Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes

1984 ◽  
Vol 3 (6) ◽  
pp. 355-361 ◽  
Author(s):  
David B. Stern ◽  
Tony P. Hodge ◽  
David M. Lonsdale
Keyword(s):  
Escherichia Coli ◽  
Mitochondrial Dna ◽  
Ribosomal Dna ◽  
Rrna Genes ◽  
Mitochondrial Rrna

Restriction fragment length polymorphisms demonstrate single origin of infection centers in Phellinus weirii

1994 ◽  
Vol 72 (4) ◽  
pp. 440-447 ◽  
Author(s):  
Hanhong Bae ◽  
Everett M. Hansen ◽  
Steven H. Strauss
Keyword(s):  
Mitochondrial Dna ◽  
Restriction Fragment ◽  
Ribosomal Dna ◽  
Fragment Length ◽  
Host Species ◽  
Root Rot ◽  
Biological Species ◽  
Douglas Fir ◽  
Dna Probes ◽  
Restriction Fragment Length

Restriction fragment length polymorphism (RFLP) markers were used to study genetic variation in the basidiomycete fungus Phellinus weirii (Murr.) Gilbertson, the cause of laminated root rot of conifers. In an initial study, three isolates each from the Douglas-fir type and the cedar-type biological species were surveyed with 12 restriction enzymes and 20 random, mitochondrial, and nuclear-ribosomal gene probes. The two biological species were distinct with most probe–enzyme combinations (91%). Variation within biological species was detected for the random and ribosomal DNA probes but not for the mitochondrial DNA probes. In a subsequent study 65 probe–enzyme combinations (13 × 5) that had detected variation within the Douglas-fir type biological species were used to analyze 27 isolates derived from six infection centers, two host species, and two geographic areas in western Oregon. Infection centers differed from one another in numerous probe–enzyme combinations but were nearly genetically uniform within. Isolates from the two host species, Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) and mountain hemlock (Tsuga mertensiana (Bong.) Carr.), showed few RFLP differences. Initiation of infection centers, and subsequent vegetative or basdiospore initiated immigration, appear to be rare events. Key words: ribosomal DNA, mitochondrial DNA, RFLP, root rot, conifer.

Initiation and termination of DNA replication in human rRNA genes

1993 ◽  
Vol 13 (10) ◽  
pp. 6600-6613
Author(s):  
R D Little ◽  
T H Platt ◽  
C L Schildkraut
Keyword(s):  
Dna Replication ◽  
Ribosomal Dna ◽  
Regulatory Elements ◽  
Transcription Unit ◽  
Replication Initiation ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Replication Forks ◽  
Nontranscribed Spacer ◽  
Dna Repeat

We have used the multicopy human rRNA genes as a model system to study replication initiation and termination in mammalian chromosomes. Enrichment for replicating molecules was achieved by isolating S-phase enriched populations of cells by centrifugal elutriation, purification of DNA associated with the nuclear matrix, and a chromatographic procedure that enriches for molecules containing single-stranded regions, a characteristic of replication forks. Two-dimensional agarose gel electrophoresis techniques were used to demonstrate that replication appears to initiate at multiple sites throughout most of the 31-kb nontranscribed spacer (NTS) of human ribosomal DNA but not within the 13-kb transcription unit or adjacent regulatory elements. Although initiation events were detected throughout the majority of the NTS, some regions may initiate more frequently than others. Termination of replication, the convergence of opposing replication forks, was found throughout the ribosomal DNA repeat units, and, in some repeats, specifically at the junction of the 3' end of the transcription unit and the NTS. This site-specific termination of replication is the result of pausing of replication forks near the sites of transcription termination. The naturally occurring multicopy rRNA gene family offers a unique system to study mammalian DNA replication without the use of chemical synchronization agents.

scholarly journals Prevalence and molecular detection of fluoroquinolone-resistant genes (qnrA and qnrS) in Escherichia coli isolated from healthy broiler chickens

2018 ◽  
pp. 1720-1724 ◽  
Author(s):  
Shahin Mahmud ◽  
K. H. M. Nazmul Hussain Nazir ◽  
Md. Tanvir Rahman
Keyword(s):  
Escherichia Coli ◽  
Broiler Chickens ◽  
Molecular Detection ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Diffusion Method ◽  
Isolation And Identification ◽  
E Coli ◽  
Pcr Targeting ◽  
Apparently Healthy

Aim: The present study was carried out to determine the prevalence and molecular detection of fluoroquinolone-resistant Escherichia coli carrying qnrA and qnrS genes in healthy broiler chickens in Mymensingh, Bangladesh, and also to identify the genes responsible for such resistance. Materials and Methods: A total of 65 cloacal swabs were collected from apparently healthy chickens of 0-14 days (n=23) and 15-35 days (n=42) old. The samples were cultured onto Eosin Methylene Blue Agar, and the isolation and identification of the E. coli were performed based on morphology, cultural, staining, and biochemical properties followed by polymerase chain reaction (PCR) targeting E. coli 16S rRNA genes. The isolates were subjected to antimicrobial susceptibility test against five commonly used antibiotics under fluoroquinolone (quinolone) group, namely gatifloxacin, levofloxacin, moxifloxacin, ofloxacin, and pefloxacin by disk diffusion method. Detection of qnrA and qnrS genes was performed by PCR. Results: Among the 65 cloacal samples, 54 (83.08%) were found to be positive for E. coli. Antibiotic sensitivity test revealed that, of these 54 isolates, 18 (33.33%) were found to be resistant to at least one fluoroquinolone antibiotic. The highest resistance was observed against pefloxacin (61.11%). By PCR, of 18 E. coli resistant to fluoroquinolone, 13 (72.22%) were found to be positive for the presence of qnrS. None of the isolates were found positive for qnrA. Conclusion: Fluoroquinolone-resistant E. coli harboring qnrS genes is highly prevalent in apparently healthy broiler chickens and possesses a potential threat to human health.

scholarly journals PSVII-16 Galactosylated chitosan-oligosaccharides have anti-adhesive effect against enterotoxigenic Escherichia coli in piglets

2019 ◽  
Vol 97 (Supplement_2) ◽  
pp. 224-224
Author(s):  
Charlotte Maria Elisabeth Heyer ◽  
Weilan Wang ◽  
Yalu Yan ◽  
Michael G Gänzle ◽  
Ruurd T Zijlstra
Keyword(s):  
Escherichia Coli ◽  
Enterotoxigenic Escherichia Coli ◽  
Rrna Genes ◽  
Saline Control ◽  
Fluid Loss ◽  
Bacterial Gene ◽  
Test Product ◽  
Chitosan Oligosaccharides ◽  
Galactosylated Chitosan ◽  
K88 Fimbriae

Abstract Enterotoxigenic Escherichia coli (ETEC) is a major cause of diarrhea in piglets. In vitro, high molecular weight β-galactosylated chitosan-oligosaccharides (Gal-COS) had strong anti-adhesive activity against ETEC-expressing K88 fimbriae (ETEC K88) binding to porcine erythrocytes. This study assessed the effects of Gal-COS differing in structure on anti-adhesive properties against ETEC in a small intestinal segment perfusion (SISP) model in 8 piglets (BW 10 kg; 5-wk old). With 10 jejunal segments in each pig, 5 segments were infected with ETEC K88, and the other 5 segments were infused with saline (non-ETEC). Every 2 paired segments (ETEC or non-ETEC) from the same pig were treated for 8 h with 64 ml of 10 g L-1 of one of the following test products: 1) α-Gal-COS; 2) β-Gal-COS; 3) exopolysaccharides produced by Lactobacillus reuteri; and 4) raffinose in a double 4 × 4 Latin square with a saline control. Infection by ETEC K88 was verified by quantitative PCR. Net fluid loss was calculated as difference of fluid loss between ETEC segment and its paired non-ETEC segment. Data were analyzed using the mixed model with segment and test product as fixed effects, and pig as random effect. Number of eubacterial rRNA genes was 10-fold greater (P < 0.001) in ETEC segments than non-ETEC segments, indicating that ETEC K88 accounted for > 90% of bacterial gene counts. Test product did not affect (P > 0.10) the number of ETEC bacteria in the outflow fluid. Furthermore, net fluid loss caused by ETEC tended (P = 0.08) to be decreased by β-Gal-COS compared to all other treatments. In conclusion, the in vivo SISP model confirmed that Gal-COS had anti-diarrheal effects, indicating that β-Gal-COS is a potential feed additive to reduce the ETEC-induced diarrhea in piglets.

scholarly journals Phylogenetic relationships of the European newts (genus Triturus) tested with mitochondrial DNA sequence data

1999 ◽  
Vol 68 (2) ◽  
pp. 73-81 ◽  
Author(s):  
I. Zajc ◽  
J.W. Arntzen
Keyword(s):  
Mitochondrial Dna ◽  
Sequence Data ◽  
A Priori ◽  
Strong Support ◽  
Species Group ◽  
Rrna Genes ◽  
Sister Taxon ◽  
Phylogenetic Position ◽  
12S Rrna ◽  
16S Rrna Sequence

European newts (genus Triturus) are widely studied, but their phylogeny is not yet unambiguously resolved. Fragments of mitochondrial DNA experiencing different rates of evolution (the ATPase and 12S rRNA genes) were sequenced in order to test a phylogenetic hypothesis derived from biochemical and behavioral data. Well-supported branches of the existing phylogeny gained support in our study. The monophyletic origin of the hypothesized T. boscai – T. italicus clade remained ambiguous, whereas strong support was gained for the sister-taxon relationship of T. vulgaris and T. montandoni. The position of T. vittatus as a sister taxon to the T. marmoratus species group was also supported. The phylogenetic position of T. alpestris could not be clarified. With an in-group taxon sampling denser than in previous molecular phylogenetic studies and under the a priori selection of species from the genera Cynops, Neurergus and Paramesotriton as out-groups, the monophyly of Triturus was strongly supported. It cannot be excluded, however, that the presumed out-group actually belongs to the in-group, rendering Triturus paraphyletic as was concluded from recently published 12S and 16S rRNA sequence data.

scholarly journals Gene activities for ribosomal components in Escherichia coli B/r

1975 ◽  
Vol 150 (3) ◽  
pp. 469-475 ◽  
Author(s):  
H Bremer ◽  
P P Dennis
Keyword(s):  
Escherichia Coli ◽  
Steady State ◽  
Ribosomal Rna ◽  
Growth Rates ◽  
Ribosomal Proteins ◽  
Rrna Genes ◽  
Steady State Growth ◽  
State Growth ◽  
Escherichia Coli B

The relative transcriptional activities of genes coding for ribosomal RNA (rRNA) and ribosomal proteins (r-proteins) at a steady-state growth rates ranging from 0.65 to 2.1 doublings/h can be estimated from previous measurements of the synthesis rates of stable and unstable RNA (Pato & von Meyenburg, 1970; Nierlich, 1972a,b; Bremer et al., 1973; Dennis & Bremer, 1973b, 1974b) and ribosomal proteins (Schleif, 1967; Dennis & Bremer, 1974a). Comparison of these transcriptional activities suggests that the expression of the r-protein genes and rRNA genes is controlled seperately.

scholarly journals Effect of gamma irradiation on viability and DNA of Staphylococcus epidermidis and Escherichia coli

2006 ◽  
Vol 55 (9) ◽  
pp. 1271-1275 ◽  
Author(s):  
Andrej Trampuz ◽  
Kerryl E. Piper ◽  
James M. Steckelberg ◽  
Robin Patel
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Gamma Irradiation ◽  
Staphylococcus Epidermidis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Molecular Diagnostic ◽  
Molecular Diagnostic Techniques ◽  
Bacterial Cells ◽  
E Coli

Gamma irradiation is widely used for sterilization; however, its effect on elimination of amplifiable DNA, an issue of relevance to molecular diagnostic approaches, has not been well studied. The effect of gamma irradiation on the viability of Staphylococcus epidermidis and Escherichia coli (using quantitative cultures) and on their DNA (using quantitative 16S rRNA gene PCR) was evaluated. Viability was abrogated at 2.8 and 3.6 kGy for S. epidermidis and E. coli, respectively. The radiation dose required to reduce viable bacteria by one log10 (D 10 value) was 0.31 and 0.35 kGy for S. epidermidis and E. coli, respectively. D 10 values for amplifiable DNA extracted from bacteria were 2.58 and 3.09 kGy for S. epidermidis and E. coli, respectively, whereas D 10 values for amplifiable DNA were significantly higher for DNA extracted from irradiated viable bacterial cells (22.9 and 52.6 kGy for S. epidermidis and E. coli, respectively; P<0.001). This study showed that gamma irradiation of DNA in viable bacterial cells has little effect on amplifiable DNA, was not able to eliminate amplifiable 16S rRNA genes at a dose of up to 12 kGy and cannot therefore be used for elimination of DNA contamination of PCR reaction components or laboratory equipment when this DNA is present in microbial cells. This finding has practical implications for those using molecular diagnostic techniques in microbiology.

scholarly journals Chabertia erschowi (Nematoda) is a distinct species based on nuclear ribosomal DNA sequences and mitochondrial DNA sequences

2014 ◽  
Vol 7 (1) ◽  
pp. 44 ◽  
Author(s):  
Guo-Hua Liu ◽  
Lei Zhao ◽  
Hui-Qun Song ◽  
Guang-Hui Zhao ◽  
Jin-Zhong Cai ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Distinct Species ◽  
Nuclear Ribosomal Dna

Structure and molecular evolution of the ribosomal DNA external transcribed spacer in the cockroach genus Blattella

Genome ◽  
2011 ◽  
Vol 54 (3) ◽  
pp. 222-234 ◽  
Author(s):  
Dmitry V. Mukha ◽  
Vera Mysina ◽  
Valeria Mavropulo ◽  
Coby Schal
Keyword(s):  
Ribosomal Dna ◽  
Multigene Family ◽  
Internal Transcribed Spacers ◽  
Rrna Genes ◽  
Nucleotide Substitutions ◽  
Rdna Cluster ◽  
Nontranscribed Spacer ◽  
External Transcribed Spacer ◽  
A New Species ◽  
Nucleolus Organizers

The ribosomal DNA (rDNA) cluster of insects contains several hundred repeating structural–functional units and, therefore, is a typical example of a multigene family. Eukaryotic ribosomal RNA (rRNA) genes (18S, 5.8S, and 28S like) are arranged in tandemly repeated clusters in the nucleolus organizers, separated by several spacers, namely the nontranscribed spacer, the external transcribed spacer (ETS), and the internal transcribed spacers. The nucleotide sequences of the ETS of the three closely related Blattella cockroach species, Blattella germanica (Linnaeus, 1767), Blattella asahinai (Mizukubo, 1981), and Blattella lituricollis (Walker, 1868), were determined and compared. The three species had relatively similar ETS lengths, and sequence differences among them could be explained by two types of rearrangements, namely deletions of subrepeats and nucleotide substitutions. Minor ETS variants in B. germanica differed from the major variant in the same way that the major ETS variants of the three Blattella species differed from each other. Concerted evolution and the birth-and-death models, which are often invoked to explain the diversity and evolution of the multigene families of rDNA clusters, are discussed in the light of our data. A new model is proposed to explain the evolutionary reorganization of the ETS region: evolution of rDNA by “magnification-and-fixation” is characterized by magnification of minor subrepeats, which become adaptive in a new rapidly changed environment, and subsequent fixation of this variant type as a major component of the multigene family of a new species.

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