Repeated Sequences and Genome Change

AbstractAn optimized method for bacterial strain differentiation, based on combination of Repeated Sequences and Whole Genome Alignment Differential Analysis (RS&WGADA), is presented in this report. In this analysis, 51 Acinetobacter baumannii multidrug-resistance strains from one hospital environment and patients from 14 hospital wards were classified on the basis of polymorphisms of repeated sequences located in CRISPR region, variation in the gene encoding the EmrA-homologue of E. coli, and antibiotic resistance patterns, in combination with three newly identified polymorphic regions in the genomes of A. baumannii clinical isolates. Differential analysis of two similarity matrices between different genotypes and resistance patterns allowed to distinguish three significant correlations (p < 0.05) between 172 bp DNA insertion combined with resistance to chloramphenicol and gentamycin. Interestingly, 45 and 55 bp DNA insertions within the CRISPR region were identified, and combined during analyses with resistance/susceptibility to trimethoprim/sulfamethoxazole. Moreover, 184 or 1374 bp DNA length polymorphisms in the genomic region located upstream of the GTP cyclohydrolase I gene, associated mainly with imipenem susceptibility, was identified. In addition, considerable nucleotide polymorphism of the gene encoding the gamma/tau subunit of DNA polymerase III, an enzyme crucial for bacterial DNA replication, was discovered. The differentiation analysis performed using the above described approach allowed us to monitor the distribution of A. baumannii isolates in different wards of the hospital in the time frame of several years, indicating that the optimized method may be useful in hospital epidemiological studies, particularly in identification of the source of primary infections.

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A second gene in a Balbiani ring. Chironomus salivary glands contain a 6.5-kb poly(A)+ RNA that is transcribed from a hierarchy of tandem repeated sequences in Balbiani ring 1.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(17)39105-6 ◽

1985 ◽

Vol 260 (21) ◽

pp. 11824-11830

Author(s):

T D Dreesen ◽

J R Bower ◽

S T Case

Keyword(s):

Salivary Glands ◽

Repeated Sequences ◽

Balbiani Ring

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Comparison of Whole-Genome Sequences from Two Colony Morphovars of Burkholderia pseudomallei

Genome Announcements ◽

10.1128/genomea.01194-15 ◽

2015 ◽

Vol 3 (5) ◽

Cited By ~ 6

Author(s):

Pei-Tan Hsueh ◽

Yao-Shen Chen ◽

Hsi-Hsu Lin ◽

Pei-Ju Liu ◽

Wen-Fan Ni ◽

...

Keyword(s):

Burkholderia Pseudomallei ◽

Repeated Sequences ◽

Whole Genome ◽

Genome Sequences ◽

Single Base

The entire genomes of two isogenic morphovars (vgh16W and vgh16R) of Burkholderia pseudomallei were sequenced. A comparison of the sequences from both strains indicates that they show 99.99% identity, are composed of 22 tandem repeated sequences with <100 bp of indels, and have 199 single-base variants.

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Clusters of interspersed repeated DNA sequences in the rice genome (Oryza)

Genome ◽

10.1139/g93-124 ◽

1993 ◽

Vol 36 (5) ◽

pp. 944-953 ◽

Cited By ~ 6

Author(s):

Xinping Zhao ◽

Gary Kochert

Keyword(s):

Dna Sequences ◽

Blot Hybridization ◽

Rice Genome ◽

Repeated Sequence ◽

Repeated Sequences ◽

Repeated Dna ◽

Rice Varieties ◽

Slot Blot Hybridization ◽

Repeated Dna Sequence ◽

Genus Oryza

We have characterized a repeated DNA sequence (RTL 122) from rice (Oryza sauva L.) with respect to its organization in the rice genome and its distribution among rice and other plants. The results indicate that the RTL 122 sequence is interspersed in the rice genome and limited to the genus Oryza. It is highly polymorphic and can be used to fingerprint rice varieties. A structure was observed in which several repeated sequences were clustered in DNA regions of 15–20 kb. We characterized three bacteriophage lambda clones that contained the RTL 122 sequence. Southern analysis using probes derived from restriction fragments of the three lambda clones indicated that all fragments except one are interspersed repeated sequences and belong to different repeated sequence families. Subsequent slot blot hybridization showed that most of them are only present within the genus Oryza. Some of the Oryza-specific, physically linked sequences show the same phylogenetic distribution, which suggests that these sequences might have evolved in a coordinate fashion. On the other hand, some of the repeated sequences have a different distribution even though they are physically adjacent in the genome. We speculate that such blocks of interspersed repeated sequences may serve as hotspots for rapid changes in the rice genome.Key words: rice, Oryza, repeated sequences, DNA fingerprinting, coordinated evolution.

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Primary Auditory Stream Segregation of Repeated Word Sequences

Perceptual and Motor Skills ◽

10.2466/pms.1976.42.3c.1071 ◽

1976 ◽

Vol 42 (3_suppl) ◽

pp. 1071-1074 ◽

Cited By ~ 4

Author(s):

Betty Tuller ◽

James R. Lackner

Keyword(s):

Spatial Separation ◽

Repeated Sequences ◽

Stream Segregation ◽

Natural Speech ◽

Auditory Stream ◽

Auditory Stream Segregation ◽

Repeated Word ◽

Auditory Sequence ◽

Constituent Order

Primary auditory stream segregation, the perceptual segregation of acoustically related elements within a continuous auditory sequence into distinct spatial streams, prevents subjects from resolving the relative constituent order of repeated sequences of tones (Bregman & Campbell, 1971) or repeated sequences of consonant and vowel sounds (Lackner & Goldstein, 1974). To determine why primary auditory stream segregation does not interfere with the resolution of natural speech, 8 subjects were required to indicate the degree of stream segregation undergone by 24 repeated sequences of English monosyllables which varied in terms of the degrees of syntactic and intonational structure present. All sequences underwent primary auditory stream segregation to some extent but the amount of apparent spatial separation was less when syntactic and intonational structure was present.

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The M26 Hotspot of Schizosaccharomyces pombe Stimulates Meiotic Ectopic Recombination and Chromosomal Rearrangements

Genetics ◽

10.1093/genetics/149.3.1191 ◽

1998 ◽

Vol 149 (3) ◽

pp. 1191-1204 ◽

Cited By ~ 1

Author(s):

Jeffrey B Virgin ◽

Jeffrey P Bailey

Keyword(s):

Homologous Recombination ◽

Schizosaccharomyces Pombe ◽

Dna Sequences ◽

Chromosomal Rearrangements ◽

Low Frequency ◽

Repeated Sequences ◽

Crossing Over ◽

Ectopic Recombination ◽

Recombination Hotspots ◽

Integration Sites

Abstract Homologous recombination is increased during meiosis between DNA sequences at the same chromosomal position (allelic recombination) and at different chromosomal positions (ectopic recombination). Recombination hotspots are important elements in controlling meiotic allelic recombination. We have used artificially dispersed copies of the ade6 gene in Schizosaccharomyces pombe to study hotspot activity in meiotic ectopic recombination. Ectopic recombination was reduced 10–1000-fold relative to allelic recombination, and was similar to the low frequency of ectopic recombination between naturally repeated sequences in S. pombe. The M26 hotspot was active in ectopic recombination in some, but not all, integration sites, with the same pattern of activity and inactivity in ectopic and allelic recombination. Crossing over in ectopic recombination, resulting in chromosomal rearrangements, was associated with 35–60% of recombination events and was stimulated 12-fold by M26. These results suggest overlap in the mechanisms of ectopic and allelic recombination and indicate that hotspots can stimulate chromosomal rearrangements.

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A Method of On-Line Analysis for Mechanical Dynamic Characteristic

13th Biennial Conference on Mechanical Vibration and Noise: Modal Analysis, Modeling, Diagnostics, and Control — Analytical and Experimental ◽

10.1115/detc1991-0361 ◽

1991 ◽

Author(s):

Fengquan Wang ◽

Huixin Wu ◽

Xiaolin Han ◽

Haomin Fu

Keyword(s):

Dynamic Characteristic ◽

Rotor System ◽

Repeated Sequences ◽

Identification Error ◽

Line Identification ◽

On Line ◽

Line Analysis

Abstract In this paper, a method of multipoint pseudorandom combined excitation with the orthogonal reciprocal repeated sequences (ORRS) is presented on the background of the on-line identification of the multivariate rotor system. The capacaty of the restraint to the identification error caused by the non-random D. C. drift of the multi-input excitation with the ORRS in the rotor system is also discussed. The validity of the method described in this paper is proved by the modelling tests of the multi-plate rotor system.

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Recombination and deletion of sequences in shuttle vector plasmids in mammalian cells

Molecular and Cellular Biology ◽

10.1128/mcb.5.9.2265-2271.1985 ◽

1985 ◽

Vol 5 (9) ◽

pp. 2265-2271

Author(s):

S Chakrabarti ◽

S Joffe ◽

M M Seidman

Keyword(s):

Shuttle Vector ◽

Marker Gene ◽

Simian Virus 40 ◽

Repeated Sequences ◽

Marker Genes ◽

Insertion Mutagenesis ◽

Direct Repeats ◽

African Green Monkey Kidney ◽

Alu Sequence ◽

Insertion Mutants

Shuttle vector plasmids were constructed with directly repeated sequences flanking a marker gene. African green monkey kidney (AGMK) cells were infected with the constructions, and after a period of replication, the progeny plasmids were recovered and introduced into bacteria. Those colonies with plasmids that had lost the marker gene were identified, and the individual plasmids were purified and characterized by restriction enzyme digestion. Recombination between the repeated elements generated a plasmid with a precise deletion and a characteristic restriction pattern, which distinguished the recombined molecules from those with other defects in the marker gene. Recombination among the following different sequences was measured in this assay: (i) the simian virus 40 origin and enhancer region, (ii) the AGMK Alu sequence, and (iii) a sequence from plasmid pBR322. Similar frequencies of recombination among these sequences were found. Recombination occurred more frequently in Cos1 cells than in CV1 cells. In these experiments, the plasmid population with defective marker genes consisted of the recombined molecules and of the spontaneous deletion-insertion mutants described earlier. The frequency of the latter class was unaffected by the presence of the option for recombination represented by the direct repeats. Both recombination and deletion-insertion mutagenesis were stimulated by double-strand cleavage between the repeated sequences and adjacent to the marker, and the frequency of the deletion-insertion mutants in this experiment was again independent of the presence of the direct repeats. We concluded that although recombination and deletion-insertion mutagenesis were both stimulated by double-strand cleavage, the molecules which underwent the two types of change were drawn from separate pools.

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