Sequences ribosomal rna genes. Medical search. Frequent questions

In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)

In a subset of 10 representative patients, bacterial DNA was extracted from ascites and whole blood, followed by 16S rRNA gene amplicon sequencing. (frontiersin.org)
MiSeq amplicon high-throughput sequencing (Illumina ® ) is able to detect species richness (the number of species within a community) and species evenness (the sizes of species populations within a community). (degruyter.com)
Lee, S., Yamamoto, N. (2015) Accuracy of the high-throughput amplicon sequencing to identify species within the genus Aspergillus . (degruyter.com)
Systematic processing of ribosomal RNA gene amplicon sequencing data. (cdc.gov)

Sequence data from nuclear 18S rRNA genes from several dennstaedtioid ferns were also analyzed and found to support some of the inferences based on rbcL data. (usu.edu)
Archaea were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox, based on their ribosomal RNA (rRNA) genes. (wikipedia.org)
Phylogenetic affiliations of mesopelagic acantharia and acantharian-like environmental 18S rRNA genes off the southern California coast. (mbl.edu)

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)
To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
The genetic homogeneity of ospC -A isolates was confi rmed agent, Borrelia burgdorferi , a spirochete that parasitizes by sequences at 6 additional chromosomal housekeeping vertebrates, is transmitted by hard-bodied ticks through- loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
Only 16S rRNA sequencing was able to determine the subspecies of P. multocida and to determine the genetic relatedness of the 2 isolates. (medscape.com)
ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. (lu.se)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)

Backward compatibility of whole genome sequencing data with MLVA typing using a new MLVAtype shiny application for Vibrio cholerae. (cdc.gov)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)

Internal transcriber spacer (ITS) sequences and several chloroplast markers, rpoB , rpoC1 , and psbA-trnH were sequenced in order to infer a preliminary phylogeny of the genus. (bioone.org)
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)
Here we obtained a well-resolved polymorphism type of intergenic spacer (IGS) sequence phylogeny of B. burgdorferi sensu stricto clonal complexes (corresponding to the ospC- A and -B groups) is associated by using multilocus sequence typing at housekeeping loci with hematogenous dissemination in patients with early as well as loci under adaptive evolution. (cdc.gov)

DNA was isolated and ribosomal RNA genes were obtained by PCR and cloning, and sequenced to identify microbes. (cdc.gov)
The regions employed to establish identity are usually ribosomal RNA genes from microbes (16S) or from invertebrates (18S). (noaa.gov)
Norm Pace for his pioneering work on characterizing microbes indirectly via sequencing their RNA and DNA, especially their ribosomal RNA genes. (blogspot.com)

This study detected fungal diversity in discolored Mongolian pine for the first time by the MiSeq approach, focusing on the nuclear ribosomal internal transcribed spacer-1 (ITS1). (degruyter.com)
Polymerase chain reaction (PCR)-restriction fragment length polymorphism (RFLP) analysis of the ribosomal RNA gene internal transcribed spacer-1 (ITS1) was used. (who.int)

The three mock communities, featuring as many as 87 microbial strains spanning 29 bacterial and archaeal phyla, were created by researchers at Oakridge National Laboratory led by Mircea Podar and are likely some of the most complex communities that could be sequenced, according to senior author Mathieu Almeida, a research fellow at INRAE. (genomeweb.com)
His lab has made headlines by sequencing microbial communities from urban environments, including subways. (genomeweb.com)
To understand these processes through comprehensive analyses of microbial ecology, evolution and metabolism, sequenced reference genomes of representative native prokaryotes are crucial. (biomedcentral.com)
Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. (medscape.com)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

Differentiation of Schistosoma haematobium from related species using cloned ribosomal RNA gene probes. (ajtmh.org)
We also described the phylogenetic relationships among these species which were analyzed using ribosomal RNA and other gene sequences. (usda.gov)
Of these, 3,114 were single genes confined to a single species. (blogspot.com)
However, for thyriothecial species, phylogenies from DNA sequence data and illustrations of scutella remain have been limited. (ubc.ca)
Of the delimited species, nine had been collected ten or more times each and were, based on morphology and sequence analysis, undescribed and restricted to North America. (ubc.ca)
These genomes represent novel species within typical freshwater and marine clades, including clades not previously sequenced. (biomedcentral.com)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)

Sixteen new sequences of the chloroplast gene rbcL were used to assess evolutionary relationships in Dennstaedtiaceae. (usu.edu)

Bacteria 16S ribosomal RNA gene, partial sequence. (nih.gov)
Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. (wikipedia.org)
The diversity of their fecal bacteria was explored using 16S ribosomal RNA gene sequencing. (frontiersin.org)
Distinguishing pathogenic bacteria that contribute to airway disease from commensal microbiota in sputum has proved challenging and remains an obstacle to clinical application of sequencing results [ 13 , 14 ]. (ersjournals.com)
2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). (nih.gov)
The researchers extracted DNA from the samples and sequenced a portion of the 16S ribosomal RNA gene, widely used in microbiome studies to help identify and compare bacteria. (news-medical.net)
Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry. (cdc.gov)
Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)
The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)

In addition, mitochondrial DNA (mtDNA) encodes 2 ribosomal RNA genes and 22 transfer RNA (tRNA) genes necessary for the intramitochondrial synthesis of these 13 polypeptides. (medscape.com)

With the advancement of next-generation sequencing and mass spectrometry, there is a growing need for the ability to merge biological features in order to study a system as a whole. (rsc.org)
We used 3 different approaches: biochemical testing, matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and 16S ribosomal RNA (rRNA) gene sequencing. (medscape.com)
A concordant identification of P. multocida was observed using biochemical testing, mass spectrometry, and 16S rRNA gene sequencing. (medscape.com)

Find regions of similarity between this sequence and other sequences using BLAST. (nih.gov)
P22 has strong 16S rRNA gene sequence similarity to Paenibacillus humicus (99.5%) ( 7 ). (asm.org)

uncultured bacterium nitrogenase reductase (nifH) gene, partial cds. (nih.gov)

The phylogenetic analysis of the strain was based on 16S rRNA gene sequencing and showed that Paenibacillus sp. (asm.org)

NEW YORK - Researchers from France's National Research Institute for Agriculture, Food, and Environment (INRAE) have published data on the performance of both short- and long-read sequencing platforms in analyzing highly complex metagenomic samples. (genomeweb.com)
When we started, we were aware of the strong requirements for long-read sequencing, requesting long DNA fragments and high DNA purity, and expected low performance for quantitative metagenomic analysis compared to conventional short-read methods in such complex mock samples," Almeida said. (genomeweb.com)
Furthermore, we were surprised by the DNBSEQ-T7 performance, providing ultra-deep sequencing in a single run with similar low error rate compared to the other technologies, making it at the time of our study one of the cheapest technologies for metagenomic sequencing. (genomeweb.com)
Access to data from complex metagenomic sequencing studies aren't often provided, "because these data are produced for the purpose of hypothesis testing," said first author Victoria Meslier, also of INRAE. (genomeweb.com)
Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)
Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)

The proposed mechanism is based on the knowledge that transcription of mtDNA is polycistronic, which means that all genes encoded on the heavy and light strands are transcribed as 2 large precursor RNA strands. (medscape.com)

Cluster of ortholog genes (COG) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) were used to detect enrichment pathways among the three groups. (frontiersin.org)
were able to cluster all genes into 15,389 groups called "gene families. (blogspot.com)

Coding sequences (CDS) were predicted based on an in-house workflow that integrates ab initio predictions from Glimmer ( 10 ), Genemark ( 11 ), Prodigal ( 12 ), and Critica ( 13 ) with homology information derived from a BLAST search against NCBI nr ( 14 ). (asm.org)

Each instrument can generate data required for a draft bacterial genome sequence in days, making them attractive for identifying and characterizing pathogens in the clinical setting. (nature.com)

Design and test primers for this sequence using Primer-BLAST. (nih.gov)
These known sequences (primers) serve to prime the reaction that amplifies the gene of interest. (noaa.gov)
For example, in the search for new antitumor compounds, primers from a conserved class of antitumor compounds can be used to find the presence of this type of gene in new organisms. (noaa.gov)

Molecular techniques make this possible through the isolation of important genes and the production of biomedical compounds through recombinant technology. (noaa.gov)

Three benchtop high-throughput sequencing instruments are now available. (nature.com)

BALF from paediatric and adult CF patients and paediatric disease controls undergoing clinically indicated bronchoscopy was analysed for total bacterial load and for microbiota by 16S rDNA sequencing. (ersjournals.com)
The A and B clones of Borrelia burgdorferi sensu stric- maintenance of these clonal complexes in natural bacterial to, distinguished by outer surface protein C ( ospC ) gene populations ( 3 , 4 ). (cdc.gov)
Some of the enzymes which generate aromatic radicals that break down most prominent bacterial strains found were isolated and tax- the complex linkages present in lignin to compounds of lower onomically identified using 16S ribosomal RNA (rRNA) se- molecular weight. (lu.se)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)

C . difficile was presumptively identified on the basis of Gram stain and detection of L-proline aminopeptidase activity (Pro Disc, Remel, Lenexa, KS, USA) and confirmed by identification of the triose phosphate isomerase gene ( 9 ). (cdc.gov)

Certain strains may also produce a ( tcdA ) and B ( tcdB ), the binding component of CDT binary toxin (known as CDT), whose clinical relevance is ( cdtB ), and the tcdC gene were performed as previously under investigation. (cdc.gov)
All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)

This is critical because, while individual genes or genome fragments provide useful information on the metabolic potential of a community, in practice most biochemical transformations take place inside a cell, involving sets of genes structured in controlled pathways. (biomedcentral.com)

The complete nucleotide sequence of the mitochondrial genome for the Senegal sole Solea senegalensis Kaup was determined. (unboundmedicine.com)
A deletion anywhere in the mitochondrial genome may affect transcription or translation of genes that were not affected by the deletion. (medscape.com)

In this review, we discuss considerations of the study design for each data feature, the limitations in gene and protein abundance and their rate of expression, the current data integration methods, and microbiome influences on gene and protein expression. (rsc.org)
In addition to the host regulatory mechanisms response to disease, the microbiome can make changes to the expression of the host features such as their genes, proteins, and/or PTMs. (rsc.org)

In 1965, Emile Zuckerkandl and Linus Pauling instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. (wikipedia.org)

Phylogenetic analysis based on gene sequences, in particular, ribosomal sequences, has provided the major supporting evidence for the composition and taxonomic subdivision of this group of organisms with diverse habitats and ecology and has become the mainstream for the Acholeplasmataceae systematics. (usda.gov)

Molecular sequencing approaches have expanded this traditional view of airway infection [ 3 - 9 ]. (ersjournals.com)
The molecular characterization was based on the RAPD markers, telomeric fingerprinting and ITS sequencing. (scielo.br)

lamina propria and mesenteric lymph node tissues were analyzed by RNA sequencing and flow cytometry. (nih.gov)

Pour identifier les espèces de Leishmania , des techniques moléculaires ont été appliquées sur des échantillons prélevés chez 64 patients atteints de leishmaniose cutanée orientés vers l'hôpital régional d'Herat en 2013. (who.int)

The obvious next step is to integrate this information and learn how genes, proteins, and/or epigenetic factors influence the phenotype of a disease in context of the system. (rsc.org)

Draft Genome Sequence of the Growth-Promoting Endophyte Paenibacillus sp. (asm.org)

results of 16S ribosomal RNA gene sequencing. (wikipedia.org)
To check their results, the researchers obtained from a database the DNA sequences of the myoglobin of 10 whales and dolphins. (newscientist.com)

The frozen sample is later thawed at 4° C and homogenized in an extraction buffer that dissolves all the cell's membranes to release nucleic acids (DNA and RNA). (noaa.gov)

We compared the performance of these instruments by sequencing an isolate of Escherichia coli O104:H4, which caused an outbreak of food poisoning in Germany in 2011. (nature.com)
A comprehensive account of Escherichia coli Sequence Type 131 in wastewater reveals an abundance of fluoroquinolone resistant clade A strains. (cdc.gov)

Accurate whole human genome sequencing using reversible terminator chemistry. (nature.com)

The biosensor probe identified a target DNA sequence that was several-folds shorter than a typical PCR-template. (hindawi.com)
In this paper, we have targeted a 27-bp AluI fragment of porcine mitochondrial cytochrome b (cytb) gene to construct porcine-specific hybrid nanobiosensor probe that was able to detect pork in heterogeneous autoclaved meat products in a single step eliminating the need of washing or separation steps. (hindawi.com)

This is a nice comparison of the long- and short-read platforms, and shows overall comparability between methods," said Chris Mason, a sequencing expert at Weill Cornell Medicine who was not involved in the study. (genomeweb.com)
The Transformation of Reference Microbiology Methods and Surveillance for Salmonella With the Use of Whole Genome Sequencing in England and Wales. (cdc.gov)

Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)

The 18S rRNA gene appeared to be evolving at about one ninth of the rate of rbcL, and therefore 18S data should provide increased resolution for phylogenetic studies of the early branches in fern evolution. (usu.edu)
Figure 2: N50 contig sizes from assemblies generated from sequence data for each sequencing platform. (nature.com)
New ITS data were therefore analyzed together with published sequences for generating a topology. (bioone.org)
Mason said that he would like to see data from the latest sequencing platforms. (genomeweb.com)

Finds sub-sequences or patterns in the sequence and highlights the matching regions. (nih.gov)
The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
Finds sub-sequence or patterns in the sequence and highlights the matching region. (nih.gov)
DCs incubated with the FFAR2 agonist no longer had gene expression patterns associated with activation or IL27 production. (nih.gov)
Scutella have distinctive cell patterns that are formed by a sequence of hyphal branching and septation. (ubc.ca)
The genomes' seasonal dynamics follow phylogenetic patterns, but with fine-grained lineage-specific variations, reflected in gene-content. (biomedcentral.com)

PCR based on the amplification of the small sub-unit ribosomal RNA (ssrRNA) gene sequences was applied. (who.int)
Small amounts of the sequence of that gene must be known. (noaa.gov)
However, single-cell sequencing requires a highly specialized laboratory facility, and single amplified genomes (SAGs) typically have fairly low genome coverage, due to the small amount of DNA in each cell and associated whole-genome amplification biases [ 9 ]. (biomedcentral.com)

Polymerase chain reaction (PCR) is an important technique for establishing the presence of a particular gene in an organism. (noaa.gov)
Although the genome is a foundation for understanding the metabolism, ecology and evolution of an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties in cultivating them. (biomedcentral.com)

The Giardia lamblia vsp gene repertoire: characteristics, genomic organization, and evolution. (mbl.edu)
As a result of ocean exploration and research, genomic libraries can be created to preserve all of the genes (DNA) found in marine organisms. (noaa.gov)
From genomic libraries, a gene that makes an important biomedical compound can be cloned and expressed as a chemical compound in an artificial system. (noaa.gov)

Also, TaqI and BamHI restriction fragments containing 5S and 18S-5.8S-26S rRNA sequences were identified as positive markers specific to Th. (nih.gov)

By sequencing the entire genome, a comprehensive understanding of the genetic composition is obtained. (folkhalsomyndigheten.se)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Of the 1860 nucleotide sites of the 18S rRNA gene examined, 215 sites (11.6%) were variable and 71 sites (3.8%) were phylogenetically informative. (usu.edu)
A novel class of nanobiosensor was developed by integrating a 27-nucleotide AluI fragment of swine cytochrome b (cytb) gene to a 3-nm diameter citrate-tannate coated gold nanoparticle (GNP). (hindawi.com)
Nanoscaffolding and nanoquenching properties of thiol-capped gold nanocrystals (GNCs), covalently linked to fluorophore-lebeled oligonucleotide through metal-sulfur bond, were extensively studied for decades to detect specific sequences and single-nucleotide mismatches [ 1 - 3 , 21 , 22 ]. (hindawi.com)

Each of these platforms have technological limitations due to sample preparation steps, amount of material needed for sequencing, and sequencing depth requirements. (rsc.org)
In just the last year, the number of companies offering short-read sequencing platforms has doubled and PacBio has introduced new long-read instruments. (genomeweb.com)

Pro Disc, Remel, Lenexa, KS, USA) and confirmed by Toxigenic strains of C . difficile typically produce 2 identification of the triose phosphate isomerase gene ( 9 ). (cdc.gov)
PCR ribotyping and gene identification for toxins A duce only toxin B ( 3 ). (cdc.gov)
PCR ribotyping and gene identification for toxins A ( tcdA ) and B ( tcdB ), the binding component of CDT ( cdtB ), and the tcdC gene were performed as previously described ( 4 , 10 ). (cdc.gov)

3 toxins and have a mutated toxin regulatory gene, tcdC , also performed ( 11 ). (cdc.gov)
PCR ribotype 027 strains produce all 3 toxins and have a mutated toxin regulatory gene, tcdC , which is thought to be associated with increased toxin production in vitro ( 2 ). (cdc.gov)

orthogonal exPeriMental changes and pathways induced by EGE investigated the impact of aSSeSSMent of ePigenetic environmental factors in cancer causation, both current H. pylori infection and driver geneS and their link to underpinning studies of etiology e , pigenetic memory of past (eradicated) environMental carcinogenS carcinogen evaluation, and prevention. (who.int)

Sequence features of the 13 protein-coding genes, two ribosomal RNAs and 22 transfer RNAs are described. (unboundmedicine.com)

Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. (wikipedia.org)
The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

Sequence accession no. 16S rRNA gene: AF009477, 16S ribosomal RNA gene, partial sequence: NR_036918. (dsmz.de)

Comparing the genomes with globally distributed metagenomes reveals significant fragment recruitment at high sequence identity from brackish waters in North America, but little from lakes or oceans. (biomedcentral.com)
We describe the gene content, temporal dynamics and biogeography of a large set of new bacterioplankton genomes assembled from metagenomes. (biomedcentral.com)
The last decade's revolution in DNA sequencing throughput and cost has provided researchers with the unprecedented possibility of obtaining sequences from thousands of genomes at a time in natural samples. (biomedcentral.com)
Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism. (medscape.com)

Pseudomonadota nitrogenase reductase (nifH) gene, partial cds. (nih.gov)
Solaneae granule-bound starch synthase (GBSSI) gene, exons 2 through 10 and partial cds. (nih.gov)

The legitimacy of using cytb gene lies on its high rate of evolution and abundant copy number [ 32 ]. (hindawi.com)

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