Ergodic Sets as Cell Phenotype of Budding Yeast Cell Cycle

It has been suggested that irreducible sets of states in Probabilistic Boolean Networks correspond to cellular phenotype. In this study, we identify such sets of states for each phase of the budding yeast cell cycle. We find that these “ergodic sets” underly the cyclin activity levels during each phase of the cell cycle. Our results compare to the observations made in several laboratory experiments as well as the results of differential equation models. Dynamical studies of this model: (i) indicate that under stochastic external signals the continuous oscillating waves of cyclin activity and the opposing waves of CKIs emerge from the logic of a Boolean-based regulatory network without the need for specific biochemical/kinetic parameters; (ii) suggest that the yeast cell cycle network is robust to the varying behavior of cell size (e.g., cell division under nitrogen deprived conditions); (iii) suggest the irreversibility of the Start signal is a function of logic of the G1 regulon, and changing the structure of the regulatory network can render start reversible.     

Quantifying the Length and Variance of the Eukaryotic Cell Cycle Phases by a Stochastic Model and Dual Nucleoside Pulse Labelling

A fundamental property of cell populations is their growth rate as well as the time needed for cell division and its variance. The eukaryotic cell cycle progresses in an ordered sequence through the phases and and is regulated by environmental cues and by intracellular checkpoints. Reflecting this regulatory complexity, the length of each phase varies considerably in different kinds of cells but also among genetically and morphologically indistinguishable cells. This article addresses the question of how to describe and quantify the mean and variance of the cell cycle phase lengths. A phase-resolved cell cycle model is introduced assuming that phase completion times are distributed as delayed exponential functions, capturing the observations that each realization of a cycle phase is variable in length and requires a minimal time. In this model, the total cell cycle length is distributed as a delayed hypoexponential function that closely reproduces empirical distributions. Analytic solutions are derived for the proportions of cells in each cycle phase in a population growing under balanced growth and under specific non-stationary conditions. These solutions are then adapted to describe conventional cell cycle kinetic assays based on pulse labelling with nucleoside analogs. The model fits well to data obtained with two distinct proliferating cell lines labelled with a single bromodeoxiuridine pulse. However, whereas mean lengths are precisely estimated for all phases, the respective variances remain uncertain. To overcome this limitation, a redesigned experimental protocol is derived and validated in silico. The novelty is the timing of two consecutive pulses with distinct nucleosides that enables accurate and precise estimation of both the mean and the variance of the length of all phases. The proposed methodology to quantify the phase length distributions gives results potentially equivalent to those obtained with modern phase-specific biosensor-based fluorescent imaging.     

Cell cycle arrest in Batten disease lymphoblast cells

Batten disease is an inherited neurodegenerative disorder caused by a CLN3 gene mutation. Batten disease is characterized by blindness, seizures, cognitive decline, and early death. Although apoptotic cell death is one of the pathological hallmarks of Batten disease, little is known about the regulatory mechanism of apoptosis in this disease. Since the CLN3 gene is suggested to be involved in the cell cycle in a yeast model, we investigated the cell cycle profile and its regulatory factors in lymphoblast cells from Batten disease patients. We found G1/G0 cell cycle arrest in Batten disease cells, with overexpression of p21, sphingosine, glucosylceramide, and sulfatide as possible cell cycle regulators.     

Control of the cell cycle ofCandida utilis by external conditions

A mathematical model of the cell cycle ofCandida utilis in a continuous culture was formulated with respect to dilution rate. It makes it possible to express the duration of morphological stages in minutes, separately for mother cells and daughter cells. These values were compared with equivalent parameters in batch cultures. Duration of the morphological stage with buds was much longer in batch cultures as compared with the same value determined for a continuous culture according to the mathematical model. When using cultivation apparatus with a higher aeration capacity the (S + G₂) phase, i.e. the stage bearing the bud, was reduced also in the batch cultures and approached the values determined for the continuous culture by means of the mathematical model.     

Mathematical modeling of fission yeast Schizosaccharomyces pombe cell cycle: exploring the role of multiple phosphatases

Cell cycle is the central process that regulates growth and division in all eukaryotes. Based on the environmental condition sensed, the cell lies in a resting phase G0 or proceeds through the cyclic cell division process (G1??S??G2??M). These series of events and phase transitions are governed mainly by the highly conserved Cyclin dependent kinases (Cdks) and its positive and negative regulators. The cell cycle regulation of fission yeast Schizosaccharomyces pombe is modeled in this study. The study exploits a detailed molecular interaction map compiled based on the published model and experimental data. There are accumulating evidences about the prominent regulatory role of specific phosphatases in cell cycle regulations. The current study emphasizes the possible role of multiple phosphatases that governs the cell cycle regulation in fission yeast S. pombe. The ability of the model to reproduce the reported regulatory profile for the wild-type and various mutants was verified though simulations.     

Human population, urban settlement patterns and their impact on Plasmodium falciparum malaria endemicity

Background

The length of the gonotrophic cycle varies the vectorial capacity of a mosquito vector and therefore its exact estimation is important in epidemiological modelling. Because the gonotrophic cycle length depends on temperature, its estimation can be satisfactorily computed by means of physiological time analysis.

Methods

A model of physiological time was developed and calibrated for Anopheles pseudopunctipennis, one of the main malaria vectors in South America, using data from laboratory temperature controlled experiments. The model was validated under varying temperatures and could predict the time elapsed from blood engorgement to oviposition according to the temperature.

Results

In laboratory experiments, a batch of An. pseudopunctipennis fed at the same time may lay eggs during several consecutive nights (2–3 at high temperature and > 10 at low temperature). The model took into account such pattern and was used to predict the range of the gonotrophic cycle duration of An. pseudopunctipennis in four characteristic sites of Bolivia. It showed that the predicted cycle duration for An. pseudopunctipennis exhibited a seasonal pattern, with higher variances where climatic conditions were less stable. Predicted mean values of the (minimum) duration ranged from 3.3 days up to > 10 days, depending on the season and the geographical location. The analysis of ovaries development stages of field collected biting mosquitoes indicated that the phase 1 of Beklemishev might be of significant duration for An. pseudopunctipennis. The gonotrophic cycle length of An. pseudopunctipennis correlates with malaria transmission patterns observed in Bolivia which depend on locations and seasons.

Conclusion

A new presentation of cycle length results taking into account the number of ovipositing nights and the proportion of mosquitoes laying eggs is suggested. The present approach using physiological time analysis might serve as an outline to other similar studies and allows the inclusion of temperature effects on the gonotrophic cycle in transmission models. However, to better explore the effects of temperature on malaria transmission, the others parameters of the vectorial capacity should be included in the analysis and modelled accordingly.     

Possible functional roles of phase resetting during walking

The walking rhythm is known to show phase shift or "reset" in response to external impulsive perturbations. We tried to elucidate functional roles of the phase reset possibly used for the neural control of locomotion. To this end, a system with a double pendulum as a simplified model of the locomotor control and a model of bipedal locomotion were employed and analyzed in detail. In these models, a movement corresponding to the normal steady-state walking was realized as a stable limit cycle solution of the system. Unexpected external perturbations applied to the system can push the state point of the system away from its limit cycle, either outside or inside the basin of attraction of the limit cycle. Our mathematical analyses of the models suggested functional roles of the phase reset during walking as follows. Function 1: an appropriate amount of the phase reset for a given perturbation can contribute to relocating the system's state point outside the basin of attraction of the limit cycle back to the inside. Function 2: it can also be useful to reduce the convergence time (the time necessary for the state point to return to the limit cycle). In experimental studies during walking of animals and humans, the reset of walking rhythm induced by perturbations was investigated using the phase transition curve (PTC) or the phase resetting curve (PRC) representing phase-dependent responses of the walking. We showed, for the simple double-pendulum model, the existence of the optimal phase control and the corresponding PTC that could optimally realize the aforementioned functions in response to impulsive force perturbations. Moreover, possible forms of PRC that can avoid falling against the force perturbations were predicted by the biped model, and they were compared with the experimentally observed PRC during human walking. Finally, physiological implications of the results were discussed.     

Luteal function during the periimplantation period and requirement for estrogen for implantation and pregnancy maintenance in the non-human primate

An attempt has been made in this paper to review our present understanding of luteal function during the periimplantation period and in particular hormonal requirement for implantation and maintenance of early pregnancy in the non-human primate.In a fertile cycle thecorpus luteum is apparently rescued from luteolysis by chorionic gonadotropin secreted by the implanted blastocyst, In the bonnet monkey the serum progesterone titers during the luteal phase of a fertile cycle seems higher compared to that of nonmated cycling monkeys. This suggested that thecorpus luteum is receiving some stimulatory signal from the blastocyst even prior to implantation. The recent demonstration that human blastocyst in culture secretes into the medium human chorionic gonadotropin essentially support the above assumption. However, attempts to extend the luteal phase of cycling unmated monkeys with exogenous human chorionic gonadotropin injection has hitherto not met with complete success suggesting that there could be other than chorionic gonadotropin, additional luteal stimulatory factors the unimplanted blastocyst is secreting.Corpus luteum is the principle source of both progesterone and estrogen produced during the periimplantation period and dysruption of luteal function, brought about by either lutectomy or ovariectomy or luteinizing hormone antiserum treatment, followed by progesterone supplementation leads to maintenance of pregnancy. This has lead to questioning the need for estrogen in the maintenance of early pregnancy. Recent work using Zuclomiphene, an antiestrogen during days 5–11 of cycle in rhesus monkeys mated between day 9–14, has however, suggested that estrogen may be required for implantation. Further work is needed to arrive at an unequivocal decision regarding the need for estrogen in maintenance of early pregnancy in the primate.     

From START to FINISH: The Influence of Osmotic Stress on the Cell Cycle

The cell cycle is a sequence of biochemical events that are controlled by complex but robust molecular machinery. This enables cells to achieve accurate self-reproduction under a broad range of different conditions. Environmental changes are transmitted by molecular signalling networks, which coordinate their action with the cell cycle. The cell cycle process and its responses to environmental stresses arise from intertwined nonlinear interactions among large numbers of simpler components. Yet, understanding of how these pieces fit together into a coherent whole requires a systems biology approach. Here, we present a novel mathematical model that describes the influence of osmotic stress on the entire cell cycle of S. cerevisiae for the first time. Our model incorporates all recently known and several proposed interactions between the osmotic stress response pathway and the cell cycle. This model unveils the mechanisms that emerge as a consequence of the interaction between the cell cycle and stress response networks. Furthermore, it characterises the role of individual components. Moreover, it predicts different phenotypical responses for cells depending on the phase of cells at the onset of the stress. The key predictions of the model are: (i) exposure of cells to osmotic stress during the late S and the early G2/M phase can induce DNA re-replication before cell division occurs, (ii) cells stressed at the late G2/M phase display accelerated exit from mitosis and arrest in the next cell cycle, (iii) osmotic stress delays the G1-to-S and G2-to-M transitions in a dose dependent manner, whereas it accelerates the M-to-G1 transition independently of the stress dose and (iv) the Hog MAPK network compensates the role of the MEN network during cell division of MEN mutant cells. These model predictions are supported by independent experiments in S. cerevisiae and, moreover, have recently been observed in other eukaryotes.     

Multi-step Loading of Human Minichromosome Maintenance Proteins in Live Human Cells

Once-per-cell cycle replication is regulated through the assembly onto chromatin of multisubunit protein complexes that license DNA for a further round of replication. Licensing consists of the loading of the hexameric MCM2–7 complex onto chromatin during G₁ phase and is dependent on the licensing factor Cdt1. In vitro experiments have suggested a two-step binding mode for minichromosome maintenance (MCM) proteins, with transient initial interactions converted to stable chromatin loading. Here, we assess MCM loading in live human cells using an in vivo licensing assay on the basis of fluorescence recovery after photobleaching of GFP-tagged MCM protein subunits through the cell cycle. We show that, in telophase, MCM2 and MCM4 maintain transient interactions with chromatin, exhibiting kinetics similar to Cdt1. These are converted to stable interactions from early G₁ phase. The immobile fraction of MCM2 and MCM4 increases during G₁ phase, suggestive of reiterative licensing. In late G₁ phase, a large fraction of MCM proteins are loaded onto chromatin, with maximal licensing observed just prior to S phase onset. Fluorescence loss in photobleaching experiments show subnuclear concentrations of MCM-chromatin interactions that differ as G₁ phase progresses and do not colocalize with sites of DNA synthesis in S phase.     

Synthesis of photoreactivating enzyme in synchronous and asynchronous cultures of Escherichia coli

The technique of flash photolysis was used to study cellular variations in the number of photoreactivating enzyme (PRE) molecules during the cell division cycle of the UV-sensitive E. coli strain B_S?1. No variations in the number of PRE molecules per genome were observed throughout the cell division cycle when synchronized cells cultured in either glucose-minimal or succinate-minimal medium were used. This is interpreted to mean that PRE synthesis is continuous throughout the cell cycle for glucose-grown cells, but may stop at the time chromosome replication ceases prior to division, in succinate-grown cells. The effect of growth rate and stage of growth on cellular PRE content in asynchronous cultures was also determined. Variations in the number of PRE per genome were observed for both synchronous and asynchronous cells cultured in different media and occurred in a manner that suggested a dependence on growth rate. PRE per genome increased with generation time. Stationary phase cells from each culture medium (nutrient broth, glucose-minimal, succinate-minimal) had more PRE per genome than did respective log phase cells. It is suggested that PRE synthesis may be controlled by some aspect of chromosome replication.     

On the mutability of the yeast mitochondrial genome.

A mechanism is proposed to explain how a mutation in a single molecule of mitochondrial DNA (mitDNA) can come to affect all the other mitDNA molecules of a yeast cell. It is suggested that an initial mutation may be “amplified” by a process which is, in fact, intended to ensure the identity of the cell's complement of mitDNA molecules. It is postulated that this process involves a small number of “reference” copies of mitDNA to which all other (“derived”) copies are compared and corrected once per cell cycle. Asymmetric gene conversion is proposed as the correction mechanism and the means of “amplifying” mutations. The model is shown to be compatible with current data on spontaneous and induced mitochondrial mutation in Saccharomyces cerevisiae.     

Synthesis and identification of 2,4-bisanilinopyrimidines bearing 2,2,6,6-tetramethylpiperidine-N-oxyl as potential Aurora A inhibitors

The Aurora kinases are a family of serine/threonine kinases that interact with components of the mitotic apparatus and serve as potential therapeutic targets in oncology. Herein, we reported a series of 2,4-bisanilinopyrimidines bearing 2,2,6,6-tetramethylpiperidine-N-oxyl with selective inhibition of Aurora A in either enzymatic assays or cellular phenotypic assays, and displaying more potent anti-proliferation compared with that of VX-680. The most potent compound 10a forms better interaction with Aurora A than Aurora B in molecular docking. Mechanistic studies revealed that 10a disrupt the spindle formation, block the cell cycle progression in the G2/M phase and induce apoptosis in HeLa cell. These results suggested that the produced series of compounds are potential anticancer agents for further development as selective Aurora A inhibitors.     

A Stochastic Model Correctly Predicts Changes in Budding Yeast Cell Cycle Dynamics upon Periodic Expression of CLN2

In this study, we focus on a recent stochastic budding yeast cell cycle model. First, we estimate the model parameters using extensive data sets: phenotypes of 110 genetic strains, single cell statistics of wild type and cln3 strains. Optimization of stochastic model parameters is achieved by an automated algorithm we recently used for a deterministic cell cycle model. Next, in order to test the predictive ability of the stochastic model, we focus on a recent experimental study in which forced periodic expression of CLN2 cyclin (driven by MET3 promoter in cln3 background) has been used to synchronize budding yeast cell colonies. We demonstrate that the model correctly predicts the experimentally observed synchronization levels and cell cycle statistics of mother and daughter cells under various experimental conditions (numerical data that is not enforced in parameter optimization), in addition to correctly predicting the qualitative changes in size control due to forced CLN2 expression. Our model also generates a novel prediction: under frequent CLN2 expression pulses, G1 phase duration is bimodal among small-born cells. These cells originate from daughters with extended budded periods due to size control during the budded period. This novel prediction and the experimental trends captured by the model illustrate the interplay between cell cycle dynamics, synchronization of cell colonies, and size control in budding yeast.     

月经周期不同阶段游离皮质醇昼夜节律的变化

为了研究皮质醇分泌的昼夜节律在月经周期中的变化,实验对15位月经周期正常的育龄期健康妇女,在月经周期的不同阶段分别于24h内每隔两小时采样,检测唾液昼夜游离皮质醇水平。采用非线性回归分析模型分析皮质醇昼夜节律。结果显示,皮质醇昼夜节律在整个月经周期都具有复杂的明显受到亚节律(ultradian)影响的分泌形式;与月经期相比,围排卵期和黄体晚期昼夜节律波峰宽度(peak-width)明显减低(P=0．005与0．031),而昼夜节律波谷(trough)有抬高趋势(P=0．0622与0．066);黄体晚期的亚节律波幅(ultradian amplitude)与月经期相比显著减低(P=0．002)而与围排卵期相比有减低趋势(P=0．05)。这些结果提示月经周期的不同阶段对皮质醇分泌的昼夜节律有影响。     

Polyamines and the Cell Cycle of Catharanthus roseus Cells in Culture

Investigation was made on the effect of partial depletion of polyamines (PAs), induced by treatment with inhibitors of the biosynthesis of PAs, on the distribution of cells at each phase of the cell cycle in Catharanthus roseus (L.) G. Don. cells in suspension cultures, using flow cytometry. More cells treated with inhibitors of arginine decarboxylase (ADC) and ornithine decarboxylase (ODC) were accumulated in the G₁ phase than those in the control, while the treatment with an inhibitor of spermidine (SPD) synthase showed no effect on the distribution of cells. The endogenous levels of the PAs, putrescine (PUT), SPD, and spermine (SPM), were determined during the cell cycle in synchronous cultures of C. roseus. Two peaks of endogenous level of PAs, in particular, of PUT and SPD, were observed during the cell cycle. Levels of PAs increased markedly prior to synthesis of DNA in the S phase and prior to cytokinesis. Activities of ADC and ODC were also assayed during the cell cycle. Activities of ADC was much higher than that of ODC throughout the cell cycle, but both activities of ODC and ADC changed in concert with changes in levels of PAs. Therefore, it is suggested that these enzymes may regulate PA levels during the cell cycle. These results indicate that inhibitors of PUT biosynthesis caused the suppression of cell proliferation by prevention of the progression of the cell cycle, probably from the G₁ to the S phase, and PUT may play more important roles in the progression of the cell cycle than other PAs.     

The influence of daily variation in foraging cost on the activity of small carnivores

The daily activity of some predators is correlated with the activity pattern of their prey. If capture efficiency varies as a function of prey activity, a predator that synchronizes its foraging activity with the time of day that prey are most vulnerable should capture more prey, and at lower cost, than a predator that initiates foraging at random. Mink, Mustela vison, and weasels, M. erminea and M. nivalis, were presented with an opportunity to maximize their intake in similar circumstances in the laboratory. An animal's ability to synchronize its foraging activity with the time of day when food was most available was tested. Energy costs (wheel revolutions) were varied to encourage an animal to redistribute its activity from a preferred 12-h phase of the light-dark cycle to the other phase, and then back again. The degree to which activity changed to coincide with the most economical phase was analysed for each individual, and weasels were compared to mink. The activity of six (of seven) animals shifted in response to modified foraging costs, but only two animals (both mink) approached the 180° redistribution of activity expected of an energy-maximizing forager. In general, all animals were active during a favoured phase (usually dark) of the light-dark cycle and relatively large variations in foraging cost during this cycle had only modest effects on activity.     

Immunolocalization of hepatic estrogen and progesterone receptors in the female lizard Uromastyx acanthinura

The hormonal regulation of hepatic synthesis of vitellogenin during the annual reproductive cycle was performed for the first time in the deserticole, oviparous, diurnal and herbivorous Uromastyx acanthinura, a lizard belonging to the Agamidae family. In order to elucidate what kind of estrogen receptor is involved in this process, an immunohistochemical study was performed. Changes were obtained in the labeling and cellular distribution of the estrogen and progesterone receptors according to the period of the reproductive cycle and the experimental administration of 17β-estradiol. Only the ERβ subtype was present; it was found in all phases of the cycle with a variable localization: nuclear and cytosolic during vitellogenesis, mainly cytosolic in the female with egg retention (luteal phase) and strictly cytosolic in females at sexual rest. The progesterone receptors were present only at the luteal phase and during sexual rest and disappeared completely from females after 17β-estradiol treatment in sexual rest. Our data suggested that mediation of action of the 17β-estradiol in the vitellogenin synthesis in the lizard U. acanthinura occured via ERβ. PRA and PRB could both be necessary for the negative effect of progesterone on the hepatic synthesis of vitellogenin.