Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

2009 ◽  
Vol 37 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Shiraz Ali Shah ◽  
Niels R. Hansen ◽  
Roger A. Garrett
Keyword(s):  
Plasmid Dna ◽  
Genomic Dna ◽  
Inhibitory Mechanism ◽  
Archaeal Viruses ◽  
Extrachromosomal Elements ◽  
Dna Strand ◽  
High Level

Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles, the chromosomal spacers show a high level of matches (∼30%) with viral or plasmid genomes. Moreover, their distribution along the virus/plasmid genomes, as well as their DNA strand specificity, appear to be random. This is consistent with the hypothesis that chromosomal spacers are taken up directly and randomly from virus and plasmid DNA and that the spacer transcripts target the genomic DNA of the extrachromosomal elements and not their transcripts.

Host–parasite genome relationships in Acridid grasshoppers. II. Patterns of variation in the plasmids of gut bacteria of Caledia captiva and Locusta migratoria

Genome ◽  
1987 ◽  
Vol 29 (2) ◽  
pp. 264-271 ◽  
Author(s):  
D. J. Colgan ◽  
D. A. Willcocks
Keyword(s):  
Southern Blotting ◽  
Locusta Migratoria ◽  
Sequence Diversity ◽  
Extrachromosomal Elements ◽  
Size Uniformity ◽  
Restriction Fragment Pattern ◽  
High Level ◽  
Host Parasite ◽  
Plasmid Diversity ◽  
Very High

Plasmid preparations were made from 110 isolates of Enterobacter cloacae taken from the guts of members of the Caledia captiva complex of grasshoppers to ascertain whether a relationship exists between these extrachromosomal elements and taxonomic variation in the grasshoppers themselves. Fifty-two plasmids, distinguishable by mobility or restriction fragment pattern differences, were identified. Thirty-seven of these were similar in size. Five plasmids were nick translated and used to probe Southern blots. Only three instances of cross homology with another plasmid were found, implying a very high level of sequence diversity in the samples. No explanation of the size uniformity and sequence diversity of the plasmids is entirely satisfactory but it appears most likely that the variation is maintained to serve a variety of adaptive functions. No plasmid was found in grasshoppers of more than one taxon of C. captiva. This may be due to geographical limitations on the distribution of plasmids. If this is so, it remains possible that there is an association of one or more plasmids with taxonomic divergence in this grasshopper complex. Plasmid preparations were also made from 68 bacterial isolates (predominantly E. aerogenes) from laboratory-reared Locusta migratoria and from 72 isolates from other acridid grasshoppers. Plasmids of the size general in C. captiva were discovered in most of these isolates. Some smaller plasmids were also found. As judged by restriction endonuclease digests and Southern blotting, plasmid diversity is much less in this sample of L. migratoria bacteria than in the field-collected C. captiva. The plasmids reported in this paper may be considered as possible vectors for use in the genetic control of locusts. Key words: host–parasite, plasmids, grasshoppers, Enterobacter.

scholarly journals Structures, Locations, and Transfer Frequencies of Genetic Elements Conferring High-Level Gentamicin Resistance in Enterococcus faecalis Isolates in Greece

2003 ◽  
Vol 47 (12) ◽  
pp. 3950-3953 ◽  
Author(s):  
George L. Daikos ◽  
George Bamias ◽  
Christos Kattamis ◽  
Marcus J. Zervos ◽  
Joseph W. Chow ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Restriction Enzyme ◽  
Plasmid Dna ◽  
Strong Association ◽  
Hybridization Analysis ◽  
Clinical Isolates ◽  
Genetic Elements ◽  
Transfer Characteristics ◽  
Gentamicin Resistance ◽  
High Level

ABSTRACT The elements conferring high-level gentamicin resistance in 64 clinical isolates of Enterococcus faecalis were characterized by PCR and by restriction enzyme hybridization analysis of genomic and plasmid DNA. There was a strong association between gentamicin resistance and the aac(6′)-aph(2") gene carried on IS256-based elements with different structures, locations, and transfer characteristics.

scholarly journals A paradoxical synergism between Resveratrol and copper (II) with respect to degradation of DNA and RNA

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 1145 ◽  
Author(s):  
Siddharth Subramaniam ◽  
Iqbal Vohra ◽  
Aishwarya Iyer ◽  
Naveen K Nair ◽  
Indraneel Mittra
Keyword(s):  
Synergistic Effect ◽  
Plasmid Dna ◽  
Genomic Dna ◽  
Oxygen Species ◽  
Molar Ratios ◽  
Dna Cleaving ◽  
Dna And Rna ◽  
Fixed Concentration ◽  
Anti Cancer ◽  
Low Levels

Resveratrol (R), a plant polyphenol, is known to reduce Cu (II) to Cu (I) generating reactive oxygen species that can cleave plasmid DNA. Here we report a surprising observation of a paradoxical synergistic effect between R and Cu whereby plasmid DNA cleaving / degrading activity of R-Cu increased progressively as the ratio of R to Cu was increased i.e., the concentration of Cu was successively reduced with respect to a fixed concentration R. Whereas cleavage of plasmid DNA occurred at low molar ratios of R to Cu, at higher ratios, complete degradation of DNA was achieved. By further increasing the ratio, whereby the concentration of Cu was reduced to very low levels, the DNA degrading activity of R-Cu was lost. This paradoxical synergistic effect is also seen with respect to eukaryotic genomic DNA and RNA. Since R-Cu may have anti-cancer and anti-viral activities, our findings may not only help to improve the therapeutic efficacy of R-Cu but also reduce its toxic side effects with the use of low concentration of Cu.

scholarly journals Fragmentation of Plasmid DNA Produced by Gamma Radiation: A Theoretical Approach

2012 ◽  
Vol 2012 ◽  
pp. 1-6
Author(s):  
R. A. S. Silva ◽  
J. D. T. Arruda-Neto ◽  
L. Nieto
Keyword(s):  
Plasmid Dna ◽  
Fragment Size ◽  
Power Laws ◽  
Double Strand Breaks ◽  
Strand Breaks ◽  
Starting Point ◽  
Dna Strands ◽  
High Let ◽  
Fragment Distribution ◽  
Dna Strand

Breaks in DNA, resulting in fragmented parts, can be produced by ionizing radiation which, in turn, is the starting point in the search for novel physical aspects of DNA strands. Double-strand breaks in particular cause disruption of the DNA strand, splitting it into several fragments. In order to study effects produced by radiation in plasmid DNA, a new simple mechanical model for this molecule is proposed. In this model, a Morse-like potential and a high-LET component are used to describe the DNA-radiation interaction. Two power laws, used to fit results of the model, suggest that, firstly, distribution of fragment size is nonextensive and, secondly, that a transition phase is present in the DNA fragment distribution pattern.

scholarly journals Plasmid DNA-based Alphavirus Vaccines

Vaccines ◽  
2019 ◽  
Vol 7 (1) ◽  
pp. 29 ◽  
Author(s):  
Kenneth Lundstrom
Keyword(s):  
Tumor Cells ◽  
Plasmid Dna ◽  
Transgene Expression ◽  
Tumor Regression ◽  
Infectious Agents ◽  
Application Range ◽  
Mammalian Cell Lines ◽  
High Level ◽  
Rna Replicon

Alphaviruses have been engineered as vectors for high-level transgene expression. Originally, alphavirus-based vectors were applied as recombinant replication-deficient particles, subjected to expression studies in mammalian and non-mammalian cell lines, primary cell cultures, and in vivo. However, vector engineering has expanded the application range to plasmid DNA-based delivery and expression. Immunization studies with DNA-based alphavirus vectors have demonstrated tumor regression and protection against challenges with infectious agents and tumor cells in animal tumor models. The presence of the RNA replicon genes responsible for extensive RNA replication in the RNA/DNA layered alphavirus vectors provides superior transgene expression in comparison to conventional plasmid DNA-based expression. Immunization with alphavirus DNA vectors revealed that 1000-fold less DNA was required to elicit similar immune responses compared to conventional plasmid DNA. In addition to DNA-based delivery, immunization with recombinant alphavirus particles and RNA replicons has demonstrated efficacy in providing protection against lethal challenges by infectious agents and tumor cells.

scholarly journals Screen for Potential Candidate Alternatives of Sargentodoxa cuneata from Its Six Adulterants Based on Their Phenolic Compositions and Antioxidant Activities

2019 ◽  
Vol 20 (21) ◽  
pp. 5427 ◽  
Author(s):  
Lingguang Yang ◽  
Peipei Yin ◽  
Xinxin Cao ◽  
Yujun Liu
Keyword(s):  
Plasmid Dna ◽  
Antioxidant Activities ◽  
Peroxyl Radicals ◽  
Potential Candidate ◽  
Total Phenols ◽  
Polygonum Cuspidatum ◽  
Caffeoylquinic Acids ◽  
Phenolic Contents ◽  
Hydroxybenzoic Acids ◽  
Dna Strand

Daxueteng, the liana stem of Sargentodoxa cuneata, is a widely used Traditional Chinese Medicine facing the overflow of its commercial adulterants. A method for discriminating adulterants and screening potential candidate alternatives of S. cuneata was thus established. Total phenols and flavonoids of S. cuneata and its six adulterants and their abilities to scavenge DPPH• and ABTS•+, to absorb peroxyl radicals (ORAC), and to inhibit AAPH-induced supercoiled plasmid DNA strand scission were comprehensively assessed. Polygonum cuspidatum and Bauhinia championii, two of the six adulterants of S. cuneate, shared considerably higher antioxidant activities as well as phenolic contents and, therefore, were considered as potential candidate alternatives. Phenolic compositions of the two potential candidate alternatives and S. cuneata itself were further determined by UPLC-QTOF-MS/MS. Totally 38 phenolics, including four hydroxybenzoic acids, two tyrosols, two caffeoylquinic acids, seven flavanol or its oligomers, two lignans, three hydroxycinnamic acids, six stilbenes, seven anthraquinones, and five flavanones were determined from three species. Furthermore, contents of different phenolic categories were semi-quantified and the major antioxidant contributors of S. cuneata and the two potential candidate alternatives were subsequently determined. It is concluded that tyrosols and caffeoylquinic acids were unique categories making great antioxidant contributions in S. cuneata and thus were considered as effective biomarkers in distinguishing its potential candidate alternatives.

scholarly journals Acquisition of telomere repeat sequences by transfected DNA integrated at the site of a chromosome break.

1993 ◽  
Vol 13 (2) ◽  
pp. 977-983 ◽  
Author(s):  
J P Murnane ◽  
L C Yu
Keyword(s):  
Plasmid Dna ◽  
Integration Site ◽  
Chromosome Breakage ◽  
Nucleotide Sequence Analysis ◽  
Parent Cell ◽  
Chromosome Break ◽  
Telomere Repeat ◽  
Repeat Sequences ◽  
Before And After ◽  
Dna Strand

Previous analysis of plasmid DNA transfected into 108 cell clones demonstrated extensive polymorphism near the integration site in one clone. This polymorphism was apparent by Southern blot analysis as diffuse bands that extended over 30 kb. In the present study, nucleotide sequence analysis of cloned DNA from the integration site revealed telomere repeat sequences at the ends of the integrated plasmid DNA. The telomere repeat sequences at one end were located at the junction between the plasmid and cell DNA. The telomere repeat sequences at the other end were located in the opposite orientation in the polymorphic region and were shown by digestion with BAL 31 to be at the end of the chromosome. Telomere repeat sequences were not found at this location in the plasmid or parent cell DNA. Although the repeat sequences may have been acquired by recombination, a more likely explanation is that they were added to the ends of the plasmid by telomerase before integration. Comparison of the cell DNA before and after integration revealed that a chromosome break had occurred at the integration site, which was shown by fluorescent in situ hybridization to be located near the telomere of chromosome 13. These results demonstrate that chromosome breakage and rearrangement can result in interstitial telomere repeat sequences within the human genome. These sequences could promote genomic instability, because short repeat sequences can be recombinational hotspots. The results also show that DNA rearrangements involving telomere repeat sequences can be associated with chromosome breaks. The introduction of telomere repeat sequences at spontaneous or ionizing radiation-induced DNA strand breaks may therefore also be a mechanism of chromosome fragmentation.

scholarly journals A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures

2020 ◽  
Vol 17 (167) ◽  
pp. 20190866 ◽  
Author(s):  
Stefan Badelt ◽  
Casey Grun ◽  
Karthik V. Sarma ◽  
Brian Wolfe ◽  
Seung Woo Shin ◽  
...  
Keyword(s):  
Dna Nanotechnology ◽  
Biophysical Model ◽  
Kinetic Properties ◽  
Strand Displacement ◽  
Natural Connection ◽  
Dna Strand Displacement ◽  
Wide Range ◽  
Dna Strand ◽  
High Level ◽  
Domain Level

Information technologies enable programmers and engineers to design and synthesize systems of startling complexity that nonetheless behave as intended. This mastery of complexity is made possible by a hierarchy of formal abstractions that span from high-level programming languages down to low-level implementation specifications, with rigorous connections between the levels. DNA nanotechnology presents us with a new molecular information technology whose potential has not yet been fully unlocked in this way. Developing an effective hierarchy of abstractions may be critical for increasing the complexity of programmable DNA systems. Here, we build on prior practice to provide a new formalization of ‘domain-level’ representations of DNA strand displacement systems that has a natural connection to nucleic acid biophysics while still being suitable for formal analysis. Enumeration of unimolecular and bimolecular reactions provides a semantics for programmable molecular interactions, with kinetics given by an approximate biophysical model. Reaction condensation provides a tractable simplification of the detailed reactions that respects overall kinetic properties. The applicability and accuracy of the model is evaluated across a wide range of engineered DNA strand displacement systems. Thus, our work can serve as an interface between lower-level DNA models that operate at the nucleotide sequence level, and high-level chemical reaction network models that operate at the level of interactions between abstract species.

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