... A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast ... A 24-base-pair DNA sequence from the MAT locus stimulates intergenic recombination in yeast ...
Molecular phylogeny ofNothofagus (Nothofagaceae) based on theatpB-rbcL intergenic spacer of the chloroplast DNA. ... Ribosomal and chloroplast DNA restriction site mutations and the radiation ofRobinsonia (Asteraceae: Senecioneae) on the Juan ... The phylogeny of the genus was elucidated by the sequences ofatpB-rbcL intergenic spacer of cpDNA for the better understanding ... Hasebe, M. andIwastuki, K. 1990.Adiantum capillus veneris chloroplast DNA clone bank: as useful heterologous probes in the ...
Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex. ...
Sequence Analysis of the Ribosomal DNA Intergenic Spacer 1 Regions of Trichosporon Species. Takashi Sugita, Masamitsu Nakajima ... Sequence Analysis of the Ribosomal DNA Intergenic Spacer 1 Regions of Trichosporon Species ... Sequence Analysis of the Ribosomal DNA Intergenic Spacer 1 Regions of Trichosporon Species ... Sequence Analysis of the Ribosomal DNA Intergenic Spacer 1 Regions of Trichosporon Species ...
Phylogeny of Camassia (Agavaceae) Inferred from Plastid rpl16 Intron and trnD-trnY-trnE-trnT Intergenic Spacer DNA Sequences: ... Inferred from Plastid rpl16 Intron and trnD-trnY-trnE-trnT Intergenic Spacer DNA Sequences: Implications for Species ... Inferred from Plastid rpl16 Intron and trnD-trnY-trnE-trnT Intergenic Spacer DNA Sequences: Implications for Species ... We estimated the phylogeny of Camassia using two noncoding plastid DNA regions: rpl16 intron and trnD-trnY-trnE-trnT spacers, ...
... and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, ... of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer ... Keywords: ribosomal DNA; intergenic spacer; 45S rDNA; Brassica oleracea var. capitata ribosomal DNA; intergenic spacer; 45S ... Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. ...
Intergenic" by people in this website by year, and whether "DNA, Intergenic" was a major or minor topic of these publications. ... "DNA, Intergenic" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH (Medical Subject ... Any of the DNA in between gene-coding DNA, including untranslated regions, 5 and 3 flanking regions, INTRONS, non-functional ... Below are the most recent publications written about "DNA, Intergenic" by people in Profiles. ...
PCR Analyses of tRNA Intergenic Spacer, 16S-23S Internal Transcribed Spacer, and Randomly Amplified Polymorphic DNA Reveal ... PCR Analyses of tRNA Intergenic Spacer, 16S-23S Internal Transcribed Spacer, and Randomly Amplified Polymorphic DNA Reveal ... PCR Analyses of tRNA Intergenic Spacer, 16S-23S Internal Transcribed Spacer, and Randomly Amplified Polymorphic DNA Reveal ... PCR Analyses of tRNA Intergenic Spacer, 16S-23S Internal Transcribed Spacer, and Randomly Amplified Polymorphic DNA Reveal ...
Two-dimensional DNA barcodes (i.e., QR codes) for the psbK-psbI and psbK-psbI + atpF-atpH regions ... By contrast, the intergenic spacers psbK-psbI and atpF-atpH were variable loci distinct for the medicinal plant < ... DNA barcoding is an emerging technology for rapid and accurate species identification. In this study, six candidate ... chloroplastid barcodes were investigated for the authentication of R. stricta. We compared the DNA sequences from fifty ...
PCR primer pair in examination of methanogenic Archaeain a digester treating plant biomass was evaluated by Ribosmal Intergenic ... similarity to the above-mentioned DNA sequence of M. barkeri. The analyzed DNA sequences were different in length. The MT-1 DNA ... Ribosomal Intergenic Spacer Analysis. After successful DNA amplification, the PCR products were separated in 8 % polyacrylamide ... Specific primers spanning Ribosomal Intergenic Spacer region were designed on the base of DNA sequences available in the ...
Interestingly, lincRNA genes appear to be much less susceptible to CNV in comparison to both protein-coding and intergenic ... Interestingly, lincRNA genes appear to be much less susceptible to CNV in comparison to both protein-coding and intergenic ... 700 nt throughout the intergenic region of the human genome. We mapped annotated or putative lincRNA genes to a subset of ... 700 nt throughout the intergenic region of the human genome. We mapped annotated or putative lincRNA genes to a subset of ...
Amplification of the VT-Intergenic Regions (IG Regions).. From the viral DNA obtained from urine (see above), the 610-bp IG ... A 610-bp segment of JCV DNA was amplified from each urine sample, and its DNA sequence was determined. A worldwide phylogenetic ... that can be calculated from mitochondrial DNA sequence diversities (37, 39, 40). Furthermore, analysis of mitochondrial DNA ... VT-intergenic region (sequence);. RFLP,. restriction fragment length polymorphism;. NJ tree,. neighbor joining tree. ...
DNA upon infection of E. coli with a filamentous helper phage, replication in S … ... A family of yeast expression vectors containing the phage f1 intergenic region Gene. 1987;52(2-3):225-33. doi: 10.1016/0378- ... The multiple cloning site as well as the ori and intergenic region of the phage f1 have been cloned in two orientations for ... DNA upon infection of E. coli with a filamentous helper phage, replication in Saccharomyces cerevisiae based on the 2 mu ...
Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host ... The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate ... Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host ... Long-range function of an intergenic retrotransposon Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12992-7. doi: 10.1073/pnas. ...
DNA extraction. M. tuberculosis and M. bovis DNA were extracted from subcultures on DifcoTM Lowenstein and Stonebrink media, ... The Enterobacterial Repetitive Intergenic Consensus sequence (ERIC) are repetitive elements of 126 bp and appear to be ... standardization of the mycobacterial DNA concentration should be carried out to have more constant intensities of the DNA bands ... DNA was further extracted by 2 volumes of phenol-chloroform-isoamyl alcohol (25:24:1, v/v), followed by two steps of ...
An automated ribosomal intergenic spacer analysis of fresh and incubated fecal DNA confirmed association between microbial ... DNA Extraction and Automated Ribosomal Intergenic Spacer Analysis (ARISA). Fresh and incubated feces samples used to analyze ... An automated ribosomal intergenic spacer analysis of fresh and incubated fecal DNA confirmed association between microbial ... VOCs also underwent DNA extraction and microbial fingerprinting by means of automated ribosomal intergenic spacer analysis ( ...
Intergenic Spacers. Intergenic spacers in Chara mtDNA vary from 0 to 1173 bp, with an average size of 91 bp and only three ... DNA Cloning and Sequencing. A random clone library was prepared from the Chara organelle DNA fraction as described previously ( ... A fraction containing chloroplast DNA and mitochondrial DNA (mtDNA) was obtained using the isolation procedure described by ... After hybridization of the clones with the original DNA used for cloning, DNA templates from positive clones were prepared with ...
DNA, Intergenic/genetics*. *Database Management Systems. *Databases, Genetic*. *Genome, Archaeal/genetics*. *Genome, Bacterial/ ...
DNA extraction.Chromosomal DNA was extracted from colonies of C. difficile by using the UltraClean soil DNA kit (Mo Bio) ... 16S-23S ribosomal DNA intergenic spacer regions in cellulolytic myxobacteria and differentiation of closely related strains. ... to do text searches for ISR DNA sequences and perform sequence alignments of ISR DNA sequences (between regions 4 and 5) using ... DNA sequence heterogeneity in the three copies of the long 16S-23S rDNA spacer of Enterococcus faecalis isolates. Microbiology ...
Eukaryotic intergenic DNA* X0 sex-determination system* ZW sex-determination system* Haplodiploid sex-determination system* ... Haplogroup N (Y-DNA)* Haplogroup O (Y-DNA)* Haplogroup P (Y-DNA)* Haplogroup Q (Y-DNA)* Haplogroup Q3 (Y-DNA)* Adapter ( ... Haplogroup O2a (Y-DNA)* Adenovirus E1B protein* Haplogroup O2b (Y-DNA)* Fosmid* Suppressor mutation* Polar effect (genetics)* ... Naked DNA* TATA box* Activator (genetics)* Canonical sequence* Polycistronic* Pribnow box* Repeated sequence (DNA)* Wobble base ...
DNA, Intergenic/genetics*. *Extrachromosomal Inheritance/genetics*. *Genes, Bacterial. *Genome, Bacterial. *Molecular Sequence ... and more generally foreign DNA expression, by coding an anti-sense RNA. The presence of gene fragments in CRISPR structures and ... the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step. ...
... and DNA sequence alterations affecting specific neuronal genes are established risk factors for Autism Spectrum Disorder (ASD ... Rare variants in intergenic regions may implicate new risk loci and genes in ASD and also present useful data for comparison ... Examples of such intergenic CNV regions include 16q21 and 2p16.3 near known ASD risk genes CDH8 and NRXN1 respectively, as well ... Examples of such intergenic CNV regions include 16q21 and 2p16.3 near known ASD risk genes CDH8 and NRXN1 respectively, as well ...
In cellular life forms, the hereditary information exists as DNA. ... intergenic), of DNA that does not code for any gene products. ... This nongene DNA has often been called "junk DNA," as scientists have yet to find a specific function for it. The junk DNA can ... In eukaryotes, this will include chromosomal DNA and non-chromosomal DNA (e.g. DNA found in mitochondria and chloroplasts).. ... Enough DNA was produced to enable determination of the genetic code. Recombinant DNA also provides the basis for the ...
Journal Article] Sunlight exposure-mediated DNA damage in young adults.2011. *. Author(s). Kato M, Iida M, Goto Y, Kondo T, ... Chromatin structure and nuclear territories of the intergenic region between inactivated and escape genes on human inactive X ...
However, the recent flood of genomic data made possible by next-generation methods of DNA sequencing, enabled scientists to ... and their effects on human health and wellbeing Despite all of the elaborate mechanisms that a cell employs to handle its DNA ... 1.1 DNA is a Text 1. 1.2 Genomes Small and Large 6. 1.3 Genes and Intergenic Regions 7. 1.4 Cells, Mitosis, and Meiosis 14. 1.5 ... 8 Functioning DNA and Junk DNA 141. 8.1 Selective Neutrality and Random Drift 141. 8.2 Effective Population Size 144. 8.3 Junk ...
... long intergenic non-protein coding RNA 2043), Authors: Dessen P. Published in: Atlas Genet Cytogenet Oncol Haematol. ...
FID, flanking intergenic DNA.. *. TABLE 2 Nucleotide diversity within D. miranda (values expressed as percentages) ...
... and the LINE-1 and satellite 2 DNA repeats. These choices were based upon previous literature or publicly available DNA ... The DNA regions studied were promoters (BRCA1, CD44, ESR1, GSTM2, GSTP1, MAGEA1, MSI1, NFE2L3, RASSF1A, RUNX3, SIX3 and TFF1), ... many other types of normal cells). The importance of considering the exact DNA region analyzed and the gene structure was ... We confirmed the frequent DNA methylation changes in invasive breast cancer at a variety of genome locations and found evidence ...
  • The phylogeny of the genus was elucidated by the sequences of atpB-rbcL intergenic spacer of cpDNA for the better understanding of its evolution and biogeography. (springer.com)
  • Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. (mdpi.com)
  • 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. (umassmed.edu)
  • However, DGGE has many limitations, such as limited sensitivity of detection for some rare community members and the co-migration of DNA fragments with different sequences. (springer.com)
  • We compared the DNA sequences from fifty locally collected and five market samples of R. stricta with database sequences of R. stricta and seven closely related species. (scirp.org)
  • Although tests for selection are routinely carried out on the ∼85-90% of bacterial genomes corresponding to protein-coding sequences, attempts to measure the strength and direction of selection operating on nontranslated intergenic regions (IGRs) are far less common. (genetics.org)
  • Nucleotide base sequences of Lactobacillus 16S ribosomal DNA (rDNA) provide an accurate basis for phylogenetic analysis and identification ( 2 , 5 , 17 ). (asm.org)
  • In this paper, based on the characteristics of base composition of sequences and conservative of nucleotides at exon/intron splicing site, a least increment of diversity al-gorithm (LIDA) is developed for studying and predicting three kinds of coding exons, introns and intergenic regions. (scirp.org)
  • However, in plants, no DNA sequences have been found to be comparable to the COI in animals. (biomedcentral.com)
  • The DNA sequences were identical to each other and had 99.6% (456/457 bp) sequence similarity with B. henselae San Antonio 2 intergenic spacer region genotype (GenBank accession no. (cdc.gov)
  • The DNA sequences were identical to each other (404/404 bp) and to GenBank sequence AF312490. (cdc.gov)
  • and large intergenic sequences. (bioworld.com)
  • Most of the latter two types of sequences lack an ascribed function and hence have been thought of as "junk" DNA. (bioworld.com)
  • Many techniques have been introduced for discriminating between the exons and the introns in the eukaryotic DNA sequences, such as the discrete Fourier transform (DFT) based techniques, but these DFT-based methods rapidly lose their effectiveness in the case of short DNA sequences. (hindawi.com)
  • Nowadays, the rapid growth of raw genome sequence data requires efficient biological interpretations, but biological experiments for gene identification in DNA sequences are costly to conduct, so there is still a real demand for accurate and fast tools to analyze these sequences, especially to find genes and determine their functions [ 3 , 4 ]. (hindawi.com)
  • For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. (medlineplus.gov)
  • For example, repeated noncoding DNA sequences at the ends of chromosomes form telomeres . (medlineplus.gov)
  • Repetitive noncoding DNA sequences also form satellite DNA, which is a part of other structural elements. (medlineplus.gov)
  • The genome of humans and other animals is composed of more than just DNA sequences that produce proteins-there are also many other types of sequences that do not code for proteins. (icr.org)
  • His lab recently develops machine-learning techniques where computers algorithms detect regulatory sequences in intergenic DNA. (hopkinsmedicine.org)
  • This set consisted of DNA sequences derived from the ribosomal internal transcribed spacer (ITS) regions, partial sequences of the ribosomal intergenic spacer (IGS) region, the beta-tubulin and translation elongation factor-1 alpha (EF-1alpha) genes, AFLP fingerprints, chromatographic data on secondary metabolites and morphological data and growth characteristics. (dtu.dk)
  • An intergenic region (IGR) is a stretch of DNA sequences located between genes. (wikipedia.org)
  • It is one of the DNA sequences sometimes referred to as junk DNA, though it is only one phenomenon labeled such and in scientific studies today, the term is less used. (wikipedia.org)
  • In particular, intergenic regions often contain enhancer DNA sequences, which can activate expression of discrete sets of genes over distances of several thousand base pairs. (wikipedia.org)
  • The DUF1874 motif has not (as of 2018) been detected in any classified organism, but rather is known only in metagenomic DNA sequences isolated from hot springs. (wikipedia.org)
  • All five New Caledonian species formed a monophyletic group with very few sequence divergences in the intergenic spacer of cpDNA, thus showing rapid adaptive radiation in the island. (springer.com)
  • We determined the sequence of the intergenic spacer (IGS) 1 region, which is located between the 26S and 5S rRNA genes, in 25 species of the genus Trichosporon . (asm.org)
  • A DNA-sequence analysis of dominant bands extracted from the gel revealed that the main role in methane synthesis was played by micro-organisms affiliated with Methanosarcina barkeri . (springer.com)
  • 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)
  • Ribotyping is generally considered the best method, but it fails to account for sequence diversity which might exist in intergenic 16S-23S rRNA spacer regions (ISRs) within and among strains of this organism. (asm.org)
  • Copy number variations (CNVs) and DNA sequence alterations affecting specific neuronal genes are established risk factors for Autism Spectrum Disorder (ASD). (biomedcentral.com)
  • Rare variants in intergenic regions may implicate new risk loci and genes in ASD and also present useful data for comparison with coming whole genome sequence datasets. (biomedcentral.com)
  • A 610-bp segment of JCV DNA was amplified from each urine sample, and its DNA sequence was determined. (pnas.org)
  • Studies by Tilsala-Timisjarvi and Alatossava ( 15 ), Berthier and Ehrlich ( 3 ), Nour ( 11 ), and Nakagawa and colleagues ( 10 ) have demonstrated that the DNA sequence between the 16S and 23S genes of lactobacilli is hypervariable. (asm.org)
  • This intergenic spacer region is about 200 bases in length if tRNA genes are absent (small spacer sequence) ( 3 ). (asm.org)
  • Two sequence motifs from intergenic ncRNAs with significant similarity against known DNA motifs.For each comparison, the upper one is the known DNA motif, and the lower one is the intergenic ncRNA sequence motif. (nih.gov)
  • The numbers of "sense" and "antisense" sequence sites in intergenic ncRNAs are almost equal for most of the identified motifs (Table S8, A & B and Figure S5). (nih.gov)
  • Analysis of the DNA sequence of this fragment revealed four tandemly repeated 36-bp units. (ajtmh.org)
  • The DNA sequence of a highly conserved region of these repeats was used to synthesize an oligonucleotide probe specific to A. aquasalis. (ajtmh.org)
  • At first, by selecting the 64 trinucleotides composition and 120 position parameters of the four bases as informational parameters, coding exon, intron and intergenic sequence are predicted. (scirp.org)
  • Nucleotide sequence of the intergenic spacer and the 18S ribosomal RNA gene from mustard (Sinapis alba). (semanticscholar.org)
  • The rDNA intergenic spacer region nucleotide sequence of Hordeum bulbosum L. (semanticscholar.org)
  • The requirement for this sequence was strictly correlated with Benham's theoretical stress-induced DNA duplex destabilization. (wikigenes.org)
  • DNA barcoding technology, which uses a short piece of DNA sequence to identify species, has wide ranges of applications. (biomedcentral.com)
  • The amplification yielded the same uniquely "sequence-scrambled" product, whether the template used for PCR was total cellular DNA, chloroplast DNA or a plasmid clone DNA corresponding to that region. (bvsalud.org)
  • Our comparison of methods suggests that without previous knowledge of the DNA sequence of the IGS and flanking regions, both methods be used to accurately measure IGS length. (biomedcentral.com)
  • Deoxyribonucleicacid (DNA) sequence consists of genic and intergenic regions. (hindawi.com)
  • Dbv4 shows a putative helix-turn-helix DNA-binding motif and shares sequence similarity with StrR, the transcriptional activator of streptomycin biosynthesis in Streptomyces griseus . (asm.org)
  • c) Nonclassical constitutional epimutations have low or no DNA methylation with no identified DNA sequence change. (els.net)
  • The majority of transgenerational similarity in DNA methylation is attributable to genetic effects, and approximately 20% of individual differences in DNA methylation in the population are caused by DNA sequence variation that is not located within CpG sites. (biomedcentral.com)
  • With genetic inheritance, an individual's underlying DNA sequence affects epigenetic state, with the extreme example being a genetic variant at a CpG locus that can disrupt DNA methylation at this site. (biomedcentral.com)
  • Less understood is the role that DNA sequence variation outside of the CpG locus plays in the observed variation in DNA methylation. (biomedcentral.com)
  • While the human genome sequence has transformed our understanding of human biology, it isn't just the sequence of your DNA that matters, but also how you use it! (coursera.org)
  • Computational techniques are used in biology to prioritize DNA sequence variants (or polymorphisms) that may be responsible for population diversity and the manifestation of species-specific traits. (plos.org)
  • His research focuses on understanding how gene regulatory information is encoded in genomic DNA sequence and how regulatory variation contributes to diseases. (hopkinsmedicine.org)
  • Dr. Beer's research focuses on understanding how gene regulatory information is encoded in genomic DNA sequence. (hopkinsmedicine.org)
  • Progress has been made in understanding how DNA sequence features specify cell-type specific mammalian enhancer activity by using kmer-based SVM machine learning approaches. (hopkinsmedicine.org)
  • A Method to Predict the Impact of Regulatory Variants from DNA Sequence. (hopkinsmedicine.org)
  • Epigenetics generally refers to modifications to DNA that alter gene expression but not the DNA sequence, and includes DNA methylation and chromatin remodeling 13 , 14 . (nature.com)
  • The AS11 and AS12 linear double-stranded DNA genomes of 41,642 base pairs (bp) and 41,402 bp share 86% nucleotide sequence identity with the most variable regions falling in host receptor-recognition genes. (mdpi.com)
  • Our data suggest that transposition of selfish DNA, low effective population size, and high fidelity replication allowed the unusual 'inflation' of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle. (osti.gov)
  • Intergenic DNA, as the name suggests, is DNA between genes which does not code for proteins. (madsci.org)
  • The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). (mdpi.com)
  • An alternative technique is Ribosomal Intergenic Spacer Analysis (RISA), which is based on the amplification of the intergenic region located between the 16S and 23S rRNA genes in the rRNA operon. (springer.com)
  • Interestingly, lincRNA genes appear to be less susceptible to CNV in comparison to both protein-coding and intergenic regions (CNV affected segments in percentage: 1.8%, 37.5%, and 60.6%, respectively). (frontiersin.org)
  • Many of them are located in intergenic regions far from genes. (nih.gov)
  • Examples of such intergenic CNV regions include 16q21 and 2p16.3 near known ASD risk genes CDH8 and NRXN1 respectively, as well as novel loci contiguous with ZHX2 , MOCS1 , LRRC4C , SEMA3C, and other genes. (biomedcentral.com)
  • Chromatin structure and nuclear territories of the intergenic region between inactivated and escape genes on human inactive X chromosome. (nii.ac.jp)
  • Recent advances in DNA sequencing technology and transcriptome analysis have challenged the traditional view that protein coding genes are the only effectors of gene function. (plantcell.org)
  • Bovine ncRNAs are abundant, primarily intergenic, conserved and associated with regulatory genes. (nih.gov)
  • The presence of gene fragments in CRISPR structures and the nuclease motifs in cas genes of both cluster types suggests that CRISPR formation involves a DNA degradation step. (nih.gov)
  • The intergenic spacer of the ribosomal genes in eukaryotes (IGS) contains duplications of the core transcription promoter. (biomedcentral.com)
  • Many of these phenotypes are mediated in part by increased expression of the vps genes, which are organized into vps- I and vps- II coding regions, separated by an intergenic region. (asm.org)
  • In this study, we generated in-frame deletions of the five genes located in the vps intergenic region, termed rbmB to - F ( r ugosity and b iofilm structure m odulators B to F) in the rugose genetic background, and characterized the mutants for rugose colony development and biofilm formation. (asm.org)
  • Taken together, these results indicate that vps intergenic region genes encode proteins that are involved in biofilm matrix production and maintenance of biofilm structure and stability. (asm.org)
  • Further investigation of one of these cis mQTL, found in the MHC region of chromosome 6, showed the most significantly associated SNP was also associated with over 200 other DNA methylation probes in this region and the gene expression level of 9 genes. (biomedcentral.com)
  • During the lytic cycle, phage-encoded recombinases promote DNA rearrangements that occasionally result in the acquisition of foreign genes, including virulence determinants. (dur.ac.uk)
  • Some noncoding DNA regions, called introns, are located within protein-coding genes but are removed before a protein is made. (medlineplus.gov)
  • Other noncoding regions are found between genes and are known as intergenic regions. (medlineplus.gov)
  • EVERY press release on science issues is over-simplified, of course, but, well, it's a PERFECTLY GOOD argument to note that there is a complex angiosperm that has basically ALL the genes of a typical plant/typical multicellular eukaryote -- with maybe even a few extra due to multiply polyploid events -- but has almost NONE of the noncoding DNA / DNA formerly known as junk / DNA which should still be known as junk. (blogspot.com)
  • It was once believed that the regions in between the protein-coding genes of the genome were wastelands of alleged nonfunctional "junk DNA. (icr.org)
  • Here we explored in the same population the contribution of a panel of DNA repair-related SNPs in genes acting downstream of ATM. (biomedcentral.com)
  • The association of 141 SNPs located in 43 DNA repair genes was examined in 75 PTC cases and 254 controls from the Gomel region in Belarus. (biomedcentral.com)
  • These findings indicate that several genes acting in distinct DNA repair mechanisms contribute to PTC risk. (biomedcentral.com)
  • ENCODE researchers found that most of our DNA has a function: controlling when and where genes are turned on and off. (embl.de)
  • Today, an international team of researchers reveal that much of what has been called 'junk DNA' in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. (embl.de)
  • it bound to regions of DNA important for the function of genes involved in the synthesis of aflatoxins. (usda.gov)
  • Using five trees to represent each major genetic group in the complex, 667 bp of the intergenic region between the chloroplast genes rbcL and atpB were amplified via the polymerase chain reaction and directly sequenced. (oregonstate.edu)
  • The sequencing of the human genome revealed that only a small fraction of the DNA in our chromosomes comprises genes that encode instructions for making proteins. (healthcanal.com)
  • We used shotgun DNA sequencing to produce a 264-MB metagenome from these soils, comprising 208,233 predicted genes ( Supplementary Table 2 ) and 451 predicted 16S/18S rRNA operational taxonomic units (OTUs) ( Supplementary Table 3 ). (nature.com)
  • Occasionally some intergenic DNA acts to control genes nearby, but most of it has no currently known function. (wikipedia.org)
  • Intergenic regions are different from intragenic regions (or introns), which are short, non-coding regions that are found within genes, especially within the genes of eukaryotic organisms. (wikipedia.org)
  • Also intergenic regions may contain as yet unidentified genes such as noncoding RNAs. (wikipedia.org)
  • DUF1874 are frequently present in consecutive intergenic regions between consecutive genes. (wikipedia.org)
  • All of these genes are encoded on the same DNA strand. (wikipedia.org)
  • attC sites are singled-stranded DNA elements that are used by integrons to enabling the rearrangement and integration of new genes into the intron. (wikipedia.org)
  • Long intergenic non-coding RNAs (lincRNA) have recently come to our attention as a result of an increased intergenic coverage of whole transcriptome and sequencing analysis. (frontiersin.org)
  • The LTR complex transcribes intergenic RNAs unidirectionally through the intervening DNA to loop with and modulate transcription factor occupancies at the far downstream globin promoters, thereby modulating globin gene switching by a competitive mechanism. (nih.gov)
  • Long intergenic noncoding RNAs ( lincRNAs ) transcribed from intergenic regions of yeast and animal genomes play important roles in key biological processes. (plantcell.org)
  • and (4) long intergenic noncoding RNAs ( lincRNAs ). (plantcell.org)
  • these are called long intergenic noncoding RNAs, or lincRNAs (a subset of lncRNAs). (icr.org)
  • Relative abundance of the three main classifications of ncRNAs.Almost 60% of ncRNAs are long intergenic non-coding RNAs (intergenic ncRNAs). (nih.gov)
  • Long intergenic noncoding RNA (lincRNA) is the largest class of these RNAs. (healthcanal.com)
  • Two other regions exist in each repeat: the internal transcribed spacer (ITS) region and the intergenic spacer (IGS) region (Fig. 1 ). (asm.org)
  • We conclude that the intergenic 16S-23S rRNA spacer regions showed a high degree of diversity, not only among the rrn operons in different strains and different rrn copies in a single strain but also among ISRs of the same length. (asm.org)
  • Nontranslated intergenic regions (IGRs) compose 10-15% of bacterial genomes, and contain many regulatory elements with key functions. (genetics.org)
  • The main cis -acting control regions for replication of the single-stranded DNA genome of maize streak virus (MSV) are believed to reside within an approximately 310 nt long intergenic region (LIR). (microbiologyresearch.org)
  • The rbc L and mat K regions have been proposed as the "core barcode" for plants and the ITS2 and psbA-trnH intergenic spacer (PTIGS) regions were later added as supplemental barcodes. (biomedcentral.com)
  • ChIP-chip/ChIP-seq often identifies non-canonical target regions for DNA-associated proteins, i.e. target regions that are inconsistent with our current understanding of the protein being studied. (biomedcentral.com)
  • To achieve these high levels of ribosome production, eukaryotes have multiple copies of ribosomal (r)DNA, arranged in tandem in the Nucleolus Organizer Regions (NORs) of one or more chromosomes. (biomedcentral.com)
  • PCR-RFLP of three intergenic regions revealed five haplotypes. (usda.gov)
  • This figure shows that eukaryotic DNA consists of genic and intergenic regions, and the exon regions are interrupted by introns in eukaryotic DNA. (hindawi.com)
  • These clusters are the most actively transcribed DNA regions in cells, as well as the most fragile sites in human chromosomes. (springer.com)
  • Other regions of noncoding DNA provide instructions for the formation of certain kinds of RNA molecules. (medlineplus.gov)
  • The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. (medlineplus.gov)
  • Our purpose was to corroborate the existence of haplotypes within the T. cruzi I group and to describe the genetic variability and phylogenetic relationships, based on single nucleotide polymorphisms (SNPs) found in the miniexon gene intergenic region, for the isolates from different hosts and epidemiological transmission cycles in Colombian regions. (hindawi.com)
  • VH-DH intergenic regions are detected in red. (babraham.ac.uk)
  • The choanoflagellates have a circular mitochondrial DNA genome with long intergenic regions. (wikipedia.org)
  • Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. (osti.gov)
  • Intergenic regions are a subset of noncoding DNA. (wikipedia.org)
  • Historically intergenic regions have sometimes been called junk DNA suggesting that they have no function. (wikipedia.org)
  • In recent years the ENCODE project has been studying intergenic regions in humans in more detail. (wikipedia.org)
  • Statistical methods have been specifically developed to detect trait- or disease-associated regions located in intergenic region using whole genome sequencing data, including the sliding window procedure and dynamic window procedure. (wikipedia.org)
  • Re: What is intergenic DNA compared to introns and exons? (madsci.org)
  • In this study, we used genomic inhibition of DNA methylation through disruption of DNA methyltransferases DNMT1 and DNMT3B and pharmacologic inhibition with 5-Aza-2′-deoxycytidine (5-Aza-dC, decitabine) to demonstrate that DNA methylation predominantly regulates expression of metastasis-suppressive miRNAs in the 14q32 cluster. (aacrjournals.org)
  • These findings implicate epigenetic modification via DNA methylation in the regulation of metastatic propensity through miRNA networks and identify a previously unrecognized action of decitabine on the activation of metastasis-suppressive miRNAs. (aacrjournals.org)
  • Epimutations are epigenetic aberrations, typically defined by deoxyribonucleic acid (DNA) methylation, that predispose individuals to cancer through soma‐wide changes in the expression of the afflicted gene. (els.net)
  • The molecular cause of most epimutations is unknown but it is hypothesised that they could be driven by hitherto unidentified genetic alterations in long‐range cis ‐regulatory elements that manifest as DNA methylation or repressive histone modifications at a gene promoter. (els.net)
  • DNA methylation at CpG island promoters (black lollipops) is the most extensively described epimutation. (els.net)
  • Despite the important role DNA methylation plays in transcriptional regulation, the transgenerational inheritance of DNA methylation is not well understood. (biomedcentral.com)
  • The genetic heritability of DNA methylation has been estimated using twin pairs, although concern has been expressed whether the underlying assumption of equal common environmental effects are applicable due to intrauterine differences between monozygotic and dizygotic twins. (biomedcentral.com)
  • We estimate the heritability of DNA methylation on peripheral blood leukocytes using Illumina HumanMethylation450 array using a family based sample of 614 people from 117 families, allowing comparison both within and across generations. (biomedcentral.com)
  • The correlations from the various available relative pairs indicate that on average the similarity in DNA methylation between relatives is predominantly due to genetic effects with any common environmental or zygotic effects being limited. (biomedcentral.com)
  • The average heritability of DNA methylation measured at probes with no known SNPs is estimated as 0.187. (biomedcentral.com)
  • Importantly, DNA methylation (along with other epigenetic changes) provides a biological link between an individual's environmental exposures and their phenotype. (biomedcentral.com)
  • The relative importance of genetic inheritance, epigenetic inheritance and common environmental influences to locus specific DNA methylation similarity among relatives has not been well estimated on a genome-wide scale. (biomedcentral.com)
  • We'll also discuss the best-characterised epigenetic modification, DNA methylation, and how it is not only implicated in regulating gene expression, but also in maintaining genome stability. (coursera.org)
  • DNA methylation may be involved in development of type 1 diabetes (T1D), but previous epigenome-wide association studies were conducted among cases with clinically diagnosed diabetes. (nature.com)
  • For example, DNA methylation at specific genomic loci may be altered in response to environmental stimuli, maintained in daughter cells, and directly influence disease development by altering gene expression 16 . (nature.com)
  • Alternately, DNA methylation may be altered as a consequence of disease progression, and therefore serve as a biomarker of pathogenesis. (nature.com)
  • We measured DNA methylation in peripheral whole blood collected prior to onset of clinical T1D from individuals enrolled in the prospective Diabetes Autoimmunity Study in the Young (DAISY) cohort, which follows high-risk children for the development of IA and T1D. (nature.com)
  • This Beadchip platform includes a total of 2,435,915 SNP loci dispersed at an average interval of ~700 nt throughout the intergenic region of the human genome. (frontiersin.org)
  • LONDON The "junk" DNA in the human genome so-called because no one knows what its function is may not be so useless after all. (bioworld.com)
  • Species-specific repeat units in the intergenic spacer of the ribosomal RNA cistron of Anopheles aquasalis Curry. (ajtmh.org)
  • The multiple cloning site as well as the ori and intergenic region of the phage f1 have been cloned in two orientations for convenient gene cloning and ssDNA strand selection. (nih.gov)
  • Objectives To explore the functional basis for the association between ankylosing spondylitis (AS) and single-nucleotide polymorphisms (SNPs) in the IL23R - IL12RB2 intergenic region. (bmj.com)
  • Both A. aquasalis-specific clones were from the intergenic spacer region of the ribosomal RNA (rRNA) cistron. (ajtmh.org)
  • The intergenic spacer region of the rDNA in Haplopappus gracilis (Nutt. (semanticscholar.org)
  • The intergenic spacer region of the rDNA in Olea europaea L. (semanticscholar.org)
  • Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat. (semanticscholar.org)
  • Prokaryotic cells tend to be very small, have few or no cytoplasmic organelles, and have the cellular DNA arranged in a "nucleoid region" that is not separated from the remainder of the cell by any membrane. (encyclopedia.com)
  • Identification of the replication-associated protein binding domain within the intergenic region of tomato leaf curl geminivirus. (microbiologyresearch.org)
  • In animals, a region of the COI gene has been found to possess properties like high PCR amplification efficiency, high DNA sequencing success rate, and high discrimination power. (biomedcentral.com)
  • One of the RAPD-markers, "P2" (1.6 kb) was cloned, sequenced and was fine mapped to the 3 kb region encompassing 3' end of 23S, full 5S and intergenic region between 5S and psbA. (bvsalud.org)
  • and intergenic spacer region genotype. (cdc.gov)
  • DNA demethylation facilitated CCCTC-binding factor (CTCF) recruitment to the maternally expressed gene 3 differentially methylated region (MEG3-DMR), which acts as a cis -regulatory element for 14q32 miRNA expression. (aacrjournals.org)
  • The A. parasiticus areA gene encoded a polypeptide of 864 amino acids which contained a nuclear localization signal (NLS), a highly acidic region from positions 497 to 542, a Cys-X2-Cys-X17-Cys-X2-Cys DNA-binding motif and a conserved carboxyl terminus. (usda.gov)
  • Electrophoretic mobility shift assays suggested that the A. parasiticus AREA DNA-binding domain fusion protein bound cooperatively to single GATA elements in the A. parasiticus niaD-niiA intergenic region. (usda.gov)
  • A. parasiticus AREA also bound to the aflR-aflJ intergenic region of the aflatoxin biosynthesis gene cluster. (usda.gov)
  • No variation was observed in the sequenced intergenic region. (oregonstate.edu)
  • The genome may have an intergenic poly (A) region. (kenyon.edu)
  • Methods We performed conditional analysis on genetic association data and used epigenetic data on chromatin remodelling and transcription factor (TF) binding to identify the primary AS-associated IL23R-IL12RB2 intergenic SNP. (bmj.com)
  • Researchers have now described a novel type of genetic mutation, which leads to disease even though it does not lie in the part of the DNA that normally contributes information to make a protein. (bioworld.com)
  • In cis DNA elements such as enhancers and insulators regulate gene expression and are potential sites of genetic alterations that give rise to epimutations. (els.net)
  • The aim of this study was to develop, refine and evaluate an alternative methodology, which enables better preservation of large numbers of individual schistosome larval stages and eggs collected in low resource endemic areas, to provide PCR-quality DNA for multi-locus genetic analysis. (biomedcentral.com)
  • Cauliflower mosaic virus , in the genus Caulimovirus of the family Caulimoviridae , was the first plant virus discovered to use DNA instead of RNA as its genetic material. (kenyon.edu)
  • Ribosomal DNA (rDNA) has been widely utilized for molecular systematics and the identification of microorganisms. (asm.org)
  • Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). (mdpi.com)
  • Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex. (genetics.org)
  • Nucleotide variation was surveyed in 21 subrepeat arrays from the ribosomal DNA intergenic spacer of three Daphnia pulex populations. (genetics.org)
  • Analysis of the distribution of nucleotide variation suggested that the populations were quite divergent, a result that is concordant with previous surveys of allozyme and mitochondrial DNA variation. (genetics.org)
  • We report here two highly reliable ribosomal DNA-based single nucleotide polymorphism (SNP) markers, CxpG2T and CxpA2d, for detecting Cx. (ajtmh.org)
  • Previously, we reported that common single nucleotide polymorphisms (SNPs) within the DNA damage recognition gene ATM contribute to PTC risk in Belarusian children exposed to fallout from the Chernobyl power plant accident. (biomedcentral.com)
  • Using a reproducibility-based bioinformatics strategy to analyze 200 Arabidopsis thaliana transcriptome data sets, we identified 13,230 intergenic transcripts of which 6480 can be classified as lincRNAs . (plantcell.org)
  • The majority of the ncRNAs in our dataset were intergenic transcripts (57% intergenic compared to 42% intronic). (nih.gov)
  • The data in Table 1 also showed that the vast majority of ncRNAs (both intergenic and intronic) were apparently unspliced transcripts. (nih.gov)
  • By contrast, the intergenic spacers psbK-psbI and atpF-atpH were variable loci distinct for the medicinal plant R. stricta. (scirp.org)
  • We compare patterns of selection operating on IGRs using two independent methods: the proportion of singleton mutations and the d I / d S ratio, where d I is the number of intergenic SNPs per intergenic site. (genetics.org)
  • During interphase, the nuclear DNA is organized in a dispersed network of chromatin , which is a complex consisting of nucleic acid and basic proteins. (encyclopedia.com)
  • We conclude that surprising ChIP-chip results are not artifacts to be ignored, but rather indications that our understanding of DNA-binding proteins is incomplete. (biomedcentral.com)
  • The data on forum domains formed by DNA double-strand break (DSB) hotspots are reviewed including forum domain identification by pulsed-field gel electrophoresis, whole genome mapping of these domains using deep sequencing strategies, analysis of gene expression in forum domains, and binding of nuclear proteins to their boundaries. (springer.com)
  • Noncoding DNA does not provide instructions for making proteins. (medlineplus.gov)
  • Importantly, proteins that inefficiently crosslink to DNA (either intrinsically or due to indirect crosslinking via another protein) and thus are very difficult to detect, are expected to be significantly detected by the kits and methods described herein. (freepatentsonline.com)
  • Finally, viruses (which are noncellular, parasitic "life forms") have genomes of double-stranded DNA, single-stranded DNA, double-stranded RNA, or single-stranded RNA. (encyclopedia.com)
  • Subviral agents associated with plant single-stranded DNA viruses. (microbiologyresearch.org)
  • The invasion reaction is typical of models for E. coli recombination at a break and requires host RecA to bind single-stranded DNA (ssDNA), locate a homologous duplex and promote strand exchange to create a recombinant joint. (dur.ac.uk)
  • Background: Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). (ufl.edu)
  • Intriguingly, and possibly contra- dicting the premise that polymerase fidelity is the major universal determinant of evolution rates, figures closer to those of RNA viruses (~10-4 subs/site/year) have been reported for the small single stranded DNA (ssDNA) anelloviruses [7-9] and parvoviruses [10-12]. (ufl.edu)
  • Thus, if the preceding hypothesis is true, then the DUF1874 motif function as single-stranded DNA. (wikipedia.org)
  • For example, the haploid complement of Homo sapiens DNA contains between 3.12 and 3.2 gigabases (the prefix "giga" denotes billions), while the haploid complement of yeast ( Saccharomyces cerevisiae ) DNA contains 12,057,500 base pairs. (encyclopedia.com)
  • The need to revise the available data on DNase I-hypersensitive sites in various genomes, including endogenous DNA breaks of different nature, is discussed. (springer.com)
  • 2014. How Reliable Are Genomes from Ancient DNA? (icr.org)
  • The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and two fold higher than that found in the gene dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. (osti.gov)
  • Enhancers can be found on the DNA strand before or after the gene they control, sometimes far away. (medlineplus.gov)
  • Khair L, Baker RE, Linehan EK, Schrader CE, Stavnezer J. Nbs1 ChIP-Seq Identifies Off-Target DNA Double-Strand Breaks Induced by AID in Activated Splenic B Cells. (umassmed.edu)
  • Two pathways of exchange predominate in phage lambda depending on whether a DNA strand is used to invade a homologous duplex or is annealed to a complementary single-strand. (dur.ac.uk)
  • Promoters are typically found just ahead of the gene on the DNA strand. (medlineplus.gov)
  • This DNA may or may not encode regulatory functions. (umassmed.edu)
  • Obviously it's a simplification to say that all noncoding DNA is not needed, but given how the media has been obsessed with the horrid ENCODE hype claiming that most of it is 'functional', using their own misleading meaning of the term, if the public needs a simplification, I'd much rather have it be that it isn't functional because that's closer to the truth. (blogspot.com)
  • Exon Promoter (biology) ENCODE Heterochromatin Noncoding DNA Repetitive DNA Regulator gene Whole genome sequencing Tropp BE (2008). (wikipedia.org)
  • But the Nature Genetics paper showed that there is more function in junk DNA than anyone would ever have thought, Baralle said. (bioworld.com)
  • In this case, the lack of four bases in the middle of what everyone thought was junk DNA is causing a disease. (bioworld.com)
  • When their genomic abundance began to be apparent, they were categorized as ""junk DNA"" and acquired the label of parasites. (wiley.com)
  • Scientists once thought noncoding DNA was "junk," with no known purpose. (medlineplus.gov)
  • Noncoding DNA-Subtlety, Punctuation, or Just Plain Junk? (medlineplus.gov)
  • So - they have redefined junk DNA as all non coding DNA? (blogspot.com)
  • At least for a plant, junk DNA really is just junk - it's not required. (blogspot.com)
  • Nobody's really known what junk DNA does or doesn't do " apparently calling into question the some 10,000 plus papers on the topic. (blogspot.com)
  • A Weird Little Plant is Nearly Free of Junk DNA. (blogspot.com)
  • The rest of the genome, about 98 percent of it, was sometimes referred to as the "dark matter" of the genome or dismissed as "junk DNA. (healthcanal.com)
  • human and plant chromosomes possessing mainly 50-to 150-kilobase stretches of DNA, Proc. (springer.com)
  • Exo serves as a functional equivalent of RecBCD exonuclease, normally responsible for generating 3' tailed DNA at broken chromosomes in E. coli . (dur.ac.uk)
  • Some structural elements of chromosomes are also part of noncoding DNA. (medlineplus.gov)
  • Satellite DNA also forms heterochromatin, which is densely packed DNA that is important for controlling gene activity and maintaining the structure of chromosomes. (medlineplus.gov)
  • We'll discuss the molecular mechanisms for regulating gene expression in some detail, from how the DNA is packaged at a local level, right up to how the chromatin is positioned within the nucleus. (coursera.org)
  • Methods, systems and kits for detecting protein-nucleic acid interactions, in particular, detecting the genomic location to near-base pair resolution at which a particular protein (e.g., transcription factor) binds includes combining steps of a convention chromatin immunoprecipitation (ChIP) assay with use of an exonuclease that digests DNA strands in the 5′-3′ or 3′-5′ direction until it reaches a bound protein including a protein crosslinked to DNA. (freepatentsonline.com)
  • Mitochondrial DNA (mtDNA) has undergone radical changes during the evolution of green plants, yet little is known about the dynamics of mtDNA evolution in this phylum. (plantcell.org)
  • This preparation of high molecular weight DNA is appropriate for use in the polymerase chain reaction (PCR)* process and other molecular biology applications. (atcc.org)
  • In viruses, which are generally subject to relatively high rates contrast and consistent with the hypothesis that of mutation due to their dependence on error-prone DNA polymerase fidelity influences evolution rates double dependent RNA polymerases. (ufl.edu)
  • 4. The method of claim 1, wherein step (c) of identifying the exonuclease-treated end comprises at least one selected from the group consisting of: DNA sequencing, microarrays, and polymerase chain reaction (PCR). (freepatentsonline.com)
  • PCR analysis of tRNA intergenic spacer (tDNA-PCR) and of the 16S-23S internal transcribed spacer (ITS-PCR) and random amplified polymorphic DNA (RAPD) analysis were evaluated for their usefulness in characterization of Enterobacter cloacae strains isolated from both clinical origins and vaccine microbial contamination. (asm.org)
  • Here, we compared the most commonly used alignment-based and alignment-free methods and developed a web server to allow the biologists to carry out PTIGS-based DNA barcoding analyses. (biomedcentral.com)
  • Much of my work involves structural and functional analyses of enzymes that initiate, process and resolve branched DNA recombination intermediates. (dur.ac.uk)
  • Initiation of DNA replication in a eukaryotic rolling-circle replicon: identification of multiple DNA-protein complexes at the geminivirus origin. (microbiologyresearch.org)
  • ChIP-chip and ChIP-seq are widely used methods to map protein-DNA interactions on a genomic scale in vivo . (biomedcentral.com)
  • The currently accepted 25 species of the genus Trichosporon were examined as shown in Table 1 Trichosporon DNA was extracted by the method of Makimura et al. (asm.org)
  • DNA barcoding is an emerging technology for rapid and accurate species identification. (scirp.org)
  • This technology identifies unknown species by using standardized DNA segments as universal product codes. (scirp.org)
  • have estimated the precision and accuracy of hierarchical clustering methods (parsimony and neighbor joining), similarity methods (BLAST, BLAT, and megaBLAST), combined clustering/similarity methods (BLAST/parsimony and BLAST/neighbor joining), diagnostic methods (DNA-BAR and DOME ID) for species identification [ 12 ]. (biomedcentral.com)
  • Chloroplast DNA (cpDNA) variability and phylogeny were studied via analysis of restriction site mutations and DNA sequencing in a complex of three closely related species of pines: Pinus radiata D. Don, P. attenuata Lemm. (oregonstate.edu)
  • Focusing on the intergenic intervals of the genome, we performed a systematic genome-wide investigation to identify rare CNVs enriched in cases compared with controls [ 16 ] to identify known and novel ASD susceptibility loci. (biomedcentral.com)
  • Chloroplast DNA (cpDNA) variation was examined in 48 northern red oaks at 14 sites representing contrasting glacial histories and age structures within the state of Indiana in the United States. (usda.gov)
  • Genomic DNA from 384 trees representing 20 populations in the complex were digested with 20 restriction enzymes and probed with cloned cpDNA fragments from Douglas-fir that comprise 85% of the chloroplast genome. (oregonstate.edu)
  • Burge, C. and Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA, J. Mol. (scirp.org)
  • Parent -specific, randomly amplified polymorphic DNA (RAPD) markers were obtained from total genomic DNA of Chlamydomonas reinhardtii . (bvsalud.org)
  • We also noticed that most ncRNAs were singletons (72.2% out of intergenic, 81.1% out of intronic and 71.3% out of overlapped ncRNAs respectively)(Table 1). (nih.gov)
  • Induces the transcription of long intergenic non-coding RNA p21 (lincRNA-p21) and lincRNA-Mkln1. (rcsb.org)
  • Epstein-Barr virus nuclear antigen 3A partially coincides with EBNA3C genome-wide and is tethered to DNA through BATF complexes. (semanticscholar.org)
  • Human-Chimp DNA Similarity: Separating Fact from Fiction. (icr.org)
  • the fact that Bartonella DNA was found suggests the possibility that persistent blood-borne infection can occur in nonmammals and that the host range for Bartonella spp. (cdc.gov)
  • Bartonella grahamii DNA was amplified from a bird tick in Korea ( 10 ). (cdc.gov)
  • Bartonella henselae-specific DNA was detected in their blood. (google.com)
  • Bartonella henselae-specific DNA was also detected in live deer ticks obtained from the households of 2 of these patients. (google.com)
  • A total of 1253 ixodid ticks (254 tick pools) collected between the end of 1995 and the spring of 1997 from six California counties (El Dorado, Los Angeles, Orange, Santa Cruz, Shasta and Sonoma) were examined for the presence of Bartonella DNA by PCR of the citrate synthase gene. (google.com)
  • Following our previous findings of Bartonella PCR-positive adult I. pacificus ticks in central coastal California, this is the first preliminary report of the presence of Bartonella DNA in I. pacificus nymphs and in Dermacentor sp. (google.com)
  • These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. (ufl.edu)
  • The genome is made of a double stranded DNA and is -RT. (kenyon.edu)