A bibliographic database that includes MEDLINE as its primary subset. It is produced by the National Center for Biotechnology Information (NCBI), part of the NATIONAL LIBRARY OF MEDICINE. PubMed, which is searchable through NLM's Web site, also includes access to additional citations to selected life sciences journals not in MEDLINE, and links to other resources such as the full-text of articles at participating publishers' Web sites, NCBI's molecular biology databases, and PubMed Central.
A publication issued at stated, more or less regular, intervals.
"The business or profession of the commercial production and issuance of literature" (Webster's 3d). It includes the publisher, publication processes, editing and editors. Production may be by conventional printing methods or by electronic publishing.
The premier bibliographic database of the NATIONAL LIBRARY OF MEDICINE. MEDLINE® (MEDLARS Online) is the primary subset of PUBMED and can be searched on NLM's Web site in PubMed or the NLM Gateway. MEDLINE references are indexed with MEDICAL SUBJECT HEADINGS (MeSH).
The determination of the pattern of genes expressed at the level of GENETIC TRANSCRIPTION, under specific circumstances or in a specific cell.
Publications in any medium issued in successive parts bearing numerical or chronological designations and intended to be continued indefinitely. (ALA Glossary of Library and Information Science, 1983, p203)
Multicomponent ribonucleoprotein structures found in the CYTOPLASM of all cells, and in MITOCHONDRIA, and PLASTIDS. They function in PROTEIN BIOSYNTHESIS via GENETIC TRANSLATION.
The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.
Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.
Guanosine 5'-diphosphate 2'(3')-diphosphate. A guanine nucleotide containing four phosphate groups. Two phosphate groups are esterified to the sugar moiety in the 5' position and the other two in the 2' or 3' position. This nucleotide serves as a messenger to turn off the synthesis of ribosomal RNA when amino acids are not available for protein synthesis. Synonym: magic spot I.
The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)
A DNA-dependent RNA polymerase present in bacterial, plant, and animal cells. It functions in the nucleoplasmic structure where it transcribes DNA into RNA. It has specific requirements for cations and salt and has shown an intermediate sensitivity to alpha-amanitin in comparison to RNA polymerase I and II. EC 2.7.7.6.
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.
The aggregation of suspended solids into larger clumps.
Refuse liquid or waste matter carried off by sewers.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.
Encrustations, formed from microbes (bacteria, algae, fungi, plankton, or protozoa) embedding in extracellular polymers, that adhere to surfaces such as teeth (DENTAL DEPOSITS); PROSTHESES AND IMPLANTS; and catheters. Biofilms are prevented from forming by treating surfaces with DENTIFRICES; DISINFECTANTS; ANTI-INFECTIVE AGENTS; and antifouling agents.
Contaminated water generated as a waste product of human activity.
The etiologic agent of CHOLERA.
Strains of VIBRIO CHOLERAE containing O ANTIGENS group 1. All are CHOLERA-causing strains (serotypes). There are two biovars (biotypes): cholerae and eltor (El Tor).
An acute diarrheal disease endemic in India and Southeast Asia whose causative agent is VIBRIO CHOLERAE. This condition can lead to severe dehydration in a matter of hours unless quickly treated.
Strains of VIBRIO CHOLERAE containing O ANTIGENS group 139. This strain emerged in India in 1992 and caused a CHOLERA epidemic.
A genus of VIBRIONACEAE, made up of short, slightly curved, motile, gram-negative rods. Various species produce cholera and other gastrointestinal disorders as well as abortion in sheep and cattle.
An ENTEROTOXIN from VIBRIO CHOLERAE. It consists of two major protomers, the heavy (H) or A subunit and the B protomer which consists of 5 light (L) or B subunits. The catalytic A subunit is proteolytically cleaved into fragments A1 and A2. The A1 fragment is a MONO(ADP-RIBOSE) TRANSFERASE. The B protomer binds cholera toxin to intestinal epithelial cells, and facilitates the uptake of the A1 fragment. The A1 catalyzed transfer of ADP-RIBOSE to the alpha subunits of heterotrimeric G PROTEINS activates the production of CYCLIC AMP. Increased levels of cyclic AMP are thought to modulate release of fluid and electrolytes from intestinal crypt cells.
A disorder with chronic or recurrent colonic symptoms without a clearcut etiology. This condition is characterized by chronic or recurrent ABDOMINAL PAIN, bloating, MUCUS in FECES, and an erratic disturbance of DEFECATION.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Chronic or recurrent colonic disorders without an identifiable structural or biochemical explanation. The widely recognized IRRITABLE BOWEL SYNDROME falls into this category.
An increased liquidity or decreased consistency of FECES, such as running stool. Fecal consistency is related to the ratio of water-holding capacity of insoluble solids to total water, rather than the amount of water present. Diarrhea is not hyperdefecation or increased fecal weight.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.

Ribotypes of clinical Vibrio cholerae non-O1 non-O139 strains in relation to O-serotypes. (1/3473)

The emergence of Vibrio cholerae O139 in 1992 and reports of an increasing number of other non-O1 serogroups being associated with diarrhoea, stimulated us to characterize V. cholerae non-O1 non-O139 strains received at the National Institute of Infectious Diseases, Japan for serotyping. Ribotyping with the restriction enzyme BglI of 103 epidemiological unrelated mainly clinical strains representing 10 O-serotypes yielded 67 different typing patterns. Ribotype similarity within each serotype was compared by using the Dice coefficient (Sd) and different levels of homogeneity were observed (serotypes O5, O41 and O17, Sd between 82 and 90%: serotypes O13 and O141 Sd of 72; and O2, O6, O7, O11, O24 Sd of 62-66%). By cluster analysis, the strains were divided into several clusters of low similarity suggesting a high level of genetic diversity. A low degree of similarity between serotypes and ribotypes was found as strains within a specific serotypes often did not cluster but clustered with strains from other serotypes. However, epidemiological unrelated O5 strains showed identical or closely related ribotypes suggesting that these strains have undergone few genetic changes and may correspond to a clonal line. Surprisingly, 10 of 16 O141 strains studied contained a cholera toxin (CT) gene, including 7 strains recovered from stool and water samples in the United States. This is to our knowledge the first report of CT-positive clinical O141 strains. The closely related ribotypes shown by eight CT-positive strains is disturbing and suggest that these strains may be of a clonal origin and have the potential to cause cholera-like disease. Despite the low degree of correlation found between ribotypes and serotypes, both methods appears to be valuable techniques in studying the epidemiology of emerging serotypes of V. cholerae.  (+info)

Molecular differentiation of Renibacterium salmoninarum isolates from worldwide locations. (2/3473)

Renibacterium salmoninarum is a genospecies that is an obligate pathogen of salmonid fish and is capable of intracellular survival. Conventional typing systems have failed to differentiate isolates of R. salmoninarum. We used two methods to assess the extent of molecular variation which was present in isolates from different geographic locations. In one analysis we investigated possible polymorphisms in a specific region of the genome, the intergenic spacer (ITS) region between the 16S and 23S rRNA genes. In the other analysis we analyzed differences throughout the genome by using randomly amplified polymorphic DNA (RAPD). We amplified the spacer region of 74 isolates by using PCR and performed a DNA sequence analysis with 14 geographically distinct samples. The results showed that the 16S-23S ribosomal DNA spacer region of R. salmoninarum is highly conserved and suggested that only a single copy of the rRNA operon is present in this slowly growing pathogen. DNA sequencing of the spacer region showed that it was the same length in all 14 isolates examined, and the same nucleotide sequence, sequevar 1, was obtained for 11 of these isolates. Two other sequevars were found. No tRNA genes were found. We found that RAPD analysis allows reproducible differentiation between isolates of R. salmoninarum obtained from different hosts and different geographic regions. By using RAPD analysis it was possible to differentiate between isolates with identical ITS sequences.  (+info)

Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles. (3/3473)

The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.  (+info)

Anaerobic oxidation of o-xylene, m-xylene, and homologous alkylbenzenes by new types of sulfate-reducing bacteria. (4/3473)

Various alkylbenzenes were depleted during growth of an anaerobic, sulfate-reducing enrichment culture with crude oil as the only source of organic substrates. From this culture, two new types of mesophilic, rod-shaped sulfate-reducing bacteria, strains oXyS1 and mXyS1, were isolated with o-xylene and m-xylene, respectively, as organic substrates. Sequence analyses of 16S rRNA genes revealed that the isolates affiliated with known completely oxidizing sulfate-reducing bacteria of the delta subclass of the class Proteobacteria. Strain oXyS1 showed the highest similarities to Desulfobacterium cetonicum and Desulfosarcina variabilis (similarity values, 98.4 and 98.7%, respectively). Strain mXyS1 was less closely related to known species, the closest relative being Desulfococcus multivorans (similarity value, 86.9%). Complete mineralization of o-xylene and m-xylene was demonstrated in quantitative growth experiments. Strain oXyS1 was able to utilize toluene, o-ethyltoluene, benzoate, and o-methylbenzoate in addition to o-xylene. Strain mXyS1 oxidized toluene, m-ethyltoluene, m-isoproyltoluene, benzoate, and m-methylbenzoate in addition to m-xylene. Strain oXyS1 did not utilize m-alkyltoluenes, whereas strain mXyS1 did not utilize o-alkyltoluenes. Like the enrichment culture, both isolates grew anaerobically on crude oil with concomitant reduction of sulfate to sulfide.  (+info)

High-affinity methane oxidation by a soil enrichment culture containing a type II methanotroph. (5/3473)

Methanotrophic bacteria in an organic soil were enriched on gaseous mixing ratios of <275 parts per million of volume (ppmv) of methane (CH4). After 4 years of growth and periodic dilution (>10(20) times the initial soil inoculum), a mixed culture was obtained which displayed an apparent half-saturation constant [Km(app)] for CH4 of 56 to 186 nM (40 to 132 ppmv). This value was the same as that measured in the soil itself and about 1 order of magnitude lower than reported values for pure cultures of methane oxidizers. However, the Km(app) increased when the culture was transferred to higher mixing ratios of CH4 (1,000 ppmv, or 1%). Denaturing gradient gel electrophoresis of the enrichment grown on <275 ppmv of CH4 revealed a single gene product of pmoA, which codes for a subunit of particulate methane monooxygenase. This suggested that only one methanotroph species was present. This organism was isolated from a sample of the enrichment culture grown on 1% CH4 and phylogenetically positioned based on its 16S rRNA, pmoA, and mxaF gene sequences as a type II strain of the Methylocystis/Methylosinus group. A coculture of this strain with a Variovorax sp., when grown on <275 ppmv of CH4, had a Km(app) (129 to 188 nM) similar to that of the initial enrichment culture. The data suggest that the affinity of methanotrophic bacteria for CH4 varies with growth conditions and that the oxidation of atmospheric CH4 observed in this soil is carried out by type II methanotrophic bacteria which are similar to characterized species.  (+info)

Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. (6/3473)

Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.  (+info)

Immunochemical detection and isolation of DNA from metabolically active bacteria. (7/3473)

Most techniques used to assay the growth of microbes in natural communities provide no information on the relationship between microbial productivity and community structure. To identify actively growing bacteria, we adapted a technique from immunocytochemistry to detect and selectively isolate DNA from bacteria incorporating bromodeoxyuridine (BrdU), a thymidine analog. In addition, we developed an immunocytochemical protocol to visualize BrdU-labeled microbial cells. Cultured bacteria and natural populations of aquatic bacterioplankton were pulse-labeled with exogenously supplied BrdU. Incorporation of BrdU into microbial DNA was demonstrated in DNA dot blots probed with anti-BrdU monoclonal antibodies and either peroxidase- or Texas red-conjugated secondary antibodies. BrdU-containing DNA was physically separated from unlabeled DNA by using antibody-coated paramagnetic beads, and the identities of bacteria contributing to both purified, BrdU-containing fractions and unfractionated, starting-material DNAs were determined by length heterogeneity PCR (LH-PCR) analysis. BrdU-containing DNA purified from a mixture of DNAs from labeled and unlabeled cultures showed >90-fold enrichment for the labeled bacterial taxon. The LH-PCR profile for BrdU-containing DNA from a labeled, natural microbial community differed from the profile for the community as a whole, demonstrating that BrdU was incorporated by a taxonomic subset of the community. Immunocytochemical detection of cells with BrdU-labeled DNA was accomplished by in situ probing with anti-BrdU monoclonal antibodies and Texas red-labeled secondary antibodies. Using this suite of techniques, microbial cells incorporating BrdU into their newly synthesized DNA can be quantified and the identities of these actively growing cells can be compared to the composition of the microbial community as a whole. Since not all strains tested could incorporate BrdU, these methods may be most useful when used to gain an understanding of the activities of specific species in the context of their microbial community.  (+info)

Dissimilatory reduction of Fe(III) and other electron acceptors by a Thermus isolate. (8/3473)

A thermophilic bacterium that can use O2, NO3-, Fe(III), and S0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a South African gold mine. This organism, designated SA-01, clustered most closely with members of the genus Thermus, as determined by 16S rRNA gene (rDNA) sequence analysis. The 16S rDNA sequence of SA-01 was >98% similar to that of Thermus strain NMX2 A.1, which was previously isolated by other investigators from a thermal spring in New Mexico. Strain NMX2 A.1 was also able to reduce Fe(III) and other electron acceptors. Neither SA-01 nor NMX2 A.1 grew fermentatively, i.e., addition of an external electron acceptor was required for anaerobic growth. Thermus strain SA-01 reduced soluble Fe(III) complexed with citrate or nitrilotriacetic acid (NTA); however, it could reduce only relatively small quantities (0.5 mM) of hydrous ferric oxide except when the humic acid analog 2,6-anthraquinone disulfonate was added as an electron shuttle, in which case 10 mM Fe(III) was reduced. Fe(III)-NTA was reduced quantitatively to Fe(II); reduction of Fe(III)-NTA was coupled to the oxidation of lactate and supported growth through three consecutive transfers. Suspensions of Thermus strain SA-01 cells also reduced Mn(IV), Co(III)-EDTA, Cr(VI), and U(VI). Mn(IV)-oxide was reduced in the presence of either lactate or H2. Both strains were also able to mineralize NTA to CO2 and to couple its oxidation to Fe(III) reduction and growth. The optimum temperature for growth and Fe(III) reduction by Thermus strains SA-01 and NMX2 A.1 is approximately 65 degrees C; their optimum pH is 6.5 to 7.0. This is the first report of a Thermus sp. being able to couple the oxidation of organic compounds to the reduction of Fe, Mn, or S.  (+info)

Write a brief summary of the theory behind the following techniques that we used to identify our bacterial species by molecular tools: genomic DNA isolation, polymerase chain amplification of part of the 16s rRNA genes, use of the Zero Blunt® TOPO® PCR Cloning Kit to create a library of unique plasmid vector with our 16S rRNA gene inserts and then select, One Shot® TOP10 Competent E. coli Cells that allowed us to select and separate our 16S rRNA genes for sequencing, and DNA sequencing by the newer fluorescent-labeled ddNPTs chain -termination (Sanger) method. Directions found at: Lab 6 Assignment: Assignment: Theory Summary ...
IVS: Intervening sequence with conserved ORF in eubacterial 23S rRNA genes; forms a homopentamer with a toroid-shaped structure containing a tapered central channel ...
Obtaining full-length 16S rRNA gene sequences is important for generating accurate taxonomy assignments of bacteria, which normally is realized via clone library construction. However, the application of clone library has been hindered due to its limitations in sample throughput and in capturing minor populations (<1 % of total microorganisms). To overcome these limitations, a new strategy, two-step denaturing gradient gel electrophoresis (2S-DGGE), is developed to obtain full-length 16S rRNA gene sequences. 2S-DGGE can compare microbial communities based on its first-round DGGE profiles and generate partial 16S rRNA gene sequences (8-534 bp, Escherichia coli numbering). Then, strain-specific primers can be designed based on sequence information of bacteria of interest to PCR amplify their remaining 16S rRNA gene sequences (515-1541 bps, E. coli numbering). The second-round DGGE can confirm DNA sequence purity of these PCR products. Finally, the full-length 16S rRNA gene sequences can be ...
Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is the most rigorous. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the ability of the method to properly represent the distances between the sequences is more important. Methods. Our analysis implemented five de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and the open and closed-reference methods. Using two previously published datasets we used the Matthews Correlation Coefficient (MCC) to assess the stability and
Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the
A polyphasic study was undertaken to clarify the taxonomic position of endospore-forming strains 433-D9, 433-E17 and 121-X1. BOX-PCR-generated fingerprints indicated that they may be members of a single species. 16S rRNA gene sequence similarity demonstrated that a representative of this group, 433-.... Full description. ...
Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The sources of these contaminants are reagents used in DNA extraction, PCR, and next-generation sequencing library preparation, and human (skin, oral and respiratory) microbiota from the investigators. For in silico removal of reagent contaminants, a pipeline was used which combines the relative abundance of operational taxonomic units (OTUs) in V3-4 16S rRNA gene amplicon datasets with bacterial DNA quantification based on qPCR targeting of the V3 segment of the 16S rRNA gene. Serially diluted cultures of Escherichia coli and Staphylococcus aureus were used for 16S rDNA profiling, and DNA from each of these species was used as a qPCR standard. OTUs assigned to Escherichia or Staphylococcus were virtually unaffected by the decontamination procedure, whereas OTUs from Pseudomonas, which is a major
Coloured scanning electron micrograph (SEM) of Viridibacillus arvi, Gram-positive, aerobic, spore forming, rod prokaryote (bacterium). Viridibacillus arvi (formerly known as Bacillus arvi) is a bacterial endospore forming bacillus (rod). Members of the genus Viridibacillus have the unique property of developing a green pigment, which is associated with sporulation. This image shows vegetative cells and terminally swollen sporulated cells. Unique chemotaxonomic characteristics including quinone and peptidoglycan cross linking structure differentiate these bacteria. Magnification: x4,000 when shortest axis printed at 25 millimetres. - Stock Image C032/2391
The five most frequent keywords within the labels of environmental samples which yielded hits were microbi (9.4%), hypersalin (9.1%), http://www.selleckchem.com/products/pazopanib.html mat (8.6%), len, miniprim, new, view, world (8.5%) and food (3.4%). The single most frequent keyword within the labels of environmental samples which yielded hits of a higher score than the highest scoring species was hypersalin, len, mat, microbi, miniprim, new, view, world (12.5%). These key words are in line with the ecology and the niche from where strains of H. praevalens have been isolated. Figure 1 shows the phylogenetic neighborhood of H. praevalens GSLT in a 16S rRNA gene based tree.. The sequences of the four 16S rRNA gene copies in the genome differ from each other by up to five nucleotides, and differ by up to five nucleotides from the previously published 16S rRNA gene sequence (type:entrez-nucleotide,attrs:text:AB022034″,term_id:4127263″,term_text:AB022034″AB022034). ...
The 16S rRNA gene sequence of this type strain is not congruent with the 16S rRNA gene sequence deposited in the GenBank database under the accession number HQ888848. Proposal for rejection of the species. Request for an opinion : http://ijs.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.000777# ...
Mouse monoclonal to 4E-BP1 continues to be questioned for their poor cooccurrence or relationship (3 -5). Some strains of FIB have already been reported to really have the ability to adjust in the surroundings also to persist in sediment and vegetation (6 7 The main restriction of FIB is normally that they can not be designated to a particular original source because of their cosmopolitan character (being frequently within different warm-blooded plus some cold-blooded pets) (8 9 When environmental waters are polluted with FIB from multiple resources it becomes incredibly difficult to put into action a robust administration plan without determining the resources of this air pollution. Within the last 2 years library-dependent and library-independent microbial supply tracking (MST) strategies have been created to differentiate between resources of fecal air pollution in environmental waters. The MST strategies created earlier were collection dependent and needed the collection and fingerprinting ...
Use 16S and ITS rRNA gene analysis to identify and compare samples from complex microbiomes or environments that are difficult or impossible to study.
Ribosomal RNA(rRNA) persists for several days estimates for rRNA half-life in vitro range from ,3 days (human fibroblasts) (primary source), through 3.8 days (18S rRNA moiety in H1299 cells) (3), to about 7.5 days (cultured rat fibroblasts) (4 ...
Download MicrobiomeUtilities for free. A set of software utilities for processing and analyzing 16S rRNA genes including generating NAST alignments, chimera checking, and assembling paired 16S rRNA reads according to reference sequence homology.
Agustín Silva, Actor: La Nana. Agustín Silva is an actor, known for The Maid (2009), Crystal Fairy & the Magical Cactus and 2012 (2013) and Aquí no ha pasado nada (2016).
Effective depletion of rRNA from bacteria (gram-positive and gram-negative organisms), from monocultures or samples with mixed bacterial species. Kit includes RNAClean® XP beads.
Ribosomal RNA. It is a part of a rybosome and has a very important function in the process of translation. The existence of rRNA is one of the clues whi...
Anderson Silva is, in the parlance of our times, shook. The longtime middleweight champion recently revealed he had tweaked his knee training for the rematch the world has been waiting for...
Genetic information processingProtein synthesistRNA and rRNA base modification16S rRNA (cytosine(967)-C(5))-methyltransferase (TIGR00563; EC 2.1.1.176; HMM-score: 27.7) ...
Genetic information processingProtein synthesistRNA and rRNA base modification16S rRNA (cytosine(967)-C(5))-methyltransferase (TIGR00563; EC 2.1.1.176; HMM-score: 27) ...
Sereniki, Adriana; Linard-Medeiros, Cybelle F. B.; Silva, Shirliane N.; Silva, Juciene B. R.; Peixoto Sobrinho, Tadeu J. S.; da Silva, Juliano R.; Alves, Lariza D. S.; Smaili, Soraya S ...
Sereniki, Adriana; Linard-Medeiros, Cybelle F. B.; Silva, Shirliane N.; Silva, Juciene B. R.; Peixoto Sobrinho, Tadeu J. S.; da Silva, Juliano R.; Alves, Lariza D. S.; Smaili, Soraya S ...
Yasmin Silva Really interesting this article. I hope someday we can play and interact with other platforms unlimitedly. This would make it easier for many players like us. Column: Cross-Play is the future · 24. September 2019 ...
Marques, M.A. (UFRJ), Oliveira, P.A.G. (UFRJ-IBqM), Pereira, E.G. (UFRJ), Dias, C.V. (UESC), Souza, T.L.F. (UFRJ-FF), Ferretti G (UFRJ), Cordeiro, Y. (UFRJ-FF), Cascardo, J.C.M. (UESC), Almeida, F.C.L. (UFRJ-IBqM), Valente, A.P. (UFRJ-IBqM), Silva, J.L. (UFRJ-IBqM ...
A novel Ferrimonas species is described on the basis of phenotypic, chemotaxonomic and phylogenetic studies. Four halophilic organisms were isolated from marine sand and marine macroalgae samples by using high-pH marine agar 2216. An analysis of the nearly complete 16S rRNA gene sequences of these new isolates indicated that they were phylogenetically close (16S rRNA gene sequence similarity |99·5 %, gyrB gene sequence similarity |97·8 %), and were most closely related to Ferrimonas balearica (16S rRNA gene sequence similarity 97·1-97·3 %, gyrB gene sequence similarity 84·4-85·0 %). Chemotaxonomic data (major menaquinone MK7; major fatty acids C16 : 0 and C18 : 1 ω9c) supported the affiliation of the new isolates to the genus Ferrimonas. The results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from F. balearica. It is therefore proposed that the new isolates represent a novel species with the name Ferrimonas marina sp. nov. and type strain A4D-4T (
Two Gram-stain-positive, aerobic, pink, curved, rod-shaped, non-motile bacterial strains, designated MI-28T and SKY-11, were isolated from freshwater samples taken from a river and fish pond, respectively. Based on characterization using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic profiles. They demonstrated 99.9 % 16S rRNA gene sequence similarity and a 93-95 % DNA-DNA relatedness value, suggesting that they represent a single genomic species. Phylogenetic analyses, based on 16S rRNA gene sequences, showed that strains MI-28T and SKY-11 form a distinct lineage with respect to closely related genera within the family Microbacteriaceae of the class Actinobacteria , which is most closely related to Rhodoluna and Pontimonas, and levels of 16S rRNA gene sequence similarity with the type species of related genera were less than 95 %. Cell-wall analysis showed that the peptidoglycan contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid.
A Gram-negative, aerobic, non-motile rod, designated GSW-M26T, was isolated from seawater from the southern coast of Korea. Strain GSW-M26T grew optimally at pH 7.0-8.0, at 30 °C and with 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain GSW-M26T fell within the cluster comprising the genus Jannaschia and clustered with Jannaschia seosinensis CL-SP26T. The isolate exhibited the highest 16S rRNA gene sequence similarity (96.9 %) with J. seosinensis CL-SP26T and 93.7-95.5 % 16S rRNA gene sequence similarity with the other members of the genus Jannaschia . Strain GSW-M26T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unidentified aminolipid. The DNA G+C content was 66.4 mol%. Phenotypic characteristics demonstrated that strain GSW-M26T could be differentiated from
Background Next-generation sequencing platforms have revolutionised our ability to investigate the microbiota composition of complex environments, frequently through 16S rRNA gene sequencing of the bacterial component of the community. Numerous factors, including DNA extraction method, primer sequences and sequencing platform employed, can affect the accuracy of the results achieved. The aim of this study was to determine the impact of these three factors on 16S rRNA gene sequencing results, using mock communities and mock community DNA. Results The use of different primer sequences (V4-V5, V1-V2 and V1-V2 degenerate primers) resulted in differences in the genera and species detected. The V4-V5 primers gave the most comparable results across platforms. The three Ion PGM primer sets detected more of the 20 mock community species than the equivalent MiSeq primer sets. Data generated from DNA extracted using the 2 extraction methods were very similar. Conclusions Microbiota compositional data ...
Identifying the organisms behind novel environmental lineages has been one of several major targets in microbial biodiversity research (9, 23, 38, 41). This is especially important in the case of evolutionarily interesting lineages at higher taxonomic levels and in the case of lineages that occur frequently in different environmental systems and whose morphological diversity and ecological function are unknown. The uncultured MAST clades identified recently (23, 44) meet all of these criteria and therefore deserve further study. Due to the information obtained as a result of the research that we conducted, we were able to determine the morphotype for the 18S rRNA gene sequence that branches within the MAST-12 clade which we retrieved from a Norwegian estuarine microbial mat sample.. Our phylogenetic reconstruction of stramenopiles using 18S rRNA gene signatures is consistent with previous analyses. The previous analyses confirmed the monophyly of phototrophic stramenopiles, resulting in ...
Figure 1. Prokaryotic 70S ribosome and eukaryotic 80S ribosome.. 18S rRNA as a marker for biodiversity studies. 18S rRNA gene is a common molecular marker for biodiversity studies since it is highly conserved intra-species (similarities close to 100%) and assist in species-level analyses. Similar to 16S rRNA, 18S rRNA gene has nine variable regions (V1-V9). Previous studies tested the taxonomic resolutions of 18S rRNA gene at different taxonomic levels (Wu et al. 2015) come to the following conclusions: i. full-length 18S rRNA sequences or partial regions (around V2, V4, and V9) of the 18S rRNA gene are useful for the discrimination of samples at both the family and order levels; ii. V9 has a higher resolution at the genus level; iii. V4 is the most divergent region in length, which would be a marker candidate for the phylogenetic study of Acartia speicies.. Once we obtained 18S rRNA sequences, they could be used for taxonomic resolutions and diversity analysis in eukaryotic communities. While ...
Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea - archaeal diversity;16S rRNA gene;marine group;Ulleung Basin;East Sea;
Relative abundance of 16S/18S rRNA gene sequences affiliated to lineages displaying metabolisms favoring carbonate precipitation in Alchichica microbialites. Si
Widdel 1981) Kuever 2006 may be the type and only species of the genus and the order GEBAproject. class represents a separate lineage within the which is only distantly related to most other members of this class. The closest relatives based on 16S rRNA gene sequence similarity values are the type strains of (87.6% sequence identity) and (87.2%) both belonging to the family within the order [9]. The most similar cloned 16S rRNA gene EUB-42 [10] shared only 95.5% sequence similarity with and was retrieved from anaerobic sludge. Strain 2st14T WYE-354 represents the only stress of this varieties obtainable from a tradition collection so far. Available data from cultivation 3rd party studies (environmental testing and genomic studies) didnt surpass 86% series similarity indicating that people of this varieties are limited to specific habitats which are undersampled generally in most conditions or are in low great quantity (status Oct 2010). The solitary genomic 16S rRNA series of stress 2st14T was ...
TY - JOUR. T1 - PCR primers and probes for the 16S rRNA gene of most species of pathogenic bacteria, including bacteria found in cerebrospinal fluid. AU - Greisen, K.. AU - Loeffelholz, M.. AU - Purohit, A.. AU - Leong, D.. PY - 1994/1/1. Y1 - 1994/1/1. N2 - A set of broad-range PCR primers for the 16S rRNA gene in bacteria were tested, along with three series of oligonucleotide probes to detect the PCR product. The first series of probes is broad in range and consists of a universal bacterial probe, a gram-positive probe, a Bacteroides- Flavobacterium probe, and two probes for other gram-negative species. The second series was designed to detect PCR products from seven major bacterial species or groups frequently causing meningitis: Neisseria meningitidis, Haemophilus influenzae, Streptococcus pneumoniae, S. agalactiae, Escherichia coli and other enteric bacteria, Listeria monocytogenes, and Staphylococcus aureus. The third series was designed for the detection of DNA from species or genera ...
We have constructed a conditional rRNA gene expression system by fusing a plasmid-encoded rrnB operon to the lambda PL promoter/operator. It was thereby possible to study the events that lead to the regulation of chromosomal rRNA and tRNA synthesis after overproduction of rRNA. rRNA induction resulted in a 2-fold increase in 30S and 50S free ribosomal subunits, whereas the polysome fraction was unaffected. Overproduction of rRNA and free ribosomes produced a large repression of rRNA and tRNA synthesis from chromosomal genes and a smaller increase in the concentration of guanosine tetraphosphate. These results lend support to the ribosome feedback regulation model: rRNA and tRNA operons are negatively regulated, either directly or through some intermediate, by free, nontranslating ribosomes.. ...
ABSTRACT: Marine photosynthetic picoeukaryotes (PPEs), representing organisms ,3 µm in size, are major contributors to global carbon cycling. However, the key members of the PPE community and hence the major routes of carbon fixation, particularly in the open ocean environment, are poorly described. Here, we have accessed PPE community structure using the plastid encoded 16S rRNA gene. Plastid 16S rRNA genes were sequenced from 65 algal cultures, about half being PPEs, representing 14 algal classes. These included sequences from 5 classes where previously no such sequences from cultured representatives had been available (Bolidophyceae, Dictyochophyceae, Eustigmatophyceae, Pelagophyceae and Pinguiophyceae). Sequences were also obtained for 6 of the 7 (according to 18S rRNA gene sequence) prasinophyte clades. Phylogenetic analysis revealed plastids from the same class as clustering together. Using all the obtained sequences, as well as plastid sequences currently in public databases, a ...
This paper describes how ground water was sampled, DNA extracted, amplified and cloned and how information available in the ribosomal 16S rRNA gene was used for mapping diversity and distribution of subterranean bacteria in groundwater at the Bangombé site in the Oklo region. The results showed that …
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This product was produced by the IAM Culture Collection (IAM) and transferred to JCM in 2007. Viability and purity assays were performed by IAM at the time of production. The authenticity of the culture was confirmed by analyzing an appropriate gene sequence, e.g., the 16S rRNA gene for prokaryotes, the D1/D2 region of LSU rRNA gene, the ITS region of the nuclear rRNA operon, etc. for eukaryotes. The characteristics and/or functions of the strain appearing in the catalogue are based on information from the corresponding literature and JCM does not guarantee them ...
Eckburg works with David Relman, MD, associate professor of medicine (infectious diseases and geographic medicine) and of microbiology and immunology. Relmans lab at the Veteran Affairs Palo Alto Heath Care System specializes in microbial pathogen discovery and human microbial ecology, and in appreciating the roles played by microbes in human health and disease.. The paper by Eckburg and Relman is intended as the first of several studies looking at how microbial communities vary according to host, diet, geography, disease and other variables.. To distinguish individual bacteria among the hundreds of types in the samples, Eckburg took advantage of a technique that compares the genetic sequence of a molecule shared by bacteria and archaea. The molecule, 16S rRNA, plays a role in the translation of the genetic code and thus is critical to the organisms. However, small variations in the 16S rRNA gene sequences allow scientists to detect distinct bacteria.. For each of the three research subjects, ...
Huisman, J.M., Sherwood, A.R. & Abbott, I.A. (2003) Morphology, reproduction, and the 18S rRNA gene sequence of Pihiella liagoraciphila gen. et sp. nov. (Rhodophyta), the so-called monosporangial discs associated with members of the Liagoraceae (Rhodophyta), and proposal of the Pihiellales ord. nov. J. Phycol. 39: 978-987 ...
The RDP Classifier was updated to version 2.13 and released 30 July 2020 on SourceForge (https://sourceforge.net/projects/rdp-classifier/). The update is based on bacterial and archaeal training set No.18 with over 800 new genera and significant rearrangements of several phyla and genera based on the latest genome analyses. For detailed explanations of these revisions, please see the release notes.. As in earlier editions, databases are also included for classification of fungal ITS sequences by UNITE and Warcup taxonomies and for classification of fungal 28S rRNA gene sequences.. ...
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There are some drawbacks to the use of the molecule primarily as they several Bacteria have more than one copy of the 16S rRNA gene on their genome often with a dissimilar collections. We should check each piece of food that you simply acquisition inside supermarket to find out whether it has trans interact. She chose to head using a Bloody Mary cake while Charlene baked up very good almond cake. Im sorry if that is challenging that your entire family can notice however it is the facts along with absolutely any diet and fitness system, and also this is the identical. It will then hit the item you may be viewing as well as a mirror underneath it and am going to return to the microscope to be viewed. Huge problem that is growing year on year is the absence of food, yet it is likely that 40% of nearly all food produced is either consumed or spoiled by insects. Sales of biotechnology products are projected that would exceed $20 billion by the year 2000. Interestingly, a retired couple filed an ...
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Dive into the research topics where Manuel Pedro Marques da Silva is active. These topic labels come from the works of this person. Together they form a unique fingerprint ...
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About the mithocondrial ribosoms: They resemble very much those of archea: size just like bacteria, but rRNA 16S in small subunit of ribosoms resembles very much 18S rRNA in the small subunit of eukaryotic cells. Another resemblence between mitocondria and archea is that they both have introns ...
背景:临床真菌引起的血流感染日益增加,其中念珠菌属引起的感染占真菌感染的90.0%以上,主要包括白色念珠菌(66.0%)、光滑念珠菌(11.2%)、热带念珠菌(7.6%)、近平滑念珠菌(5.6%)和克柔念珠菌(2.4%) 5种念珠菌,占临床念珠菌属感染的90.0%以上。目前,检测和鉴定念珠菌属/种血流感染主要依赖血培养和血清学试验,但固有的方法学缺陷难以满足临床快速、准确鉴定血流感染的需要。. 目的:分别建立念珠菌属和5种念珠菌(白色念珠菌、光滑念珠菌、近平滑念珠菌、热带念珠菌和克柔念珠菌)的real-time PCR快速检测平台,并对所建方法及其临床应用价值进行初步评价。. 方法:. 1.引物和探针设计:分别以上述5种念珠菌标准菌株的5.8S rRNA 基因(5.8S rDNA)序列和内转录间隔序列(ITS)作为参考序列,通过属、种间序列比对,在5.8S ...
Pavao, F., Castilho, M.S., Pupo, M.T., Dias, R.L., Correa, A.G., Fernandes, J.B., da Silva, M.F., Mafezoli, J., Vieira, P.C., Oliva, G ...
Kanegusuku H, Silva-Batista C, Peçanha T, Nieuwboer A, Silva ND Jr, Costa LA, de Mello MT, Piemonte ME, Ugrinowitsch C, Forjaz CL ...
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It is largely made up of specialized RNA known as ribosomal RNA (rRNA) as well as dozens of distinct proteins (the exact number ... Xue S, Barna M (May 2012). "Specialized ribosomes: a new frontier in gene regulation and organismal biology". Nature Reviews. ... Eukaryotic ribosomes are between 25 and 30 nm (250-300 Å) in diameter with an rRNA-to-protein ratio that is close to 1. ... The unit of measurement used to describe the ribosomal subunits and the rRNA fragments is the Svedberg unit, a measure of the ...
The most prominent examples of RNA genes are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the ... "housekeeping genes"), while σ32 recognizes promoters for genes required at high temperatures ("heat-shock genes"). In archaea ... However, since the late 1990s, many new RNA genes have been found, and thus RNA genes may play a much more significant role ... Control of the process of gene transcription affects patterns of gene expression and, thereby, allows a cell to adapt to a ...
Sequence analysis of a fragment of the LSU rRNA gene; Journal of Phycology, 30: 991-1011. ANDERSON, D.M., KULIS, D.M., DOUCETTE ... RFLP analysis of SSU rRNA genes; Journal of Phycology, 30: 744-754. SCHOLIN, C.A., HERZOG, M., SOGIN, M. & ANDERSON, D.M. 1994 ...
The 16S rRNA gene of Methanocaldococcus sp. FS406-22, is almost 100% similar to that of Methanocaldococcus jannaschii, a non- ... It also has a GC-content of 32.04%. The 16S rRNA gene of Methanocaldococcus sp. FS406-22, is almost 100% similar to that of ... Looking further into this methanogen, it was found that the 16S rRNA gene of Methanocaldococcus sp. FS406-22, is 99% similar to ... This divergence of genes is estimated to have happened before the separation of the Domains bacteria and methanogenic archaea. ...
Phylogenetic Relationships of the Wardiaceae (Musci); Evidence from 18s rRNA and rps4 Gene Sequences. The Bryologist 102 (1): ...
"Computer-simulated RFLP analysis of 16S rRNA genes: identification of ten new phytoplasma groups". International Journal of ... Despite their small genomes, many predicted phytoplasma genes are present in multiple copies. Phytoplasmas lack many genes ... The expression of genes involved in maintaining the apical meristem or in the development of floral organs is altered in the ... In 2009, 56 genes for secreted proteins were identified in the genome of Aster Yellows phytoplasma strain Witches Broom (AY-WB ...
The genes coding for 28S rRNA are referred to as 28S rDNA. The comparison of the sequences from these genes are sometimes used ... It has a size of 25S in plants and 28S in mammals, hence the alias of 25S-28S rRNA. Combined with 5.8S rRNA to the 5' side, it ... The 28S rRNA is typically 4000-5000 nt long. Some eukaryotes cleave 28S rRNA into two parts before assembling both into the ... 28S ribosomal RNA is the structural ribosomal RNA (rRNA) for the large subunit (LSU) of eukaryotic cytoplasmic ribosomes, and ...
"Comparison of 16S rRNA gene sequences of genus Methanobrevibacter". BMC Microbiol. 4: 20. doi:10.1186/1471-2180-4-20. PMC ... "Comparison of 16S rRNA gene sequences of genus Methanobrevibacter". BMC Microbiology. 4 (1): 20. doi:10.1186/1471-2180-4-20. ...
nov., a unique halophilic archeon, with three 16s rRNA genes, that grows only in defined medium with glycerol and acetate or ... "Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes". Journal of Bacteriology. 186 (12): ...
"Staphylococcus pseudintermedius 16S rRNA gene, type strain LMG 22219T". 2005-08-15. "Notification that new names and new ... as a novel species in 2005 using 16S rRNA sequencing of the tRNA intergenic length polymorphisms of the AJ780976 gene loci. ... are the gold standard for accurately identifying the presence of mecA genes, which confer resistance to Beta-lactam drugs in S ... "Molecular Detection and Characterization of the mecA and nuc Genes From Staphylococcus Species (S. aureus, S. pseudintermedius ...
homari by 16S rRNA gene sequence and RAPD" (PDF). Diseases of Aquatic Organisms. 63 (2-3): 237-246. doi:10.3354/dao063237. PMID ...
homari by 16S rRNA gene sequence and RAPD" (PDF). Diseases of Aquatic Organisms. 63 (2-3): 237-246. doi:10.3354/dao063237. PMID ... Sequencing of 16S rRNA has become the gold standard for identification, but other techniques such as MALDI-TOF have also been ...
... based on cytochrome b and 12S rRNA genes". Genetics and Molecular Research. 10 (1): 368-381. doi:10.4238/vol10-1gmr1048. PMID ...
Compared to 16S rRNA genes, 23S rRNA genes typically have higher sequence variations including insertions and/or deletions. The ... Pei A, Nossa CW, Chokshi P, Blaser MJ, Yang L, Rosmarin DM, Pei Z (5 May 2009). "Diversity of 23S rRNA Genes within Individual ... The 23S rRNA is a 2904 nt long (in E. coli) component of the large subunit (50S) of the bacterial/archean ribosome. The ... However, 23S rRNA positions which are G2252, A2451, U2506, and U2585 have a significant function for tRNA binding in P site of ...
Ribosomal RNA genes (rDNA) encodes for ribosomal RNA (rRNA) that constitutes the majority of the ribosome. These genes are not ... Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (May 2006). "Intergenic transcripts regulate the epigenetic state of rRNA genes ... These studies confirmed that pRNA has a role gene silencing by targeting chromatin remodelling complex to a rDNA gene promoters ... Gene silencing of rDNA requires binding of the chromatin remodelling complex, NoRC to a non-coding RNA (ncRNA) molecule that is ...
An 18S rRNA Gene Perspective". Mycologia. 85 (6): 923-936. doi:10.2307/3760675. JSTOR 3760675. Hibbett DS; et al. (2007). "A ... A phylogenetic analysis of nuclear ribosomal genes in 1993 showed that heterobasidiomycetes as originally circumscribed by ...
SSU rRNA) gene to distinguish between bacteria, archaea and eukaryotes. Out of this approach, the SSU rRNA gene made its way to ... For both bacteria and archaea the 16S rRNA/rDNA gene is used. It is a common housekeeping gene in all prokaryotic organisms and ... Nübel U, Garcia-Pichel F, Muyzer G (August 1997). "PCR primers to amplify 16S rRNA genes from cyanobacteria". Applied and ... For protists, the corresponding 18S rRNA/rDNA gene is used. To distinguish different species of fungi, the ITS (Internal ...
Tringe SG, Hugenholtz P (2008). "A renaissance for the pioneering 16S rRNA gene" (PDF). Curr Opin Microbiol. 11 (5): 442-446. ... For instance, 16S ribosomal RNA gene clone libraries revealed that the bacterial community of the lake with the highest ... For microorganisms, the phylogenetic marker gene Small Subunit (SSU) Ribosomal RNA is typically targeted, due to its good ...
These are associated with the promoters of 56% of mammalian genes, including all ubiquitously expressed genes. One to two ... tRNA, rRNA, mRNA, tmRNA, snRNA, snoRNA, miRNA, and viral RNA. Different catalytic strategies are employed for RNA methylation ... "Methylation loss at H19 imprinted gene correlates with methylenetetrahydrofolate reductase gene promoter hypermethylation in ... Methylation can modify heavy metals, regulate gene expression, RNA processing and protein function. It has been recognized as a ...
"Origin of the Mesozoa inferred from 18S rRNA gene sequences". Mol. Biol. Evol. 13 (8): 1128-32. doi:10.1093/oxfordjournals. ... "Origin of the Mesozoa inferred from 18S rRNA gene sequences". Mol. Biol. Evol. 13 (8): 1128-32. doi:10.1093/oxfordjournals. ... tool-kit genes in a highly simplified bilaterian". BMC Evol. Biol. 7: 201. doi:10.1186/1471-2148-7-201. PMC 2222250. PMID ...
"Species-specific identification of Leptospiraceae by 16S rRNA gene sequencing". J. Clin. Microbiol. 44 (10): 3510-6. doi: ...
... rapid taxonomic classification of fungal large-subunit rRNA genes". Applied and Environmental Microbiology. 78 (5): 1523-33. ... The Good Genes Hypothesis, also referred to as the sexy son hypothesis, suggests that the females will choose a male that ... Because high gene flow was still anticipated along this cline, selection was only expected to act upon the QTLs that incur ... Therefore, the mates that are more 'attractive" are more likely to be chosen for mating and pass on their genes to the next ...
The bacteria has 6349 genes and 6280 protein coding genes. It also has 69 RNA genes in its genome. The 16s ribosomal RNA gene ... Researchers identified the bacterium by using comparative 16s rRNA sequencing. Specifically, a small percentage of cultivable X ... Specifically, the gene has been determined to have high activity with the following azo dyes: Acid Orange 7, 1-(2-Pyridylazo)-2 ... All in all, it is important that more research be done on the X. azovorans azoreducatase gene due to its ability to break down ...
It has 4,169 protein-coding genes, six rRNA genes, and 44 tRNA genes on the chromosome, as well as 75 pseudogenes. The plasmid ... The GC content of the 4.26 Mb genome is 60.9%. There are 3949 protein-coding genes, 46 tRNA, and six rRNA genes in the genome ... Within the genome are 64 tRNA, and three rRNA genes. Analysis of the genome reveals the presence of two forms of rubisco. The ... These genes include a putative arsenite efflux pump and an arsenate reductase, as well as genes similar to those found in ...
"Strain Bryocella elongata partial 16S rRNA gene, type strain SN10T". Type strain of Bryocella elongata at BacDive - the ... According to analysis of 16S rRNA sequence, Bryocella elongata is a member of subdivision 1 of the phylum Acidobacteria. ... 16S ribosomal RNA gene sequence similarity to members of the genera Edaphobacter and Granulicella, 93.0-93.7% similarity to ...
2377 genes had an ortholog belonging to one of the 235 known biological pathways. There are 41 microRNA, 348 tRNA and 2017 rRNA ... It has 3,972 gene clusters containing 11,300 genes that were common to the genomes of the three previously sequenced mosquito ... possibly a significant mechanism for gene introgression in sympatric populations". Parasites & Vectors. 7 (1): 36. doi:10.1186/ ... genes. Ree, Han-Il (2005). "Studies on Anopheles sinensis, the vector species of vivax malaria in Korea". The Korean Journal of ...
The genome contains 57 RNA genes and two rRNA operons. Furthermore, there is 68 pseudo genes which makes up 2.0% of the total ... predicted 3,408 genes in the genome of 1pr3T, with 3,351 genes that encode proteins. ... japonicas with equal relation respective to the phylogenetic tree constructed using 16S rRNA sequences. Desulfobulbus ...
"Origin of the Mesozoa inferred from 18S rRNA gene sequences". Mol. Biol. Evol. 13 (8): 1128-32. doi:10.1093/oxfordjournals. ...
"Globicatella sanguinis bacteraemia identified by partial 16S rRNA gene sequencing". Scandinavian Journal of Infectious Diseases ...
This snoRNA guides pseudouridylation of position U1445 in 18S rRNA. This RNA is expressed from the intron of the host gene ...
In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated ... Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. ... Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in ... We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were ...
Gene neighbors Overlapping genes and two nearest non-overlapping genes on either side ... NIP7 NIP7, nucleolar pre-rRNA processing protein [ Homo sapiens (human) ] Gene ID: 51388, updated on 13-Jan-2019 ... Genes with a similar H3K4me3 profile Genes with a similar profile of promoter-activating H3K4me3 modifications across several ... General gene information Markers, Related pseudogene(s), Clone Names, Homology, Gene Ontology ...
Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences Message Subject (Your Name) has sent you a message ... Phylogeny of the malarial genus Plasmodium, derived from rRNA gene sequences. A A Escalante and F J Ayala ... We analyze the small subunit rRNA gene sequences of 11 Plasmodium species, including three parasitic to humans, to infer their ...
... Int J Immunopharmacol. 1994 Sep;16(9):711-21. doi: 10.1016/0192-0561(94) ... Our data indicate that this new immunosuppressive agent modulates transcription of rRNA genes via regulation of specific ... experiments using nuclei from Rapa-treated cells indicated a dose-dependent inhibition of transcription or rRNA genes. Cells ... Under similar conditions, transcriptions of U3 snRNA genes remained unaffected. Cytoplasmic extracts prepared from P1798 cells ...
IPR023165 rRNA_Ade_diMease-like. IPR020596 rRNA_Ade_Mease_Trfase_CS. IPR020598 rRNA_Ade_methylase_Trfase_N. IPR029063 SAM- ... IPR023165 rRNA_Ade_diMease-like. IPR020596 rRNA_Ade_Mease_Trfase_CS. IPR020598 rRNA_Ade_methylase_Trfase_N. IPR029063 SAM- ... The absence of this section means that the gene is located in one of the main chromosomal element(s).,p>,a href=/help/encoded_ ... rRNA adenine N(6)-methyltransferase family.PROSITE-ProRule annotation. Automatic assertion according to rulesi ...
... counts of genes for reference OTUs with known gene content), the gene content inference workflow predicts gene content for each ... Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not ... as well as the copy number of the marker gene in each OTU and the gene content of each OTU (as generated by the gene content ... Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.. Langille MG1, Zaneveld J, ...
We have determined mitochondrial DNA sequences from two genes that evolve at relatively rapid … ... Phylogenetic reconstruction of the Felidae using 16S rRNA and NADH-5 mitochondrial genes J Mol Evol. 1997;44 Suppl 1:S98-116. ... We have determined mitochondrial DNA sequences from two genes that evolve at relatively rapid evolutionary rates, 16S rRNA (379 ... Based on separate and combined gene analyses using minimum evolution, maximum parsimony, and maximum likelihood phylogenetic ...
This protein produces a dimethylation of the adenine residue at position 2085 in 23S rRNA, resulting in reduced affinity ... IPR023165 rRNA_Ade_diMease-like. IPR020596 rRNA_Ade_Mease_Trfase_CS. IPR020598 rRNA_Ade_methylase_Trfase_N. IPR029063 SAM- ... IPR023165 rRNA_Ade_diMease-like. IPR020596 rRNA_Ade_Mease_Trfase_CS. IPR020598 rRNA_Ade_methylase_Trfase_N. IPR029063 SAM- ... help/gene_ontology target=_top>More...,/a>,/p>GO - Molecular functioni. *23S rRNA (adenine(2085)-N(6))-dimethyltransferase ...
Gene Model ID. Feature Type. Coordinates. Select Strains. C57BL/6J MGI_C57BL6J_2144566. protein coding gene. Chr11:74898071- ... protein coding gene. Chr11:75014809-75027277 (+). BALB/cJ MGP_BALBcJ_G0018641. protein coding gene. Chr11:73175259-73186530 (+) ... protein coding gene. Chr11:75204796-75216077 (+). PWK/PhJ MGP_PWKPhJ_G0017779. protein coding gene. Chr11:73104953-73115529 (+) ... protein coding gene. Chr11:74780029-74794051 (+). WSB/EiJ MGP_WSBEiJ_G0018061. protein coding gene. Chr11:75014593-75026809 (+) ...
... chromosomes has recently been called into question after finding several cases of gene activity on them. The grasshopper ... B chromosomes showing active ribosomal RNA genes contribute insignificant amounts of rRNA in the grasshopper Eyprepocnemis ... we also infer that the relative contribution of B chromosome rRNA genes to ribosome biogenesis is insignificant, at least in ... Long EO, David IB (1980) Repeated genes in eukaryotes. Annu Rev Biochem 49:727-764PubMedCrossRefGoogle Scholar ...
Internal transcribed spacer rRNA gene sequencing analysis of fungal diversity in Kansas City indoor environments.. ... Fungi; Bronchial-asthma; Children; Indoor-air-pollution; Indoor-environmental-quality; Genes; Exposure-assessment; ...
The gene in this thermophile was systematically replaced with a diverse array of heterologous genes, resulting in the discovery ... Here we show the genetic interoperability and promiscuity of 16S rRNA in the ribosomes of an extremely thermophilic bacterium, ... However, a growing number of reports suggest the occurrence of horizontal gene transfer, raising genealogical questions. ... Remarkably, cold-adapted mutants were obtained carrying chimeric or full-length heterologous genes, indicating that horizontal ...
Direct Amplification of rRNA Genes in Diagnosis of Bacterial Infections. Kaisu Rantakokko-Jalava, Simo Nikkari, Jari Jalava, ... Direct Amplification of rRNA Genes in Diagnosis of Bacterial Infections. Kaisu Rantakokko-Jalava, Simo Nikkari, Jari Jalava, ... Direct Amplification of rRNA Genes in Diagnosis of Bacterial Infections. Kaisu Rantakokko-Jalava, Simo Nikkari, Jari Jalava, ... Direct Amplification of rRNA Genes in Diagnosis of Bacterial Infections Message Subject (Your Name) has forwarded a page to you ...
Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. ... Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. (1996) by M T Suzuki, S J ... PCR-amplified 16S rRNA genes from particle-attached and free-living bacteria in the Columbia River, its estuary, and the ... Levels of bacterial community diversity in four arid soils compared by cultivation and 16S rRNA gene cloning by John Dunbar, ...
Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes. R ... Overproduction of rRNA and "free" ribosomes produced a large repression of rRNA and tRNA synthesis from chromosomal genes and a ... Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes ... Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes ...
... followed by water chemistry and whole community 16S rRNA gene-based metabarcoding analysis. Results: We found that different ... membrane filters to efficiently capture environmental DNA for further microbial diversity estimation using 16S rRNA gene-based ... 16S rRNA gene; membrane filters; metabarcoding; pathogenic bacteria spring water; karst; 16S rRNA gene; membrane filters; ... Testing Different Membrane Filters for 16S rRNA Gene-Based Metabarcoding in Karstic Springs by Oana Teodora Moldovan ...
... 0-9. A. B. C. D. E. F. G. H. I. J. K. L. M. N. O. P. Q. R. S ...
High throughput 16S rRNA gene amplicon sequencing: A fast and cheap method to study the influence of microbial community ... In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling ... In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling ... In this study we show how 16S rRNA gene amplicon sequencing can be used to reveal factors of importance for the operation of ...
... comparison of the gene sequences of bacterial species showed that the 16S rRNA gene is highly conserved within a species and ... Identification by 16S rRNA Gene Sequencing of Lactobacillus salivarius Bacteremic Cholecystitis. Patrick C. Y. Woo, Ami M. Y. ... Identification by 16S rRNA Gene Sequencing of Lactobacillus salivarius Bacteremic Cholecystitis. Patrick C. Y. Woo, Ami M. Y. ... Identification by 16S rRNA Gene Sequencing of Lactobacillus salivarius Bacteremic Cholecystitis. Patrick C. Y. Woo, Ami M. Y. ...
106 rRNA genes per cubic meter of sampled air in summer. The presence and high concentration of rRNA genes in air suggests that ... The abundance of Oomycetes rRNA genes was low in winter and enhanced during spring, summer, and fall, with a dominance of ... FIGURE 3. Oomycetes rRNA gene abundance retrieved from qPCR analysis. (A) The gene abundance (rRNA genes m-3 air) of selected ... 106 rRNA genes per cubic meter of sampled air in summer. The presence and high concentration of rRNA genes in air suggests that ...
Sequence Characterization of Mitochondrial 12S rRNA Gene in Mouse Deer (Moschiola indica) for PCR-RFLP Based Species ... characterization and polymerase chain reaction-restriction fragment length polymorphism of the mitochondrial DNA 12S rRNA gene ... mitochondrial 12S rRNA sequence and its use in differentiation from closely related poultry species," British Poultry Science, ...
Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing.. T M Schmidt, E F DeLong, N R Pace ... Thirty-eight clones containing 16S rRNA genes were identified in a screen of 3.2 x 10(4) recombinant phage, and portions of the ... Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. ... Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. ...
All assays targeted 16S rRNA gene phylotypes putatively associated with IBS, based on 16S rRNA gene library sequence analysis. ... 16S rRNA Gene-targeted TTGE in Determining Diversity of Gut Microbiota during Acute Diarrhoea and Convalescence. Monira, ... Analysis of the D1/D2 domains of the large subunit (LUS) rRNA gene and internal transcribed spacer (ITS) regions of these ... Eight of the target phylotypes had less than 95% similarity to cultured bacterial species according to their 16S rRNA gene ...
... Dataset homepage ... Murray A (2015). Antarctic Peninsula Bacterioplankton 16S rRNA gene surveys and metagenomes from Winter 2002 and Summer 2006… ... We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic ...
The mitochondrial 12S rRNA gene was amplified using universal primers: 12S-rRNA-F and 12S-rRNA-R (Girish et al., 2005). This ... mitochondrial 12S rRNA gene using universal primers and restriction fragment length polymorphism of mitochondrial 12S rRNA gene ... The mitochondrial 12S rRNA gene fragment was clearly amplified in all samples of the fresh meat by PCR using universal and ... Our PCR-RFLP of mitochondrial 12S rRNA gene using restriction enzymes (AluI and ApoI) aimed to confirm the accuracy of the meat ...
Broad range 16S rRNA gene PCR was performed from whole blood (SepsiTest) or blood plasma (IHP) and compared to blood culture ... We compared a commercial broad range 16S rRNA gene PCR assay (SepsiTest) to an in-house developed assay (IHP). We assessed ... Diagnostic Utility of Broad Range Bacterial 16S rRNA Gene PCR with Degradation of Human and Free Bacterial DNA in Bloodstream ...
Survey of the Collective 16s rRNA Genes From Bacterial Populations From Exercising and Non-exercising Participants. The safety ... Changes in DNA sequence of the 16S rRNA gene of each member of the bacterial population in the oral cavity of each participant ... Changes in DNA sequence of the 16S rRNA genes will be assessed at 5 weeks after an exercise intervention and and compared to ... MedlinePlus related topics: Exercise and Physical Fitness Genes and Gene Therapy Tooth Decay ...
We report a case of chagasic encephalitis diagnosed by 28S rRNA sequencing. The diagnosis of chagasic encephalitis is ... Sequencing of the internal transcribed spacer 2 and D2 regions of the 28S rRNA gene in paraffin-embedded tissue identified the ... Diagnosis of Chagasic Encephalitis by Sequencing of 28S rRNA Gene. Emerging Infectious Diseases. 2019;25(7):1370-1372. doi: ... Newer diagnostic methods, such as rRNA gene sequencing, can enable rapid diagnosis and should be considered as part of the ...
... and sequencing of 16S rRNA genes. Strejcek et al. [44] also compared whole-cell MALDI-TOF MS with 16S rRNA gene analysis for ... 2.5 16S rRNA gene sequencing. The DNA extraction was performed using single colony enriched in TY agar. The 16S rDNA was ... Strejcek M, Smrhova T, Junkova P, Uhlik O (2018) Whole-cell MALDI-TOF MS versus 16S rRNA gene analysis for identification and ... 16S rRNA gene sequencing and MALDI-TOF mass spectrometry based comparative assessment and bioprospection of psychrotolerant ...
  • We analyze the small subunit rRNA gene sequences of 11 Plasmodium species, including three parasitic to humans, to infer their evolutionary relationships. (pnas.org)
  • Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. (nih.gov)
  • We have determined mitochondrial DNA sequences from two genes that evolve at relatively rapid evolutionary rates, 16S rRNA (379 bp) and NADH dehydrogenase subunit 5 (NADH-5, 318 bp), from multiple individuals of 35 species. (nih.gov)
  • Since the discovery of PCR and DNA sequencing, comparison of the gene sequences of bacterial species showed that the 16S rRNA gene is highly conserved within a species and among species of the same genus and hence can be used as the new "gold standard" for determination of the species of bacteria. (asm.org)
  • The sequence of the PCR product was compared with known 16S rRNA gene sequences in GenBank by multiple-sequence alignment with the CLUSTAL W program ( 20 ). (asm.org)
  • The phylogenetic diversity of an oligotrophic marine picoplankton community was examined by analyzing the sequences of cloned ribosomal genes. (asm.org)
  • The resulting sequences were used to establish the identities of the picoplankton by comparison with an established data base of rRNA sequences. (asm.org)
  • In addition to sequences closely related to those of described bacteria, sequences were obtained from two phylogenetic groups of organisms that are not closely related to any known rRNA sequences from cultivated organisms. (asm.org)
  • The rRNA sequences of the alpha-related group are nearly identical to those of some Sargasso Sea picoplankton, suggesting a global distribution of these organisms. (asm.org)
  • Most of the genotypic identification methods are mainly based on the polymorphism of the 16S rRNA gene sequences. (springer.com)
  • The phylogenetic position of subfamily Monotropoideae (Ericaceae) inferred from large ribosomal subunit (26S) rRNA gene DNA sequences. (thefreelibrary.com)
  • Aphylogeny inferred from partial 28S rRNA gene sequences by Cullings (1994) indicated that the myco-heterotropic Monotropoideae are polyphyletic. (thefreelibrary.com)
  • A phylogenetic study using 18S rRNA sequences separately and combined with rbcL sequences by Kron (1996) recovered topologies that suggested various positions for the Monotropoideae with Ericaceae. (thefreelibrary.com)
  • This Relationship is inferred from a maximum parsimony analysis using large ribosomal subunit (26S) rRNA gene DNA sequences. (thefreelibrary.com)
  • 2. 16SpathDB offers efficient and accurate analysis of 16S rRNA gene sequences of medically important bacteria. (hkmj.org)
  • Problems remain in that the sequences in some databases are not accurate, there is no consensus quantitative definition of genus or species based on 16S rRNA gene sequence data, the proliferation of species names based on minimal genetic and phenotypic differences raises communication difficulties, and microheterogeneity in 16S rRNA gene sequence within a species is common. (asm.org)
  • procaryotes), and Eucarya , as well as the major branches within the procaryotes based on these gene sequences ( 62 , 64 , 111 , 113 ). (asm.org)
  • Two new exons (1A and 1B) encoding sequences in the 5' untranslated region (5'UTR) of mRNA were discovered in the human RAG1 gene. (diva-portal.org)
  • Appendix C. A photograph of DGGE analysis of 16S rRNA gene sequences of ammonia oxidizers from the intensive grazing (IG) and light grazing (LG) grassland sites, at two topographical locations (downslope and upslope). (figshare.com)
  • The nucleotide sequences of partial 16S rRNA and bacterial RNA polymerase ß-subunit (rpoB) genes for 57 mycobacterial strains were determined. (stir.ac.uk)
  • Compared to the 16S rRNA gene sequences, variable regions were scattered along the whole fragment sequence, indicating that therpoBgene is more polymorphic. (stir.ac.uk)
  • Unlike 16S rRNA sequences, species variation was observed within M. fortuitum strains. (stir.ac.uk)
  • The overall mean distance forrpoB-gene?based sequences was 2.5 times greater than that of the 16S rRNA gene for all 57 mycobacterial strains examined. (stir.ac.uk)
  • Moreover, a bootstrap value above 70% was observed for 13 nodes, while this value was 14 nodes in the case of 16S rRNA sequences. (stir.ac.uk)
  • Alternatively, does anyone know the primer sequences that can extract the 16s gene? (biostars.org)
  • How To Extract Rrna Sequences (In Fasta Format) From Genbank (Bacterial Genome)? (biostars.org)
  • In the second part of the thesis, the goals were to amplify the cryptophyte plastome 16S rRNA-rbcL fragments by MasterAmpTM Extra-long PCR kit and read their DNA sequences by BigDye Terminator v1.1 Cycle sequencing kit and automated ABI3730 sequencer, then exploited the sequencing information for further understanding the evolutionary history of cryptophyte plastomes. (uni-koeln.de)
  • Two novel gull-specific quantitative PCR (qPCR) assays were developed using 16S rRNA gene sequences from gull fecal clone libraries: a SYBR green assay targeting Streptococcus spp. (semanticscholar.org)
  • Phylogenies of housekeeping gene and 16S rRNA gene sequences were compared to improve the classification of the bacterial family Pasteurellaceae and knowledge of the evolutionary relationships of its members. (semanticscholar.org)
  • Deduced partial protein sequences of the housekeeping genes atpD, infB and rpoB were compared in 28, 36 and 28 representative taxa of the Pasteurellaceae, respectively. (semanticscholar.org)
  • 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. (peerj.com)
  • A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. (peerj.com)
  • As a result, the diversity of 16S rRNA genes within biological samples may be underestimated, because multiple sequences can migrate at the same rate to form a single band. (rian.ie)
  • Here we introduce an integrated database, called EzBioCloud, that holds the taxonomic hierarchy of the Bacteria and Archaea , which is represented by quality-controlled 16S rRNA gene and genome sequences. (microbiologyresearch.org)
  • EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. (microbiologyresearch.org)
  • Since then, many 16S rRNA gene sequences of newly isolated strains or clones representing the genus Methanobrevibacter have been deposited. (biomedcentral.com)
  • We tried to reorganize the 16S rRNA gene sequences of this genus and revise the taxonomic affiliation of the isolates and clones representing the genus Methanobrevibacter . (biomedcentral.com)
  • The cophenetic correlation coefficient, a test for the ultrametric properties of the 16S rRNA gene sequences used for the tree was found to be 0.913 indicating the high degree of goodness of fit of the tree topology. (biomedcentral.com)
  • Conclusion: Comparative analysis of minicircle sequences has allowed us to identify previously unrecognised features of dinoflagellate chloroplast genomes, including additional protein and RNA genes. (cam.ac.uk)
  • The chloroplast rRNA gene sequences are radically different from those in other organisms, and in many ways resemble the rRNA genes found in some highly reduced mitochondrial genomes. (cam.ac.uk)
  • All sequences were obtained from the bacterial 16S rRNA gene, which was amplified from microbial DNA extracted from a human fecal sample. (biomedcentral.com)
  • We found that the microbiota composition of 16S rRNA gene sequences obtained using Sanger, 454 and SOLiD sequencing provide results comparable to the result based on shotgun sequencing. (biomedcentral.com)
  • DNA based identification of microorganisms using 16S rRNA gene amplicon sequencing has been developed over the past few years and is now ready to use for more comprehensive studies related to plant operation and optimization thanks to short analysis time, low cost, high throughput, and high taxonomic resolution. (aau.dk)
  • In this study we show how 16S rRNA gene amplicon sequencing can be used to reveal factors of importance for the operation of full-scale nutrient removal plants related to settling problems and floc properties. (aau.dk)
  • In conclusion, 16S rRNA gene amplicon sequencing provides a high throughput approach for a rapid and cheap community profiling of activated sludge that in combination with multivariate statistics can be used to reveal important correlations that provide solutions for plant operation problems and can contribute to process performance optimization. (aau.dk)
  • Alignment of amplicon sequence isolated from the patient was compared with a reference Trypanosoma cruzi 5.8S rRNA. (cdc.gov)
  • Nevertheless, the nanopore sequencer would be very useful for pathogen detection in patients with bacterial infections because it enables full-length 16S rRNA amplicon sequencing and the real-time analysis of the reads. (nanoporetech.com)
  • Conclusions Here, we provide the most comprehensive study of performance and bias inherent to a 16S rRNA gene amplicon sequencing method to date. (uio.no)
  • DNA extracts were subjected to amplification of the 16S rRNA gene pool, T-RFLP with the HaeIII restriction enzyme, 454 tag encoded FLX amplicon pyrosequencing, and PyroTRF-ID analysis. (epfl.ch)
  • Spatial- and temporal-based 16S rRNA gene amplicon profile analysis from recovered communities further revealed contrasting results. (scielo.org.za)
  • Here, we report 16S rRNA amplicon pyrosequencing data on the water and sediment microbial communities of eight alkaline lakes in the Sandhills of western Nebraska. (asm.org)
  • The melting profiles and melting temperatures (Tm) of the amplicon targeting 18S rRNA revealed differences that can discriminate the four Babesia spp. (biomedcentral.com)
  • Background: Amplicon sequencing methods targeting the 16S rRNA gene have been used extensively to investigate microbial community composition and dynamics in anaerobic digestion. (gla.ac.uk)
  • In this research, the archaeal and bacterial community of 48 full-scale anaerobic digestion plants were evaluated on DNA (total community) and RNA (active community) level via 16S rRNA (gene) amplicon sequencing. (gla.ac.uk)
  • Internal transcribed spacer rRNA gene sequencing analysis of fungal diversity in Kansas City indoor environments. (cdc.gov)
  • Recently, we have reported on the application of 16S rRNA gene sequencing to the identification of clinical isolates with ambiguous biochemical profiles ( 23 , 24 , 26 , 27 ) and a bacterium that was noncultivable ( 6 ). (asm.org)
  • Bacterial DNA extraction, PCR amplification, and DNA sequencing of the 16S rRNA gene were performed as described in our previous publications ( 6 , 22 , 23 , 24 , 25 , 26 , 27 ). (asm.org)
  • Analysis of a marine picoplankton community by 16S rRNA gene cloning and sequencing. (asm.org)
  • We report a case of chagasic encephalitis diagnosed by 28S rRNA sequencing. (cdc.gov)
  • This case was diagnosed by sequencing of the parasite 28S rRNA gene. (cdc.gov)
  • Sequencing of the internal transcribed spacer 2 and D2 regions of the 28S rRNA gene in paraffin-embedded tissue identified the organism as Trypanosoma cruzi ( Figure 3 ) ( 1 , 2 ). (cdc.gov)
  • The present paper deals with the evaluation of bacterial diversity in high-altitude soil samples from IHR following polyphasic approach including comparison between the MALDI-TOF mass spectrometry and 16S rRNA gene sequencing for species-level identification. (springer.com)
  • Performing morphological and biochemical screenings, sixty-one representative isolates were selected for mass spectrometry and gene sequencing. (springer.com)
  • We evaluated the use of 16S rRNA gene sequencing to rapidly identify these two species and differentiate them from each other as well as from closely related species and genera such as Pandoraea spp. (unboundmedicine.com)
  • Using 16S rRNA gene and gyrB gene sequencing as a gold standard, the performance of two MALDI-TOF MS instruments in the identification of 181 VGS clinical isolates was studied. (frontiersin.org)
  • Based on MALDI-TOF analysis and selected 16S rRNA gene plus gyrB genes sequencing, we designed a practical VGS identification algorithm. (frontiersin.org)
  • Our offering includes DNA sequencing, as well as RNA and gene expression analysis and future technology for analysing proteins. (nanoporetech.com)
  • The usual approach is sequencing specific hypervariable regions of the 16S rRNA gene, which fails to assign taxonomy to genus and species level. (nanoporetech.com)
  • Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger. (bioportfolio.com)
  • Nanopore sequencing of the 16S rRNA gene allowed the identification of C. fetus at the subspecies level. (nanoporetech.com)
  • pallidum in clinical samples: sequencing of TP0136, TP0548 and 23S rRNA genes. (muni.cz)
  • High-throughput sequencing of small subunit ribosomal RNA (SSU rRNA) genes from marine environments is a widely applied method used to uncover the composition of micro- bial communities. (bios.edu)
  • Thus, a future challenge is to translate information from 16S rRNA gene sequencing into convenient biochemical testing schemes, making the accuracy of the genotypic identification available to the smaller and routine clinical microbiology laboratories. (asm.org)
  • Fecal and blood microbiota were investigated by high-throughput IllUmina Miseq sequencing targeted on the V3-V4 functional region of 16s rRNA gene. (iospress.com)
  • The microbial communities from three upflow anaerobic bioreactors treating purified terephthalic acid (PTA) wastewater were characterized with 16S ribosomal RNA gene sequencing surveys. (iwaponline.com)
  • Quantifying the technical versus biological variation expected in targeted 16S rRNA gene sequencing studies and how this variation changes with input biomass is critical to guide meaningful interpretation of the current literature and plan future research. (biomedcentral.com)
  • Data were compiled from 469 sequencing libraries across 19 separate targeted 16S rRNA gene sequencing runs over a 2.5-year time period. (biomedcentral.com)
  • Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. (biostars.org)
  • I would like to identify as many bacteria as possible from the 16s rRNA sequencing data. (biostars.org)
  • Materials and methods: Molecular analysis of these genes was investigated by PCR amplification and direct DNA sequencing. (alliedacademies.org)
  • At the first stage of the thesis, the cryptophyte plastid rbcL gene (1,5- biphosphate carboxylase/oxygenase [RuBisCO] large subunit) was chosen to amplify by BioTherm� Taq DNA Polymerase and read their DNA compositions by SequiTherm EXCEL� II DNA Sequencing Kit-LC and Li-Cor 4200L bidirectional sequencer. (uni-koeln.de)
  • Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. (biomedcentral.com)
  • Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach. (biomedcentral.com)
  • The objective of many high-throughput sequencing studies is to identify those genes or features that make a significant difference between two or more conditions. (biomedcentral.com)
  • These methods are diverse and include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and metagenomic and 16S rRNA gene amplification analysis of microbial populations. (biomedcentral.com)
  • The entities can be genes, other expressed or non-expressed genomic features (RNA-seq and metagenomics), operational taxonomic units (OTUs) (16S rRNA gene sequencing) or genomic segments (ChIP-seq). (biomedcentral.com)
  • Pinto, A. J. , de Vrieze, J. , Sloan, W. T. and Ijaz, U. Z. (2018) The active microbial community more accurately reflects the anaerobic digestion process: 16S rRNA (gene) sequencing as a predictive tool. (gla.ac.uk)
  • PCR and DNA sequencing were used to identify 16S rRNA methylase and extended-spectrum β-lactamase (ESBL) genes, including armA and rmtB , and in situ hybridization was performed to determine the location of 16S rRNA methylase genes. (biomedcentral.com)
  • Identification of Bacillus Probiotics Isolated from Soil Rhizosphere Using 16S rRNA, recA, rpoB Gene Sequencing and RAPD-PCR. (semanticscholar.org)
  • The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. (nature.com)
  • Based on separate and combined gene analyses using minimum evolution, maximum parsimony, and maximum likelihood phylogenetic methods, we recognized eight significant clusters or species clades that likely reflect separate monophyletic evolutionary radiations in the history of this family. (nih.gov)
  • Based on the structural complexity of ribosomes, 16S rRNA genes are considered species-specific and hence used for bacterial phylogenetic analysis. (nature.com)
  • These idiosyncratic mutations gradually shaped the species-specificity of the gene, which became the basis of the use of 16S rRNA gene sequence for the phylogenetic classification of bacteria-indeed all living organisms on earth-based on the small subunit of rRNA 11 , 12 (Fig. 1A ). (nature.com)
  • Sequence specificity is ensured but rRNA are not interoperable between species because functionally essential interactions are species-specific and would be lost upon interspecies exchange. (nature.com)
  • Eight of the target phylotypes had less than 95% similarity to cultured bacterial species according to their 16S rRNA gene sequence. (ebscohost.com)
  • Our PCR-RFLP of mitochondrial 12S rRNA gene using restriction enzymes ( AluI and ApoI ) aimed to confirm the accuracy of the meat species labeling, based on fresh and processed meat collected in central markets along the main cities in the Amazonas Region (Bagua, Bagua Grande, Chachapoyas, Luya, Pedro Ruiz, Rodriguez de Mendoza). (scielo.br)
  • Although the MALDI-TOF technique appeared to be advantageous as less time-consuming in comparison with 16S rRNA-based method, the discrepancies at species level indicated the limited database of MALDI Biotyper and species complexity in the genera. (springer.com)
  • Strikingly, they also show that the same 5S rRNA species that regulates Hdm2 is also a positive effector of Hdm4, a negative regulator of p53. (healthcanal.com)
  • We are proposing PCR-DGGE and 16S rRNA gene libraries as an alternative to improve the detection and identification rate of bacterial species from endophthalmitis cases. (scielo.br)
  • The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. (biomedcentral.com)
  • Results: Full-length 16S rRNA and the rrn operon retrieved the microbiota composition from the bacterial isolate, the mock communities and the complex skin samples, even at the genus and species level. (nanoporetech.com)
  • For the Staphylococcus pseudintermedius isolate, when using EPI2ME, the amplicons were assigned to the correct bacterial species in ~98% of the cases with rrn operon as the marker, and ~68% of the cases with 16S rRNA gene respectively. (nanoporetech.com)
  • For identification to the species level, partial sequence analysis of the hsp65 and 16S rRNA genes were used. (iwaponline.com)
  • Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. (microbiologyresearch.org)
  • Fox GE , Wisotzkey JD , Jurtshuk P . How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. (microbiologyresearch.org)
  • Kim M , Oh HS , Park SC , Chun J . Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (microbiologyresearch.org)
  • A previous study of the North American biogeography of the red algal genus Hildenbrandia noted the presence of group I introns in the nuclear small subunit (SSU) rRNA gene of the marine species H. rubra (Sommerf. (academicconcepts.net)
  • 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)
  • Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community's functional capabilities. (nih.gov)
  • Our results demonstrate that phylogeny and function are sufficiently linked that this 'predictive metagenomic' approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available. (nih.gov)
  • Antarctic Peninsula Bacterioplankton 16S rRNA gene surveys and metagenomes from Winter 2002 and Summer 2006… SCAR - Microbial Antarctic Resource System. (gbif.org)
  • Conclusions: Both full-length 16S rRNA and the rrn operon retrieved the microbiota composition of simple and complex microbial communities, even from the low-biomass samples such as dog skin. (nanoporetech.com)
  • To explore the alterations of microbial 16s ribosomal (rRNA) gene in the feces and blood of Chinese patients with multiple system atrophy (MSA) and its relationships with clinical features. (iospress.com)
  • We confirmed the alterations of microbial 16s rRNA gene in the feces and blood occurs in Chinese patients with MSA. (iospress.com)
  • Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. (nih.gov)
  • Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (jax.org)
  • Universal phylogenetic tree based on the 16S rRNA gene sequence comparisons. (asm.org)
  • The topology of therpoB-based phylogenetic tree was almost the same as that of the 16S rRNA sequence analysis. (stir.ac.uk)
  • In recent phylogenetic analyses combining nuclear and nucleomorph RNA genes of the ribosomal operons, three different colourless lineages were found in the genus Cryptomonas. (uni-koeln.de)
  • Another additional gene � ORF403 encoding Tic22 protein � also was examined the conserved domains and done a phylogenetic analysis. (uni-koeln.de)
  • Three protein-coding genes � chlI, rps4 and rbcL � were used as separated phylogenetic markers or in combined. (uni-koeln.de)
  • Although having moderate size (609 bp), rps4 had an evolution rate neither as high as in chlI gene nor as low as in rbcL gene, producing acceptable phylogenetic trees for both nucleotide and protein levels. (uni-koeln.de)
  • It has been proposed that isolates of Trypanosoma cruzi, the agent of American trypanosomiasis, can be ordered into two primary phylogenetic lineages, first based on multilocus enzyme electrophoresis and random amplified polymorphic DNA, and subsequently based on the 24Salpha rRNA and mini-exon genes. (pasteur.fr)
  • Thirty-eight clones containing 16S rRNA genes were identified in a screen of 3.2 x 10(4) recombinant phage, and portions of the rRNA gene were amplified by polymerase chain reaction and sequenced. (asm.org)
  • Differential amplification of rRNA genes by polymerase chain reaction. (asm.org)
  • Quantitative real-time reverse transcriptase-polymerase chain reaction was used to determine the expression level of 18S rRNA, β-actin mRNA, GAPDH mRNA and mRNA for six cytokines in carefully counted samples of resting human peripheral blood mononuclear cells (PBMCs), intestinal lymphocytes and PBMCs subjected to polyclonal T-cell activation. (diva-portal.org)
  • Heterotrophic plate count using ISO 6222 agar (HPC) vs. in situ bacterial (DF) community structure from corresponding samples of a drinking water distribution system were investigated by 16S rRNA gene-based polymerase chain reaction denaturing gradient gel electrophoresis (PCR DGGE) profiling. (scielo.org.za)
  • The results show that, under the action of DRB transcribed rRNA, genes spread throughout the nucleoplasm and finally appear in the form of several rows, each containing several (up to 30) granules positive for RNA polymerase I and argyrophilic proteins. (rupress.org)
  • We further propose that each RNA polymerase-positive granular unit represents a single transcription unit and that each continuous array of granules ("string of nucleolar beads") reflects the linear distribution of rRNA genes along a nucleolar organizer region. (rupress.org)
  • Based on the total number of polymerase I-positive granules we estimate that a minimum of 60 rRNA genes are active during interphase of DRB-treated rat cells. (rupress.org)
  • It is necessary to develop a rapid and reliable method for detecting bacteria in blood and cerebrospinal fluid (CSF) Polymerase chain reaction (PCR) and reverse hybridization of the 16S rRNA gene would permit fast and sensitive determination of the presence of bacteria and differentiate gram-positive bacteria from gram-negative ones in clinical specimens. (academicconcepts.net)
  • In this model, idiosyncratic mutations accumulate both in essential and non-essential sites of rRNA and cradle (r-proteins). (nature.com)
  • Identification of mutations in 23S rRNA gene of clarithromycin-resistant Mycobacterium intracellulare. (asm.org)
  • Mutations in the 23S rRNA gene (A2058G and A2059G), causing macrolide resistance of TPA strains, were found in samples taken from 28.6% of patients. (muni.cz)
  • A PCR-oligonucleotide ligation assay to determine the prevalence of 23S rRNA gene mutations in clarithromycin-resistant Helicobacter pylori. (asm.org)
  • Govorun, V. 2005-11-11 00:00:00 To detect point mutations A2115C, A2143G/C, and A2144G in the 23S rRNA gene of Helicobacter pylori associated with resistance of the microorganism to clarithromycin, a new powerful way of analysis was used. (deepdyve.com)
  • Objective: In our study, mutational analysis of these genes were examined to determine the prevalence of gene mutations in Vietnamese non-syndromic deaf children. (alliedacademies.org)
  • Therefore, the small introns must have retained their ability to splice in order to allow the production of functional small subunit rRNA. (biomedcentral.com)
  • Twenty-two of 23 B. mallei isolates showed 16S rRNA gene sequence identity and were designated 16S type 10, whereas the remaining isolate was designated type 11. (unboundmedicine.com)
  • Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. (nature.com)
  • In the genome of Neisseria meningitidis (serogroup B), the gene for this protein is present (NMB0066). (uniprot.org)
  • Bearing in mind that B chromosomes carry the largest rDNA cluster in the E. plorans genome, we also infer that the relative contribution of B chromosome rRNA genes to ribosome biogenesis is insignificant, at least in the body parts analyzed. (springer.com)
  • The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. (g3journal.org)
  • The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. (biomedcentral.com)
  • Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. (biomedcentral.com)
  • The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. (biomedcentral.com)
  • Is there a search that you can just enter the whole bacteria genome ID and then specify the 16srRNA gene. (biostars.org)
  • how can we extract 16s rrna from an assembled genome. (biostars.org)
  • Whole-genome assemblies in the NCBI Assembly Database were screened for low quality and subjected to a composite identification bioinformatics pipeline that employs gene-based searches followed by the calculation of average nucleotide identity. (microbiologyresearch.org)
  • Genome reduction appears to be the result of extensive transfer of genes to the nuclear genome. (cam.ac.uk)
  • The retention of certain tRNA genes in the dinoflagellate chloroplast genome has important implications for models of chloroplast-mitochondrion interaction. (cam.ac.uk)
  • The part of the DNA now most commonly used for taxonomic purposes for bacteria is the 16S rRNA gene ( 7 , 36 , 44 , 52 , 64 , 101 ). (asm.org)
  • However, there have been few studies that examine how the similarities of both taxonomic and functional genes co‐vary over geographic distance within a group of ecologically related microbes. (darkenergybiosphere.org)
  • The grasshopper Eyprepocnemis plorans harbors B chromosomes containing large amounts of ribosomal DNA (rDNA) units, some of which are eventually active, but the amount of rRNA transcripts contributed by B chromosomes, compared to those of the standard (A) chromosomes, is unknown. (springer.com)
  • The 16S rRNA gene is also designated 16S rDNA, and the terms have been used interchangeably: current ASM policy is that "16S rRNA gene" be used. (asm.org)
  • The chromatin remodelling complex B-WICH, which comprises the William syndrome transcription factor (WSTF), SNF2h, and nuclear myosin 1 (NM1), is involved in regulating rDNA transcription, and SiRNA silencing of WSTF leads to a reduced level of 45S pre-rRNA. (diva-portal.org)
  • rRNA genes (rDNA) exist in two distinct epigenetic states, active promoters being unmethylated and marked by euchromatic histone modifications, whereas silent ones are methylated and exhibit heterochromatic features. (elsevier.com)
  • Repression of rDNA transcription in growtharrested and differentiated cells correlateswith elevated association of NuRD and increased levels of poised rRNA genes. (elsevier.com)
  • We have used this experimental system, which does not inhibit transcription of the rRNA genes, to study by immunocytochemistry the distribution of active rRNA genes and their transcriptional products during nucleolar dispersal and recovery to normal morphology. (rupress.org)
  • In conclusion, 18S rRNA was the most stable housekeeping gene and hence superior for normalization in comparative analyses of mRNA expression levels in human T lymphocytes. (diva-portal.org)
  • To the best of our knowledge, this is the first investigation evaluating the use of 16S rRNA andrpoBsequence analyses for identification of aquatic mycobacteria obtained from diverse geographical locations. (stir.ac.uk)
  • Distance-decay, ordination and statistical analyses revealed that the distribution of 16S rRNA genes is strongly influenced by geographic distance and environmental factors, whereas the dsrA gene is not. (darkenergybiosphere.org)
  • The variability of the 16S rRNA gene in bacterial genomes and its consequences for bacterial community analyses. (biostars.org)
  • Since Estuarine Turbidity Maxima (ETM) are sites of accumulation and transformation of this phytoplankton-derived OM, to further characterize the ETM protist assemblage, we collected in August 2007 bottom waters throughout an ETM event, as well as surface water during the peak of bottom turbidity, and performed biogeochemical, microscopic and molecular (18S rRNA gene clone libraries) analyses. (stccmop.org)
  • This information is precomputed for 16S based on Greengenes and IMG , but all functionality is accessible in PICRUSt for use with other marker genes and reference genomes. (nih.gov)
  • Ribosomal RNA (rRNA) multigene families are organized into two distinct classes that are tandemly arrayed in eukaryotic genomes. (biomedcentral.com)
  • This raised questions about the evolutionary history of these interesting objects and their relatives as well as the role of plastid genomes such as whether these three lineages resulted from similar or from different evolutionary events or what are the mutual relationship or/and roles of photosynthetic genes in the absence of photosynthetic activities, etc. (uni-koeln.de)
  • The features include further protein coding genes, unusual rRNA genes, which we show are transcribed, and the first examples of tRNA genes from peridinin-containing dinoflagellate chloroplast genomes. (cam.ac.uk)
  • We report here an environmental genomic and small subunit ribosomal RNA (SSU rRNA) analysis of winter and summer Antarctic Peninsula coastal seawater bacterioplankton. (gbif.org)
  • In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. (biomedcentral.com)
  • Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. (nature.com)
  • More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea. (nature.com)
  • rRNA operon copy number reflects ecological strategies of bacteria. (nature.com)
  • Fecal 16S rRNA copy number of selected bacteria was studied using qPCR in 47. (ebscohost.com)
  • 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, can be routinely used for identification of mycobacteria, and can lead to the recognition of novel pathogens and noncultured bacteria. (asm.org)
  • Candidates for this genetic area in bacteria included the genes that code for the 5S, the 16S (also called the small subunit), and the 23S rRNA and the spaces between these genes. (asm.org)
  • The 16S rRNA gene can be compared not only among all bacteria but also with the 16S rRNA gene of archeobacteria and the 18S rRNA gene of eucaryotes. (asm.org)
  • Hey, I have a list of NCBI ID and gi number and they are the ID/number for the whole bacteria gene. (biostars.org)
  • I want to build a fasta file with only the 16s rRNA gene from the bacteria associated these ID and gi#. (biostars.org)
  • Methods: We developed a pair of primers according to the gene encoding 16SrRNA found in all bacteria. (academicconcepts.net)
  • Control of rRNA transcription in Escherichia coli . (nature.com)
  • Gourse RL, Gaal T, Bartlett MS, Appleman JA, Ross W. rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli . (nature.com)
  • Run-on transcription experiments using nuclei from Rapa-treated cells indicated a dose-dependent inhibition of transcription or rRNA genes. (nih.gov)
  • Cytoplasmic extracts prepared from P1798 cells treated with 1 microgram/ml Rapa for 24 h failed to support transcription from cloned mouse rRNA promoter. (nih.gov)
  • Our data indicate that this new immunosuppressive agent modulates transcription of rRNA genes via regulation of specific transcription factor function. (nih.gov)
  • Given that rRNA gene transcription is limiting for growth silencing of half the rRNA gene capacity seems counter intuitive. (edu.au)
  • This project will use mouse embryonic stems (ES) cells to explore the biological function of rRNA gene silencing by manipulating levels of the Pol I transcription factor UBF and levels of the methyltransferase DNMT1. (edu.au)
  • Background: One requisite of quantitative reverse transcription PCR (qRT-PCR) is to normalise the data with an internal reference gene that is invariant regardless of treatment, such as virus infection. (lboro.ac.uk)
  • A widely used method for normalisation involves measuring the expression of an internal reference or "housekeeping" gene, which takes into account the potential error of RNA/cDNA loading, and variation of reverse transcription efficiency [ 3 ]. (biomedcentral.com)
  • In the RNA pol III transcription, the chromatin outside of the gene is more open, leading to binding of c-Myc, with the subsequent recruitment of histone acetylation resulting in H3-Ac. (diva-portal.org)
  • The importance of the chromatin remodelling around the genes was particularly clear in WSTF knock-down cells, in which the binding of RNA pol III and auxiliary transcription factors at the 5S rRNA and 7SL RNA gene promoters were totally abolished. (diva-portal.org)
  • Here we show that the nucleosome remodeling and deacetylation (NuRD) complex establishes a specific chromatin structure at rRNA genes that are poised for transcription activation. (elsevier.com)
  • The promoter of poised rRNA genes is unmethylated, associated with components of the preinitiation complex, marked by bivalent histone modifications and covered by a nucleosome in the "off" position, which is refractory to transcription initiation. (elsevier.com)
  • Hartmann RK, Ulbrich N, Erdmann VA. An unusual rRNA operon constellation: in Thermus thermophilus HB8 the 23S/5S rRNA operon is a separate entity from the 16S rRNA operon. (nature.com)
  • Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. (nature.com)
  • Munson MA, Baumann L, Baumann P. Buchnera aphidicola (a prokaryotic endosymbiont of aphids) contains a putative 16S rRNA operon unlinked to the 23s rRNA-encoding gene: sequence determination, and promoter and terminator analysis. (nature.com)
  • We have constructed a conditional rRNA gene expression system by fusing a plasmid-encoded rrnB operon to the lambda PL promoter/operator. (pnas.org)
  • By using a cloned Escherichia coli rRNA operon as the probe, Southern blot hybridization of restriction endonuclease-digested total DNA was carried out. (elsevier.com)
  • Why is 18S ribosomal RNA (rRNA) used as a housekeeping gene to normalize sample-to-sample, systematic variation in qPCR assays? (qiagen.com)
  • To further characterize the treponemal strains, two sequentially variable genes including TP0136 and TP0548 were amplified and sequenced together with the 23S rRNA gene. (muni.cz)
  • Identified subtypes of TPA strains were further typed with the CDC typing system for TPA treponemes (comprising analysis of the arp and tpr genes). (muni.cz)
  • B to E) The indicated mutant strains were patched from a yeast deletion library in which ∼4,800 nonessential genes have been individually disrupted in the BY strain background. (asm.org)
  • They were combined with other result done by Dr. Kerstin Hoef-Emden such as analyzing the shift from NNC to NNU in two-fold degenerate NNY codon in rbcL gene in Cryptomonas to discuss some hypotheses of the loss of photosynthetic activities in the colorless C. paramaecium strains. (uni-koeln.de)
  • Strain C. erosa CCAC 0018 and C. obovoidea CCAC 0031 seemed to have the largest plastomes as their 16S-rbcL fragments contained an additional gene � ycf26 � that was not found in other Cryptomonas strains. (uni-koeln.de)
  • Using the 24Salpha rRNA and mini-exon markers in combination, five sets of strains were distinguished, corresponding to the multilocus enzyme electrophoresis/random amplified polymorphic DNA lineages I, IIa, IIc, IId and to lineages IIb/IIe together, respectively. (pasteur.fr)
  • We studied the restriction endonuclease cleavage patterns of rRNA genes (ribotypes) of 72 clinical isolates of Shigella flexneri representing eight serotypes to determine whether ribotyping could be used to distinguish S. flexneri strains and to compare the discriminating ability of the method with that of serotyping. (elsevier.com)
  • However, HindIII produced the optimum digestion pattern of the rRNA genes and was more useful than the other enzymes used in differentiating strains. (elsevier.com)
  • It was thereby possible to study the events that lead to the regulation of chromosomal rRNA and tRNA synthesis after overproduction of rRNA. (pnas.org)
  • Overproduction of rRNA and "free" ribosomes produced a large repression of rRNA and tRNA synthesis from chromosomal genes and a smaller increase in the concentration of guanosine tetraphosphate. (pnas.org)
  • These results lend support to the ribosome feedback regulation model: rRNA and tRNA operons are negatively regulated, either directly or through some intermediate, by free, nontranslating ribosomes. (pnas.org)
  • A genotyping method for Entamoeba histolytica based on PCR amplification of tRNA gene-linked short tandem repeats. (microbiologyresearch.org)
  • However, a number of lines of evidence suggest that the relative abundance of PCR rDNAs reasonably reflects the relative in situ abundance of bacterial and archaeal rRNA genes in the samples taken. (psu.edu)
  • Result: There were four kinds of nucleotide changes in the GJB2 gene, including a pathogenic 235delC mutation that was identified in only patients with HL. (alliedacademies.org)
  • The minor class (5S rRNA genes) consists of multiple copies of a highly conserved 120 bp transcribing region that is separated by a variable non-transcribed region (NTS) [ 1 , 2 ]. (biomedcentral.com)
  • These results suggest that therpoBgene is a highly conserved gene, and taxonomical studies based on this gene may be comparable with similar studies based on the 16S rRNA gene. (stir.ac.uk)
  • Pourahmad F & Richards R (2016) Comparative evaluation of sequence analysis of 16S rRNA and rpoB genes for identification of aquatic mycobacteria, Turkish Journal of Veterinary and Animal Sciences, 40 (4), pp. 406-416. (stir.ac.uk)
  • Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. (semanticscholar.org)
  • Comprehensive Bioinformatic Analysis Genes Associated to the Prognosis of Liposarcoma. (nih.gov)
  • All assays targeted 16S rRNA gene phylotypes putatively associated with IBS, based on 16S rRNA gene library sequence analysis. (ebscohost.com)
  • A multivariate analysis of the relative quantities of all 14 bacterial 16S rRNA gene phylotypes suggested that the intestinal microbiota of the IBS-D patients differed from other sample groups. (ebscohost.com)
  • An approximate 1 kb DNA segment of the 26S gene was sequenced for the taxa included in this analysis. (thefreelibrary.com)
  • This dataset contains the digitized treatments in Plazi based on the original journal article Lu, Borong, Huang, Jie, Chen, Xiangrui (2013): The morphology and SSU rRNA gene sequence analysis of a poorly-known brackish water ciliate, Pinacocoleps tesselatus (Kahl, 1930) (Ciliophora, Colepidae) from Hangzhou Bay, China. (gbif.org)
  • The analysis of a sequence such as a region of a chromosome, a haplotype, a gene, or an allele for its involvement in controlling the phenotype of a specific trait, metabolic pathway, or disease. (bioportfolio.com)
  • Despite its accuracy, 16S rRNA gene sequence analysis lacks widespread use beyond the large and reference laboratories because of technical and cost considerations. (asm.org)
  • The goal of this review is to describe not only the mechanism and limits of bacterial 16S rRNA gene sequence analysis but also the impact and potential contribution that the 16S rRNA gene sequence analysis can make to the understanding of clinical microbiology and infectious diseases. (asm.org)
  • The accuracy of 18S rRNA, β-actin mRNA and glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA as indicators of cell number when used for normalization in gene expression analysis of T lymphocytes at different activation stages was investigated. (diva-portal.org)
  • Cytokine analysis revealed that only normalization to 18S rRNA gave a result that satisfactorily reflected their mRNA expression levels per cell. (diva-portal.org)
  • Recipient(s) will receive an email with a link to 'Identification of nontuberculous mycobacteria isolated from hospital water by sequence analysis of the hsp65 and 16S rRNA genes' and will not need an account to access the content. (iwaponline.com)
  • In order to ensure accurate and reproducible 16S rRNA gene profile analysis, rigorous methodical evaluation and standardisation procedures were undertaken (DGGE optimisation, replication of PCR, multiple-lane standardisation, representative sampling volume determination, application of multiple similarity coefficients). (scielo.org.za)
  • In many habitats, microorganisms exhibit significant distance-decay patterns as determined by analysis of the 16S rRNA gene and various other genetic elements. (darkenergybiosphere.org)
  • Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error. (biomedcentral.com)
  • The culturable gill bacterial populations associated with amoebic gill disease (AGO) in Atlantic salmon (Salmo salar) were identified using bio chemical test, cluster an analysis and 16S r RNA gene based approaches. (edu.au)
  • Analysis of qRT-PCR data from virus and mock infected cells using NormFinder and BestKeeper software programmes found that 18S rRNA was the most stable gene in HBECs, PTECs and avian lung cells. (lboro.ac.uk)
  • Ribosomal database project: data and tools for high throughput rRNA analysis. (microbiologyresearch.org)
  • Sequence analysis of a 4.6-kb HindIII fragment containing the malic enzyme gene (mae2) of Schizosaccharomyces pombe, revealed the presence of an open reading frame of 1695 nucleotides, coding for a 565 amino acid polypeptide. (sun.ac.za)
  • Analysis of the 72 isolates showed 11 different HindIII cleavage patterns of their rRNA genes. (elsevier.com)
  • Here, we employed a pyrosequencing-based analysis of the V2-V3 16S rRNA gene region to characterize the overall and horizon-specific (A and B horizons) bacterial community compositions in nine grassland soils, which covered three different land use types. (mpg.de)
  • Here, we show that the B-WICH complex affects the chromatin structure and that silencing of the WSTF protein results in a compaction of the chromatin structure over a 200 basepair region at the rRNA promoter. (diva-portal.org)
  • WSTF knock down does not show an effect on the binding of the rRNA-specific enhancer and chromatin protein UBF, which contributes to the chromatin structure at active genes. (diva-portal.org)
  • We propose that the B-WICH complex remodels the chromatin structure at actively transcribed rRNA genes, and this allows for the association of specific histone acetyl-transferases. (diva-portal.org)
  • Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. (nih.gov)
  • The abundance of Oomycetes rRNA genes was low in winter and enhanced during spring, summer, and fall, with a dominance of Phytophthora , reaching a maximum concentration of ∼1.6 × 10 6 rRNA genes per cubic meter of sampled air in summer. (frontiersin.org)
  • Pairwise distances increased with more dilute samples, and estimates of relative abundance became unreliable below approximately 100 copies of the 16S rRNA gene per microliter. (biomedcentral.com)
  • The ALDEx2 approach is shown to be suitable for all three types of data: it correctly identifies both the direction and differential abundance of features in the differential growth experiment, it identifies a substantially similar set of differentially expressed genes in the RNA-seq dataset as the leading tools and it identifies as differential the taxa that distinguish the tongue dorsum and buccal mucosa in the Human Microbiome Project dataset. (biomedcentral.com)
  • The formation of the 60S involves many molecular constituents, including L5, L11 and 5S rRNA, which form a pre-ribosomal complex before being incorporated into the mature 60S subunit. (healthcanal.com)
  • A broad-range bacterial PCR targeting rRNA genes (rDNAs) was used to directly analyze 536 clinical samples obtained from 459 hospitalized patients during a 4-year study period. (asm.org)
  • Summary A target-primed in situ rolling circle amplification (in situ RCA) protocol was developed for detection of single-copy genes inside bacterial cells and optimized with Pseudomonas stutzeri, targeting nitrite and nitrous oxide reductase genes (nirS and nosZ). (academicconcepts.net)
  • The 18S rRNA level in activated and resting PBMCs and intestinal lymphocytes was essentially the same, while the levels of β-actin and GAPDH mRNAs fluctuated markedly upon activation. (diva-portal.org)
  • Several studies have found variability in the expression of commonly used housekeeping genes, such as beta-actin (ACTB) and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), under different experimental settings. (lboro.ac.uk)
  • However, ACTB and GAPDH remain widely used in the studies of host gene response to virus infections, including influenza viruses. (lboro.ac.uk)
  • This protein produces a dimethylation of the adenine residue at position 2085 in 23S rRNA, resulting in reduced affinity between ribosomes and macrolide-lincosamide-streptogramin B antibiotics. (uniprot.org)
  • Here we show the genetic interoperability and promiscuity of 16S rRNA in the ribosomes of an extremely thermophilic bacterium, Thermus thermophilus . (nature.com)
  • According to the complexity hypothesis 9 , genes involved in complex biosystems, which are constrained by many interactions (as represented by ribosomes), tend to experience horizontal gene transfer (HGT) less frequently than those coding for products not involved in complex systems. (nature.com)
  • The Thomas team have shown that when there is damage to ribosomes, or potentially when ribosome biogenesis is hyperactivated, the L5/L11/5S rRNA pre-ribosomal complex is redirected from nascent ribosomes to the binding and inhibition of Hdm2, allowing p53 to rise, leading to cell death. (healthcanal.com)
  • Group I introns (specifically subgroup IC1) are common in the nuclear ribosomal RNA genes of fungi. (biomedcentral.com)
  • Here, we describe eight short putative group I introns, ranging in length from 63 to 75 nt, in the rRNA small subunit genes of Phialophora isolates, a fungal genus that ranges from saprobic to pathogenic on plants and animals. (biomedcentral.com)
  • A few hypotheses have been proposed to explain how group I introns became established in the rRNA gene locus. (biomedcentral.com)
  • Establishment of group I introns in the rRNA gene locus appears to have occurred tens to hundreds of millions of years ago, since the introns are found in phylogentically diverse organisms and the sequence diversity is large. (biomedcentral.com)
  • Beginning with a reference OTU tree and a gene content table (i.e., counts of genes for reference OTUs with known gene content), the gene content inference workflow predicts gene content for each OTU with unknown gene content, including predictions of marker gene copy number. (nih.gov)
  • In ten analyzed clarithromycin-resistant clinical isolates of H. pylori obtained in Russia, the resistance was found to be mediated only by mutation A2144G in the 23S rRNA gene. (deepdyve.com)
  • Expression levels of the other housekeeping genes evaluated in this study (including ACTB and GPADH) were highly affected by influenza virus infection and hence are not reliable as reference genes for RNA normalisation. (lboro.ac.uk)
  • The phylogeny of the genus Methanobrevibacter was established almost 25 years ago on the basis of the similarities of the 16S rRNA oligonucleotide catalogs. (biomedcentral.com)
  • A significant relationship was found between the 16S rRNA sequence similarity ( S ) and the extent of DNA hybridization ( D ) for the genus with the correlation coefficient ( r ) for log D and log S , and for [ln(-ln D ) and ln(-ln S )] being 0.73 and 0.796 respectively. (biomedcentral.com)
  • Primary screening of clinical specimens included nested PCR detection of two TPA specific loci (tmpC and polA genes). (muni.cz)
  • The aim of this study was to investigate the occurrence of 16S rRNA methylase genes in E. coli clinical isolates from a teaching hospital in Wenzhou, China. (biomedcentral.com)
  • We developed a diagnostic highly sensitive and specific real-time TaqMan PCR assay for detection of S. tigurinus in clinical samples, based on the 16S rRNA gene. (biomedcentral.com)
  • PCR primers to amplify 16S rRNA genes from cyanobacteria. (asm.org)
  • Universal PCR primers were used to amplify the V1-2 hyper-variable region of bacterial 16S rRNA genes present in DNA samples from I. holocyclus and I. ricinus ticks, collected in Australia and Germany respectively. (biomedcentral.com)
  • Results: PCR was used to amplify several minicircles from Amphidinium carterae so that a homologous set of gene-containing minicircles was available for Amphidinium carterae and Amphidinium operculatum, two apparently closely related peridinin-containing dinoflagellates. (cam.ac.uk)
  • Conclusions: Based on the presented data from cell culture models (HBECs, PTECs, chicken and duck lung cells) infected with a range of influenza viruses, we found that 18S rRNA is the most stable reference gene for normalising qRT-PCR data. (lboro.ac.uk)
  • Instead, WSTF knock down results in a reduced level of acetylated H3-Ac, in particular H3K9-Ac, at the promoter and along the gene. (diva-portal.org)
  • The remodelling at the 45S genes occurs at the promoter, leading higher accessibility to histone acetyltransferases, such as PCAF and p300. (diva-portal.org)
  • I concluded that B-WICH functions in a similar manner on both RNA pol I and RNA pol III genes, remodels chromatin locally at the promoter and around the genes, which allows other factors to bind. (diva-portal.org)
  • However, due to its extremely high expression in most cell types, it can sometimes be challenging to use 18S rRNA as an endogenous normalizer for several gene expression assays in the same reaction. (qiagen.com)
  • Comparison of gull feces-specific assays targeting the 16S rRNA genes of Catellicoccus marimammalium and Streptococcus spp. (semanticscholar.org)
  • The results presented in this work indicate a close functional interaction between NIP7 and FTSJ3 during pre-rRNA processing and show that FTSJ3 participates in ribosome synthesis in human cells. (nih.gov)
  • In our view it seems unlikely it is to simply to limit rRNA synthesis rates and growth. (edu.au)
  • Virus infection of cells leads to a general inhibition of cellular macromolecular synthesis that is referred to as shut-off [ 11 ] and causes changes in global gene expression. (biomedcentral.com)
  • We examined the bacterial composition of chlorinated drinking water using 16S rRNA gene clone libraries derived from RNA and DNA extracted from twelve water samples collected in three different months (June, August, and September of 2007). (epa.gov)
  • DNAs corresponding to 17 vitreous samples from a total of 24, exhibited the expected fragment size of 16S rRNA gene (1500 base pairs), which indicated the presence of bacterial infection. (scielo.br)
  • The task also attempted to find new evidence to explain the relationship between the changing from autotrophic to heterotrophic lifestyle in colorless Cryptomonas lineages and the elevation of evolutionary rates of photosynthetic genes that were located in the plastome 16S rRNA-rbcL fragment. (uni-koeln.de)
  • Mitochondrial rRNA methyltransferase 1 is a protein that in humans is encoded by the MRM1 gene. (wikipedia.org)
  • Functional predictions indicated that gene functions involving biosynthetic metabolism and bacterial secretion systems were significantly different between the MSA and HC. (iospress.com)
  • Here, we determined the biogeographic patterns of the functional dissimilatory sulfite reductase gene ( dsrA ) and the 16S rRNA gene in sulfate‐reducing bacterial communities of US East Coast salt marsh sediments. (darkenergybiosphere.org)
  • Although small, previously we demonstrated that the Pa SSU intron in the rRNA small subunit gene of Phialophora americana isolate Wang 1046 is capable of in vitro splicing using a standard group I intron pathway, thus qualifying it as a functional ribozyme. (biomedcentral.com)
  • Each subunit consists of one or more ribosomal RNA (rRNA) molecules and many ribosomal proteins (RPs or r-proteins). (wikipedia.org)