The Experts below are selected from a list of 141 Experts worldwide ranked by ideXlab platform
Eugene I Shakhnovich - One of the best experts on this subject based on the ideXlab platform.
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Semiconservative Replication, genetic repair, and many-gened genomes: Extending the quasispecies paradigm to living systems
Physics of Life Reviews, 2005Co-Authors: Emmanuel Tannenbaum, Eugene I ShakhnovichAbstract:Quasispecies theory has emerged as an important tool for modeling the evolutionary dynamics of biological systems. We review recent advances in the field, with an emphasis on the quasispecies dynamics of Semiconservatively replicating genomes. Applications to cancer and adult stem cell growth are discussed. Additional topics, such as genetic repair and many-gene genomes, are covered as well.
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Imperfect DNA lesion repair in the Semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape.
Physical review. E Statistical nonlinear and soft matter physics, 2004Co-Authors: Emmanuel Tannenbaum, James L. Sherley, Eugene I ShakhnovichAbstract:This paper develops a Hamming class formalism for the Semiconservative quasispecies equations with imperfect lesion repair, first presented and analytically solved in Y. Brumer and E.I. Shakhnovich (q-bio.GN/0403018, 2004). Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of fitness landscapes defined by a master genome. We use these equations to solve for a generalized single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. We determine the mean equilibrium fitness and error threshold for this class of landscapes, and show that when lesion repair is imperfect, Semiconservative Replication displays characteristics from both conservative Replication and Semiconservative Replication with perfect lesion repair. The work presented here provides a formulation of the model which greatly facilitates the analysis of a relatively broad class of fitness landscapes, and thus serves as a convenient springboard into biological applications of imperfect lesion repair.
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Semiconservative Replication in the quasispecies model II: Generalization to arbitrary lesion repair probabilities
arXiv: Populations and Evolution, 2004Co-Authors: Emmanuel Tannenbaum, James L. Sherley, Eugene I ShakhnovichAbstract:This paper extends the Semiconservative quasispecies equations to account for arbitrary post-Replication lesion repair efficiency. Such an extension could be an important tool for understanding processes such as cancer development and stem cell growth. Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of ``master-genome''-based fitness landscapes. We use these equations to solve for a ``generalized'' single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. The central pattern that emerges from our studies is that imperfect lesion repair often leads to increased mutational robustness over Semiconservative Replication with completely efficient lesion repair. The reason for this is that imperfect lesion repair breaks some of the correlation between the parent and daughter strands, thereby preventing Replication errors from destroying the information in the original genome. The result is a delayed error catastrophe over that expected from the original Semiconservative quasispecies model. In particular, we show that when only of the strands is necessary for conferring viability, then, when lesion repair is turned off, a Semiconservatively replicating system becomes an effectively conservatively replicating one.
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Semiconservative Replication in the quasispecies model.
Physical review. E Statistical nonlinear and soft matter physics, 2004Co-Authors: Emmanuel Tannenbaum, Eric J Deeds, Eugene I ShakhnovichAbstract:This paper extends Eigen's quasispecies equations to account for the Semiconservative nature of DNA Replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when micro, the product of sequence length and per base pair mismatch probability, exceeds 2 ln [2/ ( 1+1/k ) ], where k>1 is the first-order growth rate constant of the viable "master" sequence (with all other sequences having a first-order growth rate constant of 1 ). This is in contrast to the result of ln k for conservative Replication. In particular, as k--> infinity, the error catastrophe is never reached for conservative Replication, while for Semiconservative Replication the critical micro approaches 2 ln 2. Semiconservative Replication is therefore considerably less robust than conservative Replication to the effect of Replication errors. We also show that the mean equilibrium fitness of a Semiconservatively replicating system is given by k ( 2 e(-micro/2) -1 ) below the error catastrophe, in contrast to the standard result of k e(-micro) for conservative Replication (derived by Kimura and Maruyama in 1966). From this result it is readily shown that Semiconservative Replication is necessary to account for the observation that, at sufficiently high mutagen concentrations, faster replicating cells will die more quickly than more slowly replicating cells. Thus, in contrast to Eigen's original model, the Semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents.
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Semiconservative Replication in the quasispecies model.
Physical Review E, 2004Co-Authors: Emmanuel Tannenbaum, Eric J Deeds, Eugene I ShakhnovichAbstract:This is the publisher's version, also available electronically from http://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.061916.
Emmanuel Tannenbaum - One of the best experts on this subject based on the ideXlab platform.
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Semiconservative Replication, genetic repair, and many-gened genomes: Extending the quasispecies paradigm to living systems
Physics of Life Reviews, 2005Co-Authors: Emmanuel Tannenbaum, Eugene I ShakhnovichAbstract:Quasispecies theory has emerged as an important tool for modeling the evolutionary dynamics of biological systems. We review recent advances in the field, with an emphasis on the quasispecies dynamics of Semiconservatively replicating genomes. Applications to cancer and adult stem cell growth are discussed. Additional topics, such as genetic repair and many-gene genomes, are covered as well.
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Imperfect DNA lesion repair in the Semiconservative quasispecies model: derivation of the Hamming class equations and solution of the single-fitness peak landscape.
Physical review. E Statistical nonlinear and soft matter physics, 2004Co-Authors: Emmanuel Tannenbaum, James L. Sherley, Eugene I ShakhnovichAbstract:This paper develops a Hamming class formalism for the Semiconservative quasispecies equations with imperfect lesion repair, first presented and analytically solved in Y. Brumer and E.I. Shakhnovich (q-bio.GN/0403018, 2004). Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of fitness landscapes defined by a master genome. We use these equations to solve for a generalized single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. We determine the mean equilibrium fitness and error threshold for this class of landscapes, and show that when lesion repair is imperfect, Semiconservative Replication displays characteristics from both conservative Replication and Semiconservative Replication with perfect lesion repair. The work presented here provides a formulation of the model which greatly facilitates the analysis of a relatively broad class of fitness landscapes, and thus serves as a convenient springboard into biological applications of imperfect lesion repair.
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Semiconservative Replication in the quasispecies model II: Generalization to arbitrary lesion repair probabilities
arXiv: Populations and Evolution, 2004Co-Authors: Emmanuel Tannenbaum, James L. Sherley, Eugene I ShakhnovichAbstract:This paper extends the Semiconservative quasispecies equations to account for arbitrary post-Replication lesion repair efficiency. Such an extension could be an important tool for understanding processes such as cancer development and stem cell growth. Starting from the quasispecies dynamics over the space of genomes, we derive an equivalent dynamics over the space of ordered sequence pairs. From this set of equations, we are able to derive the infinite sequence length form of the dynamics for a class of ``master-genome''-based fitness landscapes. We use these equations to solve for a ``generalized'' single-fitness-peak landscape, where the master genome can sustain a maximum number of lesions and remain viable. The central pattern that emerges from our studies is that imperfect lesion repair often leads to increased mutational robustness over Semiconservative Replication with completely efficient lesion repair. The reason for this is that imperfect lesion repair breaks some of the correlation between the parent and daughter strands, thereby preventing Replication errors from destroying the information in the original genome. The result is a delayed error catastrophe over that expected from the original Semiconservative quasispecies model. In particular, we show that when only of the strands is necessary for conferring viability, then, when lesion repair is turned off, a Semiconservatively replicating system becomes an effectively conservatively replicating one.
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Semiconservative Replication in the quasispecies model.
Physical review. E Statistical nonlinear and soft matter physics, 2004Co-Authors: Emmanuel Tannenbaum, Eric J Deeds, Eugene I ShakhnovichAbstract:This paper extends Eigen's quasispecies equations to account for the Semiconservative nature of DNA Replication. We solve the equations in the limit of infinite sequence length for the simplest case of a static, sharply peaked fitness landscape. We show that the error catastrophe occurs when micro, the product of sequence length and per base pair mismatch probability, exceeds 2 ln [2/ ( 1+1/k ) ], where k>1 is the first-order growth rate constant of the viable "master" sequence (with all other sequences having a first-order growth rate constant of 1 ). This is in contrast to the result of ln k for conservative Replication. In particular, as k--> infinity, the error catastrophe is never reached for conservative Replication, while for Semiconservative Replication the critical micro approaches 2 ln 2. Semiconservative Replication is therefore considerably less robust than conservative Replication to the effect of Replication errors. We also show that the mean equilibrium fitness of a Semiconservatively replicating system is given by k ( 2 e(-micro/2) -1 ) below the error catastrophe, in contrast to the standard result of k e(-micro) for conservative Replication (derived by Kimura and Maruyama in 1966). From this result it is readily shown that Semiconservative Replication is necessary to account for the observation that, at sufficiently high mutagen concentrations, faster replicating cells will die more quickly than more slowly replicating cells. Thus, in contrast to Eigen's original model, the Semiconservative quasispecies equations are able to provide a mathematical basis for explaining the efficacy of mutagens as chemotherapeutic agents.
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Semiconservative Replication in the quasispecies model.
Physical Review E, 2004Co-Authors: Emmanuel Tannenbaum, Eric J Deeds, Eugene I ShakhnovichAbstract:This is the publisher's version, also available electronically from http://journals.aps.org/pre/abstract/10.1103/PhysRevE.69.061916.
Maria Zannis-hadjopoulos - One of the best experts on this subject based on the ideXlab platform.
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Electron microscopic analysis of in vitro Replication products ofors 8, a mammalian origin enriched sequence
Somatic Cell and Molecular Genetics, 1994Co-Authors: Christopher E. Pearson, Awatef Shihab-el-deen, Gerald B. Price, Maria Zannis-hadjopoulosAbstract:Electron microscopy was used to map the initiation site of ors 8 DNA Replication in vitro in a system that is capable of initiating and supporting one round of Semiconservative Replication of cloned mammalian DNA origin-enriched sequences (ors). Using unique restriction sites in ors 8 plasmid DNA, we have mapped the Replication bubble within the monkey DNA sequence. In addition to site-specific initiation within the ors, the results also indicate bidirectional Replication.
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Structural and Functional Characteristics of Autonomously Replicating Mammalian Origin-Enriched Sequences ( ORS )
DNA Replication: The Regulatory Mechanisms, 1992Co-Authors: Maria Zannis-hadjopoulos, Christopher E. Pearson, David Bell, David C. W. Mah, Michael A. Mcalear, Gerald B. PriceAbstract:Cloned origin-rich sequences (ors) isolated by strand extrusion from mammalian (monkey and human) cells are capable of transient autonomous Semiconservative Replication in transfected HeLa cells. Sequence analyses reveal no primary consensus sequence features that can be associated with origin function, but several common structural features have been noted which include A/T-rich stretches of DNA and inverted repeats that can potentially give rise to cruciform structures. Some similarities to the yeast ARS consensus, the consensus for attachment to nuclear scaffold and for other regulatory elements have also been noted. The data suggest that origin activation is most probably dependent on the presence of structural determinants rather than on primary sequence.
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Plasmids bearing mammalian DNA-Replication origin-enriched (ors) fragments initiate Semiconservative Replication in a cell-free system.
Biochimica et biophysica acta, 1991Co-Authors: Christopher E. Pearson, Lori Frappier, Maria Zannis-hadjopoulosAbstract:Four plasmids containing monkey (CV-1) origin-enriched sequences ( ors ), which we have previously shown to replicate autonomously in CV-1, COS-7 and HeLa cells ( Frappier and Zannis-Hadjopoulos (1987) Proc. Natl. Acad. Sci. USA 84, 6668–6672) , were found to replicate in an in vitro Replication system using HeLa cell extracts. De novo site-specific initiation of Replication on plasmids required the presence of an ors sequence, soluble low-salt cytosolic extract, poly(ethylene glycol), a solution containing the four standard deoxyribonucleoside triphosphates and an ATP regenerating system. The major reaction products migrated as relaxed circular and linear plasmid DNAs, both in the presence and absence of high-salt nuclear extracts. Inclusion of high-salt nuclear extract was required to obtain closed circular supercoiled molecules. Replicative intermediates migrating slower than form II and topoisomers migrating between forms II and I were also included among the Replication products. Replication of the ors plasmids was not inhibited by ddTTP, an inhibitor of DNA polymerase β and γ, and was sensitive to aphidicolin indicating that DNA polymerase α and/or σ was responsible for DNA synthesis. Origin mapping experiments showed that early in the in vitro Replication reaction, incorporation of nucleotides occurs preferentially at ors -containing fragments, indicating ors specific initiation of Replication. In contrast, the limited incorporation of nucleotides into pBR322, was not site specific. The observed synthesis was Semiconservative and appeared to be bidirectional.
Susan M. Gasser - One of the best experts on this subject based on the ideXlab platform.
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Cyclin B-Cdk1 Kinase Stimulates ORC- and Cdc6-Independent Steps of Semiconservative Plasmid Replication in Yeast Nuclear Extracts
Molecular and cellular biology, 1999Co-Authors: Bernard P. Duncker, Philippe Pasero, Diego Braguglia, Patrick Heun, Michael Weinreich, Susan M. GasserAbstract:Nuclear extracts from Saccharomyces cerevisiae cells synchronized in S phase support the Semiconservative Replication of supercoiled plasmids in vitro. We examined the dependence of this reaction on the prereplicative complex that assembles at yeast origins and on S-phase kinases that trigger initiation in vivo. We found that Replication in nuclear extracts initiates independently of the origin recognition complex (ORC), Cdc6p, and an autonomously replicating sequence (ARS) consensus. Nonetheless, quantitative density gradient analysis showed that S- and M-phase nuclear extracts consistently promote Semiconservative DNA Replication more efficiently than G1-phase extracts. The observed Semiconservative Replication is compromised in S-phase nuclear extracts deficient for the Cdk1 kinase (Cdc28p) but not in extracts deficient for the Cdc7p kinase. In a cdc4-1 G1-phase extract, which accumulates high levels of the specific Clb-Cdk1 inhibitor p40 SIC1 , very low levels of Semiconservative DNA Replication were detected. Recombinant Clb5-Cdc28 restores Replication in a cdc28-4 S-phase extract yet fails to do so in the cdc4-1 G1-phase extract. In contrast, the addition of recombinant Xenopus CycB-Cdc2, which is not sensitive to inhibition by p40 SIC1 , restores efficient Replication to both extracts. Our results suggest that in addition to its well-characterized role in regulating the origin-specific preReplication complex, the Clb-Cdk1 complex modulates the efficiency of the Replication machinery itself. Replication of the eukaryotic genome occurs exclusively during S phase and requires strict coordination among cisacting sequences, the replicative enzymes, and their regulatory factors to ensure that origins of Replication fire only once per cell cycle. The presence of multiple origins of Replication on eukaryotic chromosomes permits the simultaneous engage
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ORC-dependent and origin-specific initiation of DNA Replication at defined foci in isolated yeast nuclei.
Genes & development, 1997Co-Authors: Philippe Pasero, Diego Braguglia, Susan M. GasserAbstract:We describe an in vitro Replication assay from yeast in which the addition of intact nuclei to an S-phase nuclear extract results in the incorporation of deoxynucleotides into genomic DNA at spatially discrete foci. When BrdUTP is substituted for dTTP, part of the newly synthesized DNA shifts to a density on CsCl gradients, indicative of Semiconservative Replication. Initiation occurs in an origin-specific manner and can be detected in G1- or S-phase nuclei, but not in G2-phase or mitotic nuclei. The S-phase extract contains a heat- and 6-DMAP-sensitive component necessary to promote Replication in G1-phase nuclei. Replication of nuclear DNA is blocked at the restrictive temperature in an orc2-1 mutant, and the inactive Orc2p cannot be complemented in trans by an extract containing wild-type ORC. The initiation of DNA Replication in cln-deficient nuclei blocked in G1 indicates that the ORC-dependent preReplication complex is formed before Start. This represents the first nonviral and nonembryonic Replication system in which DNA Replication initiates in an ORC-dependent and origin-specific manner in vitro.
Christopher E. Pearson - One of the best experts on this subject based on the ideXlab platform.
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Electron microscopic analysis of in vitro Replication products ofors 8, a mammalian origin enriched sequence
Somatic Cell and Molecular Genetics, 1994Co-Authors: Christopher E. Pearson, Awatef Shihab-el-deen, Gerald B. Price, Maria Zannis-hadjopoulosAbstract:Electron microscopy was used to map the initiation site of ors 8 DNA Replication in vitro in a system that is capable of initiating and supporting one round of Semiconservative Replication of cloned mammalian DNA origin-enriched sequences (ors). Using unique restriction sites in ors 8 plasmid DNA, we have mapped the Replication bubble within the monkey DNA sequence. In addition to site-specific initiation within the ors, the results also indicate bidirectional Replication.
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Structural and Functional Characteristics of Autonomously Replicating Mammalian Origin-Enriched Sequences ( ORS )
DNA Replication: The Regulatory Mechanisms, 1992Co-Authors: Maria Zannis-hadjopoulos, Christopher E. Pearson, David Bell, David C. W. Mah, Michael A. Mcalear, Gerald B. PriceAbstract:Cloned origin-rich sequences (ors) isolated by strand extrusion from mammalian (monkey and human) cells are capable of transient autonomous Semiconservative Replication in transfected HeLa cells. Sequence analyses reveal no primary consensus sequence features that can be associated with origin function, but several common structural features have been noted which include A/T-rich stretches of DNA and inverted repeats that can potentially give rise to cruciform structures. Some similarities to the yeast ARS consensus, the consensus for attachment to nuclear scaffold and for other regulatory elements have also been noted. The data suggest that origin activation is most probably dependent on the presence of structural determinants rather than on primary sequence.
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Plasmids bearing mammalian DNA-Replication origin-enriched (ors) fragments initiate Semiconservative Replication in a cell-free system.
Biochimica et biophysica acta, 1991Co-Authors: Christopher E. Pearson, Lori Frappier, Maria Zannis-hadjopoulosAbstract:Four plasmids containing monkey (CV-1) origin-enriched sequences ( ors ), which we have previously shown to replicate autonomously in CV-1, COS-7 and HeLa cells ( Frappier and Zannis-Hadjopoulos (1987) Proc. Natl. Acad. Sci. USA 84, 6668–6672) , were found to replicate in an in vitro Replication system using HeLa cell extracts. De novo site-specific initiation of Replication on plasmids required the presence of an ors sequence, soluble low-salt cytosolic extract, poly(ethylene glycol), a solution containing the four standard deoxyribonucleoside triphosphates and an ATP regenerating system. The major reaction products migrated as relaxed circular and linear plasmid DNAs, both in the presence and absence of high-salt nuclear extracts. Inclusion of high-salt nuclear extract was required to obtain closed circular supercoiled molecules. Replicative intermediates migrating slower than form II and topoisomers migrating between forms II and I were also included among the Replication products. Replication of the ors plasmids was not inhibited by ddTTP, an inhibitor of DNA polymerase β and γ, and was sensitive to aphidicolin indicating that DNA polymerase α and/or σ was responsible for DNA synthesis. Origin mapping experiments showed that early in the in vitro Replication reaction, incorporation of nucleotides occurs preferentially at ors -containing fragments, indicating ors specific initiation of Replication. In contrast, the limited incorporation of nucleotides into pBR322, was not site specific. The observed synthesis was Semiconservative and appeared to be bidirectional.
