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Genes, rRNARNA, Ribosomal, 16SDNA, RibosomalPhylogenyRNA, RibosomalDNA, BacterialRNA, BacterialRNA, Ribosomal, 23SSequence Analysis, DNAMolecular Sequence DataBase CompositionRNA, Ribosomal, 5SBacterial Typing TechniquesrRNA OperonSoil MicrobiologyBase SequenceRNA, Ribosomal, 28SRNA, Ribosomal, 18SBacteriaNucleic Acid ConformationNucleic Acid HybridizationSpecies SpecificitySeawaterFatty AcidsGeologic SedimentsPolymerase Chain ReactionRibosomesActinomycetalesSequence Homology, Nucleic AcidWater MicrobiologyCluster AnalysisAlphaproteobacteriaRibosomal ProteinsFresh WaterBacteroidetesRNA Processing, Post-TranscriptionalDNA, ArchaealPolymorphism, Restriction Fragment LengthKoreaGammaproteobacteriaRNA, Ribosomal, 5.8SActinobacteriaQuinonesPhenotypeEscherichia coliBiodiversityRNA, ArchaealVitamin K 2RNA PrecursorsBetaproteobacteriaDNA PrimersRNA, FungalDNA, Ribosomal SpacerSodium ChlorideAerobiosisCell NucleolusSewagePigments, BiologicalProteobacteriaHot SpringsMethyltransferasesEcosystemEnvironmental MicrobiologyDeltaproteobacteriaRNA, TransferBacillaceaeBacterial ProteinsNocardiaGenetic VariationFlavobacteriaceaeEndoribonucleasesOligonucleotide ProbesAnaerobiosisTemperatureDiaminopimelic AcidMethaneRhodobacteraceaeGenes, BacterialDenaturing Gradient Gel ElectrophoresisTranscription, GeneticRibosome Subunits, SmallDNA FingerprintingTranscription Factor TFIIIAGentian VioletChloroflexiBiodegradation, EnvironmentalChinaAnti-Bacterial AgentsMetagenomeRNA, ProtozoanComamonadaceaeMycoplasmaMicrobial ConsortiaBacteria, AnaerobicMycobacteriumHalobacteriaceaeSequence AlignmentWaste Disposal, FluidArchaeaPlankton
SequencesGenesNEBNext rRNA Depletion KitSmall subunitBacteriaBacterial 16S rRNAAmpliconSpeciesMitochondrial rRNARibosomal proteinsEscherichiaAbstractPhylogeneticCytoplasmicDepletionMetagenomeMoleculeIntergenicSequence AnalysisMicrobiota compositionDatasetOperonProkaryoticSubunitHybridizationGene sequenceHighly abundantAmplificationTRNANucleolarMethylatesLibrariesDiversityPrimersStrainsCompositionMolecularGenusAnalysisPreviouslyHumanPartialResearchersMethodRegionsSingleSpecific
Sequences14
  • SSU rRNA sequences are widely used for determining evolutionary relationships among organisms, since they are of ancient origin and are found in all known forms of life. (wikipedia.org)
  • The CRISPRclean Plus kit depletes over 200 bacteria species and human rRNA sequences to enable identification of lower-expressed transcripts. (genomeweb.com)
  • Effective depletion of sequences overlapping with annotated rRNA regions was observed at 100 ng and 10 ng of input RNA for most of the organisms. (neb.com)
  • The 16S rRNA sequences of 128 valid and invalid Pseudomonas species, which included almost valid species of the genus Pseudomonas listed in the Approved Lists of Bacterial Names, were obtained: sequences of 59 species were determined and those of 69 species were obtained from the GenBank/EMBL/DDBJ databases. (microbiologyresearch.org)
  • 18S-NemaBase: Curated 18S rRNA Database of Nematode Sequences" by Kaitlin Gattoni, Eli M. S. Gendron et al. (unl.edu)
  • To improve molecular identification and the assessment of nematode diversity, we created and curated an 18S rRNA database specific to nematodes (18S-NemaBase) using sequences sourced from the most recent publicly available 18S rRNA SILVA v138 database. (unl.edu)
  • The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). (asm.org)
  • In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. (asm.org)
  • The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. (asm.org)
  • These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. (microbiologyresearch.org)
  • Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable. (microbiologyresearch.org)
  • Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. (peerj.com)
  • The rate of gene conversion was 10-fold less than the fixation of point mutations in the same region of the chromosome but was apparently sufficient to homogenize the sequences of rRNA genes in E. coli. (northwestern.edu)
  • Sequence alignment analysis showed 5-14.8% SNP in the partial sequences of the 18 s rRNA of P. falciparum . (biomedcentral.com)
Genes7
  • QIAseq FastSelect -rRNA Worm Kits provide highly efficient removal of rRNA (figure QIAseq FastSelect -rRNA Worm Kits provide highly efficient removal of rRNA) and consistent read mapping (figures QIAseq FastSelect -rRNA Worm exon/intron/intergenic mapping, QIAseq FastSelect ‒rRNA Worm dramatically shifts read allocation from rRNA to genes and QIAseq FastSelect ‒rRNA Worm dramatically shifts read allocation from rRNA to genes: bar chart). (qiagen.com)
  • Twenty-six strains from 16 hospitals harbored 16S rRNA methylase genes, which suggests sparse but diffuse spread of pan-aminoglycoside-resistant microbes in Japan. (cdc.gov)
  • Twenty-nine strains (17 P . aeruginosa , 4 A . baumannii , 3 E . coli , 2 P . mirabilis , 1 E . cloacae , 1 K. pneumoniae , and 1 Enterobacter aerogenes ) that grew on LB agar plates supplemented with 500 mg of arbekacin per liter were subjected to the typing of 16S rRNA methylase genes by a multiplex PCR. (cdc.gov)
  • 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)
  • 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)
  • These findings are discussed in the context of a conceptual model describing the presence of sequence heterogeneity in coevolving rRNA genes. (northwestern.edu)
  • The presence of Helicobacter genus-specific DNA (16S rRNA genes) was determined by nested polymerase chain reaction assay. (who.int)
NEBNext rRNA Depletion Kit4
  • The NEBNext ® rRNA Depletion Kit (Bacteria) employs the NEBNext RNase H-based RNA depletion workflow to target removal of rRNA from gram-positive and gram-negative organisms. (neb.com)
  • Ribosomal RNA was depleted using the NEBNext rRNA Depletion Kit (Bacteria). (neb.com)
  • Thank you for testing a sample of the NEBNext rRNA Depletion Kit (Bacteria). (neb.com)
  • For each of the species tested, how well did the NEBNext rRNA Depletion Kit (Bacteria) perform? (neb.com)
Small subunit4
  • Small subunit ribosomal ribonucleic acid (SSU rRNA) is the smaller of the two major RNA components of the ribosome. (wikipedia.org)
  • Associated with a number of ribosomal proteins, the SSU rRNA forms the small subunit of the ribosome. (wikipedia.org)
  • Ribosomal protein S15 is of particular interest because it binds primarily to 16S rRNA and is required for assembly of the small subunit and for intersubunit association, thus representing a key element in the assembly of a whole ribosome. (unboundmedicine.com)
  • A mutant strain of Escherichia coli was created by inserting a cassette encoding sucrose sensitivity and neomycin resistance (sacB-neo) into the small-subunit rRNA-encoding gene rrs in the rrnB operon. (northwestern.edu)
Bacteria6
  • The great majority of RNA in bacteria is ribosomal RNA (rRNA). (neb.com)
  • To investigate the exact isolation frequency of 16S rRNA methylase-producing, gram-negative pathogenic bacteria, we tested 87,626 clinical isolates from 169 hospitals. (cdc.gov)
  • Although the production of aminoglycoside-modifying enzymes is the most common mechanism of resistance in aminoglycosides, the emergence of pan-aminoglycoside-resistant, 16S rRNA methylase-producing, gram-negative bacteria has been increasingly reported in recent years. (cdc.gov)
  • Thus, this investigation was conducted to determine the exact isolation frequency of 16S rRNA methylase-producing, gram-negative pathogenic bacteria in Japanese medical facilities and assess the possibility of the future prevalence of these hazardous microbes. (cdc.gov)
  • Furthermore, the total bacterial population was visualized with an rRNA probe targeting the domain Bacteria. (ruc.dk)
  • A set of broad-range PCR primers for the 16S rRNA gene in bacteria, as well as three series of oligonucleotide probes to detect the PCR product, were examined. (alliedacademies.org)
Bacterial 16S rRNA1
  • 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)
Amplicon3
  • 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)
  • While bacterial community composition recovered using Illumina 16S rRNA amplicon sequencing was not detectably biased by any method, the quantity of bacterial DNA varied drastically, reducing the number of samples that could be amplified and sequenced. (harvard.edu)
  • 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)
Species5
  • Depending on rRNA sequence homology, QIAseq FastSelect −rRNA Worm will work on additional worm species (dependent upon target rRNA sequence homology with C. elegans ). (qiagen.com)
  • QIAseq FastSelect can be used with RNA from fresh samples from many species of worm (dependent upon target rRNA sequence homology with C. elegans ), and delivers reliable rRNA removal and high reproducibility in downstream applications. (qiagen.com)
  • In 2002, an ad hoc committee for the reevaluation of species definition in bacteriology ( 24 ) advised that all new bacterial species descriptions include an rRNA sequence from the type strain, and in 2001, Bergey's Trust published a revised higher-order taxonomy attempting to reconcile bacterial taxonomy with rRNA-based phylogeny ( 12 , 13 ). (asm.org)
  • Comparative analysis of Bacillus anthracis, Bacillus cereus , and related species on the basis of reverse transcriptase sequencing of 16S rRNA. (microbiologyresearch.org)
  • The use of random hexamer priming allows for analyzing a broader range of RNA species, but comes with the drawback that ribosomal RNA (rRNA) - that can constitute up to 90% of total RNA - is reverse transcribed together with the RNA of interest. (biomedcentral.com)
Mitochondrial rRNA1
  • In particular, the present invention provides compositions comprising affinity-tagged antisense rRNA molecules corresponding to substantially all of at least one rRNA molecule (e.g., 28S, 26S, 25S, 18S, 5.8S and 5S eukaryotic cytoplasmic rRNA molecules, 12S and 16S eukaryotic mitochondrial rRNA molecules, and 23S, 16S and 5S prokaryotic rRNA molecules) and methods for using such compositions to generate rRNA-depleted samples or to isolate rRNA molecules from samples. (justia.com)
Ribosomal proteins1
Escherichia2
  • Spatial distribution of Escherichia coli in the mouse large intestine inferred from rRNA in situ hybridization. (ruc.dk)
  • Fluorescent oligonucleotide probes targeting rRNA were used to develop an in situ hybridization technique by which the spatial distribution of Escherichia coli in the large intestines of streptomycin-treated mice was determined. (ruc.dk)
Abstract1
  • Abstract The two ruminant parasites, Paramphistomum cervi and Carmyerius gregarius, were collected from freshslaughtered native cattle at local abattoirs in Sadat district, Menoufia province and identified morphologically, then molecularly by sequencing the nucleotides of 18S ribosomal RNA gene (18S rRNA). (sohag-univ.edu.eg)
Phylogenetic3
  • Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. (microbiologyresearch.org)
  • Starting in the mid-1980s, Carl Woese revolutionized the field of microbiology with his rRNA-based phylogenetic comparisons delineating the three main branches of life ( 28 ). (asm.org)
  • Phylogenetic trees based on 18 s rRNA placed the P. falciparum isolates into three sub-clusters and P. vivax into one cluster. (biomedcentral.com)
Cytoplasmic1
  • QIAseq FastSelect -rRNA Worm Kits are designed for quick, efficient removal of cytoplasmic and mitochondrial worm ribosomal RNA from total RNA during NGS RNA library preparation. (qiagen.com)
Depletion1
  • The CRISPRclean Stranded Total RNA Prep kit with rRNA depletion offers unbiased depletion and library preparation for RNA sequencing. (genomeweb.com)
Metagenome2
Molecule1
  • Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule. (gsea-msigdb.org)
Intergenic1
  • 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)
Sequence Analysis1
Microbiota composition1
Dataset1
  • The incorporation of 16S rRNA sequencing as a supportive dataset complemented the analysis of the metabolome data. (lu.se)
Operon1
  • In the present study, 6 rRNA operon libraries constructed along the salinity gradient in the Chesapeake Bay in 2 different seasons were analyzed and sequenced. (stroudcenter.org)
Prokaryotic1
  • The by far most often used marker for prokaryotic diversity studies is the 16S rRNA or its corresponding gene. (frontiersin.org)
Subunit2
Hybridization1
  • Seven subclusters were formed in the cluster of the genus Pseudomonas (sensu stricto), and the resulting clusters conformed well to the rRNA-DNA hybridization study by Palleroni (1984). (microbiologyresearch.org)
Gene sequence1
  • Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. (asm.org)
Highly abundant2
  • Ribosomal RNA (rRNA) is highly abundant in bacterial samples, and its removal is desirable in order to reveal the biological significance of less abundant transcripts. (neb.com)
  • QIAseq FastSelect -rRNA Worm Kits use a novel method to remove highly abundant RNA that is of low scientific value from your RNA-seq libraries. (qiagen.com)
Amplification3
  • 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)
TRNA1
  • Es gibt drei RNA-Typen, die in der Proteinsynthese eine Rolle spielen: Boten-RNA (englisch messenger RNA, mRNA), Transfer-RNA (tRNA) und die ribosomale RNA (rRNA). (jove.com)
Nucleolar2
  • The rid2-1 mutation was shown to cause nucleolar vacuolation and excessive accumulation of various intermediates of pre-rRNA processing. (nih.gov)
  • It can be inferred from these findings that RID2 contributes to the nucleolar activity for pre-rRNA processing, probably through some methylation reaction. (nih.gov)
Methylates1
  • The enzyme specifically methylates guanine(1207) at N(2) in 16S rRNA. (expasy.org)
Libraries2
  • We here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps. (biomedcentral.com)
  • The kit provided a straightforward procedure for generating random hexamer primed stranded RNAseq libraries from 1-5 ng of total RNA, although an effective solution for reducing the rRNA contribution to the library was lacking. (biomedcentral.com)
Diversity1
  • Today, rRNA-based analysis remains a central method in microbiology, used not only to explore microbial diversity but also as a day-to-day method for bacterial identification. (asm.org)
Primers1
  • 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)
Strains1
  • Geographic distribution of hospitals where 16S rRNA methylase gene-positive strains were isolated. (cdc.gov)
Composition1
  • DNA was extracted from each sample, and quantitative polymerase chain reaction (qPCR) and 16S rRNA Illumina MiSeq gene sequencing were performed to determine relative concentrations of biomass and microbial community composition, respectively. (usgs.gov)
Molecular3
  • QIAseq FastSelect -rRNA Worm Kits are intended for molecular biology applications. (qiagen.com)
  • Another new 16S rRNA methylase was initially identified in C. freundii in Poland, submitted to European Molecular Biology Laboratory (EMBL)/GenBank in 2002 (accession no. (cdc.gov)
  • Molecular weight and chain length of rabbit reticulocyte rRNA. (wikidata.org)
Genus1
  • When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. (peerj.com)
Analysis4
  • Researchers using RNA-seq for whole transcriptome analysis can use QIAseq FastSelect -rRNA Worm Kits to remove all annotated rRNAs in RefSeq and Ensembl for Caenorhabditis elegans (worm). (qiagen.com)
  • 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)
  • Structural analysis of their complexes with rRNA requires identification of their binding sites in the 5S rRNA. (unboundmedicine.com)
  • In particular, the present invention provides methods for generating compositions comprising affinity-tagged antisense rRNA molecules, kits comprising such compositions, and methods for using such compositions to generate rRNA-depleted samples or to isolate rRNA from a sample (e.g., for further analysis and use). (justia.com)
Previously1
  • Previously, a TL5-binding site has been identified, a TL5-RNA complex crystallized, and its structure determined to 2.3 A. The sites for L5 and L18 were characterized, and two corresponding 5S rRNA fragments constructed. (unboundmedicine.com)
Human2
  • I have some 16S rRNA sequencing data from human tissue, which was performed on NovaSeq 6000 platform. (biostars.org)
  • 16S rRNA sequencing data on human skin microbiome samples collected before and after swimming in the ocean. (mendeley.com)
Partial1
  • Blood samples from 511 febrile patients were collected and a partial region of the 18 s ribosomal RNA (18 s rRNA) gene was amplified using nested PCR. (biomedcentral.com)
Researchers1
  • This study aimed to recommend an adequate sampling plan for field researchers obtaining microbial biomass for 16S rRNA gene sequencing, applicable specifically to oil and gas-producing environments. (usgs.gov)
Method2
  • Still further, better methods for removing rRNA, including degraded rRNA, from non-rRNA RNA molecules of interest would greatly improve the applicability and success of methods that comprise deliberately degrading the RNA as part of the particular method (such as the method of Ingolia et al. (justia.com)
  • Method of measurement: Measured by 16s rRNA method. (who.int)
Regions2
  • For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. (asm.org)
  • Repair of this lesion required flanking regions of DNA that were similar to the six remaining intact rRNA operons and reestablished the full complement of seven rRNA operons. (northwestern.edu)
Single1
  • Single E. coli cells were identified in thin frozen sections from the large intestines by the use of a probe specific for E. coli 23S rRNA. (ruc.dk)
Specific1
  • Specific enrichment of bacterial mRNAs is challenging due to their lack of poly(A) tails, and so the converse - efficient and specific removal of bacterial rRNA - is necessary. (neb.com)