DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.Genome, Mitochondrial: The genetic complement of MITOCHONDRIA as represented in their DNA.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.National Library of Medicine (U.S.): An agency of the NATIONAL INSTITUTES OF HEALTH concerned with overall planning, promoting, and administering programs pertaining to advancement of medical and related sciences. Major activities of this institute include the collection, dissemination, and exchange of information important to the progress of medicine and health, research in medical informatics and support for medical library development.Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Molecular Sequence Data: Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.DNA Barcoding, Taxonomic: Techniques for standardizing and expediting taxonomic identification or classification of organisms that are based on deciphering the sequence of one or a few regions of DNA known as the "DNA barcode".DNA, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).Winteraceae: A plant family of the order Magnoliales, subclass Magnoliidae, class Magnoliopsida. The wood lacks water-conducting cells but has acrid sap. The leaves are gland-dotted, leathery, and smooth-margined. The flowers are small, in clusters, with two to six sepals, petals in two or more series, several stamens, and one to several carpels.Authorship: The profession of writing. Also the identity of the writer as the creator of a literary production.Cuba: An island in the Greater Antilles in the West Indies, south of Florida. With the adjacent islands it forms the Republic of Cuba. Its capital is Havana. It was discovered by Columbus on his first voyage in 1492 and conquered by Spain in 1511. It has a varied history under Spain, Great Britain, and the United States but has been independent since 1902. The name Cuba is said to be an Indian name of unknown origin but the language that gave the name is extinct, so the etymology is a conjecture. (From Webster's New Geographical Dictionary, 1988, p302 & Room, Brewer's Dictionary of Names, 1992, p132)Pseudotsuga: A plant genus in the family PINACEAE, order Pinales, class Pinopsida, division Coniferophyta. They are coniferous evergreen trees with long, flat, spirally arranged needles that grow directly from the branch.Corbicula: A genus of freshwater clams, in the family Corbiculidae, class BIVALVIA. It originated in Asia but was introduced in North America and is now found throughout the United States.Foraminifera: An order of amoeboid EUKARYOTES characterized by reticulating pseudopods and a complex life cycle with an alternation of generations. Most are less than 1mm in size and found in marine or brackish water.Cape Verde: The republic consists of islands that are located in the mid-Atlantic Ocean about 300 miles off the west coast of Africa. The archipelago includes 10 islands and 5 islets, divided into the windward (Barlavento) and leeward (Sotavento) groups. The capital is Praia.Bivalvia: A class in the phylum MOLLUSCA comprised of mussels; clams; OYSTERS; COCKLES; and SCALLOPS. They are characterized by a bilaterally symmetrical hinged shell and a muscular foot used for burrowing and anchoring.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.DNA Contamination: The presence of DNA from a source foreign to the sample being analysed.Drug Contamination: The presence of organisms, or any foreign material that makes a drug preparation impure.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Equipment Contamination: The presence of an infectious agent on instruments, prostheses, or other inanimate articles.Brassica: A plant genus of the family Cruciferae. It contains many species and cultivars used as food including cabbage, cauliflower, broccoli, Brussel sprouts, kale, collard greens, MUSTARD PLANT; (B. alba, B. junica, and B. nigra), turnips (BRASSICA NAPUS) and rapeseed (BRASSICA RAPA).DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Molecular Biology: A discipline concerned with studying biological phenomena in terms of the chemical and physical interactions of molecules.Electronic Mail: Messages between computer users via COMPUTER COMMUNICATION NETWORKS. This feature duplicates most of the features of paper mail, such as forwarding, multiple copies, and attachments of images and other file types, but with a speed advantage. The term also refers to an individual message sent in this way.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Fungal Proteins: Proteins found in any species of fungus.Genes, Fungal: The functional hereditary units of FUNGI.Ranidae: The family of true frogs of the order Anura. The family occurs worldwide except in Antarctica.Rana catesbeiana: A species of the family Ranidae (true frogs). The only anuran properly referred to by the common name "bullfrog", it is the largest native anuran in North America.Balantidium: A genus of protozoa parasitic in the digestive tract of vertebrate or invertebrate hosts. Asexual multiplication is accomplished by transverse binary fission. Its organisms are ovoidal in shape and have a ciliated covering over the entire body.Balantidiasis: Infection by parasites of the genus BALANTIDIUM. The presence of Balantidium in the LARGE INTESTINE leads to DIARRHEA; DYSENTERY; and occasionally ULCER.Genes, rRNA: 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.N-Terminal Acetyltransferases: Enzymes that catalyze the transfer of an acetyl group, usually from ACETYL COENZYME A, to the N-terminus of a peptide chain.N-Terminal Acetyltransferase E: An N-terminal acetyltransferase subtype that consists of the Naa50p catalytic subunit, and the Naa10p and Naa15p auxiliary subunits. It has specificity for the N-terminal METHIONINE of peptides where the next amino acid in the chain is hydrophobic.Carcinoma, Ehrlich Tumor: A transplantable, poorly differentiated malignant tumor which appeared originally as a spontaneous breast carcinoma in a mouse. It grows in both solid and ascitic forms.Acetyltransferases: Enzymes catalyzing the transfer of an acetyl group, usually from acetyl coenzyme A, to another compound. EC 2.3.1.N-Terminal Acetyltransferase A: An N-terminal acetyltransferase subtype that consists of the Naa10p catalytic subunit and the Naa15p auxiliary subunit. The structure of this enzyme is conserved between lower and higher eukaryotes. It has specificity for N-terminal SERINE; ALANINE; THREONINE; GLYCINE; VALINE; and CYSTINE residues and acts on nascent peptide chains after the removal of the initiator METHIONINE by METHIONYL AMINOPEPTIDASES.Histone Code: The specific patterns of changes made to HISTONES, that are involved in assembly, maintenance, and alteration of chromatin structural states (such as EUCHROMATIN and HETEROCHROMATIN). The changes are made by various HISTONE MODIFICATION PROCESSES that include ACETYLATION; METHYLATION; PHOSPHORYLATION; and UBIQUITINATION.Acetylation: Formation of an acetyl derivative. (Stedman, 25th ed)Arabidopsis: A plant genus of the family BRASSICACEAE that contains ARABIDOPSIS PROTEINS and MADS DOMAIN PROTEINS. The species A. thaliana is used for experiments in classical plant genetics as well as molecular genetic studies in plant physiology, biochemistry, and development.Arabidopsis Proteins: Proteins that originate from plants species belonging to the genus ARABIDOPSIS. The most intensely studied species of Arabidopsis, Arabidopsis thaliana, is commonly used in laboratory experiments.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.Gene Expression Regulation, Plant: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.Genes, Plant: The functional hereditary units of PLANTS.

In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron. (1/10320)

The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron-supplied ribozyme activity and adaptation to the general RNA polymerase II pathway of mRNA expression to allow a protein to be produced from the RNA polymerase I-transcribed rDNA.  (+info)

p53 represses ribosomal gene transcription. (2/10320)

Induction of the tumor suppressor protein p53 restricts cellular proliferation. Since actively growing cells require the ongoing synthesis of ribosomal RNA to sustain cellular biosynthesis, we studied the effect of p53 on ribosomal gene transcription by RNA polymerase I (Pol I). We have measured rDNA transcriptional activity in different cell lines which either lack or overexpress p53 and demonstrate that wild-type but not mutant p53 inhibits cellular pre-rRNA synthesis. Conversely, pre-rRNA levels are elevated both in cells which express mutant p53 and in fibroblasts from p53 knock-out mice. Transient transfection assays with a set of rDNA deletion mutants demonstrate that intergenic spacer sequences are dispensable and the minimal rDNA promoter is sufficient for p53-mediated repression of Pol I transcription. However, in a cell-free transcription system, recombinant p53 does not inhibit rDNA transcription, indicating that p53 does not directly interfere with the basal Pol I transcriptional machinery. Thus, repression of Pol I transcription by p53 may be a consequence of p53-induced growth arrest.  (+info)

A new rapidly growing mycobacterial species, Mycobacterium murale sp. nov., isolated from the indoor walls of a children's day care centre. (3/10320)

Scotochromogenic mycobacterial isolates from water-damaged parts of indoor building materials of a children's day care centre represented a phenetically and genetically distinct group of strains. A 16S rDNA dendrogram (1243 bp) showed that the closest species to the new strain MA112/96T was Mycobacterium abscessus. Phylogenetic and phenetic analyses (100 characteristics) grouped the new isolates with M. abscessus, Mycobacterium vaccae, Mycobacterium aurum and Mycobacterium austroafricanum. Ribotyping with Pvull restriction distinguished the 5 isolates from the other 12 most closely related species by the major bands at 6.5-7 kb and 13-15 kb. The cell morphology of the new isolates was typical of mycobacteria, electron microscopy revealed a triple-layered cell wall with an irregular electron-dense outer layer. They grew at 10-37 degrees C, with no growth at 45 degrees C in 5 d. The gene encoding the secreted 32 kDa protein, specific to mycobacteria, was detected by PCR. The main whole-cell fatty acids were characterized by high tuberculostearic acid 10Me-C18:0 (17% at 28 degrees C), which increased with increasing growth temperature (22% at 37 degrees C). The other main fatty acids were C18:1 cis9 and C16:0 (21-20% each), followed by, C17:1 cis9 (14%), C16:1 cis10 (8%) and also a high amount of C20 alcohol (9%). alpha-Mycolic acids, keto-mycolates and wax esters were present (C60-C90), MK-9(H2) (90%) and MK-8(H2) were the main menaquinones. The cellular phospholipids were phosphatidylethanolamine, phosphatidylinositol, phosphatidyl inositolmannosides and diphosphatidylglycerol. Polyamine content was low. G+C content was 72.9 mol%. The new isolates are proposed as a new species, Mycobacterium murale sp. nov. The type strain is MA112/96T (= DSM 44340T).  (+info)

Treponema brennaborense sp. nov., a novel spirochaete isolated from a dairy cow suffering from digital dermatitis. (4/10320)

A novel Treponema species was isolated from an ulcerative lesion of a cow suffering from digital dermatitis (DD), a disease which causes painful ulcerations along the coronary band. Among other anaerobic bacteria, high numbers of spirochaetes have been regularly found in DD lesions. Here data are presented of a spirochaete isolated from a DD ulcer. By chemotaxonomy, protein analysis and comparative 16S rDNA sequence analysis this isolate was classified as a treponeme that differed from all Treponema species described previously. The only isolate, DD5/3T, for which the name Treponema brennaborense is proposed, is designated the type strain of the novel species. The strain is a small, highly motile spirochaete that has two periplasmic flagella, one flagellum being attached at each cell pole. Strain DD5/3T exhibits alpha-glucosidase and N-acetyl-beta-glucosaminidase activity and growth is inhibited by rabbit serum. T. brennaborense was phylogenetically most closely related (89.5% 16S rRNA similarity) to Treponema maltophilum, an oral spirochaete isolated from a periodontitis patient.  (+info)

RFLP of rRNA genes and sequencing of the 16S-23S rDNA intergenic spacer region of ammonia-oxidizing bacteria: a phylogenetic approach. (5/10320)

It has been established that 16S rRNA gene-based phylogeny gives a low resolution between members of the chemoautotrophic ammonia-oxidizing bacteria (AOB) belonging to the beta-subclass of the Proteobacteria. In this study, 12 isolates of AOB were ribotyped, and the sequences of the 16S-23S rDNA intergenic spacer region (ISR) were determined and used in a phylogenetic study. 16S and 23S rDNA ribotyping revealed that the AOB studied contain only one rrn operon per genome, in contrast to most bacteria, which have 5-10 copies of the rRNA genes per genome. It is likely that the presence of only one set of rRNA genes is related to the slow growth of the AOB. The 16S and 23S rRNA genes of the AOB were shown to be arranged in the classical way: a 16S rRNA gene, an ISR and a 23S rRNA gene. Despite the close phylogenetic relationship among the AOB, the relative location of the rRNA genes in the genome appears to vary considerably. The size of the ISR was approximately 400 bp in the Nitrosomonas isolates and 645-694 bp in the Nitrosospira isolates, suggesting a species-specific size difference in the ISR. The ISR contained two potential tRNA genes in the 5' end in all isolates studied. The similarity values between the ISR sequences of the AOB are low (42.9-96.2%) compared with the 16S rDNA sequence similarity values, and therefore the ISR sequences are valuable as a complementary phylogenetic tool in combination with 16S rRNA gene sequences. The phylogenetic analysis of the AOB based on ISR sequences confirms the 16S rRNA gene-based phylogeny but has the benefit of giving a higher resolution.  (+info)

New genus-specific primers for the PCR identification of members of the genera Pseudonocardia and Saccharopolyspora. (6/10320)

Members of the family Pseudonocardiaceae are difficult to identify on the basis of their micromorphology only. The biochemical characterization of each new isolate is a painstaking and time-consuming task which cannot always be undertaken when handling large numbers of strains as is the case in natural product screening programmes. In this study, two sets of genus-specific oligonucleotides were designed which allow rapid detection of members of the genera Pseudonocardia and Saccharopolyspora by means of PCR-specific amplification. The genus specificity of these primers was validated on a wide range of collection strains and the primers were subsequently used to study a group of 106 wild-type isolates that possessed morphological characteristics of the family. Out of this group, 51 strains could be identified as members of the genus Pseudonocardia and only nine isolates could be assigned to the genus Saccharopolyspora. The diversity indicated by whole-cell fatty acid profiles of both wild-type and reference strains was compared with that identified using the oligonucleotide primers. The partial 16S rDNA sequencing of representative wild-type strains was used to validate their genus assignment by PCR-specific amplification. This study shows the industrial usefulness of the application of these direct identification tools as well as the complementary use of two sources of data, PCR-specific amplification results and fatty acid composition, to assess the diversity of a microbial population.  (+info)

Reclassification of Brevibacterium oxydans (Chatelain and Second 1966) as Microbacterium oxydans comb. nov. (7/10320)

Phylogenetic and chemotaxonomic analyses indicate that Brevibacterium oxydans is closely related to species of the genus Microbacterium, namely Microbacterium liquefaciens, Microbacterium luteolum and Microbacterium saperdae. DNA-DNA reassociation values of less than 60% between Brevibacterium oxydans and these three Microbacterium species support the distinctness of this misclassified Brevibacterium species, which is reclassified as Microbacterium oxydans comb. nov.  (+info)

Reclassification of Brevibacterium incertum (Breed 1953) as Desemzia incerta gen. nov., comb. nov. (8/10320)

Phylogenetic analysis of 16S rDNA indicates that Brevibacterium incertum is not a member of the genus Brevibacterium but related to species of the genus Carnobacterium. Hence, Brevibacterium incertum is not a member of the class Actinobacteria but belongs to the phylogenetically defined broad Bacillus-Lactobacillus cluster. Based upon properties that taxonomically clearly distinguishes Brevibacterium incertum from species of the phylogenetic sister genus Carnobacterium, Brevibacterium incertum is reclassified as Desemzia incerta gen. nov., comb. nov.  (+info)

Background Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. Methodology/Principal Findings A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These
Chronic wounds affect millions of people and cost billions of dollars in the United States each year. These wounds harbor polymicrobial biofilm communities, which can be difficult to elucidate using culturing methods. Clinical molecular microbiological methods are increasingly being employed to investigate the microbiota of chronic infections, including wounds, as part of standard patient care. However, molecular testing is more sensitive than culturing, which results in markedly different results being reported to clinicians. This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing), and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. Parallel samples from 51 chronic wounds were studied using aerobic culturing and 16S DNA sequencing for the identification of bacteria. One hundred
Strain D-14T, a brown-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from oil-contaminated soil. It was able to grow at 20-40 °C, at pH 6.0-10.0 and at 0-1 % (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain D-14T belonged to the genus Lysobacter and was closely related to Lysobacter caeni BUT-8T (99.0 % sequence similarity), Lysobacter ruishenii CTN-1T (98.5 %), Lysobacter daejeonensis GH1-9T (98.2 %) and Lysobacter panacisoli CJ29T (97.2 %). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl-N-methyl-ethanolamine. The predominant fatty acids of strain D-14T were iso-C15 : 0, iso-C16 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C14 : 0, C11 : 0iso 3-OH, C15 : 1iso F and C16 : 0. The genomic DNA G+C content of this novel strain
The nuclear ribosomal repeats for the 18S, 5.8S, and 26S RNAs of two closely related Picea (spruce) species were characterized by restriction mapping and Southern blot hybridization. Restriction polymorphisms were identified in the IGS and ITS sequences; however, no polymorphism was species specific. As many as five different rDNA repeat units were observed in individual genomes. The repeat size for these gymnosperms ranged from a minimum of 32 kbp to greater than 40 kbp, two- to threefold larger than the typical angiosperm rDNA unit. Slot-blot hybridizations were used to determine the nuclear rDNA copy concentration. Among P. rubens individuals threefold variation was observed in the rDNA copy concentration, and among P. mariana individuals such variation was as much as sixfold. At a size greater than 32 kbp and at a concentration averaging 1.2-1.3 x 10(4) copies/pg, the rDNA constitutes approximately 4% of the total genome. Regression analysis revealed a significant relationship between copy
Vol 63: Ribosomal DNA Sequence Heterogeneity Reflects Intraspecies Phylogenies and Predicts Genome Structure in Two Contrasting Yeast Species.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Vol 13: Molecular identification of clinical difficult-to-identify microbes from sequencing 16S ribosomal DNA and internal transcribed spacer 2.. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Ben Hanelt, D. Van Schyndel, C. M. Adema, L. A. Lewis, E. S. Loker. The Phylogenetic Position of Rhopaluva ophiocomae (Orthonectida) Based on 18s Ribosomal DNA Sequence Analysis. -Molecular Biology and Evolution, 1996,. 13 (9), lk 1187-1191. Veebiversioon. ...
Learn about Exubera (Insulin Human [rDNA origin]) may treat, uses, dosage, side effects, drug interactions, warnings, patient labeling, reviews, and related medications.
Aime, M. C., P. B. Matheny, D. A. Henk, E. M. Frieders, R. H. Nilsson, M. Piepenbring, D. J. McLaughlin, L. J. Szabo, D. Begerow, J. P. Sampaio, R. Bauer, M. Wei , F. Oberwinkler, and D. S. Hibbett. 2006. An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98: 896 905.. Bauer, R., D. Begerow, J. Sampaio, M. Weiβ, F. Oberwinkler. 2006. The simple-septate basidiomycetes: a synopsis. Mycological Progress 5: 41 66.. Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. E. Eriksson, S. Huhndorf, T. James, P. M. Kirk, R. L cking, T. Lumbsch, F. Lutzoni, P. B. Matheny, D. J. Mclaughlin, M. J. Powell, S. Redhead, C. L. Schoch, J. W. Spatafora, J. A. Stalpers, R. Vilgalys, M. C. Aime, A. Aptroot, R. Bauer, D. Begerow, G. L. Benny, L. A. Castlebury, P. W. Crous, Y.-C. Dai, W. Gams, D. M. Geiser, G. W. Griffith, C. Gueidan, D. L. Hawksworth, G. Hestmark, K. Hosaka, R. A. Humber, K. ...
Strange looking elevated amplification plots from ChIP-qPCR samples - posted in PCR, RT-PCR and Real-Time PCR: Hi everyone, I am hoping that you all can help as I am not an expert in qPCR. I performed a ChIP experiment to assess binding to human ribosomal gene repeats. I used primers that have been published in multiple papers and a positive ChIP control: UBF. I have attached the strange amplification plots that I get when doing a standard curve using a dilution series of 1:10 of...
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 ...
Addgene NGS Result TTAATGATTAACCCGCCATGCTACTTATCTACGTAGCCATGCTCTAGGAAGATCCAACATATCCTGGTGT GGAGTAGGGGACGCTGCTCTGACAGAGGCTCGGGGGCCTGAGCTGGCTCTGTGAGCTGGGGAGGAGGCAG ACAGCCAGGCCTTTGTCTGCAAGCAGACCTGGCAGCATTGGGCTGGCCGCCCCCCAGGGCCTCCTCTTCA TGCCCAGTGAATGACTCACCTTGGCACAGACACAATGTTCGGGGTGGGCACAGTGCCTGCTTCCCGCCGC ACCCCAGCCCCCCTCAAATGCCTTCCGAGAAGCCCATTGAGCAGGGGGCTTGCATTGCACCCCAGCCTGA CAGCCTGGCATCTTGGGATAAAAGCAGCACAGCCCCCTAGGGGCTGCCCTTGCTGTGTGGCGCCACCGGC GGTGGAGAACAAGGCTCTATTCAGCCTGTGCCCAGGAAAGGGGATCAGGGGATGCCCAGGCATGGACAGT GGGTGGCAGGGGGGGAGAGGAGGGCTGTCTGCTTCCCAGAAGTCCAAGGACACAAATGGGTGAGGGGAGA GCTCTCCCCATAGCTGGGCTGCGGCCCAACCCCACCCCCTCAGGCTATGCCAGGGGGTGTTGCCAGGGGC ACCCGGGCATCGCCAGTCTAGCCCACTCCTTCATAAAGCCCTCGCATCCCAGGAGCGAGCAGAGCCAGAG CAGGTTGGAGAGGAGACGCATCACCTCCGCTGCTCGCGGGGATCCCGCCACCATGGAGACAGACACACTC CTGCTATGGGTACTGCTGCTCTGGGTTCCAGGTTCCACTGGTGACAGATCTGCCGCAGGCAGCACGCTGG ACAAAATCGCCAAAAACGGTGTGATTGTCGTCGGTCACCGTGAATCTTCAGTGCCTTTCTCTTATTACGA ...
Abstract: 对大连某城市污水处理厂活性污泥进行长期驯化,筛选得到好氧条件下以对氨基苯磺酸(4-aminobenzenesulphonate,4-ABS)为唯一碳源和能源生长的高效降解菌株W1.根据菌株W1的形态特征、生理生化特征及16S rDNA序列分析,初步鉴定为Pannonibacter菌属.通过考察生长条件对降解效果的影响,确定了该菌株降解4-ABS的优化条件为:接种量10%、 30℃、 pH 7、摇床转速150 r/min,并且在有外加碳源的情况下仍保持较高的4-ABS降解活性.在4-ABS的降解过程中,4-ABS自身含有的氨基和磺酸基会以NH+4和SO2-4的形式释放到水体中,但浓度仅为理论释放量的77.6%和91.5%,推测原因是部分释放的NH+4和SO2-4被菌株W1作为氮源和硫源利用;菌株W1可以耐受2 500 mg/L的4-ABS,且在32 ...
هدف: نگرانی از وجود آفلاتوکسین در مواد غذایی و خطراتی که این سم برای سلامت انسان و حیوانات دارد، باعث پیدایش راه‌های مختلف حذف یا کاهش این سم شده است؛ از جمله این روش‌ها، کنترل زیستی قارچ توسط ریززنده‌های دیگر است. در این تحقیق از باکتری باسیلوس آمیلولیکوفاسینس جدا شده از خاک باغ پسته از باغات شهرستان دامغان به‌عنوان عامل کنترل زیستی برای مهار رشد و تولید آفلاتوکسین قارچ آسپرژیلوس پارازیتیکوس استاندارد NRRL2999 استفاده شد. مواد و روش‌ها: پس از 72 ساعت کشت باکتری در دمای 30 درجه سانتی‌گراد، مایع‌رویی آن به‌عنوان منبع ترکیبات ضد قارچی جداسازی شد. غلظت‌های
A polyphasic study was carried out to clarify the taxonomic position of two Gram-positive bacteria isolated from soil samples of the Grotta dei Cervi (Italy), a relatively unexplored hypogean environment. The strains, 20-5T and 23-23T, showed phenotypic and phylogenetic characteristics that were consistent with their classification in the genus Agromyces. 16S rRNA gene sequence comparisons revealed that the two strains formed distinct phyletic lines within the genus Agromyces. Based on 16S rRNA gene sequence similarity, chemotaxonomic data and the results of DNA-DNA relatedness studies, it is proposed that the two isolates represent two novel species of the genus Agromyces. Pronounced differences in a broad range of phenotypic characteristics and DNA G+C content distinguished the two strains from each other and from previously described species of the genus Agromyces. Two novel species are proposed: Agromyces salentinus sp. nov. (type strain, 20-5T=HKI 0320T=DSM 16198T=NCIMB 13990T) and Agromyces
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 (
A Gram-stain-positive, aerobic, non-motile, rod-shaped bacterium, strain 0704C9-2T, was isolated from hydrothermal sediment of the Indian Ocean. The organism grew with 0-5 % (w/v) NaCl and at 10-37 °C, with optimal growth occurring with 1 % NaCl and at 28-30 °C. Comparative 16S rRNA gene sequence analysis revealed that strain 0704C9-2T belonged to the genus Microbacterium . It exhibited highest 16S rRNA gene sequence similarity with Microbacterium testaceum DSM 20166T (98.4 %). Levels of similarity with the type strains of all other recognized species of the genus Microbacterium were less than 98.0 %. DNA-DNA hybridization experiments with strain 0704C9-2T and its closest relative, M. testaceum DSM 20166T, revealed a low reassociation value of 42.9 %. The DNA G+C content of strain 0704C9-2T was 73.3 mol%. The cell-wall peptidoglycan contained ornithine and the acyl type was glycolyl. The major whole-cell sugars were mannose, galactose, rhamnose and glucose. The major cellular fatty acids were
A bacterial strain, B5-2(T), was isolated from an ice core drilled from Muztagh Glacier, China. Strain B5-2(T) was a Gram-stainnegative, short rod-shaped, motile by polar flagella, aerobic bacterium. The major fatty acids of strain B5-2(T) were summed feature 8 (C-18 : 1 omega 7c and/ or C-18 : 1 omega 6c) and iso-C-13 : 0. The G+C content of the DNA from strain B5-2(T) was 69.3 mol%. The predominant isoprenoid quinone of strain B5-2(T) was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, an unidentified phospholipid and sulfoquinovosyldiacylglycerol. Comparative 16S rRNA gene sequence analysis revealed that the novel strain B5-2(T) shared highest similarity (96.7 %) with Aureimonas altamirensis S21B(T). On the basis of the results of this polyphasic study, strain B5-2(T) represents a novel species of the genus Aureimonas, for which the name Aureimonas glaciei sp. nov. is ...
The identification of mycobacteria can be a complicated, expensive, and difficult process; many laboratories are now referring uncommon organisms to laboratories that have the capability of using additional technology. Nucleic acid probes have offered laboratories the ability to rapidly and accurately identify four of the most common mycobacterial species, and they have rarely misidentified an organism (3).. A more important issue is the inaccuracy of phenotypic methods in providing a reliable and timely identification of the other mycobacteria (14). Nucleic acid sequencing of 16S rDNA has been investigated as a definitive method for the identification of many microorganisms, including mycobacteria (3, 5, 8, 11, 12, 16-18, 23), and its use is becoming more extensive. Most of the studies used a small number of organisms for evaluation or included only common species and/or the type species from culture collections.. We sought to determine whether 16S rDNA sequencing with a commercially available ...
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;
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 ...
Bacillus tusciae Bonjour & Aragno 1994 is a hydrogen-oxidizing, thermoacidophilic spore former that lives as a facultative chemolithoautotroph in solfataras. Although 16S rRNA gene sequencing was well established at the time of the initial description of the organism, 16S sequence data were not available and the strain was placed into the genus Bacillus based on limited chemotaxonomic information. Despite the now obvious misplacement of strain T2(T) as a member of the genus Bacillus in 16S rRNA-based phylogenetic trees, the misclassification remained uncorrected for many years, which was likely due to the extremely difficult, analysis-hampering cultivation conditions and poor growth rate of the strain. Here we provide a taxonomic re-evaluation of strain T2(T) (= DSM 2912 = NBRC 15312) and propose its reclassification as the type strain of a new species, Kyrpidia tusciae, and the type species of the new genus Kyrpidia, which is a sister-group of Alicyclobacillus. The family Alicyclobacillaceae da ...
18-26S rDNA loci were mapped on chromosomes in four species of Paris, and the number and position of rDNA sites in these species were compared for analysis of the distribution of the sites. All the plants were diploids, and the genome consisted of five chromosomes, A, B, C, D and E. (1) P. polyphylla var. yunnanensis, 2n = 10 = 6m + 4t. Two 18-26S rDNA loci were detected on the short arms of C and D chromosomes; (2) P. forrestii, 2n = 10 = 6m + 4t. One locus was detected on the long arm of B chromosome, and also two loci on the short arms of C and D chromosomes; (3) P. axialis. 2n = 10 = 6m(2sat) + 4t(2sat) + 1 - 2B. Two loci were detected on the short arms of C and D chromosomes. One locus was detected in the cell with two B-chromosomes (B), but none was detected in that with only one B chromosome, indicating that rRNA gene existed on B chromsome, and an unequal division occurred during mitotic cycle of B-chromosomes. (4) P. daliensis, 2n = 10 = 4m + 2sm + 2st + 2t. One locus was detected on ...
Background: In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement) or, less commonly, linked to 35 S rDNA units (L-type). The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results: We found that homogenization of L-type units went to completion in most (4/6) but not all species. Two species contained major L-type and minor S-type units (termed L-s-type). The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, ...
We isolated Saccharomyces cerevisiae yeast strains that are able to carry out the second fermentation of sparkling wine from spontaneously fermenting musts in El Penedès (Spain) by specifically designed selection protocols. All of them (26 strains) showed one of two very similar mitochondrial DNA (mtDNA) restriction patterns, whereas their karyotypes differed. These strains showed high rates of karyotype instability, which were dependent on both the medium and the strain, during vegetative growth. In all cases, the mtDNA restriction pattern was conserved in strains kept under the same conditions. Analysis of different repetitive sequences in their genomes suggested that ribosomal DNA repeats play an important role in the changes in size observed in chromosome XII, whereas SUC genes or Ty elements did not show amplification or transposition processes that could be related to rearrangements of the chromosomes showing these sequences. Karyotype changes also occurred in monosporidic diploid ...
Green algae (Chlorophyta) are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences (nuclear gene) as well as rbcL sequences (chloroplast, protein-coding gene). Phylogeny obtained from the sequence data can be subsequently used as a starting point for further research: well supported clades can be examined for defining traits. Like other coccoid genera, Bracteacoccus has very simple morphology and therefore few characters to be scored. Transmission electron microscopy may provide one or several taxonomically useful ...
Green algae (Chlorophyta) are a morphologically heterogeneous group that is undergoing considerable revisions at present. Especially in coccoid genera, there have been striking cases of polyphyly, when species originally placed in one genus were shown to belong to up to three different classes. The coccoid chlorophycean genus Bracteacoccus Tereg was until recently considered monophyletic, but with the advent of new molecular data, it no longer appears as such. The goal of my project is to monograph the genus Bracteacoccus. I collect 18S ribosomal DNA sequences (nuclear gene) as well as rbcL sequences (chloroplast, protein-coding gene). Phylogeny obtained from the sequence data can be subsequently used as a starting point for further research: well supported clades can be examined for defining traits. Like other coccoid genera, Bracteacoccus has very simple morphology and therefore few characters to be scored. Transmission electron microscopy may provide one or several taxonomically useful ...
Changes in the structure and composition of a protistan community were characterized through the analysis of small-subunit ribosomal RNA gene (18S) sequences for a 3-day bottle incubation using a single sample collected in the western North Atlantic. Cloning and sequencing was used to investigate changes in perceived species richness and diversity as a consequence of environmental perturbation. The treatments included a control (unamended seawater), inorganic nutrient enrichment, and enrichment with a complex organic mixture. Five clone libraries were constructed and analyzed at the time of collection (t-0 h) and after 24 (t-24 h) and 72 (t-72 h) h for the control, and at t-72 h for the inorganic and organic enrichments, resulting in an analysis of 1,626 partial 18S rDNA sequences that clustered into 238 operational taxonomic units (OTUs). Analysis of the clone libraries revealed that protistan assemblages were highly dynamic and changed substantially at both the OTU level and higher taxonomic ...
The higher proliferation rate of cancer cells requires an increased rate of protein synthesis. Thus, cancer cells often show increased rates of ribosomal DNA (rDNA) transcription and have more ribosomes and larger nucleoli, which are nuclear structures that function in ribosome biogenesis. Neumüller et al. identified genes in yeast that, when ablated, resulted in smaller or larger nucleoli. A similar analysis in Drosophila enabled the identification of evolutionarily conserved molecular complexes that increase or decrease nucleolar size when the complex constituents were targeted by RNA interference. Understanding how cells regulate rDNA transcription could provide new therapeutic avenues for interfering with the unrestricted growth that occurs in cancer.. ...
Under the intluence of 5-tluoro-uridine, the ultrastructure of the rDNA transcription units in Xenopus oocytes is altered. Whereas part of the matrix units maintains anormal aspect or shows various degrees of inhibition, in a strong proportion of the transcription units the alternating pattern of matrix units and fibril-free spacer regions is no longer recognized. Transcriptional complexes are found along the entire DNP axis, including the regions of the spacers. These observations support biochemical data on transcription in rDNA spacer region ...
H1S186ph. H1.4 serine 186 (reported as H1S187) phosphorylation is preferentially associated with active rDNA promoters and enriched at hormone response element (PMID: 20439994). ...
A Gram-negative bacterium, designated TF5-37.2-LB10T, was isolated from subsurface water of the Toarcian geological layer of Tournemire, France. Cells were non-motile straight rods that formed cream to light pink colonies on 10-fold diluted LB agar. Strain TF5-37.2-LB10T contained menaquinone 7 and its major fatty acids were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C ...
Sulfitobacter sp. ATCC ® BAA-1142D™ Designation: Genomic DNA from EE-36 TypeStrain=False Application: Genome sequencing strain
Thermobaculum terrenum ATCC ® BAA-798D-5™ Designation: Genomic DNA from Thermobaculum terrenum strain YNP1 (ATCC ® BAA-798™) TypeStrain=False Application:
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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 ...
A Gram-stain-positive, aerobic, non-spore-forming, atrichous and short rod-shaped endophytic actinomycete, designated strain BGMRC 2075 , was isolated from the leaves of Kandelia candel, and was subjected to polyphasic characterization to unravel its taxonomic position. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain BGMRC 2075 belongs to the genus Nocardioides ,showing the highest 16S rRNA gene sequence similarity to Nocardioides aestuarii JC2056 (96.1 %), Nocardioides agariphilus MSL-28 (95.1 %) andNocardioides islandiensis MSL-26 (95.1 %). The predominant cellular fatty acids of strain BGMRC 2075 were iso-C16 : 0, C17 : 1ω8c and C17 : 0. The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were composed of ribose and glucose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylcholine, ...
Strains VIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were isolated from marine sediments collected from the Xisha Islands in the South China Sea. All three isolates were able to grow optimally at pH 7.0, 28-37 degrees C and 0-3% (w/v) NaCl. Comparison of 16S rRNA gene sequences showed that these strains are members of the genus Streptomyces, exhibiting moderately high 16S rRNA gene sequence similarities of 97.0-98.8% to members of the most closely related Streptomyces species. Morphological characteristics, physiological characteristics and compositions of whole-cell sugars and phospholipids are consistent with the diagnostic characteristics of the genus Streptomyces, but still allowed differentiation amongst the three strains and their neighbours. Based on 16S rRNA gene sequence analysis, DNA DNA relatedness, phenotypic characteristics and chemotaxonomic data, strains VIM M 10366(T), VIM M 10378(T) and VIM M 10400(T) were identified as members of three novel species of the genus ...
A Gram-staining-positive, cocci, halotolerant bacterial strain, designated as SV-16T, was isolated from marine sediment and subjected to a polyphasic taxonomic study. The strain exhibited phenotypic properties that included chemotaxonomic characteristics consistent with its classification in the genus Salinicoccus. Growth occurs at temperatures in the range between 25-37 °C (optimum 30 °C), pH 7.0-11.0 (optimum 8.0) and at NaCl concentrations up to 25 .0 % (optimum 15.0 %). The highest level of 16S rRNA gene sequence similarity was with Salinicoccus carnicancri CrmT (98.6 %) followed by Salinicoccus halodurans W24T (96.6 %). The predominant polar lipids are diphosphatidylglycerol (DPG), phosphatidylinositol (PI) and phosphatidylglycerol (PG). The major cellular fatty acids are iso-C15: 0, anteiso-C15: 0, iso-C17: 0 and anteiso C17: 0. The draft genome of strain SV-16T consisted of 2,591,284 bp with G+C content of 48.7 mol %. On the basis of the phenotypic characteristics and genotypic ...
INTRODUCTION. The genus Bacillus is a phenotypically large, diverse collection of Gram-positive or Gram-variable staining, endospore-forming, aerobic or facultatively anaerobic, rod-shaped bacteria that have undergone considerable reclassification as advances in molecular biology have revealed a high phylogenetic heterogeneity (5, 21). The genus Bacillus and related genera are distributed widely in nature and include thermophilic, psychrophilic, acidophilic, alkalophilic and halophilic bacteria that utilize a wide range of carbon sources for heterotrophic growth or grow autotrophically.. The investigations on phylogenetic divergence of the genus Bacillus and its mesophilic and thermophilic members indicated the need for further and extensive studies to place some of these bacilli in appropriate taxonomic levels (1, 23, 21). With the accumulation of further 16S rRNA gene sequence data, Bacillus has been divided into more manageable and better-defined groups (16). According to Ludwig et al. (2007) ...
In Egypt, four species of Tilapia have been described based on morphometric, meristic and cytotaxonomical characteristics. These species are Tilapia zillii, Oreochromis niloticus, Oreochromis aureus and Sarotherodon galilaeus. The accurate identification of these fishes is complicated by the high variation in these characters,similarity among species and in some cases by the size of the fish. In this paper, we examined the use of polymerase chain reaction (PCR)and restriction fragment length polymorphisms (RFLPs) analysis of the nuclear small subunit ribosomal RNA gene (srDNA) for molecular identification of Tilapia spp. in Egypt. The present study aims to evaluate such advanced molecular biological approach for identification of Tilapia spp. Genomic DNA was extracted from the four species of Tilapia. About 2000 bp 18S ribosomal DNA was amplified by PCR using specific primers. The technique of restriction fragment length polymorphisms was used to identify the specific 18S rDNA for each species. O.
article{7225551, abstract = {A Gram-stain-positive, ovoid, lactic acid bacterium, strain LMG 27676(T), was isolated from a spoiled sous-vide-cooked rutabaga. 16S rRNA gene sequence analysis indicated that the novel strain belongs to the genus Leuconostoc, with Leuconostoc kimchii and Leuconostoc miyukkimchii as the nearest neighbours (99.1 and 98.8\% 16S rRNA gene sequence similarity towards the type strain, respectively). Phylogenetic analysis of the 16S rRNA gene, multilocus sequence analysis of the pheS, rpoA and atpA genes, and biochemical and genotypic characteristics allowed differentiation of strain LMG 27676(T) from all established species of the genus Leuconostoc. Strain LMG 27676(T) (=R-50029(T)=MHB 277(T)=DSM 27776(T)) therefore represents the type strain of a novel species, for which the name Leuconostoc rapi sp. nov. is proposed.}, author = {Lyhs, Ulrike and Snauwaert, Isabel and Pihlajaviita, Seija and De Vuyst, Luc and Vandamme, Peter}, issn = {1466-5026}, journal = {INTERNATIONAL ...
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
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Replication follows the DNA strand displacement model. DNA templated transcription, with some alternative splicing mechanism is ... Translation takes place by ribosomal shunting. The virus exits the host cell by nuclear envelope breakdown, viroporins, and ... Intermediate genes activate replication of the DNA genome by DNA strand displacement in the nucleus. Expression of L4-22K and ...
... assessed by nuclear ribosomal DNA sequences (ITS)". Plant Systematics and Evolution. 262 (1-2): 1-12. doi:10.1007/s00606-006- ...
... spans about 90 million base pairs (the building material of DNA) and represents just under 3% of the total DNA in ... RPS15A: encoding protein 40S ribosomal protein S15a. *RSL1D1: encoding protein Ribosomal L1 domain-containing protein 1 ...
Crampton, A.; McKay, I.; Barker, S. C. (May 1996). "Phylogeny of ticks (Ixodida) inferred from nuclear ribosomal DNA". ...
Dracunculus (Asteraceae) based on ribosomal and chloroplast DNA sequences". Taxon. 60 (3): 691-704. doi:10.1002/tax.603006.. ... Chloroplast and ribosomal DNA sequence analysis in 2011 supported monophyly with two clades, one of which includes some North ... For example, in 2011 using ribosomal DNA analysis of their own and a review of molecular data (such as ITS sequence analysis) ... of nuclear ribosomal DNA". American Journal of Botany. 85 (12): 1787-95. doi:10.2307/2446513. JSTOR 2446513. PMID 21680339.. ...
Phylogeny of GFAJ-1 based on ribosomal DNA sequences.[12] Molecular analysis based on 16S rRNA sequences shows GFAJ-1 to be ... Arsenate esters, such as those that would be present in DNA, are generally expected to be orders of magnitude less stable to ... Subsequent independent studies published in 2012 found no detectable arsenate in the DNA of GFAJ-1, refuted the claim, and ... DNA. He believes that it is more likely that arsenic is being sequestered elsewhere in the cells.[2][10] University of British ...
1997). "A cladistic analysis of mitochondrial ribosomal DNA from the Bovidae". Molecular Phylogenetics and Evolution. 7 (3): ... 2003). "Phylogenetic relationships of Chinese antelopes (subfamily Antilopinae) based on mitochondrial ribosomal RNA gene ...
... using a small-subunit ribosomal DNA". Canadian Journal of Zoology. 75 (12): 2112-2119. doi:10.1139/z97-846. CS1 maint: Multiple ...
Colgan, D. J.; Flannery, T. F. (1995). "A Phylogeny of Indo-West Pacific Megachiroptera Based on Ribosomal DNA". Systematic ... Internal relationships of African Pteropodidae based on combined evidence of mitochondrial and nuclear DNA.[24] ... A 2011 DNA study concluded that not all of these subfamilies were clades, or consisting of all the descendants of a common ... A 2016 DNA study focused only on African pteropodids (Harpyionycterinae, Rousettinae, and Epomophorinae) also challenged the ...
"Ribosomal DNA in diploid and polyploid Setaria (Poaceae) species: number and distribution". Comp Cytogenet. 9 (4): 645-60. doi: ... Mahendran B, Ghosh SK, Kundu SC (2006). "Molecular phylogeny of silk-producing insects based on 16S ribosomal RNA and ... Wang W, Lan H (2000). "Rapid and parallel chromosomal number reductions in muntjac deer inferred from mitochondrial DNA ... "DNA rearrangements directed by non-coding RNAs in ciliates". Wiley Interdiscip Rev RNA. 1 (3): 376-87. doi:10.1002/wrna.34 ...
... based on ribosomal DNA". BMC Evolutionary Biology. 13: 166. doi:10.1186/1471-2148-13-166. PMC 3751017. PMID 23927069.. ... According to the molecular work on the nuclear DNA and mitochondrial DNA, the lesser kudu and the nyala are the basal most ... based on ribosomal DNA". Journal of Mammalogy. 73 (2): 262-275. doi:10.2307/1382056. JSTOR 1382056.. ... Willows-Munro, S.; Robinson, T.J.; Matthee, C.A. (2005). "Utility of nuclear DNA intron markers at lower taxonomic levels: ...
Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. „Science". 267 (5204), s. 1641-1643, 1995. DOI: ... Evidence from 18S ribosomal DNA that the lophophorates are protostome animals. „Science". 267 (5204), s. 1641-1643, 1995. DOI: ... Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes. „Proceedings of the ...
... inferred from ribosomal DNA restriction maps". Zoological Research. 17: 89-93.. *. Wiens, Frank (2002). Behavior and ecology of ... In 2006, the Bornean slow loris was elevated to the species level (as Nycticebus menagensis) based on molecular analysis of DNA ... and DNA sequences[49] were focused on understanding the relationships between a few species, not the phylogeny of the entire ... an approach using mitochondrial DNA restriction enzyme analysis". International Journal of Primatology. 14 (1): 167-175. doi: ...
... based on ribosomal DNA sequences and morphology" (PDF). American Journal of Botany. 87 (9): 1342-1357. Retrieved 2018-04-22.. ...
"Molecular Systematics and Biogeographical History of Pit Vipers as Determined by Mitochondrial Ribosomal DNA Sequences". Copeia ... Note: the authors of the DNA sequence study of Equus (Amerhippus) use "E. caballus" as an alternative specific name for "E. ... Orlando, L.; Male, D.; Alberdi, M. T.; Prado, J. L.; Prieto, A.; Cooper, A.; Hänni, C. (2008). "Ancient DNA Clarifies the ... Mitochondrial DNA obtained from Macrauchenia corroborates this and gives an estimated divergence date of 66 Ma ago.[14] ...
"Phylogenetic Studies in the Commelinaceae Subfamily Commelinoideae Inferred from Nuclear Ribosomal and Chloroplast DNA ... et al. (2011).[8] The following is a phylogeny, or evolutionary tree, of most of the genera in Commelinaceae based on DNA ...
"Primers, 16S ribosomal DNA - François Lutzoni's Lab". lutzonilab.net. Arquivado dende o orixinal o 2012-12-27.. ... The Ribosomal Database Project[editar , editar a fonte]. The Ribosomal Database Project (RDP) é unha base de datos revisados ... Kolbert CP, Persing DH (June 1999). "Ribosomal DNA sequencing as a tool for identification of bacterial pathogens". Current ... "16S ribosomal DNA amplification for phylogenetic study". Journal of Bacteriology 173 (2): 697-703. PMC 207061. PMID 1987160. ...
... based on nuclear ribosomal DNA ITS sequences" (PDF). Aliso. 22: 372-395. Retrieved 13 October 2015.. ... ramosum as assessed by random amplified polymorphic DNA (RAPD). Retrieved 14 October 2015.. in Zeder et al (2006, Chapter 10. ... "Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and ...
Gonzalo Giribet & Carles Ribera (June 2000). "A review of arthropod phylogeny: new data based on ribosomal DNA sequences and ... The molecular data consists of comparisons of nuclear ribosomal RNA genes, mitochondrial ribosomal RNA genes, and protein ... and ribosomal DNA data Oakley et al. obtained support for three pancrustacean clades: Oligostraca (Ostracoda, Mystacocarida, ...
A Phylogeny of Cockroaches and Related Insects Based on DNA Sequence of Mitochondrial Ribosomal RNA genes. Proceedings of the ...
"Evaluating Hypotheses of Deuterostome Phylogeny and Chordate Evolution with New LSU and SSU Ribosomal DNA Data". Molecular ... 2002). "Complete Mitochondrial DNA of the Hagfish, Eptatretus burgeri: The Comparative Analysis of Mitochondrial DNA Sequences ... Some chordate lineages may only be found by DNA analysis, when there is no physical trace of any chordate-like structures.[29] ... There is still much ongoing differential (DNA sequence based) comparison research that is trying to separate out the simplest ...
Won H, Renner SS: The internal transcribed spacer of nuclear ribosomal DNA in the gymnosperm Gnetum. Molecular Phylogenetics ...
... based on chloroplast rbcL and nuclear 18S ribosomal DNA Sequences". American Journal of Botany. 90 (1): 123-130. doi:10.3732/ ... by analyzing combined nuclear and chloroplast DNA sequences, indicated that Dionaea and Aldrovanda were closely related and ...
Dna templated transcription, specifically dsdna(rt) transcription, with some alternative splicing mechanism is the method of ... Translation takes place by ribosomal shunting. The virus exits the host cell by budding, and nuclear pore export. Birds serve ...
... by analysis of their ribosomal and mitochondrial DNA". Annals of tropical medicine and parasitology. 101 (7): 621-641. doi: ... Bargues M. D., Artigas P., Khoubbane M. & Mas-Coma S. (2011). "DNA sequence characterisation and phylogeography of Lymnaea ...
1 DNA-Viren *1.1 Doppelsträngige DNA-Viren (dsDNA: double stranded DNA). *1.2 Einzelsträngige DNA-Viren (ssDNA: single stranded ... Orsay virus utilizes ribosomal frameshifting to express a novel protein that is incorporated into virions, in: Virology 450-451 ... Viren mit DNA-Genom bilden keine taxonomische Einheit. Doppelsträngige DNA-Viren (dsDNA: double stranded DNA)[Bearbeiten , ... Einzelsträngige DNA-Viren (ssDNA: single stranded DNA)[Bearbeiten , Quelltext bearbeiten]. Viren mit Einzelstrang-DNA-Genom ...
Small Subunit Ribosomal DNA Suggests that the Xenophyophorean Syringammina corbicula1 is a Foraminiferan. Authors. *. JAN ...
... signaling stimulates ribosomal DNA amplification in budding yeast, linking external nutrient availability to ribosomal DNA copy ... 2001) Identification of DNA cis elements essential for expansion of ribosomal DNA repeats in Saccharomyces cerevisiae. Mol Cell ... forms a key element in the control of ribosomal DNA amplification as overexpression of PNC1 substantially reduces ribosomal DNA ... Regulation of ribosomal DNA amplification by TOR. Carmen V. Jack, Cristina Cruz, Ryan M. Hull, Markus A. Keller, Markus Ralser ...
Ribosomal DNA polymorphisms in the yeast Geotrichum candidum.. Alper I1, Frenette M, Labrie S. ... Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA ... We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 ...
Yamashitas team looked specifically at ribosomal DNA (rDNA) loci that contain the genes for ribosomal RNA (rRNA). These loci ... Aging Clues Found in Stem Cell Ribosomal DNA. February 14, 2018. 0 ... in which DNA copy number is rapidly expanded in the male germline of animals that are deficient in rDNA due to large rDNA ...
Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA. Ribosomes are assemblies of proteins and rRNA molecules ... Keil RL, Roeder GS (1984). "Cis-acting, recombination-stimulating activity in a fragment of the ribosomal DNA of S. cerevisiae ... Weisburg WG, Barns SM, Pelletier DA, Lane DJ (January 1991). "16S ribosomal DNA amplification for phylogenetic study". J. ... Hillis, D. M.; Dixon, M. T. (1991). "Ribosomal DNA: Molecular evolution and phylogenetic inference". The Quarterly Review of ...
Redistribution of ribosomal DNA after blocking of transcription induced by actinomycin D.. Schöfer C1, Weipoltshammer K, ...
16S ribosomal DNA amplification for phylogenetic study.. W G Weisburg, S M Barns, D A Pelletier, D J Lane ... 16S ribosomal DNA amplification for phylogenetic study. Message Subject (Your Name) has forwarded a page to you from Journal of ... One pair of primers is capable of amplifying nearly full-length 16S ribosomal DNA (rDNA) from many bacterial genera; the ...
Of the 3.2 billion DNA building blocks of a human genome, ribosomal DNA accounts for only 13,000, but its puny representation ... "rDNA" stands for ribosomal DNA. Ribosomes are the roundish structures upon which the amino acids of a protein are strung ... A New Biological Aging Clock: Ribosomal DNA Posted March 28, 2019 by Ricki Lewis, PhD in Uncategorized ... For the new clock, the researchers dub the prophetic process of ribosomal DNA methylation "rDNAm." Rdamn? Im stymied. ...
Dna, ribosomal explanation free. What is Dna, ribosomal? Meaning of Dna, ribosomal medical term. What does Dna, ribosomal mean? ... Looking for online definition of Dna, ribosomal in the Medical Dictionary? ... ribosomal DNA. (redirected from Dna, ribosomal). Also found in: Dictionary. ribosomal DNA (rDNA), species of DNA present in ... ribosomal DNA. n. Abbr. rDNA. Any of various regions of DNA in eukaryotes that are transcribed into precursors of ribosomal RNA ...
In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete ... Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics ... Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were ... Conclusions/Significance Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis ...
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Conrad L. Schoch, Keith ... Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi ... Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi ... Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi ...
... suggest that ribosomal DNA copy number could be used to predict which cancers will be sensitive to DNA-damaging ... Ribosomal DNA plays a critical role in healthy cells and cancer cells alike. It encodes structural components of ribosomes, the ... Cancer cells may lose copies of ribosomal DNA to enable faster proliferation, study shows. *Download PDF Copy ... The few studies that have included analysis of ribosomal DNA thus far have shown that the number of copies of the repetitive ...
Szostak, J. W., and R. Wu, 1980 Unequal crossing over in the ribosomal DNA of Saccharomyces cerevisiae. Nature 284: 426-430. ... Merker, R. J., and H. L. Klein, 2002 hpr1Δ affects ribosomal DNA recombination and cell life span in Saccharomyces cerevisiae. ... Crease, T., and M. Lynch, 1991 Ribosomal DNA variation in Daphnia pulex. Mol. Biol. Evol. 8: 620-640. ... THE ribosomal (r)DNA of metazoan animals is a large multigene family consisting of one or more arrays of tandemly repeated ...
Amplified Ribosomal DNA Restriction Analysis. Amplified Ribosomal DNA Restriction Analysis. Amplified rDNA (Ribosomal DNA) ... Other articles related to amplified ribosomal dna restriction analysis, restriction, ribosomal:. Amplified Ribosomal DNA ... Read more about Amplified Ribosomal DNA Restriction Analysis: ARDRA Rationale and Procedure ... Famous quotes containing the words analysis, restriction and/or dna:. "Ask anyone committed to Marxist analysis how many angels ...
Amplified rDNA (Ribosomal DNA) Restriction Analysis is the extension of the technique of RFLP (restriction fragment length ... Identification of Acinetobacter Genomic Species by Amplified Ribosomal DNA Restriction Analysis. J. Clin. Microbiol. 33:11-15. ... Overnight digestion (10-16 hours) of about 300-500 ng of amplicon DNA in a 20 μL system with 4-5 units of Restriction Enzyme ... of more than 4bp would be irrelevant with respect to a gene of approximately 1500bp such as that coding for the 16s ribosomal ...
Ribosomal DNA is the sequence of DNA that codes for ribosomal RNA. In eukaryotes, the ribosomal DNA contains a tandem repeat of ... Ribosomal RNA is a specialized RNA molecule present in the ribosome. The ribosomal RNA does not carry the code in making ... The ribosomal RNAs form two subunits, i.e. large subunit and small subunit. The large subunit serves as a ribozyme. Apart from ... Retrieved from "https://www.biology-online.org/dictionary/index.php?title=Ribosomal_DNA&oldid=100624" ...
Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs. Cytogenet ... Cytogenetic Analysis of Populus trichocarpa - Ribosomal DNA, Telomere Repeat Sequence, and Marker-selected BACs ...
Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction.. K H Wilson, R B Blitchington, R C Greene ... Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. Message Subject (Your Name) has forwarded a page ...
Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex.. T J Crease ... Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex. ...
DNA studies of 23 taxa (20 platyhelminths, 1 nemertean, Homo and Artemia) and electron-microscopic studies of the ... Human 18s ribosomal RNA sequence inferred from DNA sequence. Biochem.J. 232: 725-733.Google Scholar ... Contributions to the phylogeny of Platyhelminthes based on partial sequencing of 18S ribosomal DNA. Int. J. Parasitol. 23: 705- ... The phylogenetic relationships of Kronborgia (Platyhelminthes, Fecampiida) based on comparison of 18S ribosomal DNA sequences. ...
LUPATINI, Manoeli; MELLO, Andrea Hentz de e ANTONIOLLI, Zaida Inês. Ribosomal dna characterization of Scleroderma UFSMSc1 of ... The DNA of the Scleroderma UFSMSc1 isolate was extracted with CTAB solution. PCR reactions were carried out with the universal ...
Three DNA regions were sequenced, including the trnLintron... ... DNA sequences were used to assess the monophyly and inter- ... based on DNA sequences from ITS nuclear ribosomal DNA and plastid trnL intron and trnL-F intergenic spacers. ... including the trnL intron and the trnL-F intergenic spacer of the plastid genome and the ITS region of nuclear ribosomal DNA ( ... DNA sequences were used to assess the monophyly and inter-relationships of Miscanthus, Saccharum and related genera in the ...
... implying a higher complexity of evolutionary patterns in the ribosomal genes than generally recognized. Modeling the ITS1, 5.8S ...
By 16S Ribosomal DNA Sequence Analysis Int J Syst Bacteriol. 1997 Oct;47(4):921-5. doi: 10.1099/00207713-47-4-921. ... which was consistent with data from previous DNA-DNA hybridization experiments (D. Postic, M. V. Assous, P. A. D. Grimont, and ... In accordance with DNA relatedness values, our findings suggest that genomic species PotiB2 can be more clearly defined and ...
... we present a protocol for tracing genomic DNA (gDNA) contamination in RNA samples. The presented method utilizes primers ... Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA. Seyyed Hamidreza Hashemipetroudi1, Ghorbanali Nematzadeh ... of ribosomal DNA (rDNA) genes. The method is suited for reliable and sensitive detection of DNA contamination in most ... Assessment of DNA Contamination in RNA Samples Based on Ribosomal DNA. J. Vis. Exp. (131), e55451, doi:10.3791/55451 (2018). ...
  • Repeated regions are widespread in eukaryotic genomes, and key functional elements such as the ribosomal DNA tend to be formed of high copy repeated sequences organized in tandem arrays. (pnas.org)
  • Genomic origin and organization of the hybrid Poa jemtlandica (Poaceae) verified by genomic in situ hybridization and chloroplast DNA sequences. (springer.com)
  • We report here two highly reliable ribosomal DNA-based single nucleotide polymorphism (SNP) markers, CxpG2T and CxpA2d, for detecting Cx. (ajtmh.org)
  • Objective: The present study was conducted to evaluate the efficacy of restriction fragment length polymorphism (RFLP) analysis of PCR amplified ribosomal (r) DNA including internal transcribed spacers (ITS), as an identification tool. (aber.ac.uk)
  • Polymorphism and evolution of ribosomal DNA in tea (Camellia sinensis, Theaceae). (semanticscholar.org)
  • Ribosomal RNA multigene loci: nomads of the Triticeae genomes. (springer.com)
  • With the advent of DNA sequencing technology to infer phylogenetic relationships, investigators began searching for genetic loci that were both phylogenetically informative and readily sequenced in most organisms. (peerj.com)
  • In this study, we examine the bacterial components of the wound bioburden using two clinical laboratory tests: traditional aerobic culturing and recently developed culture-free sequencing of bacterial 16S DNA. (biomedcentral.com)
  • and other types of DNA damage ( e.g. , methylation or oxidation), can stimulate recombination during mitosis. (genetics.org)
  • However, little is known about the mechanisms that specify and maintain the patterns of NOR DNA methylation. (beds.ac.uk)
  • Here, we explored the extent of naturally-occurring variation in NOR DNA methylation among accessions of the flowering plant Arabidopsis thaliana . (beds.ac.uk)
  • We investigated the inheritance of NOR DNA methylation patterns in natural accessions with hypomethylated NORs in inter-strain crosses and defined three different categories of inheritance in F1 hybrids. (beds.ac.uk)
  • In addition, subsequent analysis of F2 segregation for NOR DNA methylation patterns uncovered different patterns of inheritance. (beds.ac.uk)
  • We also revealed that NOR DNA methylation in the Arabidopsis accession Bor-4 is influenced by the vim1-1 ( variant in methylation 1-1 ) mutation, but the primary effect is specified by the NORs themselves. (beds.ac.uk)
  • Our results indicate that the NORs themselves are the most significant determinants of natural variation in NOR DNA methylation. (beds.ac.uk)
  • However, the inheritance of NOR DNA methylation suggests the operation of a diverse set of mechanisms, including inheritance of parental methylation patterns, reconfiguration of parental NOR DNA methylation, and the involvement of trans -acting modifiers. (beds.ac.uk)
  • This study compares the results of aerobic culturing and molecular testing (culture-free 16S ribosomal DNA sequencing), and it examines the relative abundance score that is generated by the molecular test and the usefulness of the relative abundance score in predicting the likelihood that the same organism would be detected by culture. (biomedcentral.com)
  • The few studies that have included analysis of ribosomal DNA thus far have shown that the number of copies of the repetitive sequences expand and contract all the time. (news-medical.net)
  • First author Baoshan Xu, Ph.D., a former postdoctoral research associate in the Gerton Lab now starting his own lab at Sun Yat-sen University in China, worked with Hua Li, Ph.D., to use computational methods to count the number of copies of ribosomal DNA in normal and cancer cells of 162 patients from the eight projects. (news-medical.net)
  • This time, Xu used a sophisticated technique called droplet digital PCR to count the ribosomal DNA copies in normal and cancer cells from the mice. (news-medical.net)
  • The cells somehow managed to be highly proliferative, made more ribosomal RNA, and synthesized more protein, all with fewer copies of ribosomal DNA. (news-medical.net)
  • The nucleosome is the basic unit of chromatin and comprises 147 base pairs of DNA wrapped around a histone octamer, which contains two copies of each of the four histones H2A, H2B, H3 and H4. (prolekare.cz)
  • Six DNA regions were evaluated as potential DNA barcodes for Fungi , the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. (pnas.org)
  • Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. (pnas.org)
  • A phylogenetic study of Gagea and Lloydia (Liliaceae) was conducted using sequences of nuclear ribosomal internal transcribed spacer (ITS) and plastid ( rpl16 intron, trnL intron, trnL-F spacer, matK and the psbA - trnH spacer) DNA regions. (oup.com)
  • Other regions of noncoding DNA provide instructions for the formation of certain kinds of RNA molecules. (medlineplus.gov)
  • The identity of regulatory elements and other functional regions in noncoding DNA is not completely understood. (medlineplus.gov)
  • The latter obstacle was circumvented by cloning and sequencing of 16S ribosomal DNAs (rDNAs) from uncultured marine microbial communities. (asm.org)
  • The 16S ribosomal DNAs (rDNAs) of two strains of Francisella tularensis and one strain of Francisella philomiragia were sequenced. (microbiologyresearch.org)
  • The findings, published June 22, 2017, in PLoS Genetics, suggest that ribosomal DNA copy number could be used to predict which cancers will be sensitive to DNA-damaging chemotherapeutics. (news-medical.net)
  • Lack of the H4 N-alpha acetyltransferase (Nat4) activity results specifically in increased deposition of asymmetric dimethylation of histone H4 arginine 3 (H4R3me2a) and in enhanced ribosomal-DNA silencing. (prolekare.cz)