117,211 research outputs found
Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
No full textOne of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information
Inscriptions of T. Peverel and the Earl of Arundel in the Beauchamp Tower
No full text'INSCRIPTIONS OF T. PEVEREL AND THE EARL OF ARUNDEL, IN THE BEAUCHAMP TOWER. Drawn by F. Nash. Engraved by J. Pye. London, Published March 6, 1821, by T. Cadell, in the Strand. Printed by Mc.Queen & Co. Proof.' Above right 'PLATE XV.
Dynamics of DNA replication loops reveal temporal control of lagging-strand synthesis
No full textIn all organisms, the protein machinery responsible for the replication of DNA, the replisome, is faced with a directionality problem. The antiparallel nature of duplex DNA permits the leading-strand polymerase to advance in a continuous fashion, but forces the lagging-strand polymerase to synthesize in the opposite direction. By extending RNA primers, the lagging-strand polymerase restarts at short intervals and produces Okazaki fragments. At least in prokaryotic systems, this directionality problem is solved by the formation of a loop in the lagging strand of the replication fork to reorient the lagging-strand DNA polymerase so that it advances in parallel with the leading-strand polymerase. The replication loop grows and shrinks during each cycle of Okazaki fragment synthesis. Here we use single-molecule techniques to visualize, in real time, the formation and release of replication loops by individual replisomes of bacteriophage T7 supporting coordinated DNA replication. Analysis of the distributions of loop sizes and lag times between loops reveals that initiation of primer synthesis and the completion of an Okazaki fragment each serve as a trigger for loop release. The presence of two triggers may represent a fail-safe mechanism ensuring the timely reset of the replisome after the synthesis of every Okazaki fragment.
Expression of catalytic mutants of the mtDNA helicase Twinkle and polymerase POLG causes distinct replication stalling phenotypes.
No full textThe mechanism of mitochondrial DNA replication is a subject of intense debate. One model proposes a strand-asynchronous replication in which both strands of the circular genome are replicated semi-independently while the other model proposes both a bidirectional coupled leading- and lagging-strand synthesis mode and a unidirectional mode in which the lagging-strand is initially laid-down as RNA by an unknown mechanism (RITOLS mode). Both the strand-asynchronous and RITOLS model have in common a delayed synthesis of the DNA-lagging strand. Mitochondrial DNA is replicated by a limited set of proteins including DNA polymerase gamma (POLG) and the helicase Twinkle. Here, we report the effects of expression of various catalytically deficient mutants of POLG1 and Twinkle in human cell culture. Both groups of mutants reduced mitochondrial DNA copy number by severe replication stalling. However, the analysis showed that while induction of POLG1 mutants still displayed delayed lagging-strand synthesis, Twinkle-induced stalling resulted in maturated, essentially fully double-stranded DNA intermediates. In the latter case, limited inhibition of POLG with dideoxycytidine restored the delay between leading- and lagging-strand synthesis. The observed cause-effect relationship suggests that Twinkle-induced stalling increases lagging-strand initiation events and/or maturation mimicking conventional strand-coupled replication
Application of Pulsed Field Gel Electrophoresis to Determine γ-ray-induced Double-strand Breaks in Yeast Chromosomal Molecules
No full textThe frequency of DNA double-strand breaks (dsb) was determined in yeast cells exposed to γ-rays under anoxic conditions. Genomic DNA of treated cells was separated by pulsed field gel electrophoresis, and two different approaches for the evaluation of the gels were employed: (1) The DNA mass distribution profile obtained by electrophoresis was compared to computed profiles, and the number of DSB per unit length was then derived in terms of a fitting procedure; (2) hybridization of selected chromosomes was performed, and a comparison of the hybridization signals in treated and untreated samples was then used to derive the frequency of dsb
Remains of the ancient conventual church at Ely
No full text'Remains of the Ancient Conventual Church at Ely. Drawn by T. Hearne F. S. A. Engraved by Wm. Byrne F. S. A. LONDON, Published May 4. 1808. by T. Cadell and W. Davies, Strand.' Accompanied by notes
Stone stalls in Bitton Church
No full text'Stone Stalls in Bitton Church. SL 1792 Publish'd as the Act directs, April 3. 1792, by T. Cadell, Strand. Above right 'Pl. XXVI.
Inscriptions of Arthur and Edmund Poole in the Beauchamp Tower
No full text'INSCRIPTIONS OF ARTHUR AND EDMUND POOLE, IN THE BEAUCHAMP-TOWER. Drawn by F. Nash. Engraved by W. Smith. London, Published March 6, 1821, by T. Cadell, in the Strand. Printed by McQueen & Co. Proof.' Above right 'PLATE XVIII.
Carving by Hugh Draper in the Salt Tower
No full text'CARVING BY HUGH DRAPER IN THE SALT TOWER. Drawn by F. Nash. Engraved by W. Smith. London, Published March 6, 1821, by T. Cadell, in the Strand. Printed by Mc.Queen & Co. Proof.' Above right 'PLATE XXII.
Inscriptions of Thomas Clarke and others in the Beauchanp Tower
No full text'INSCRIPTIONS OF THOMAS CLARKE AND OTHERS, IN THE BEAUCHAMP TOWER. Drawn by F. Nash. Engraved by W. Cook. London, Published March 6, 1821, by T. Cadell, in the Strand. Printed by Mc.Queen & Co. Proof.' Above right 'PLATE XIX.
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