• DNA sequences [ 4-6 ]. (who.int)
  • Comparison of the conserved sequences of the small subunit rDNA clearly established the close relationship of B. akodoni with other members of the geus. (usda.gov)
  • However, sequences of the more variable first internal transcribed spacer portion of the ribosomal DNA repeat support its differentiation from the other species of the genera. (usda.gov)
  • Sequencing and further analysis of the HDP2 DNA fragments of 19 Asiatic isolates of T. saginata and T. asiatica indicated that the HDP2 sequences of both species exhibited clear genomic variability, due to polymorphic variable fragments, that could correspond to the non-transcribed region of ribosomal DNA. (biomedcentral.com)
  • The genetic makeup of many species, including humans, contains crucial components known as ribosomal DNA (rDNA) sequences. (scitechdaily.com)
  • During our initial phylogenetic study of the monocot genus Erythronium (Liliaceae), we observed peculiar eudicot-type internal transcribed spacer (ITS) sequences in a dataset derived from genomic DNA of Erythronium dens-canis. (cas.cz)
  • The identification of species was addressed through a combination of biochemical and genetic methods (API ® 50 CHL test, 16S rDNA and recA gene sequences, Amplified Ribosomal DNA Restriction Analysis -ARDRA- and 16S-26S intergenic region analysis). (mdpi.com)
  • These ribosomal sequences was functional for the phylogenetic analysis and molecular taxonomic of any bacteria. (ispub.com)
  • Recently, metagenomics a new approach to identify culturable and non culturable bacteria with the help of 16S rDNA sequences isolate total DNA from HCH contaminated soil and amplified 16S rDNA through universal primers and confirmed its total population with denaturing gradient gel electrophoresis and sequencing. (ispub.com)
  • A BLAST search found that the newly obtained 18 rDNA sequence had a low sequence similarity with available sequences for Myxobolus on GenBank. (edu.sa)
  • A phylogenetical analysis based on ribosomal DNA partial sequences showed that M. opsaridiumi sp. (edu.sa)
  • Forty-nine isolates of Trichoderma from the Brazilian Midwest were evaluated for their antagonistic activity in vitro against Sclerotinia sclerotiorum (causal agent of white mold), which were then identified based on their nuclear ribosomal ITS sequences. (scielo.br)
  • The 16S rDNA nucleotide sequences of all isolates were sequenced in the 3-terminal end of the molecule using a buy MK-0359 solitary primer as explained by Leser et al. (exposed-skin-care.net)
  • 19). To determine the closest relatives of the partial and near-full-length 16S rDNA sequences retrieved, searches were carried out in GenBank using the BLAST algorithm (1). (exposed-skin-care.net)
  • DNA methylation is a process that determines whether genes are expressed or not. (foodnavigator.com)
  • Within rDNA, rRNA genes are separated by large intergenic spacers (IGSs) (Extended Data Fig. 1a ). (nature.com)
  • Studies of genes transcribed by RNA polymerase II (Pol II) have shown that open and closed chromatin structures are dynamically regulated through multiple mechanisms, including histone modifications, histone variant incorporation, and DNA methylation (reviewed in reference 17 ). (asm.org)
  • A comparison of the dendrogram of the tfdA genes with that of the SSU rDNA genes demonstrated incongruency in phylogenies, and hence 2,4-D degradation must have originated from gene transfer between species. (nih.gov)
  • Research in the Paralkar Lab spans the spectrum from human patient sample studies and mouse models to cutting-edge molecular biology tools, high-throughput sequencing approaches, and novel computational algorithms, all with the goal of gaining insight into how the transcription of coding genes and noncoding ribosomal DNA genes is regulated in hematopoietic stem cells, myeloid progenitors, and in leukemia. (upenn.edu)
  • To exert stimulatory or repressive effects on transcription, accessible regulatory DNA elements must be in close spatial proximity to susceptible genes. (biomedcentral.com)
  • We tested for recombination using the alignments of the concatenated nuclear rDNA genes. (eawag.ch)
  • This document describes some of the target genes and primers that can be used for DNA sequence-based identification of fungi and the PCR conditions with which to use those primers. (cdc.gov)
  • Pyrosequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) amplicon from genomic DNA extracted from the stool samples was used to analyze the gut microbiome. (news-medical.net)
  • Genetically modified food simply means that the original DNA (deoxyribonucleic acid) structure of plants has been altered or tempered with. (intechopen.com)
  • Small-subunit ribosomal DNA (SSU rDNA) from 20 phenotypically distinct strains of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria was partially sequenced, yielding 18 unique strains belonging to members of the alpha, beta, and gamma subgroups of the class Proteobacteria. (nih.gov)
  • Sequencing of the large subunit region of ribosomal (r)DNA places the fungus close to the Pezizellaceae, Porodiplodiaceae, and Sclerotiniaceae, with analyses of internal transcribed spacer regions of rDNA indicating that it has affinities to previously unnamed soil and root fungi from alpine, cool temperate and Low Arctic regions. (bas.ac.uk)
  • The ribosomal RNAs form two subunits, i.e. large subunit and small subunit. (biologyonline.com)
  • Although the ITS primers are universal for fungi, the D1D2 region of the large ribosomal subunit has better discrimination for yeasts, with primers NL-1 and NL-4. (cdc.gov)
  • Ribosomal RNA (rRNA) forms the majority of cellular RNA, and its transcription in the nucleolus by RNA Polymerase I from ribosomal DNA (rDNA) repeats accounts for the bulk of all transcription. (upenn.edu)
  • 16S ribosomal RNA (rRNA) gene sequencing is the current gold standard in bacterial and other pathogenic microorganism identification and classification. (unboundmedicine.com)
  • New gene-based technologies can now be employed to examine microbial diversity through the use of small sub-unit ribosomal DNA analysis (e.g. 16S rDNA) and to understand the function of complex microbial ecosystems in the rumen through metagenomic analysis. (nhbs.com)
  • Similarly, the large ribosomal RNA gene clusters that reside on different chromosomes manage to find each other in almost every cell nucleus to form another easily discernable nuclear entity, the nucleolus [ 27 - 29 ]. (biomedcentral.com)
  • Also included are topics on DNA replication during interphase of the cell cycle, DNA mutation and repair mechanisms, gene pool, modification, and diseases. (biologyonline.com)
  • This hypothesis was tested based on phylogenetic analysis of the rDNA ITS region, morphological characters of basidiomes and pure cultures, growth rates and optimum growth temperature experiments, mycelial confrontation tests, enzyme activity tests and volatile organic compound (VOC) production. (springer.com)
  • Phylogenetic analysis of DNA sequence data confirmed B. ostreae to be a member of the Haplosporidia. (int-res.com)
  • Alien rDNA, nested among Potentilla species in phylogenetic analysis, likely entered the Erythronium lineage in the common ancestor of E. dens-canis and E. caucasicum. (cas.cz)
  • On the basis of 16S rDNA phylogenetic analysis of bacteria was done. (ispub.com)
  • This slowed the expression of their rDNA, which could be influencing the function of ribosomes, and resulted in smaller offspring - as much as 25% lighter. (foodnavigator.com)
  • Ribosomal DNA (rDNA) is found in ribosomes where proteins are mainly produced. (foodnavigator.com)
  • Existing models suggest that RNA polymerases I and III (Pol I and Pol III) are the only enzymes that directly mediate the expression of the ribosomal RNA (rRNA) components of ribosomes. (nature.com)
  • Apart from the ribosomal RNA, ribosomes also have protein s (about 40% by weight). (biologyonline.com)
  • At present little is known about the genetic diversity of rDNA amongst the hundreds of copies within an individual genome or across the genomes of individuals, i.e. at a population level in humans. (foodnavigator.com)
  • This raised the possibility of horizontal transfer of a eudicot alien ribosomal DNA (rDNA) into the Erythronium genome. (cas.cz)
  • Genome skimming coupled by PacBio HiFi sequencing of a bacterial artificial chromosome clone derived from flow-sorted nuclei was used to characterise the alien 45S rDNA. (cas.cz)
  • Integration of alien rDNA in the recipient genome was further proved by Southern blotting and fluorescence in situ hybridization using specific probes. (cas.cz)
  • Current bioinformatic pipelines for high-throughput studies like whole genome sequencing, RNA-seq, ChIP-seq, and single cell RNA-seq are limited in their ability to map repetitive elements of the genome like ribosomal DNA. (upenn.edu)
  • The 16S rDNA is present in scattered form in the entire genome of bacteria. (ispub.com)
  • RESUME Une PCR (amplification en chaîne par polymérase) diagnostique avec des amorces spécifiques d'espèces et un séquençage direct ont été utilisés pour la détermination des membres du complexe Ano- pheles maculipennis dans les régions du nord-ouest et du centre de la République islamique d'Iran. (who.int)
  • DNA extraction and PCR amplification. (exposed-skin-care.net)
  • The nucleic acid extraction from isolates cultured over night at 37C in reinforced clostridial bouillon (MERCK 5411) with an added 0.005 g of hemin, and the subsequent PCR amplification of 16S ribosomal DNA (rDNA), were performed as explained by Knarreborg (18). (exposed-skin-care.net)
  • Foi usado um total de 78 primers RAPD, sendo que 8 apresentaram 54% de fragmentos de DNA polimórficos. (scielo.br)
  • In general, for unknown molds, the ITS region of the rDNA is used as the primary target with primers ITS-1 and ITS-4 as the most general primer set. (cdc.gov)
  • These primers amplify approximately 600 basepairs of the ITS1-5.8S-ITS2 region of the ribosomal cistron. (cdc.gov)
  • These primers amplify approximately 620 basepairs of the 28S region of the ribosomal cistron. (cdc.gov)
  • These primers amplify a section of the intergenic spacer in the ribosomal cistron. (cdc.gov)
  • Different shape of hybridization signals of the 18S-25S rDNA (yellow-green) on two chromosomes K showing different degrees of condensation of the chromatin of the rDNA. (nenno.it)
  • Chromatin immunoprecipitation (ChIP) showed that pS2 and another active form of Pol II, phosphorylated on serine 5 (pS5), were enriched across rDNA, with the highest levels-at IGS28 and IGS38-being comparable to those at known Pol-II-transcribed loci (Fig. 1b and Extended Data Fig. 1a, d-f ). (nature.com)
  • Although it is clear that switching among BESs does not involve DNA rearrangements and that regulation is probably epigenetic, it remains unknown why BESs are transcribed by Pol I and what roles are played by chromatin structure and histone modifications. (asm.org)
  • Chromatin endogenous cleavage (ChEC) and psoralen experiments indicated that active rDNA is devoid of histones ( 23 ), whereas chromatin immunoprecipitation (ChIP) and genetic studies led to the conclusion that active rDNA has at least a few histones and is associated with chromatin-remodeling enzymes ( 15 , 31 , 34 ). (asm.org)
  • For identification of Trichosporon species, the intergenic region of the ribosomal cistron is used (Sugita, 2002). (cdc.gov)
  • The epigenetic study revealed that a diet low in protein resulted in a direct link between restricted growth and DNA modifications during protein production. (foodnavigator.com)
  • Early-life nutrition modulates the epigenetic state of specific rDNA genetic variants in mice. (foodnavigator.com)
  • The Paralkar Lab has developed customized genomes and computational pipelines to map datasets to rDNA, and we are interested in developing advanced tools to map and interpret the genetic and epigenetic profiles of rDNA in normal and malignant cells. (upenn.edu)
  • Based on the grouping, representative isolates were selected and subjected to near-full-length 16S rDNA sequencing according to the process layed out by Leser et al. (exposed-skin-care.net)
  • The genetic variability of the isolates was first assessed using Random Amplified Polymorphic DNA (RAPD) markers. (bvsalud.org)
  • I delimited species in the mushroom genus Russula based on the fungal nuclear internal transcribed spacer 2 (ITS2) DNA barcode region. (ubc.ca)
  • In these clinical situations, 16S rDNA sequencing can help establish a definitive microbiologic diagnosis, that is, to rule in (with positive identification) or rule out an infection. (unboundmedicine.com)
  • Recent advances in genomic DNA sequencing of microbial species from single cells. (unboundmedicine.com)
  • Emergency Central , emergency.unboundmedicine.com/emergency/view/GDT/619539/all/Ribosomal_DNA__16S_rDNA__sequencing. (unboundmedicine.com)
  • All purified colonies detected from the surface of the agar plate were used for a partial sequencing of 16S rDNA. (nih.gov)
  • Based on the analysis of 16s rDNA sequencing, compared to the saline-treated group, oral administration of spirulina once daily for 24 consecutive days altered the diversity, structure, and composition of colonic microbial community at the genus level. (frontiersin.org)
  • The diversity of a microbial community covering the surface of a marine nematode was analyzed by performing a 16S ribosomal DNA (rDNA) restriction cutting and sequencing analysis. (harvard.edu)
  • Sequencing of 16S rDNA. (exposed-skin-care.net)
  • High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. (springer.com)
  • We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. (springer.com)
  • In the last two decades, DNA barcoding, the sequencing of short species-specific amplicons, has considerably simplified community analyses (Hebert et al. (springer.com)
  • However, traditional Sanger sequencing-based DNA barcoding protocols can be prohibitively expensive and laborious when large community samples have to be processed. (springer.com)
  • High throughput sequencing showed that up to 92% of DNA reads, and 68% of RNA reads, in soils from the islands were accounted for by the fungus. (bas.ac.uk)
  • The human gut microbiota from three healthy subjects were compared by the use of a sequence analysis of 16S rDNA libraries and a culture-based method. (nih.gov)
  • We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. (springer.com)
  • We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities. (springer.com)
  • Mature rRNAs are packaged into 40S and 60S ribosomal subunits for export to the cytoplasm. (nature.com)
  • In mammalian cells, active and silent rDNA promoters are characterized by specific histone modifications, DNA methylation, and positioning of the promoter-bound nucleosome (reviewed in reference 22 ). (asm.org)
  • The Paralkar Lab has identified that key hematopoietic and leukemic transcription factors bind to rDNA and regulate rRNA transcription, and we are interested in understanding how the binding of cell-type-specific transcription factors regulates the activity of Polymerase I and the transcription of rRNA in normal hematopoiesis, and how this regulation is co-opted in leukemia to drive abundant ribosome biogenesis. (upenn.edu)
  • Ribosomal RNA is a specialized RNA molecule present in the ribosome. (biologyonline.com)
  • The ribosomal operons mainly 16S rDNA has proven to be a stable and specific molecular marker for bacterial identification. (ispub.com)
  • New genomic based methods such as polymerase chain reaction ( PCR ) detect bacterial forms based on the presence of bacterial DNA or RNA. (mpkb.org)
  • Loci of the 18S-25S rDNA (yellow-green) on chromosomes A, I, and K. The scale bar represents 10 µm. (nenno.it)
  • The 3 NO-chromosomes A,I, and K with loci of the 18S-25S rDNA probe. (nenno.it)
  • Loci of the 18S-25S rDNA (yellow-green) using directly with FITC-labeled (FITC-dUTP) probe. (nenno.it)
  • In order to confirm the number of 3 chromosomes with 18S-25S rDNA loci also interphase nuclei and chromosomes in meiosis studied by FISH. (nenno.it)
  • The co-localization with the 18S-25S and the 5S rDNA probe confirm that the loci of both rDNA types are found on chromosomes I and K. (nenno.it)
  • Loci of the 5S (pink) und 18S-25S (green) rDNA on the chromosomes I and K. The scale bar represents 10 µm. (nenno.it)
  • We analyzed the geographic distribution of Tubifex tubifex from various river drainages in central Colorado by genetic screening with specific mitochondrial 16S ribosomal DNA (mt 16S rDNA) markers. (usgs.gov)
  • Moreover, we found a discrepancy between the different nuclear ribosomal DNA markers, indicating a possible recombination with fragments of 28S DNA of N. ruffoi s. lat. (eawag.ch)
  • RAPD (Random Amplified Polymorphic DNA) markers have been most widely used for this purpose 8-10 . (bvsalud.org)
  • However, for thyriothecial species, phylogenies from DNA sequence data and illustrations of scutella remain have been limited. (ubc.ca)
  • In Chapter 2, I present a comprehensive phylogeny of thyriothecial Dothideomycetes based on 4251 nucelotides for 320 taxa, contributing new nuclear rDNA sequence data for 14 thyriothecial fungi. (ubc.ca)
  • rDNA coding regions are also depleted of nucleosomes, relative to the rDNA spacer. (asm.org)
  • Regulation of nucleosome density is therefore an important mechanism to enable the transcription machinery to access the DNA. (asm.org)
  • I compared the morphology within and among DNA-delimited species, according to morphological character state data that Woo had recorded for each of specimen. (ubc.ca)
  • Since the DNA is the finger print of every organism consequently, changes made within the genetic code could possible lead to alteration in the quality or characteristic of the plant in question. (intechopen.com)
  • The probe for 5S rDNA showed hybridization signals in the cHC of the NO-Chromosomes I and K. On Chromosome I the 5S rDNA locus is situated on the distal part of the cHC on the long arm in position Iq12. (nenno.it)
  • In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. (springer.com)
  • The researchers then studied the difference in the offspring's DNA methylation, from mothers exposed to low protein and those that were not. (foodnavigator.com)
  • 1980) ribosomal DNA (rDNA) in bulk DNA from oyster gill and hemolymph. (int-res.com)
  • Given that rRNA accounts for the bulk of the transcriptional output of the cell, the inability to map datasets to rDNA has historically been a major limitation, and has created a significant knowledge gap in our understanding of the most abundant RNA in the cell. (upenn.edu)
  • A caracterização molecular foi baseada em marcadores RAPD, sequenciamento da região do espaçador interno transcrito do DNA ribossomal e "fingerprinting" telomérico. (scielo.br)
  • These species share a high sequence homology of 16S rDNA and several molecular techniques already applied to discriminate among them give ambiguous results. (biomedcentral.com)
  • This study adds a new example to the rarely documented nuclear-to-nuclear jumps of DNA between eudicots and monocots while holding the scientific community continually in suspense about the mode of DNA transfer. (cas.cz)
  • Quarenta e nove isolados de Trichoderma obtidos no centro-oeste do Brasil foram avaliados quanto a sua atividade antagônica in vitro contra Sclerotinia sclerotiorum (agente causal do mofo branco) e identificados com base nas sequências ITS do DNA ribossômico nuclear. (scielo.br)
  • "The genetic variation of ribosomal DNA could be the reason why we've only been able to explain a small fraction of the heritability of many health conditions, which makes a lot of sense in the context of metabolic diseases, such as type 2 diabetes," ​ added Rakyan. (foodnavigator.com)
  • 2003 ). DNA barcodes can provide information on genetic variation within and between species, rapidly assign taxonomic status across divergent lineages (Hebert and Gregory 2005 ), and identify the prey composition of predators' gut contents (Agustí et al. (springer.com)
  • Four distinct mt 16S rDNA lineages are evident. (usgs.gov)
  • The rDNA ITS region is useful for delimitation of Fomes species. (springer.com)
  • To fit it into a nucleus with a diameter of ~10 μm, DNA is wrapped around histone octamers, creating strings of nucleosomes that can be further organized into higher-order levels of compaction [ 1 ]. (biomedcentral.com)
  • A previously described Taenia saginata HDP2 DNA sequence, a 4-kb polymorphic fragment, was previously used as the basis for developing PCR diagnostic protocols for the species-specific discrimination of T. saginata from T. solium and for the differentiation of T. saginata from T. asiatica . (biomedcentral.com)
  • Coding regions of active rDNA were initially thought to be devoid of nucleosomes, as suggested by electron microscopy and psoralen cross-linking experiments ( 4 ). (asm.org)
  • it does not describe the procedure for purification of fungal DNA. (cdc.gov)
  • In our low protein mice mothers, we saw that their offspring had methylated ribosomal DNA (rDNA). (foodnavigator.com)
  • The relative abundances of its DNA and RNA reads were positively associated with soil carbon and nitrogen concentrations and δ13C values, with the relative abundance of its DNA being negatively associated with soil pH value. (bas.ac.uk)
  • The second 5S rDNA locus was found on chromosome K at about the middle of the cHC of the long arm, the position of the weak DAPI band named Kq25. (nenno.it)
  • Transferred eudicot-type rDNA preserved its tandemly arrayed feature on a single chromosome and was found to be transcribed in the monocot host, albeit much less efficiently than the native counterpart. (cas.cz)