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Genes, rRNARNA, Ribosomal, 16SDNA, RibosomalRNA, RibosomalrRNA OperonPhylogenyRNA, BacterialRNA, Ribosomal, 23SDNA, BacterialMolecular Sequence DataSequence Analysis, DNABase CompositionRNA, Ribosomal, 5SBase SequenceBacterial Typing TechniquesRNA, Ribosomal, 28SSoil MicrobiologyNucleic Acid ConformationBacteriaNucleic Acid HybridizationRibosomesSpecies SpecificitySeawaterPolymerase Chain ReactionGeologic SedimentsFatty AcidsSequence Homology, Nucleic AcidRibosomal ProteinsRNA Processing, Post-TranscriptionalCell NucleolusWater MicrobiologyActinomycetalesCluster AnalysisAlphaproteobacteriaEscherichia coliRNA, FungalRNA PrecursorsFresh WaterPolymorphism, Restriction Fragment LengthRNA, ArchaealBacteroidetesRNA Polymerase IDNA, ArchaealPhenotypeRibosome Subunits, SmallBiodiversityActinobacteriaGammaproteobacteriaTranscription, GeneticDNA PrimersKoreaRNA, TransferQuinonesRNA, ProtozoanMethyltransferasesVitamin K 2BetaproteobacteriaSodium ChlorideSewageProteobacteriaRibosome Subunits, Small, BacterialEndoribonucleasesEcosystemOligonucleotide ProbesDeltaproteobacteriaAerobiosisEnvironmental MicrobiologyGenetic VariationHot SpringsPigments, BiologicalBacterial ProteinsOperonRNA, Small NucleolarSaccharomyces cerevisiaeTemperatureMutationBacillaceaeSequence AlignmentNocardiaPol1 Transcription Initiation Complex ProteinsCloning, MolecularDNA FingerprintingPseudouridineMethaneAnaerobiosisNucleic Acid PrecursorsFlavobacteriaceaeRNADenaturing Gradient Gel ElectrophoresisProtein BiosynthesisDiaminopimelic AcidPlanktonPlasmidsAnti-Bacterial AgentsChloroflexiEukaryotaRhodobacteraceaeMycoplasmaDNA, MitochondrialTranscription Factor TFIIIA
SequencesSequenceMicrobiomeBacterialAmplificationAmpliconTranscriptHigh-throughputPhylogeneticRDNAFecalMicrobiota compositionDiversityMitochondrialMolecularDetectionIsolationResearchersRibosomal RNAAnalysisMarkerGenomePrimersVariantsDataEvaluationRegionProteinTranscriptsProteinsRegionsReactionProcedureExpressionMethodPresentSamplesHistoryEvent
Sequences7
  • Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. (frontiersin.org)
  • of the 5 S rRNA gene sequences of rice variety IR20 and 17 S and 25 S rRNA gene sequences of rice variety Mangetsumochi revealed the presence of 39 hexa, 4 hepta, and 2 octa nucleotide homologies between 5 S and 17 S rRNA genes and 48 hexa, 11 hepta, 6 octa and 1 nano nucleotide homologies between 5 S and 25 S rRNA genes. (iisc.ac.in)
  • Using QIIME to analyze 16S rRNA gene sequences from microbial communities. (nau.edu)
  • The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community. (qub.ac.uk)
  • The highest producer of acetic acid (11.2) was selected for identification by 16S rRNA gene sequences, and phylogenetic analysis confirmed their position in the genes Acetobacter. (kombuchabrewers.org)
  • To determine the genotypic composition of sporozoites carried by the Type C oocysts, we analyzed their 18S rRNA gene sequences using a single sporozoite isolation procedure. (elsevierpure.com)
  • It has been shown by the author in previous articles that the Greengenes Classifier can be successfully used as a bioinformatics program that performs taxonomic classification of 16S rRNA gene sequences. (edu.ba)
Sequence6
  • Alignment of amplicon sequence isolated from the patient was compared with a reference Trypanosoma cruzi 5.8S rRNA internal transcribed spacer sequence (GenBank accession no. (cdc.gov)
  • alias" : "DRX002801", "center_name" : "UT_COB", "accession" : "DRX002801", "TITLE" : "PCR amplification of 16S rRNA gene (V1-V2 region) sequence", "STUDY_REF" : { "refname" : "DRP000910", "refcenter" : "UT_COB", "accession" : "DRP000910", "IDENTIFIERS" : { "PRIMARY_ID" : { "label" : "BioProject ID", "content" : "PRJDB2343" } } }, "DESIGN" : { "DESIGN_DESCRIPTION" : "", "SAMPLE_DESCRIPTOR" : { "refname" : "DRS002885", "refcenter" : "UT_COB", "accession" : "DRS002885", "IDENTIFIERS" : { "PRIMARY_ID" : { "label" : "BioSample ID", "content" : "SAMD00010272" } } }, "LIBRARY_DESCRIPTOR" : { "LIBRARY_STRATEGY" : "AMPLICON", "LIBRARY_SOURCE" : "METAGENOMIC", "LIBRARY_SELECTION" : "PCR", "LIBRARY_LAYOUT" : { }, "LIBRARY_CONSTRUCTION_PROTOCOL" : "PCR amplification of the SSU rRNA gene V1-V2 region using forward primer (5? (nig.ac.jp)
  • A single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. (ensembl.org)
  • To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. (pacb.com)
  • There was no hybridization between 5 S rRNA and 5.8 S rRNA genes, though a hexa and a hepta nucleotide sequence homologies are found between them. (iisc.ac.in)
  • In this article we used Longest Common Subsequence similarity measure to classify bacterial 16S rRNA gene sequence short reads against the Greengenes library. (edu.ba)
Microbiome3
  • While microbiome data generated using high-throughput 16S rRNA marker gene surveys are appealing for this purpose, 16S surveys also generate a plethora of spurious microbial taxa. (nevinmanimala.com)
  • rRNA-genes for phylogenetic classifications started to be used in 1980s first time by Carl Woese which made a ground breaking contribution to microbiome science. (edu.ba)
  • In a previous article, the accuracy of the program is also tested when it is applied to common PCR products of the 16S rRNA variable regions, which are the only product of laboratories in microbiome projects. (edu.ba)
Bacterial5
  • We sequenced DNA using the bacterial 16S rRNA high-throughput next-generation sequencing and analyzed changes in microbial profiles for taxonomy comparison between samples. (nature.com)
  • Bacterial strains isolated from food products sold in Lagos, Nigeria, were subjected to phenotypic techniques and 16S rRNA gene sequencing for specie level identification. (edu.ng)
  • Bacterial identification was performed using colonial morphology, Gram staining, conventional biochemical tests, and 16S rRNA gene sequencing. (edu.ng)
  • Anammox bacterial diversity and abundance were studied from the organic-rich hypoxic sediments of the Arabian Sea utilizing the partial 16S rRNA, and hydrazine synthase, hzsA and hydrazine oxidoreductase, hzo genes. (nio.res.in)
  • rRNA-genes are used to explore microbial diversity as well as a method for bacterial annotation. (edu.ba)
Amplification5
  • Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. (frontiersin.org)
  • PCR amplification of the SSU rRNA gene V1-V2 region using forward primer (5? (nig.ac.jp)
  • The universal 16S rRNA gene is used as a control for DNA extraction and amplification for each reaction. (cdc.gov)
  • The objective of this study was to identify Mycobacterium species isolated in cattle in Zimbabwe using 16S ribosomal RNA gene amplification and sequencing. (openmicrobiologyjournal.com)
  • Supplemental Fig. S1B,C). rRNA gene subtypes in isolated nuclei or nucleoli have been identified by PCR amplification applying primers flanking the variable area (see Fig. 1A). (btkinhibitor.com)
Amplicon4
  • Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community structure analysis. (frontiersin.org)
  • This workshop will give you theoretical and most of all practical knowledge on how to analyze high-throughput sequencing data based on 16S rRNA gene amplicon libraries. (tum.de)
  • In brief, DNA extracted from whole blood and controls were used for 16S rRNA gene profiling using MiSeq Illumina technology (2 x 300 paired-end MiSeq kit V3, set to encompass 467-bp amplicon). (unimi.it)
  • The PCR amplicon is shown inside a.and variant 1 genes are silenced (Fig. 1E, RT CR primer locations are shown within a). (btkinhibitor.com)
Transcript2
  • This gene has 1 transcript ( splice variant ). (ensembl.org)
  • rRNA gene or transcript FISH signals are shown in green, immunolocalized HDA6 is in red, and DAPI-stained DNA is in blue. (btkinhibitor.com)
High-throughput1
  • The fecal samples were then analyzed using high-throughput sequencing of 16S rRNA V3-V4 amplicons. (hindawi.com)
Phylogenetic1
  • This study explains the phylogenetic relationship of stingless bees in the Special Region of Yogyakarta, Indonesia based on the 16S rRNA gene. (ugm.ac.id)
RDNA1
  • B) Localization of rRNA genes (rDNA) and Pol I. DNA-FISH using an rRNA gene probe (red signals) and immunolocalization of Flag-tagged Pol I utilizing an anti-Flag D3 Receptor Antagonist drug antibody (green signals) had been performed within a. thaliana interphase nuclei. (btkinhibitor.com)
Fecal1
  • In this study, we investigated fecal 16S rRNA gene sequencing analysis of changes in the gut microbiota of rats with LDA-related intestinal injury. (hindawi.com)
Microbiota composition1
Diversity1
  • The by far most often used marker for prokaryotic diversity studies is the 16S rRNA or its corresponding gene. (frontiersin.org)
Mitochondrial4
  • Mutation in the mitochondrial 12S rRNA gene in two families from Mongolia with matrilineal aminoglycoside ototoxicity. (bmj.com)
  • In 1993 it was shown that an A to G substitution at base pair 1555 of the mitochondrial 12S ribosomal RNA gene was the only mutation common to all the families with aminoglycoside ototoxicity. (bmj.com)
  • We have thus confirmed the clinical relevance of the 1555 A to G mitochondrial mutation in the 12S rRNA gene by identifying it in affected subjects with familial aminoglycoside ototoxicity in another ethnic group. (bmj.com)
  • 2014. Molecular phylogeny of Malaysian stingless bee (Hymenoptera: Apidae: Meliponini) revealed using partial 16s rRNA mitochondrial gene. (ugm.ac.id)
Molecular5
  • Our phylogenetical investigations inferred from partial paralogous 18S-28S rRNA genes suggest that the event resulting in the presence of two classes of rRNA genes would have occurred at approximately 300-400 million years and prior to the radiation of extant chaetognath, whereas the taxon, according to both molecular and paleontological data, would be dated from at least the Early Cambrian. (scialert.net)
  • Molecular characterization studies have been conducted 16S rRNA gene micro symbiont of sponge origin Melawai Beach, Balikpapan in East Kalimantan. (unhas.ac.id)
  • Objective analysis of histomorphological research, isolation-purification, molecular characterization of micro-symbiont genes in order to search symbiont bacteria that can live in extreme environments contaminated hydrocarbon waste. (unhas.ac.id)
  • The research method that morphological identification, isolation-purification and molecular characterization of the 16S rRNA gene with Chain Reaction Polymerization method. (unhas.ac.id)
  • Analysis of potensial and molecular characterization of 16S rRNA gene of isolation cellulolytic bacteria from Eucheuma sp. (unhas.ac.id)
Detection3
  • D) DNA-FISH detection of rRNA genes in wild-type (Col-0) and hda6 nuclei. (btkinhibitor.com)
  • E) Detection of rRNA gene variant forms and their transcripts by PCR utilizing genomic DNA or reversetranscribed (RT) cDNA of wild-type (Col-0) or hda6 plants. (btkinhibitor.com)
  • I) PCR detection of rRNA gene variant kinds in DNA of purified nuclei (N) or nucleoli (No) of wild-type (Col-0) or hda6 plants. (btkinhibitor.com)
Isolation1
  • The object of this work was to study the volatile production in established shoot and callus cultures of Haplophyllum canaliculatum as well as isolation, identification and sequencing of 18S rRNA gene from callus culture. (fatcat.wiki)
Researchers1
  • Many researchers followed rRNA-based analysis track as a central method in microbiology. (edu.ba)
Ribosomal RNA4
  • Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). (wikipedia.org)
  • It is largely made up of specialized RNA known as ribosomal RNA (rRNA) as well as dozens of distinct proteins (the exact number varies slightly between species). (wikipedia.org)
  • These proteins are involved in the production of a molecule called ribosomal RNA (rRNA), a chemical cousin of DNA. (medlineplus.gov)
  • Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the ribosomal RNA gene internal transcribed spacer-1 (ITS1) was used. (who.int)
Analysis3
  • We describe two models of change in the urinary tract microbiota after prostate biopsy using 16S RNA gene analysis. (nature.com)
  • Amplified mtDNA, obtained from transformed lymphoblastoid cell lines using previously described primers, showed the A to G point mutation in the 12S rRNA gene in two of the three families by restriction analysis as well as direct sequencing. (bmj.com)
  • Gene analysis showed 98% homology with certain species of Rutaceae, Meliaceae, Simaroubaceae, Burseraceae and Cneoraceae. (fatcat.wiki)
Marker1
  • From these analyses, it is inferred that searching for hzo gene yields robust evidence for detecting anammox community than the widely used 16S rRNA gene marker. (nio.res.in)
Genome1
  • Genome-wide association analyses identify variants in developmental genes associated with hypospadias. (nih.gov)
Primers1
Variants6
  • Variants (also known as mutations) in the TCOF1 , POLR1C , or POLR1D gene can cause Treacher Collins syndrome. (medlineplus.gov)
  • TCOF1 gene variants are the most common cause of the disorder, accounting for 81 to 93 percent of all cases. (medlineplus.gov)
  • POLR1C and POLR1D gene variants cause an additional 2 percent of cases. (medlineplus.gov)
  • Variants in the TCOF1 , POLR1C , or POLR1D gene reduce the production of rRNA. (medlineplus.gov)
  • When Treacher Collins syndrome results from variants in the TCOF1 or POLR1D gene, it is considered an autosomal dominant condition, which means one copy of the altered gene in each cell is sufficient to cause the disorder. (medlineplus.gov)
  • Autosomal recessive inheritance means both copies of the gene in each cell have variants. (medlineplus.gov)
Data3
  • 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. (frontiersin.org)
  • We generated sequencing data from the V4, V3-V5, V1-V3, V1-V5, V1-V6, and V1-V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. (pacb.com)
  • Meanwhile, for the morphospecies T. biroi , the closest hit is on T. pagdeni 16S rRNA DNA because the T. biroi 16S rRNA DNA data is not available on the database. (ugm.ac.id)
Evaluation1
  • Evaluation of Feed-Related Differences Using 16S rRNA Gene Metabarcoding. (bvsalud.org)
Region1
  • In a. thaliana, insertions/deletions inside the 39 external transcribed region define rRNA gene variant types. (btkinhibitor.com)
Protein1
  • To identify no matter if each active and silenced rRNA genes are connected with nucleoli, we performed fluorescence-activated sorting of entire nuclei or AT1 Receptor Inhibitor drug isolated nucleoli from plants expressing the nucleolar protein FIBRILLARIN2 fused to YFP (yellow fluorescent protein) (Barneche et al. (btkinhibitor.com)
Transcripts2
  • As inferred from mouse cell models, intergenic spacer regions (IGS) located between rRNA transcription units contain upstream promoters and are transcribed by RNA Polymerase I. The IGS transcripts originate approximately 2 Kb upstream of the start of rRNA transcription and proceed though the main promoter of the rRNA gene. (reactome.org)
  • C) Subnuclear localization of rRNA genes, pre-rRNA transcripts, and Flag-tagged HDA6. (btkinhibitor.com)
Proteins1
  • The proteins produced from the TCOF1 , POLR1C , and POLR1D genes all appear to play important roles in the early development of bones and other tissues of the face. (medlineplus.gov)
Regions1
  • In this study, V1-V3 hyper variable regions from 16S rRNA genes of some known bacteria is taken from the work of A. Cosic. (edu.ba)
Reaction1
Procedure1
  • Volatiles from fresh callus and shoot cultures were extracted and analyzed by GC/MS. For 18S rRNA gene study, DNA content was extracted using PCR procedure. (fatcat.wiki)
Expression1
  • Nonetheless, in nucleoli of wild-type plants, variant 2- and 3-type rRNA genes are enriched (Fig. 1I, top row), correlating with their selective expression (see Fig. 1E). (btkinhibitor.com)
Method1
  • Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. (pacb.com)
Present1
  • In hda6 mutants, in which variant 1 gene silencing will not take place, variant 1 genes are also present in nucleoli (Fig. 1I, bottom row). (btkinhibitor.com)
Samples2
  • Output from the 16s rRNA gene sequencing in Vagina samples. (vu.nl)
  • The 16S rRNA gene was successfully amplified by PCR in 41 (84%) of the samples. (openmicrobiologyjournal.com)
History1
  • in the gene and occur in people with no history of the disorder in their family. (medlineplus.gov)
Event1
  • These divergent rRNA genes could be the result of a whole ribosomal cluster duplication or of an allopolyploid event during a crisis period, since, the fossil are lacking posterioly to the post-Carboniferous period ( c.a ., 300 million years). (scialert.net)