Synchronous cultures from the baby machine. A model for animal cells

A baby-machine system that produces newborn Escherichia coli cells from cultures immobilised on a membrane was developed many years ago in an attempt to attain optimal synchrony with minimal disturbance of steady-state growth, and a model designed to characterise the nature and quality of the synchrony of such cells in a quantitative manner has been published. The baby machine has now been adapted for animal cells, and the present article is an attempt to modify the model to include these cells as well. The model consists of five elements, giving rise to five adjustable parameters (and a proportionality constant): a major, essentially synchronous group of cells with ages distributed normally about zero; a minor, random component from a steady-state population on the membrane that had undergone only very little age selection during the elution process; a fixed background count, to allow for the signals recorded by the electronic particle counter produced by debris and electronic noise; a time-shift, to account for differences between time of cell division and end of sample collection; and the coefficient of variation of the interdivision-time distribution, taken to be reciprocal-normal. It is this last feature, a reciprocal-normal rather than a Pearson type III interdivision-time distribution, that distinguishes this version of the model from its predecessor. The model is fitted by unconstrained non-linear least-squares to data from three different leukemia cell lines. The standard errors of the parameters are quite small in all cases, making their estimates highly significant; the quality of the fit is striking. The five parameters of the model can be divided into two nuisance parameters, two that are associated with the methodology and one that describes an inherent property of the cell itself; it turns out that both methodology parameters are zero in all three data sets studied. We also discuss the partition of the transition-time dispersion between the age distribution of the newborn cells and the age distribution of dividing cells and show that a reliable estimate of the corresponding parameters requires an experiment that extends over at least two and a half doubling times.     

SYNCHRONOUS GROWTH OF CHLAMYDOMONAS REINHARDTII (CHLOROPHYCEAE): A REVIEW OF OPTIMAL CONDITIONS1

Chlamydomonas reinhardtii Dangeard was synchronized at optimal growth conditions under a 12:4 LD regime at 35 C and 20,000 lx with serial dilution to a standard starting cell density of (1.4 ± 0.2) × 10⁶ cells/ml. Synchronous growth and division were characterized by measuring cell number, cell volume and size distribution, dry weight, protein, carbon, nitrogen, chlorophyll, carotenoids, nucleic acids, nuclear and cytoplasmic division during the vegetative life cycle. The main properties of the present system are: Exponential growth with high productivity, high degrees of synchrony and reproducibility during repeated life cycles. The degree of synchrony of this light-dark synchronization system was evaluated and compared with those described in the literature using probit analysis of the time course of DNA synthesis, nuclear and cytoplasmic division and sporulation (increase in cell number). The results showed that the degree of synchrony is highest for cells grown under optimal conditions.     

Sporulation Synchrony of Saccharomyces cerevisiae Grown in Various Carbon Sources

Sporulation of several strains of Saccharomyces cerevisiae grown in a variety of carbon sources that do not repress the tricarboxylic acid cycle enzymes was more synchronous than the sporulation of cells grown in medium containing dextrose which does repress those enzymes. Dextrose-grown cells showed optimal sporulation synchrony when inoculated into sporulation medium from early stationary phase when the dextrose in the medium is exhausted. Logarithmic-phase cells grown in either non-fermentable carbon sources (acetate and glycerol) or a fermentable carbon source that does not repress tricarboxylic acid cycle enzymes (galactose) sporulated more synchronously than the early stationary-phase dextrose cells. Attempts were made to sporulate cells taken from both complex and semidefined media. The semidefined acetate medium failed to support the growth of a number of strains. However, cells grown in the complex acetate medium, as well as both complex and semidefined glycerol and galactose media, sporulated with better synchrony than did the dextrose-grown cells.     

Synchronous cultures from the baby machine: anatomy of a model

The baby-machine system, which produces newborn Escherichia coli cells from cultures immobilized on a membrane, was developed many years ago in an attempt to attain optimal synchrony with minimal disturbance of steady-state growth. In the present article, we describe in some detail a model designed to analyse such cells with a view to characterizing the nature and quality of the synchrony in a quantitative manner; it can also serve to evaluate the methodology itself, its potential and its limitations. The model consists of five elements, giving rise to five adjustable parameters (and a proportionality constant): a major, essentially synchronous group of cells with ages distributed normally about zero; a minor, random component from a steady-state population on the membrane that had undergone only very little age selection during the elution process; a fixed background count, to account for the signals recorded by the electronic particle counter produced by debris and electronic noise; a time-shift, to allow for differences between collection time and sampling time; and the coefficient of variation of the interdivision-time distribution, taken to be a Pearson type III. The model is fitted by nonlinear least-squares to data from cells grown in glucose minimal medium. The standard errors of the parameters are quite small, making their estimates all highly significant; the quality of the fit is striking. We also provide a simple yet rigorous procedure for correcting cell counts obtained in an electronic particle counter for the effect of coincidence. An example using real data produces an excellent fit.     

Metapopulation dynamics in a changing climate: Increasing spatial synchrony in weather conditions drives metapopulation synchrony of a butterfly inhabiting a fragmented landscape

Habitat fragmentation and climate change are both prominent manifestations of global change, but there is little knowledge on the specific mechanisms of how climate change may modify the effects of habitat fragmentation, for example, by altering dynamics of spatially structured populations. The long‐term viability of metapopulations is dependent on independent dynamics of local populations, because it mitigates fluctuations in the size of the metapopulation as a whole. Metapopulation viability will be compromised if climate change increases spatial synchrony in weather conditions associated with population growth rates. We studied a recently reported increase in metapopulation synchrony of the Glanville fritillary butterfly (Melitaea cinxia) in the Finnish archipelago, to see if it could be explained by an increase in synchrony of weather conditions. For this, we used 23 years of butterfly survey data together with monthly weather records for the same period. We first examined the associations between population growth rates within different regions of the metapopulation and weather conditions during different life‐history stages of the butterfly. We then examined the association between the trends in the synchrony of the weather conditions and the synchrony of the butterfly metapopulation dynamics. We found that precipitation from spring to late summer are associated with the M. cinxia per capita growth rate, with early summer conditions being most important. We further found that the increase in metapopulation synchrony is paralleled by an increase in the synchrony of weather conditions. Alternative explanations for spatial synchrony, such as increased dispersal or trophic interactions with a specialist parasitoid, did not show paralleled trends and are not supported. The climate driven increase in M. cinxia metapopulation synchrony suggests that climate change can increase extinction risk of spatially structured populations living in fragmented landscapes by altering their dynamics.     

Amplification of Asynchronous Inhibition-Mediated Synchronization by Feedback in Recurrent Networks

Synchronization of 30–80 Hz oscillatory activity of the principle neurons in the olfactory bulb (mitral cells) is believed to be important for odor discrimination. Previous theoretical studies of these fast rhythms in other brain areas have proposed that principle neuron synchrony can be mediated by short-latency, rapidly decaying inhibition. This phasic inhibition provides a narrow time window for the principle neurons to fire, thus promoting synchrony. However, in the olfactory bulb, the inhibitory granule cells produce long lasting, small amplitude, asynchronous and aperiodic inhibitory input and thus the narrow time window that is required to synchronize spiking does not exist. Instead, it has been suggested that correlated output of the granule cells could serve to synchronize uncoupled mitral cells through a mechanism called “stochastic synchronization”, wherein the synchronization arises through correlation of inputs to two neural oscillators. Almost all work on synchrony due to correlations presumes that the correlation is imposed and fixed. Building on theory and experiments that we and others have developed, we show that increased synchrony in the mitral cells could produce an increase in granule cell activity for those granule cells that share a synchronous group of mitral cells. Common granule cell input increases the input correlation to the mitral cells and hence their synchrony by providing a positive feedback loop in correlation. Thus we demonstrate the emergence and temporal evolution of input correlation in recurrent networks with feedback. We explore several theoretical models of this idea, ranging from spiking models to an analytically tractable model.     

The Fis Protein Has a Stimulating Role in Initiation of Replication in Escherichia coli In Vivo

The Fis protein is a nucleoid associated protein that has previously been reported to act negatively in initiation of replication in Escherichia coli. In this work we have examined the influence of this protein on the initiation of replication under different growth conditions using flow cytometry. The Fis protein was found to be increasingly important with increasing growth rate. During multi-fork replication severe under-initiation occurred in cells lacking the Fis protein; the cells initiated at an elevated mass, had fewer origins per cell and the origins were not initiated in synchrony. These results suggest a positive role for the Fis protein in the initiation of replication.     

Minimally disturbed,multicycle, and reproducible synchrony using a eukaryotic "baby machine"

A eukaryotic "baby machine" has been developed that produces synchronized cultures that display up to four synchronous cell cycles. That such cells can be produced implies that methods unable to produce successive synchronized cell cycles may not actually synchronize cells. But most important, the baby machine method now opens the way for the study of the cell cycle of minimally disturbed, artifact-free, well-synchronized, mammalian cells.     

The Escherichia coli baby cell column: a novel cell synchronization method provides new insight into the bacterial cell cycle

We describe a new method for synchronizing bacterial cells. Cells that have transiently expressed an inducible mutant 'sticky' flagellin are adhered to a volume of glass beads suspended in a chromatography column though which growth medium is pumped. Following repression of flagellin synthesis, newborn cells are eluted from the column in large quantities exceeding that of current baby machine techniques by approximately 10-fold. Eluted cultures of 'baby cells' are highly synchronous as determined by analysis of DNA replication, cell division and other events, over time after elution from the column. We also show that use of 'minutes after elution' as a time metric permits much greater temporal resolution among sequential chromosomal events than the commonly used metric of cell size (length). The former approach reveals the existence of transient intermediate stages that are missed by the latter approach. This finding has two important implications. First, at a practical level, the baby cell column is a particularly powerful method for temporal analysis. Second, at a conceptual level, replication-related events are more tightly linked to cell birth (i.e. cell division) than to absolute cell mass.     

Does nesting habitat predict hatch synchrony between brood parasitic brown‐headed cowbirds Molothrus ater and two host species?

Nestling brown-headed cowbirds Molothrus ater typically hatch earlier and grow faster than young of the many host species of this generalist obligate brood parasite. However, a cowbird chick also benefits from the presence of some host nest mates as the parasite is provisioned disproportionately more with increasing brood size. Since asynchronous hatching affects both cowbird and host nestlings' growth and survival, mechanisms that optimize the timing of egg-laying by female parasites should be prevalent. Several habitat features might facilitate optimal timing of parasitic egg-laying and we examined whether aspects of host nesting habitat predicted cowbird hatching synchrony. We tested whether synchronous nests were less concealed, closer to perches, and located in areas of higher host density than asynchronous nests using a broad-scale information theoretic approach. There was no support for these predictions regarding song sparrow ( Melospiza melodia ; n=55) or yellow warbler ( Dendroica petechia ; n=67) nests parasitized by brown-headed cowbirds at Mono Lake, USA. For example, the best statistical models for predicting hatching synchrony in yellow warbler nests included nesting-patch width and nest-substrate shrub species. However, these relationships were relatively weak: both synchronous and asynchronous nests were in patches with statistically indistinguishable widths and the two dominant shrub species at our site contained similar proportions of synchronous and asynchronous nests. We conclude that the variability of host nesting habitats does not contribute to a biologically consistent effect on hatching synchrony by this generalist brood parasite.     

Partial synchrony in soybean cell suspension cultures induced by ethylene

Partial synchrony of cell division in continuous cultures of soybean cell suspensions was obtained by flushing the cultures with ethylene at intervals of 36 h. The most pronounced synchrony resulted from flushing the suspensions with 3% ethylene for 3 h, followed immediately by 3% CO₂ for 3 h and 30 h aeration prior to the next ethylene treatment. Soybean cells responded to this regime of gassing also with a significant enhancement of growth.     

Selective synchrony of cells of differing cycle times

If a growth inhibiting agent is applied periodically to a system of proliferating cells, travelling density waves in maturity space appear. These are synchrony waves; their group velocity depends on the average cycle time of the cells. If the cycle times of two types of cells differ significantly, only the type whose intermitotic period is close to the period at which the growth inhibitor is being applied comes into synchrony. A mathematical model is solved numerically to show the effect.     

Geographically partitioned spatial synchrony among cyclic moth populations

Many species of forest lepidopterans exhibit regular population cycles, which culminate in outbreak densities at approximately ten-year intervals. Population peaks and mass outbreaks typically occur synchronously and may lead to extensive forest damages over large geographic areas. Here, we report patterns of spatial synchrony among cyclic autumnal moth ( Epirrita autumnata ) populations across Fennoscandia, as inferred from 24 long-term (10–33 years) data sets. The study provides the first formal analysis of spatial synchrony of this pest species which damages mountain birch ( Betula pubescens ssp. czerepanovii ) forests in the sub Arctic. We detected positive cross-correlations in population growth rates between the time series, indicating overall spatial synchrony. However, we found the strongest degree of synchrony within geographically and climatically distinct regional clusters, into which time series were partitioned using cluster analyses. Within regional clusters, moth populations were exposed to the synchronizing effects of common, spatially autocorrelated environmental conditions, i.e. a Moran effect. Consequently, we conclude that a geographically and climatically restricted Moran effect, perhaps interacting with dispersal, is the most likely explanation for the regionally partitioned pattern of synchrony among autumnal moth populations in Fennoscandia. Our results emphasize that high amounts of environmental variation may result in a clear structuring of spatial synchrony at unexpectedly small scales.     

Statistical Detection of EEG Synchrony Using Empirical Bayesian Inference

There is growing interest in understanding how the brain utilizes synchronized oscillatory activity to integrate information across functionally connected regions. Computing phase-locking values (PLV) between EEG signals is a popular method for quantifying such synchronizations and elucidating their role in cognitive tasks. However, high-dimensionality in PLV data incurs a serious multiple testing problem. Standard multiple testing methods in neuroimaging research (e.g., false discovery rate, FDR) suffer severe loss of power, because they fail to exploit complex dependence structure between hypotheses that vary in spectral, temporal and spatial dimension. Previously, we showed that a hierarchical FDR and optimal discovery procedures could be effectively applied for PLV analysis to provide better power than FDR. In this article, we revisit the multiple comparison problem from a new Empirical Bayes perspective and propose the application of the local FDR method (locFDR; Efron, 2001) for PLV synchrony analysis to compute FDR as a posterior probability that an observed statistic belongs to a null hypothesis. We demonstrate the application of Efron''s Empirical Bayes approach for PLV synchrony analysis for the first time. We use simulations to validate the specificity and sensitivity of locFDR and a real EEG dataset from a visual search study for experimental validation. We also compare locFDR with hierarchical FDR and optimal discovery procedures in both simulation and experimental analyses. Our simulation results showed that the locFDR can effectively control false positives without compromising on the power of PLV synchrony inference. Our results from the application locFDR on experiment data detected more significant discoveries than our previously proposed methods whereas the standard FDR method failed to detect any significant discoveries.     

Synchrony in human,mouse and bacterial cell cultures--a comparison

Growth characteristics of synchronous human MOLT-4, human U-937 and mouse L1210 cultures produced with a new minimally-disturbing technology were compared to each other and to synchronous Escherichia coli B/r. Based on measurements of cell concentrations during synchronous growth, synchrony persisted in similar fashion for all cells. Cell size and DNA distributions in the mammalian cultures also progressed synchronously and reproducibly for multiple cell cycles. The results demonstrate that unambiguous multi-cycle synchrony, critical for verifying the absence of significant growth imbalances induced by the synchronization procedure, is feasible with these cell lines, and possibly others.     

Encoding whisker deflection velocity within the rodent barrel cortex using phase-delayed inhibition

The primary sensory feature represented within the rodent barrel cortex is the velocity with which a whisker has been deflected. Whisker deflection velocity is encoded within the thalamus via population synchrony (higher deflection velocities entail greater synchrony among the corresponding thalamic population). Thalamic (TC) cells project to regular spiking (RS) cells within the barrel cortex, as well as to inhibitory cortical fast-spiking (FS) neurons, which in turn project to RS cells. Thus, TC spikes result in EPSPs followed, with a small time lag, by IPSPs within an RS cell, and hence the RS cell decodes TC population synchrony by employing a phase-delayed inhibition synchrony detection scheme. As whisker deflection velocity is increased, the probability that an RS cell spikes rises, while jitter in the timing of RS cell spikes remains constant. Furthermore, repeated whisker deflections with fixed velocity lead to system adaptation – TC →RS, TC →FS, and FS →RS synapses all weaken substantially, leading to a smaller probability of spiking of the RS cell and increased jitter in the timing of RS cell spikes. Interestingly, RS cell activity is better able to distinguish among different whisker deflection velocities after adaptation. In this work, we construct a biophysical model of a basic ‘building block’ of barrel cortex – the feedforward circuit consisting of TC cells, FS cells, and a single RS cell – and we examine the ability of the purely feedforward circuit to explain the experimental data on RS cell spiking probability, jitter, adaptation, and deflection velocity discrimination. Moreover, we study the contribution of the phase-delayed inhibition network structure to the ability of an RS cell to decode whisker deflection velocity encoded via TC population synchrony.     

Synchrony in Human,Mouse and Bacterial Cell Cultures: A Comparison

Growth characteristics of synchronous human MOLT-4, human U-937 and mouse L1210 cultures produced with a new minimally-disturbing technology were compared to each other and to synchronous Escherichia coli B/r. Based on measurements of cell concentrations during synchronous growth, synchrony persisted in similar fashion for all cells. Cell size and DNA distributions in the mammalian cultures also progressed synchronously and reproducibly for multiple cell cycles. The results demonstrate that unambiguous multi-cycle synchrony, critical for verifying the absence of significant growth imbalances induced by the synchronization procedure, is feasible with these cell lines, and possibly others.     

Growth of functional primary cultures of kidney epithelial cells in defined medium

Primary cultures of baby mouse kidney epithelial cells can grow without fibroblast overgrowth in a hormone-supplemented serum-free medium (Medium K-1) designed for an established kidney epithelial cell line, MDCK. The five supplements in Medium K-1 are insulin, transferrin, PGE1, T3, and hydrocortisone. Medium K-1 also supports the growth of kidney epithelial cell cultures from a number of animals, including man, without fibroblast overgrowth. Outgrowth of kidney epithelial cells from kidney explants was also observed with Medium K-1. Thus, the medium appears to be selective for epithelial cell growth. The physiological properties of primary cultures of baby mouse kidney epithelial cells were studied in detail. Baby mouse kidney epithelial cells grew at equal rates (0.5 doublings/day) in Medium K-1 and serum-supplemented medium. Medium K-1 also supported the formation of baby mouse kidney epithelial colonies at low cell densities. The dependence of baby mouse kidney epithelial colony formation upon the five factors in Medium K-1 was examined. These studies indicated that the formation of baby mouse kidney epithelial colonies in defined medium depended upon all the five supplements in Medium K-1, in a manner similar, although not identical, to MDCK colonies. Primary cultures of baby mouse kidney epithelial cells grown in Medium K-1 retained kidney cell-associated properties, including the ability to form multicellular domes, a phenomenon associated with transepithelial salt transport. Amiloride-sensitive Na+ uptake and the mucosal surface enzyme leucine aminopeptidase were also observed in baby mouse kidney cultures. Similar functions were observed in MDCK monolayers.     

Induction of division synchrony in Tetrahymena pyriformis by a single hypoxic shock. Its use in elucidating control of the cell cycle by adenosine 3':5'-monophosphate.

A single hypoxic shock was used to induce division synchrony in Tetrahymena pyriformis. Hypoxia results in accumulation of the cells in the G2 phase of the cell cycle. Cyclic AMP and adenyl cyclase activity were measured in this system. Cell-cycle blockade was associated with extraordinarily high levels of intracellular cyclic AMP. After release from hypoxia, the cells retain a characteristic pattern of modulation of cyclic AMP associated with division that is found in selection-synchronized cells. The results are discussed with reference to other methods of induction synchrony and related studies on the natural cell cycle in this organism.