Mathematical modeling of the processes of DNA synthesis in irradiated cells and cell populations. Modeling of the initiation and elongation of DNA chains in irradiated mammalian cells

Dose-dependence of DNA synthesis inhibition in cells of HeLa suspension culture, bone marrow and thymus of mice was investigated. A contribution of inhibition of replicon synthesis and DNA chain elongation to the total effect of DNA synthesis inhibition by gamma-radiation was estimated by mathematical simulation. The method is proposed for evaluation of Di that characterizes cell radiosensitivity. Radiosensitivity of HeLa cells after preirradiation or exposure to 5-fluorodeoxyuridine was assessed.     

Analysis of the kinetics of cell transition to DNA synthesis in systems with stimulated proliferation. I. Properties of a mathematical model of cell kinetics]

Some features of the mathematical model of cell kinetics in the systems stimulated or induced to proliferate are under consideration in this work. The proposed model serves as a basis of the kinetics analysis of the transition of cells to the DNA synthesis.     

Direct observation of translocation in individual DNA polymerase complexes

Complexes of phi29 DNA polymerase and DNA fluctuate on the millisecond time scale between two ionic current amplitude states when captured atop the α-hemolysin nanopore in an applied field. The lower amplitude state is stabilized by complementary dNTP and thus corresponds to complexes in the post-translocation state. We have demonstrated that in the upper amplitude state, the DNA is displaced by a distance of one nucleotide from the post-translocation state. We propose that the upper amplitude state corresponds to complexes in the pre-translocation state. Force exerted on the template strand biases the complexes toward the pre-translocation state. Based on the results of voltage and dNTP titrations, we concluded through mathematical modeling that complementary dNTP binds only to the post-translocation state, and we estimated the binding affinity. The equilibrium between the two states is influenced by active site-proximal DNA sequences. Consistent with the assignment of the upper amplitude state as the pre-translocation state, a DNA substrate that favors the pre-translocation state in complexes on the nanopore is a superior substrate in bulk phase for pyrophosphorolysis. There is also a correlation between DNA sequences that bias complexes toward the pre-translocation state and the rate of exonucleolysis in bulk phase, suggesting that during DNA synthesis the pathway for transfer of the primer strand from the polymerase to exonuclease active site initiates in the pre-translocation state.     

Modelling the fission yeast cell cycle.

The molecular networks regulating basic physiological processes in a cell can be converted into mathematical equations (eg differential equations) and solved by a computer. The division cycle of eukaryotic cells is an important example of such a control system, and fission yeast is an excellent test organism for the computational modelling approach. The mathematical model is tested by simulating wild-type cells and many known cell cycle mutants. This paper describes an example where this approach is useful in understanding multiple rounds of DNA synthesis (endoreplication) in fission yeast cells that lack the main (B-type) mitotic cyclin, Cdc13. It is proposed that the key physiological variable driving progression through the cell cycle during balanced growth and division is the mass/DNA ratio, rather than the mass/nucleus ratio.     

Analysis of DNA synthesis rate of cultured cells from flow cytometric data

The rate of DNA synthesis along S phase is estimated from flow cytometric histograms on the basis of a mathematical model of a cell population. In the absence of loss, the model expresses the population kinetics in terms of DNA synthesis rate, S-phase influx, and population size. A single histogram is sufficient to determine the DNA synthesis rate when the population is in balanced exponential growth. Two suitably chosen histograms are necessary if the S-phase influx is exponential in a time interval longer than the S-phase duration. The analysis procedure was tested on published autoradiographic data and applied to three cultured cell lines (CM-S, 3LL, and M14 cells) that show various patterns of DNA distribution. In each case the cell-cycle fractions, the DNA synthesis rate, and the S-phase duration were obtained.     

Beta-adrenergic, cAMP-mediated stimulation of proliferation of brown fat cells in primary culture. Mediation via beta 1 but not via beta 3 adrenoceptors.

The ability of adrenergic stimulation to affect the rate of DNA synthesis in mouse brown adipocyte precursor cells proliferating in primary culture was investigated. Addition of 1 microM norepinephrine to the cells at day 4 in culture (proliferating cells) significantly increased the rate of DNA synthesis, whereas no significant effect was seen at day 9 (confluent cells). The effect of norepinephrine could be mimicked by forskolin, cholera toxin, and by cAMP analogues. Specific [3H]thymidine incorporation (per unit of DNA) was reduced by norepinephrine stimulation, indicating saturation of the salvage pathway for dTTP synthesis already in unstimulated cells and implying a beta-adrenergic stimulation of dTTP synthesis. Pharmacological characterization of this effect indicated it was mediated by beta 1 receptors, with alpha 2 receptors exerting an opposing effect. Notably, the stimulation of DNA synthesis was not observed with the beta 3-specific agonist CGP-12177. In contrast, both norepinephrine and CGP-12177 were able to induce the expression of the uncoupling protein thermogenin in the confluent cultured cells. This coincided with a shift in the cAMP-elevating potential of CGP-12177, from being antagonistic to norepinephrine stimulation in proliferating cells to being itself a full agonist in confluent cells, implying occurrence of coupled beta 3 receptors as part of the differentiation process. It was concluded that brown fat precursor cells respond directly to norepinephrine stimulation with an increased DNA synthesis, and that this response is mediated via the classical beta 1 receptors. This probably represents the cellular basis for the hyperplasia observed in the tissue in physiologically recruited states.     

Gene conversion in Escherichia coli. Resolution of heteroallelic mismatched nucleotides by co-repair

We have constructed heteroduplex plasmid DNA that is similar in structure to the heteroduplex DNA expected to be produced during genetic recombination of plasmids, and studied its repair after transformation into different Escherichia coli strains. The heteroduplex DNA was constructed using two different parental plasmids, each of which contained a different ten-nucleotide insertion mutation. The effect of different defined states of dam-methylation on repair was also examined. We found that heteroduplex DNA repair occurred prior to the replication of the substrate DNA 60 to 80% of the time, regardless of the state of DNA methylation. Most excision/synthesis tracts covered two markers separated by 1243 base-pairs, and this process has been termed co-repair. The most efficient co-repair pathway was the Dam-instructed repair pathway that required the mutH, mutL, mutS and uvrD gene products and preferentially used the methylated strand as the template for DNA synthesis. If there was no methylation asymmetry, mismatch nucleotide repair occurred with a similar frequency; however, no strand bias was observed. Co-repair of symmetrically methylated heteroduplex DNA required the mutS and uvrD gene products, while repair of unmethylated heteroduplex DNA also required the mutL and mutH gene products.     

Inheritance of epigenetic chromatin silencing

Maintenance of alternative chromatin states through cell divisions pose some fundamental constraints on the dynamics of histone modifications. In this paper, we study the systems biology of epigenetic inheritance by defining and analyzing general classes of mathematical models. We discuss how the number of modification states involved plays an essential role in the stability of epigenetic states. In addition, DNA duplication and the consequent dilution of marked histones act as a large perturbation for a stable state of histone modifications. The requirement that this large perturbation falls into the basin of attraction of the original state sometimes leads to additional constraints on effective models. Two such models, inspired by two different biological systems, are compared in their fulfilling the requirements of multistability and of recovery after DNA duplication. We conclude that in the presence of multiple histone modifications that characterize alternative epigenetic stable states, these requirements are more easily fulfilled.     

Induction of proliferating cell nuclear antigen (PCNA) complex formation in quiescent fibroblasts from a xeroderma pigmentosum patient.

Accumulated evidence indicates that proliferating cell nuclear antigen (PCNA) is an auxiliary protein of DNA polymerase delta and forms tight association with DNA replication sites during DNA replication or DNA repair synthesis. In this study, such PCNA complex formation was investigated by the indirect immunofluorescence method, using both normal human fibroblasts and those derived from a xeroderma pigmentosum group A (XP-A) patient. XP-A fibroblasts in both proliferating and quiescent states did not show any differences from normal fibroblasts in the properties of PCNA-staining in the untreated conditions. The PCNA complex formation was induced in quiescent normal fibroblasts by both ultraviolet light (UV)- and X-irradiation, whereas in XP-A fibroblasts it was induced by X-irradiation, but not by UV-irradiation. However, PCNA complex was induced in quiescent XP-A fibroblasts by UV-irradiation when the cells had previously incorporated 5-bromodeoxyuridine (BrdU). These observations indicate a close correlation of PCNA complex formation and unscheduled DNA synthesis (UDS). Thus, it was concluded that PCNA complex formation was commonly induced in at least three conditions to produce UDS in spite of different types of DNA damages and DNA repair mechanisms.     

A model for protein translation: polysome self-organization leads to maximum protein synthesis rates

The genetic information in DNA is transcribed to mRNA and then translated to proteins, which form the building blocks of life. Translation, or protein synthesis, is hence a central cellular process. We have developed a gene-sequence-specific mechanistic model for the translation machinery, which accounts for all the elementary steps of the translation mechanism. We performed a sensitivity analysis to determine the effects of kinetic parameters and concentrations of the translational components on protein synthesis rate. Utilizing our mathematical framework and sensitivity analysis, we investigated the translational kinetic properties of a single mRNA species in Escherichia coli. We propose that translation rate at a given polysome size depends on the complex interplay between ribosomal occupancy of elongation phase intermediate states and ribosome distributions with respect to codon position along the length of the mRNA, and this interplay leads to polysome self-organization that drives translation rate to maximum levels.     

Vaccinia virus infection of HeLa cells. I. Synthesis of vaccinia DNA in host cell nuclei.

The replication of vaccinia virus is thought to take place exclusively in the cytoplasm of host cells. However, using DNA-DNA hybridization techniques, it can be shown that a significant fraction of the synthesis of vaccinia DNA takes place in the nucleus as well as the cytoplasm. The (3H) thymiding pulse-labeled vaccinia DNA synthesized in the nucleus reaches a maximum at about 3 h after infection, corresponding to the time of maximal DNA synthesis in infected cells. At this time host DNA synthesis drops to about 25% of the rate of the uninfected cells. Even with short labeling times (2 min) the nucleus is found to contain 60% of the incorporated (3H)thymidine, much of which is in vaccinia DNA. Prior inhibition of host nuclear DNA synthesis with mitomycin C, followed by removal of the antibiotic causes a subsequent inhibition of vaccinia DNA synthesis and complete suppression of mature virus. Purified nuclei, isolated from vaccinia-infected cells, also synthesize vaccinia DNA in vitro. Over 90% of the DNA synthesized in vitro by isolated nuclei contain vaccinia-specific sequences.     

A Mathematical Model for Basepair Opening in a DNA Double Helix

In this paper, we consider a mathematical model that draws an analogy between a DNA molecule and a mechanical system consisting of two chains of interconnected pendulums. This model is designed to explore the dynamics of the system determined by rotational movements of nucleobases around a double-stranded pentose phosphate backbone. The workability of this model is assessed with respect to various factors: inhomogeneity of the chain of nucleobases, the properties of bonds in complementary pairs, and the formation of open states. It has been shown that simplified models for averaging the characteristics of the chain of nucleobases or simplification of the type of hydrogen bond in their complementary pairs influence the type of solution significantly, impairing the validity of the results. Therefore, the approach to the solution of rotational DNA molecule dynamics developed here is more consistent with its actual biomechanics. It is shown that the emergence of open states within nucleobase pairs and restoration of the closed structure may occur in the tested mathematical model.     

The acquisition and maintenance of cytolytic activity by CD4+ murine T-lymphocyte clones.

The class II MHC antigen-specific CTL clones described in this report lose lytic activity when grown in exogenous rIL-2, but regain lytic activity when rIL-2 is removed from the culture medium. Using this cell model, we have investigated the metabolic activities (i.e., DNA, RNA, and protein synthesis) required for CTL to acquire or down-regulate lytic activity. DNA synthesis inhibitors (hydroxyurea and cytosine-arabinoside) and irradiation did not prevent CTL from gaining lytic activity. However, when protein or RNA synthesis was inhibited, these CTL could no longer acquire lytic activity. Furthermore, evidence showed that continuous RNA and protein syntheses were essential for CTL to exert their lytic function. Studies on cell surface antigen expression of CD3, CD4, Thy-1, and LFA-1 revealed no significant difference of antigen expression between a cloned CTL in its lytic and nonlytic states. Our data suggested that the synthesis of certain proteins and their encoded mRNA are essential for CTL to exert its lytic function and these proteins are not the cell surface antigens involved in CTL-target recognition or binding. Data also indicated that a granule enzyme, serine-esterase, was not involved in the expression of lytic activity in these CTL clones.     

Effects of base damages on DNA replication.

Understanding the response of DNA polymerase to the encountered damage in a template is a key to assessing lethal and mutagenic events of cells exposed to genotoxic agents. In the present study M13 (or f1) DNA templates containing 4 types of thymine damages were prepared, and DNA synthesis was carried out in vitro with the templates. The extent of inhibition of DNA synthesis by the damages was evaluated by measuring [3H]dTMP incorporation. Furthermore, newly synthesized DNA was analyzed on a sequencing gel to determine termination sites of DNA synthesis. The results showed that DNA synthesis was differentially inhibited by the damages, and the termination sites of DNA synthesis were dependent on the structures of the damages and the 3'-5' exonuclease activity of DNA polymerase used.     

Mechanism of T5-induced DNA polymerase. I. Replication of short primer templates.

Bacteriophage T5-induced DNA polymerase shows an initial phase of rapid synthesis, followed by a slower steady rate for much longer periods, with short DNA primer-templates (400 to 600 nucleotides long), in vitro. On extrapolating the line of steady rate back to 0 min, an intercept is obtained on the ordinate. With large DNA primer-templates, such as denatured T5 DNA (average chain length approximately 50,000 bases), the rate of synthesis remains constant and is equal to the initial rate obtained with short primer-templates. The zero time intercept was proportional to the amount of enzyme used and independent of temperature. Polymer challenge experiments indicate that the initial phase of rapid synthesis can be attributed to the processive mode of synthesis by T5 DNA polymerase. After synthesizing a stretch of DNA processively for about 200 nucleotide residues, the enzyme apparently forms a "dead-end complex" with the primer-templates used and must dissociate from the primer-template in order to resume synthesis. The average size of the product made processively, during various phase of synthesis, remains invariant and is in good agreement with the size of the zero time intercept per enzyme molecule.     

Model Predictions of MDM2 Mediated Cell Regulation

In this work we present a mathematical approach to elucidate possible mechanisms involving mdm2 in the regulation of the cell cycle. It has been experimentally shown that the over-expression of MDM2 leads to decoupling of DNA synthesis with mitosis resulting in polyploidy cells with multiple copies of their genomes. The function of MDM2 that decouples the DNA synthesis phase (S) and the Mitosis phase (M) is unclear. To answer this question, we first formulate a mathematical model of the dynamics of the cell cycle regulatory proteins during the DNA synthesis phase and mitosis. This model is then tested for bifurcation that produces period doubling cascades that we relate to the biological event of polyploidy. The model formulation, the underlying biology, and the bifurcation results to delineate the unknown function of MDM2 are presented. Based on reproducing known experimental result of polyploidy in MDM2 overexpressed cells, we propose several possible functions of mdm2, i.e., possible interactions with the other cell cycle regulating proteins that will result in decoupling the S and M phases. We conclude that the most likely unknown function of MDM2 leading to the decoupling of the S and M phases is an obstruction of the activation of cdc25C by MDM2.     

Model predictions of MDM2 mediated cell regulation

In this work we present a mathematical approach to elucidate possible mechanisms involving mdm2 in the regulation of the cell cycle. It has been experimentally shown that the over-expression of MDM2 leads to decoupling of DNA synthesis with mitosis resulting in polyploidy cells with multiple copies of their genomes. The function of MDM2 that uncouples the DNA synthesis phase (S) and the Mitosis phase (M) is unclear. To answer this question, we first formulate a mathematical model of the dynamics of the cell cycle regulatory proteins during the DNA synthesis phase and mitosis. This model is then tested for bifurcation that produces period doubling cascades that we relate to the biological event of polyploidy. The model formulation, the underlying biology, and the bifurcation results to delineate the unknown function of MDM2 are presented. Based on reproducing known experimental result of polyploidy in MDM2 overexpressed cells, we propose several possible functions of mdm2, i.e., possible interactions with the other cell cycle regulating proteins that will result in uncoupling the S and M phases. We conclude that the most likely unknown function of MDM2 leading to the decoupling of the S and M phases is an obstruction of the activation of Cdc25C by MDM2.     

Temperature-sensitive deoxyribonucleic acid replication in a dnaC mutant of Bacillus subtilis.

A temperature-sensitive mutant of Bacillus subtilis is defective in deoxyribonucleic acid (DNA) synthesis, contains a lesion in the dnaC locus, and is not primarily an initiation mutant. The amount of DNA synthesized by this mutant at temperatures above 40 C decreases with increasing temperature. DNA synthesis resumes within 20 min after the temperature is lowered to 30 C. In the presence of chloramphenical, DNA synthesis begins at a reduced rate after the temperature is lowered to 30 C. Spores germinated at 46 C cannot initiate DNA replication. The capacity for residual DNA synthesis is stable at the restrictive temperature during inhibition of DNA synthesis. When the temperature is lowered to 30 C after a period of incubation at 43 C, DNA synthesis starts at the origin of the chromosome as well as at preexisting growing points. Similar DNA synthesis patterns are found in mutant cells in vivo and after toluene treatment.     

Measurements and models of synchronous growth of fission yeast induced by temperature oscillations

Pulsing of temperature in a fermentor at intervals coincident with cell generation time was used to induce synchrony in a population of the fission yeast Schizosaccharomyces pombe. Measurements of culture protein, RNA, and DNA during synchronous growth confirm continuous synthesis of protein and RNA and discontinuos synthesis of DNA as previously reported. Flow microfluorometry of populations at different times during the synchrony cycle was used to monitor the changes in single-cell protein. RNA, and DNA frequency functions. These measurements illustrate very clearly the degree of synchrony and patterns of macromolecular synthesis and also confirm previous estimates of the cellular protein contents characteristic of dividing cells. Additional insights into single-cell kinetics and division controls are provided by two-parameter flow microfluorometry measurements and by mathematical modeling of population dynamics. Such data are necessary foundations for robust population balance models of microbial processes.