Clocked cell cycle clocks

A Self-Operating Time Crystal Model of the Human Brain: Can We Replace Entire Brain Hardware with a 3D Fractal Architecture of Clocks Alone?

Time crystal was conceived in the 1970s as an autonomous engine made of only clocks to explain the life-like features of a virus. Later, time crystal was extended to living cells like neurons. The brain controls most biological clocks that regenerate the living cells continuously. Most cognitive tasks and learning in the brain run by periodic clock-like oscillations. Can we integrate all cognitive tasks in terms of running clocks of the hardware? Since the existing concept of time crystal has only one clock with a singularity point, we generalize the basic idea of time crystal so that we could bond many clocks in a 3D architecture. Harvesting inside phase singularity is the key. Since clocks reset continuously in the brain–body system, during reset, other clocks take over. So, we insert clock architecture inside singularity resembling brain components bottom-up and top-down. Instead of one clock, the time crystal turns to a composite, so it is poly-time crystal. We used century-old research on brain rhythms to compile the first hardware-free pure clock reconstruction of the human brain. Similar to the global effort on connectome, a spatial reconstruction of the brain, we advocate a global effort for more intricate mapping of all brain clocks, to fill missing links with respect to the brain’s temporal map. Once made, reverse engineering the brain would remain a mere engineering challenge.

Quantitative Studies for Cell-Division Cycle Control

The cell-division cycle (CDC) is driven by cyclin-dependent kinases (CDKs). Mathematical models based on molecular networks, as revealed by molecular and genetic studies, have reproduced the oscillatory behavior of CDK activity. Thus, one basic system for representing the CDC is a biochemical oscillator (CDK oscillator). However, genetically clonal cells divide with marked variability in their total duration of a single CDC round, exhibiting non-Gaussian statistical distributions. Therefore, the CDK oscillator model does not account for the statistical nature of cell-cycle control. Herein, we review quantitative studies of the statistical properties of the CDC. Over the past 70 years, studies have shown that the CDC is driven by a cluster of molecular oscillators. The CDK oscillator is coupled to transcriptional and mitochondrial metabolic oscillators, which cause deterministic chaotic dynamics for the CDC. Recent studies in animal embryos have raised the possibility that the dynamics of molecular oscillators underlying CDC control are affected by allometric volume scaling among the cellular compartments. Considering these studies, we discuss the idea that a cluster of molecular oscillators embedded in different cellular compartments coordinates cellular physiology and geometry for successful cell divisions.

Planktonic food web structure and trophic transfer efficiency along a productivity gradient in the tropical and subtropical Atlantic Ocean

Oligotrophic and productive areas of the ocean differ in plankton community composition and biomass transfer efficiency. Here, we describe the plankton community along a latitudinal transect in the tropical and subtropical Atlantic Ocean. Prochlorococcus dominated the autotrophic community at the surface and mixed layer of oligotrophic stations, replaced by phototrophic picoeukaryotes and Synechococcus in productive waters. Depth-integrated biomass of microzooplankton was higher than mesozooplankton at oligotrophic stations, showing similar biomasses in productive waters. Dinoflagellates dominated in oligotrophic waters but ciliates dominated upwelling regions. In oligotrophic areas, microzooplankton consumed ca. 80% of the production, but ca. 66% in upwelling zones. Differences in microzooplankton and phytoplankton communities explain microzooplankton diel feeding rhythms: higher grazing rates during daylight in oligotrophic areas and diffuse grazing patterns in productive waters. Oligotrophic areas were more efficient at recycling and using nutrients through phytoplankton, while the energy transfer efficiency from nutrients to mesozooplankton appeared more efficient in productive waters. Our results support the classic paradigm of a shorter food web, and more efficient energy transfer towards upper food web levels in productive regions, but a microbially dominated, and very efficient, food web in oligotrophic regions. Remarkably, both models of food web exist under very high microzooplankton herbivory.

Rhythmicity of coastal marine picoeukaryotes, bacteria and archaea despite irregular environmental perturbations

Seasonality in marine microorganisms has been classically observed in phytoplankton blooms, and more recently studied at the community level in prokaryotes, but rarely investigated at the scale of individual microbial taxa. Here we test if specific marine eukaryotic phytoplankton, bacterial and archaeal taxa display yearly rhythms at a coastal site impacted by irregular environmental perturbations. Our seven-year study in the Bay of Banyuls (North Western Mediterranean Sea) shows that despite some fluctuating environmental conditions, many microbial taxa displayed significant yearly rhythms. The robust rhythmicity was found in both autotrophs (picoeukaryotes and cyanobacteria) and heterotrophic prokaryotes. Sporadic meteorological events and irregular nutrient supplies did, however, trigger the appearance of less common non-rhythmic taxa. Among the environmental parameters that were measured, the main drivers of rhythmicity were temperature and day length. Seasonal autotrophs may thus be setting the pace for rhythmic heterotrophs. Similar environmental niches may be driving seasonality as well. The observed strong association between Micromonas and SAR11, which both need thiamine precursors for growth, could be a first indication that shared nutritional niches may explain some rhythmic patterns of co-occurrence.

Growth and cell cycle of Ulva compressa (Ulvophyceae) under LED illumination

The cell-cycle progression of Ulva compressa is diurnally gated at the G1 phase in accordance with light-dark cycles. The present study was designed to examine the spectral sensitivity of the G1 gating system. When blue, red, and green light-emitting diodes (LEDs) were used for illumination either alone or in combination, the cells divided under all illumination conditions, suggesting that all colors of light were able to open the G1 gate. Although blue light was most effective to open the G1 gate, red light alone or green light alone was also able to open the G1 gate even at irradiance levels lower than the light compensation point of each color. Occurrence of a period of no cell division in the course of a day suggested that the G1 gating system normally functioned as under ordinary illumination by cool-white fluorescent lamps. The rise of the proportion of blue light to green light resulted in increased growth rate. On the other hand, the growth rates did not vary regardless of the proportion of blue light to red light. These results indicate that the difference in growth rate due to light color resulted from the difference in photosynthetic efficiency of the colors of light. However, the growth rates significantly decreased under conditions without blue light. This result suggests that blue light mediates cell elongation and because the spectral sensitivity of the cell elongation regulating system was different from that of the G1 gating system, distinct photoreceptors are likely to mediate the two systems.

Effect of Phosphorus on the Synechococcus Cell Cycle in Surface Mediterranean Waters during Summer

The effect of phosphorus (P) and nitrogen (N) additions on the Synechococcus cell cycle was tested with natural populations from the Mediterranean Sea in summer. In the absence of stimulation, the Synechococcus cell cycle was synchronized to the light-dark cycle. DNA synthesis began around 1600, a maximum of S-phase cells was observed at around dusk (2100), and a maximum of G(inf2)-phase cells was observed at around 2400. Addition of P (as PO(inf4)(sup3-)) caused, in all cases, a decrease in the fraction of cells in G(inf2) at around 1800, no change at around 2400, and an increase at around 1200 the next day, while addition of N (as NO(inf3)(sup-)) had no effect. We hypothesize that P addition induced a shortening of the G(inf1) phase, resulting in cells entering and leaving the S and G(inf2) phases earlier. These data suggest very strongly that the Synechococcus cells were P limited rather than N limited during this period of the year. In most cases, additions as low as 20 nM P induced a cell cycle response. From dose-response curves, we established that the P concentration inducing a 50% change in the percentage of cells in G(inf2) was low, close to 10 nM, at the beginning of the sampling period (30 June) and increased to about 50 nM by the end (9 July), suggesting a decrease in the severity of P limitation. This study extends recent observations that oligotrophic systems may be P rather than N limited at certain times of the year.

Circadian-independent cell mitosis in immortalized fibroblasts

Two prominent timekeeping systems, the cell cycle, which controls cell division, and the circadian system, which controls 24-h rhythms of physiology and behavior, are found in nearly all living organisms. A distinct feature of circadian rhythms is that they are temperature-compensated such that the period of the rhythm remains constant (approximately 24 h) at different ambient temperatures. Even though the speed of cell division, or growth rate, is highly temperature-dependent, the cell-mitosis rhythm is temperature-compensated. Twenty-four-hour fluctuations in cell division have also been observed in numerous species, suggesting that the circadian system is regulating the timing of cell division. We tested whether the cell-cycle rhythm was coupled to the circadian system in immortalized rat-1 fibroblasts by monitoring cell-cycle gene promoter-driven luciferase activity. We found that there was no consistent phase relationship between the circadian and cell cycles, and that the cell-cycle rhythm was not temperature-compensated in rat-1 fibroblasts. These data suggest that the circadian system does not regulate the cell-mitosis rhythm in rat-1 fibroblasts. These findings are inconsistent with numerous studies that suggest that cell mitosis is regulated by the circadian system in mammalian tissues in vivo. To account for this discrepancy, we propose two possibilities: (i) There is no direct coupling between the circadian rhythm and cell cycle but the timing of cell mitosis is synchronized with the rhythmic host environment, or (ii) coupling between the circadian rhythm and cell cycle exists in normal cells but it is disconnected in immortalized cells.

Cell cycle arrest as a hallmark of insect diapause: changes in gene transcription during diapause induction in the drosophilid fly, Chymomyza costata

The division cycle of CNS cells was arrested in G0/G1 (86.6%) and G2 (12.8%) phases in diapausing larvae of Chymomyza costata. A two-step response was observed when the diapause was induced by transferring the 3rd instar larvae from long-day to short-day conditions: first, the proportion of G2-arrested cells increased rapidly within a single day after transfer; and second, the increase of G0/G1-arrested cells started with a delay of 5 days after transfer. The changes of relative mRNA levels of seven different genes, which code for important cell cycle regulatory factors [Cyclins D and E, kinases Wee1 and Myt1, phosphatase Cdc25 (String), Dacapo (p27), and PCNA] were followed using qRT-PCR technique. Two reference genes (Rp49 and ss-tubulin) served as a background. Significant transcriptional responses to photoperiodic transfer were observed for two genes: while the relative levels of dacapo mRNA increased during the rapid entry into the G2 arrest, the pcna expression was significantly downregulated during the delayed onset of G0/G1 arrest. In addition, moderate transcriptional upregulations of the genes coding for two inhibitory kinases, wee1 and myt1 accompanied the entry into diapause. The other genes were expressed equally in all photoperiodic conditions.

DIURNAL CELL DIVISION REGULATED BY GATING THE G1 /S TRANSITION IN ENTEROMORPHA COMPRESSA (CHLOROPHYTA)(1)

The cell-cycle progression of Enteromorpha compressa (L.) Nees (=Ulva compressa L.) was diurnally regulated by gating the G1 /S transition. When the gate was open, the cells were able to divide if they had attained a sufficient size. However, the cells were not able to divide while the gate was closed, even if the cells had attained sufficient size. The diurnal rhythm of cell division immediately disappeared when the thalli were transferred to continuous light or darkness. When the thalli were transferred to a shifted photoperiod, the rhythm of cell division immediately and accurately synchronized with the shifted photoperiod. These data support a gating-system model regulated by light:dark (L:D) cycles rather than an endogenous circadian clock. A dark phase of 6 h or longer was essential for gate closing, and a light phase of 14 h was required to renew cell division after a dark phase of >6 h.

Circadian tempo: A paradigm for genome stability?

Circadian clocks are molecular time-keeping systems that underlie daily biological rhythms in anticipation of the changing light and dark cycles. These clocks mediate daily rhythms in physiology and behavior that are thought to confer an adaptive advantage for organisms. It is hypothesized that cell cycle checkpoints are gated to an intrinsic circadian clock to protect DNA from diurnal exposure to mutagens (e.g.; UV radiation peaks with daylight and dissolved genotoxins that fluctuate with feeding periods). It is proposed that DNA replication arrest in response to genotoxic stress is a likely basis for the evolution of circadian-gated DNA replication. This protective mechanism is highly conserved and can be traced along the evolutionary time-line to the early prokaryotes, unicellular eukaryotes and viruses. Peak DNA repair capacity is normally synchronous to the crest of mutagenic stress as they oscillate with respect to time. Mutator phenotypes with increased vulnerability to genotoxic stress may therefore develop when the circadian pattern of cell cycle control, DNA repair or apoptotic response are phase-shifted relative to the rhythm of mutagenic stress. The accumulating mutations would lead to accelerated aging, genome instability and neoplasia. The proposed model delineates areas of research with potentially profound implications for carcinogenesis.

Influence of endostatin on embryonic vasculo- and angiogenesis

The proteolytic fragment of collagen XVIII, endostatin, acts as an inhibitor of angiogenesis. To date, only limited knowledge exists on the effects of endostatin on endothelial cells during embryonic development. Therefore, we analysed the role of endostatin on embryonic vasculo- and angiogenesis. Endostatin is accumulated in embryonic tissue of mouse embryos. Similarly, in vessels of embryoid bodies (EBs), endostatin and its binding sites are distributed in vessels and sprouting areas. In EBs, endostatin increases endothelial cells (control, 279.3 +/- 76.5; 50 ng/ml, 566.3 +/- 90.1; 200 ng/ml, 594.5 +/- 166.3 tube-like structures per EB) and endothelial tubes by proliferation (control, 21.4 +/- 7.5; 50 ng/ml, 160.2 +/- 9.9; 200 ng/ml, 184.2 +/- 16.5 Ki67-positive nuclei per 50 tube-like structures); it also enhances migration (control, 380.5 +/- 159.8 cells; 50 ng/ml, 718.3 +/- 251 cells; 200 ng/ml, 706 +/- 89.4 cells) and apoptosis (control, 16.8 +/- 6.7; 50 ng/ml, 94.4 +/- 23.6; 200 ng/ml, 106 +/- 42 PARP-positive nuclei per 50 tube-like structures). Furthermore, endostatin modulates the morphology of the endothelial tubes by inducing contraction. Endostatin modulates the embryonic vascular development by enhancing proliferation, migration, and apoptosis as well as by regulating morphogenesis.

Growth of Prochlorococcus, a Photosynthetic Prokaryote, in the Equatorial Pacific Ocean

The cell cycle of Prochlorococcus, a prokaryote that accounts for a sizable fraction of the photosynthetic biomass in the eastern equatorial Pacific, progressed in phase with the daily light cycle. DNA replication occurred in the afternoon and cell division occurred at night. Growth rates were maximal (about one doubling per day) at 30 meters and decreased toward the surface and the bottom of the ocean. Estimated Prochlorococcus production varied between 174 and 498 milligrams of carbon per square meter per day and accounted for 5 to 19 percent of total gross primary production at the equator. Because Prochlorococcus multiplies close to its maximum possible rate, it is probably not severely nutrient-limited in this region of the oceans.

Daily rhythm of cell proliferation in the teleost retina

To determine whether the number of cell divisions in the teleost retina exhibited a regular daily variation, we labeled dividing cells with an antibody to proliferating cell nuclear antigen. The number of dividing rod precursor cells in the outer nuclear layer of the retina were counted in retinas from the telost fish Haplochromis burtoni, sacrificed at 4-h intervals during a standard light-dark cycle and in constant darkness. These rod precursor cells exhibited a striking rhythm of cell division. The highest number of cell divisions (acrophase) was found to occur at night when it was approximately 3 times higher than during the day. The observed rhythm persisted in animals held in constant darkness. We suggest that this endogenous 24-h rhythm of rod precursor cell division may be controlled by a circadian clock. Although there are several examples of continuously proliferating cell populations which exhibit circadian or diurnal rhythms, this appears to be the first documentation of a rhythm of division in cells destined to become neurons.

A constant of temporal structure in the human hierarchy and other systems

The levels that compose biological hierarchies each have their own energetic, spatial and temporal structure. Indeed, it is the discontinuity in energy relationships between levels, as well as the similarity of sub-systems that support them, that permits levels to be defined. In this paper, the temporal structure of living hierarchies, in particular that pertaining to Human society, is examined. Consideration is given to the period defining the lifespan of entities at each level and to a periodic event considered fundamental to the maintenance of that level. The ratio between the duration of these two periods is found to be approximately 2.5 x 10(4). A similar relationship is found when lower, non-living levels of molecules and atoms are considered. This suggests that there is a constant factor of amplification between analogous periodic events at successive levels of the Human hierarchy.

Tyrosine kinase regulation of a molluscan circadian clock

On a formal level the clocks regulating circadian and cell division cycles are related in that both have been modeled as limit cycle oscillations (Science, 211 (1981) 1002-1013; Brain Res., 504 (1989) 211-215; Proc. Natl. Acad. Sci. USA, 88 (1991) 7328-7332). Furthermore, in several organisms each clock system is able to modulate the other (Science, 211 (1981) 1002-1013). However, in spite of the similarities at the formal level, and the connections at the physiological level, no common cellular elements have been identified linking the two processes. In the current series of experiments we show that one key element of cell cycle regulation, tyrosine phosphorylation/dephosphorylation is intimately associated with circadian rhythm generation in the eye of the marine snail, Bulla gouldiana. The importance of tyrosine kinase activity in the generation of circadian rhythms provides a possible point of similarity between the fundamental biochemical mechanisms underlying both circadian and cell cycle clocks.

Functions of Intracellular Protein Degradation in Yeast

Diverse vacuolar and nonvacuolar pathways of protein degradation have been described in yeast. In several cases, much is known about the proteases involved, but most of these studies utilized nonphysiological model substrates. On the other hand, many regulatory proteins, such as those involved in cell cycle control, cell type determination, and the regulation of metabolite fluxes through biosynthetic pathways, have been shown to be rapidly and selectively destroyed in vivo, either constitutively or in response to specific regulatory signals. Precisely what molecular features of this class of proteins target them for degradation is largely unknown; this question is an area of intense current interest. A connection has been made between a particular proteolytic mechanism and a specific naturally short-lived protein in only a handful of examples. It is in this regard that the powerful molecular and genetic techniques available in yeast will probably have their greatest impact in the near future. The promise of this type of approach is already becoming apparent with the molecular genetic analysis of the yeast ubiquitin system. Although this work began less than ten years ago, the genes encoding at least 22 proteins involved in ubiquitin-dependent processes have already been isolated, and questions of their physiological and mechanistic function are being answered at an ever quickening pace.

The timer

This article reviews the evidence that living systems at all levels, including cells, organs, organisms, groups, organizations, communities, societies, and supranational systems, have an information-processing system, the timer. The timer consists of one or more oscillators known as clocks or pacemakers, the phase of which can be reset. They measure duration or order in time or underlie rhythms of various sorts. The timer subsystem synchronizes internal processes of the system and coordinates the system with its environment. By 1965, 19 matter-energy and information processing subsystems were identified in living systems theory. Based on scientific evidence accumulated particularly in recent years, the timer is now recognized as an information processing subsystem, the 20th subsystem, which carries out an essential life process.

Effect of changing the light/dark schedule, the time of onset of the light or dark period, or the daylength, on rhythms of epidermal cell proliferation

Rhythms of labeling and mitotic indices were studied in the hindlimb epidermis of the anuran tadpole Rana pipiens under different light/dark (LD) cycles and daylengths in order to examine the role of the various parameters of the lighting regimen in setting the periods of the rhythms and the timing of the cell proliferation peaks. Altering the time of, or inverting, the 12 h light period on a 24 h day resulted in phase shifting of basically bimodal circadian rhythms with peaks in the light and dark. Thus the cell proliferation rhythms were entrained to the LD cycle. These rhythms also entrained to noncircadian schedules since they lengthened on a 15L:15D cycle and shortened on a 9L:9D cycle, although the bimodal characteristic of a peak in the light and a peak in the dark remained. Studies of 18L:6D and 6L:18D cycles in which either the time of onset of light or dark was changed relative to the 12L:12D control indicated that the onset of dark may regulate the timing of the labeling index peaks while the onset of light may determine the time of occurrence of mitotic index peaks. Control of the timing of labeling and mitotic index peaks by different parameters of the LD cycle suggests a mechanism for cell cycle regulation by the environmental lighting schedule. Analysis of the rhythms on all the cycles studied suggested that labeling index rhythms equal the length of, or twice the length of, the dark period. Mitotic index rhythms equal the daylength or a multiple of the length of the dark period.

Ultradian photosynchronization in Tetrahymena pyriformis GLC is related to modal cell generation time: further evidence for a common timer model

This study contains the first report of the photosynchronization of Tetrahymena in the ultradian mode of cell division. Ultradian mode cultures of T. pyriformis GLC were grown at low cell titers in a nephelostat under five different ultradian photocycles and also under constant conditions of illumination. Entrainment was achieved only when the period of the synchronizer did not exceed the nearest modal generation time observed in free-running single cells. Thus, the discrete ranges for photentrainment of ultradian rhythms in Tetrahymena were restricted to modal windows for the generation times in free-run. Cell division was found to be a function of the phase of the ultradian zeitgeber cycle. The cells did not behave as if they had been forced into synchrony by physiological shock; the synchronous populations obtained by this technique behaved like the populations commonly used in circadian studies which had been phased by a cyclic variation within the tolerance range of the organism.

Rhythm and blues. Neurochemical, neuropharmacological and neuropsychological implications of a hypothesis of circadian rhythm dysfunction in the affective disorders

Current views on the organisation and functions of the circadian rhythm system are outlined. Evidence is presented supportive of the notion that the pathophysiology of the affective disorders involves a disruption of circadian rhythms and that the primary locus of action of agents effective in the affective disorders is on the circadian rhythm system. Potential disruptions of this system are enumerated. Such a hypothesis, it is argued, might potentially unite the disparate neurochemical and neuroendocrinological findings emerging in both depression and mania. There are in addition neuropsychological and nosological implications of such a framework, which may help bridge the divide between molecular and behavioural approaches to research on the affective disorders which are outlined.

Light and dark control of the cell cycle in two marine phytoplankton species

The effect of light and dark on growth, DNA replication and cell division of two marine phytoplankters Thalassiosira weissflogii (a diatom) and Hymenomonas carterae (a coccolithophorid) was investigated using flow cytometry. The two species displayed very differing behavior. When transferred from light to prolonged darkness, all coccolithophorid cells were arrested at the beginning of the G1 stage of the cell cycle. When shifted back into light, they resumed cycling at a rate slightly slower than prior to arrest. In contrast, diatom cells were arrested either in the G1 or G2 stage of the cell cycle in the dark. Upon re-exposure to light, cells which had been dark-arrested in G1 resumed cycling at the same rate as prior to arrest, while cells arrested in G2 cycled much more slowly. These results suggest that in both species, light control of cell cycle progression is effective only over a restricted part of the cell cycle, as has been hypothesized by Spudich & Sager (J cell biol 83 (1980) 136) [38] for Chlamydomonas. In the coccolithophorid there is a single light-dependent segment located at the beginning of G1, whereas the diatom appears to have two such segments, one in G1 and the other in G2, corresponding to two different light requiring processes.

Gene networks in development

A model is presented for the formation of temporal and spatial patterns of cell types during the development of organisms. It is demonstrated that very simple random networks of interactions among genes that affect expression may lead to the autonomous development of patterns of cell types. It is required that the networks contain active feedback loops and that there is limited communication among cells. The only elements of the model, gene interactions, are specified by the DNA nucleotide sequences of the genes. Therefore, the model readily explains how the control of development is specified by the organism's DNA. In the context of this model, the formation of positional information and its interpretation becomes a single process.

Circadian-clock control of protein synthesis and degradation in Gonyaulax polyedra

In growing cultures of the dinoflagellate, Gonyaulax polyedra, total protein synthesis showed a circadian rhythm with a maximum during the phase of the cycle which corresponded to the previous darktime. The maximum coincided with the maximal phase shift of the glow rhythm caused by lower concentrations of the antibiotic anisomycin (Taylor, W., et al., 1982). J. Comp. Physiol. 148 B, 11-25. The dose reponses of inhibition of protein synthesis correlated well with the phase shifting by anisomycin. The amplitude and level of the total-protein synthesis rhythm increased with the growth rate, indicating that the majority of proteins controlled by the circadian clock were cell cycle-dependent. The degradation rate showed the same circadian rhythm as the synthesis rate. Slight variations in uptake and pool size of amino acids were not responsible for the rhythm in the protein-synthesis rate.

Biochemical modeling of an autonomously oscillatory circadian clock in Euglena

Eukaryotic microorganisms, as well as higher animals and plants, display many autonomous physiological and biochemical rhythmicities having periods approximating 24 hours. In an attempt to determine the nature of the timing mechanisms that are responsible for these circadian periodicities, two primary operational assumptions were postulated. Both the perturbation of a putative element of a circadian clock within its normal oscillatory range and the direct activation as well as the inhibition of such an element should yield a phase shift of an overt rhythm generated by the underlying oscillator. Results of experiments conducted in the flagellate Euglena suggest that nicotinamide adenine dinucleotide (NAD+), the mitochondrial Ca2+-transport system, Ca2+, calmodulin, NAD+ kinase, and NADP+ phosphatase represent clock "gears" that, in ensemble, might constitute a self-sustained circadian oscillating loop in this and other organisms.

Quasi-exponential generation time distributions from a limit cycle oscillator

In spite of the apparently random behaviour and the often exponential distribution of generation times expressed in cell populations, there is evidence for rather precise timekeeping in the cell cycle. In experiments using time-lapse video-tape microscopy, we have noted that cell generation times are often not distributed smoothly but in many cases seem to cluster at roughly 4 hr intervals. Phase shift responses following application of heat shock, ionizing radiation or serum pulses in each case show a pattern which is repeated twice in cells with an 8-9 hr modal generation time. We describe here a cell cycle model with an independent cellular clock controlling cell cycle events which accounts for the phase response data, while also reconciling the stochastic and periodic behaviour characteristic of animal cells.

Circadian oscillators, cell cycles, and singularities: light perturbations of the free-running rhythm of cell division in Euglena

The free-running circadian rhythm of cell division in the algal flagellate, Euglena gracilis (Z) was perturbed by 3-h light signals of varying intensities imposed at different circadian times (CT). Light pulses within the range of 700 to 7,500 lux were found to yield the same 'strong' (Type 0) phase response curve (PRC) comprising both advance and delay phase shifts as great as 15 h. Dark signals generated a PRC of reduced amplitude with very little, if any, phase advance being observed. Light perturbations of lower intensity, however, elicited quite different responses if applied at a quite specific circadian time: A 40- to 400-lux pulse given at approximately CT 0 (late subjective night) induced total arrhythmicity, and the culture reverted to asynchronous, exponential growth. Different degrees of arrhythmicity were induced by the same low-intensity perturbations (I*) given slightly before or after this sensitive phase point (T*), but if imposed at other circadian times, they generated normal type 0 phase resetting. The demonstration of the existence of this critical pulse (T*, I*) provides further evidence that the cell division cycle of Euglena (and presumably other microorganisms) is regulated by a circadian oscillator and, in particular, by one having limit cycle dynamics.

Cell cycle oscillators. Temperature compensation of the circadian rhythm of cell division in Euglena

The effects of different constant temperatures ranging from 16 degrees to 32 degrees C on the free-running, circadian rhythm of cell division were examined in axenic, photoautotrophic batch cultures of the unicellular algal flagellate Euglena gracilis Klebs. A comparative study was undertaken on the wild-type (Z strain) and a diuron-(DCMU)-resistant (ZR) strain. Although the overall growth rate (g) of both strains was rather dependent on temperature, lengthening increasingly at temperatures both higher and lower than the optimum range (about 23 degrees-29 degrees C), the free-running period (tau) of the oscillator hypothesized to underlie the overt rhythmicity in the cell division cycle (CDC) was found to be temperature-compensated over at least a 10 degrees C range. The degree of temperature compensation was most striking in the Z strain (Q10 = 1.05) over the permissive temperature interval of 22 degrees-32 degrees C, where periodic growth could occur. This Z strain had a slightly faster growth rate and displayed a higher degree of synchrony than that observed in the ZR strain, whose circadian clock was not as well compensated (Q10 = 1.23) over the permissive temperature interval of 18 degrees-28 degrees C. These results imply that the CDC is regulated by a circadian oscillator sharing the same features as those generating the many other overt biochemical and physiological circadian periodicities that have been documented for Euglena.

Clonal attenuation in chick embryo fibroblasts. Experimental data, a model and computer simulations

When cells from mass cultures of chick embryo fibroblasts are grown at very low density, some cells yield large clones while others produce smaller clones, and some cells fail to divide at all. The distribution of clone sizes is related to the number of population doublings which the donor mass culture has undergone: the more doublings which have occurred, the smaller the average clone size. In this report we describe a model which analyses this phenomenon, referred to as 'clonal attenuation', in detail. The model is based on the concept that a cell with hypothetically unlimited replicative potential--i.e. a 'stem' cell--can become 'committed' to a programme of limited replicative potential. This event is assumed to be stochastic and to have a fixed probability per stem cell division. The parameters of the model are: Pc, the probability of commitment; N, the number of differentiative divisions; and Tc, the cell-cycle times. By computer simulation, it is shown that Pc increases roughly exponentially at each successive stem cell division. According to the model, when the daughter of a stem cell becomes committed, its progeny proceed through N obligatory divisions before becoming terminally differentiated (post-mitotic). The best-fit value of N was found to be seven. The simulations also reveal that the absolute number of stem cells in the total population increases for most of the lifespan of the culture. When Pc becomes much greater than 0.5, the number of stem cells declines rapidly to zero, and the culture nears senescence. Sensitivity analysis shows that Pc can assume only a limited range of values at each stem-cell division.

Cell division cycles and circadian oscillators in Euglena

The algal flagellate Euglena grown photoautotrophically in L:D 3:3 displays a circadian rhythm of cell division. Oscillatory models for cell cycle (CDC) control (particularly those of the limit cycle variety) include the property of phase perturbation, or resetting. This prediction has been tested in synchronous cultures in which the free-running rhythm has been scanned by 3-hr light signals. A strong (Type 0) phase response curve (PRC), yielding both advances and delays as great as 15 hr, has been derived. A second prediction of the limit cycle model is that there exists a pulse of a critical intensity, which, if given at one specific phase of the rhythm (the singularity point), should result in a phaseless, motionless state in which the rhythmicity disappears. Such a point has been found in Euglena in the late subjective night for light pulses having an intensity ranging from 40 to 700 lx. Finally, circadian oscillators typically display temperature-compensated period lengths within the physiological range of steady-state temperatures, although the length of the CDC is commonly thought to be highly temperature dependent. We have found that over a range of at least 10 degrees C, the period of the division rhythm is only slightly affected, exhibiting a Q10 of about 1.05-1.20. These observations, therefore, collectively implicate a circadian oscillator in the control of the CDC.

Chronobiology at the cellular and molecular levels: models and mechanisms for circadian timekeeping

This review considers cellular chronobiology and examines, at least in a superficial way, several classes of models and mechanisms that have been proposed for circadian rhythmicity and some of the experimental approaches that have appeared to be most productive. After a brief discussion of temporal organization and the metabolic, epigenetic, and circadian time domains, the general properties of circadian rhythms are enumerated. A survey of independent oscillations in isolated organs, tissues, and cells is followed by a review of selected circadian rhythms in eukaryotic microorganisms, with particular emphasis placed on the rhythm of cell division in the algal flagellate Euglena as a model system illustrating temporal differentiation. In the ensuing section, experimental approaches to circadian clock mechanisms are considered. The dissection of the clock by the use of chemical inhibitors is illustrated for the rhythm of bioluminescence in the marine dinoflagellate Gonyaulax and for the rhythm of photosynthetic capacity in the unicellular green alga Acetabularia. Alternatively, genetic analysis of circadian oscillators is considered in the green alga Chlamydomonas and in the bread mold Neurospora, both of which have yielded clock mutants and mutants having biochemical lesions that exhibit altered clock properties. On the basis of the evidence generated by these experimental approaches, several classes of biochemical and molecular models for circadian clocks have been proposed. These include strictly molecular models, feedback loop (network) models, transcriptional (tape-reading) models, and membrane models; some of their key elements and predictions are discussed. Finally, a number of general unsolved problems at the cellular level are briefly mentioned: cell cycle interfaces, the evolution of circadian rhythmicity, the possibility of multiple cellular oscillators, chronopharmacology and chronotherapy, and cell-cycle clocks in development and aging.

Cell cycle control by timer and sizer in Chlamydomonas

Conservation of cell cycle control mechanisms is indicated by the presence of functionally homologous division control genes in unrelated yeasts and by the nonspecific action of oncogenes, but it remains uncertain what property of a growing cell results in the initiation of events leading to division. Response to a critical size is indicated by the longer growth period of smaller cells prior to division, which is consistent with deferment of division events until a minimum size is attained; however, in the same cell types faster growing cells are larger and this is more easily explained if division follows a timed period during which faster growing cells grow more, as is postulated for mammalian cells. Therefore, either time- or size-dependent controls might be the sole significant mechanism; we report here, however, that both controls do function in Chlamydomonas since cycle duration is under timer control and cell size determines the number of division rounds committed at the end of each cycle, and hence whether 2, 4, 8 or 16 daughter cells are formed.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

The action spectrum and phototransformations of pterobilin (biliverdin IX gamma)

Pterobilin 1 (biliverdin IX gamma), a butterfly bile pigment, is photocyclized into phorcabilin 2 and sarpedobilin 3 by irradiation in visible light. Selective irradiations have now been performed at the absorption maxima of pterobilin 1. The 650-nm radiations are responsible for the observed photocyclizations while the 375-nm radiations lead to decomposition products. These results are discussed in connection with a hypothesis concerning the biological role of pterobilin in butterfly larvae.

Importance of circadian rhythms in animal cell cultures

Circadian rhythms are a characteristic feature of many cell and organ cultures. Such rhythms may be important in the interpretation of data from cells in culture. More examples of circadian rhythms in tissue culture are badly needed to understand this phenomena. However, they will only be expressed under optimum and well-understood conditions.

Phase locking of biological clocks

Radial isochron clocks (RICs) and their response to external signals and coupling with other RICs are studied. RICs are derived as phase approximations to self-sustained oscillators. Their response to single impulses (phase resetting) and to repetitive impulses is determined. This response may be harmonic or chaotic. Finally, the effect of coupling between clocks is studied. Simple coupling is shown to exhibit rhythm splitting like that observed in fish and small mammals. New phase locking results for general weakly coupled RIC systems are also derived.