Direct cell-cell communication: a new approach derived from recent data on the nature and self-organisation of ultradian (circahoralian) intracellular rhythms

Neuronal metabolism in learning and memory: The anticipatory activity perspective

Current research on the molecular mechanisms of learning and memory is based on the "stimulus-response" paradigm, in which the neural circuits connecting environmental events with behavioral responses are strengthened. By contrast, cognitive and systems neuroscience emphasize the intrinsic activity of the brain that integrates information, establishes anticipatory actions, executes adaptive actions, and assesses the outcome via regulatory feedback mechanisms. We believe that the difference in the perspectives of systems and molecular studies is a major roadblock to further progress toward understanding the mechanisms of learning and memory. Here, we briefly overview the current studies in molecular mechanisms of learning and memory and propose that studying the predictive properties of neuronal metabolism will significantly advance our knowledge of how intrinsic, predictive activity of neurons shapes a new learning event. We further suggest that predictive metabolic changes in the brain may also take place in non-neuronal cells, including those of peripheral tissues. Finally, we present a path forward toward more in-depth studies of the role of cell metabolism in learning and memory.

A non-parametric model: free analysis of actigraphic recordings of acute insomnia patients

Both parametric and non-parametric approaches to time-series analysis have advantages and drawbacks. Parametric methods, although powerful and widely used, can yield inconsistent results due to the oversimplification of the observed phenomena. They require the setting of arbitrary constants for their creation and refinement, and, although these constants relate to assumptions about the observed systems, it can lead to erroneous results when treating a very complex problem with a sizable list of unknowns. Their non-parametric counterparts, instead, are more widely applicable but present a higher detrimental sensitivity to noise and low density in the data. For the case of approximately periodic phenomena, such as human actigraphic time series, parametric methods are widely used and concepts such as acrophase are key in chronobiology, especially when studying healthy and diseased human populations. In this work, we present a non-parametric method of analysis of actigraphic time series from insomniac patients and healthy age-matched controls. The method is fully data-driven, reproduces previous results in the context of activity offset delay and, crucially, extends the concept of acrophase not only to circadian but also for ultradian spectral components.

Self-Organization and Information Processing: From Basic Enzymatic Activities to Complex Adaptive Cellular Behavior

One of the main aims of current biology is to understand the origin of the molecular organization that underlies the complex dynamic architecture of cellular life. Here, we present an overview of the main sources of biomolecular order and complexity spanning from the most elementary levels of molecular activity to the emergence of cellular systemic behaviors. First, we have addressed the dissipative self-organization, the principal source of molecular order in the cell. Intensive studies over the last four decades have demonstrated that self-organization is central to understand enzyme activity under cellular conditions, functional coordination between enzymatic reactions, the emergence of dissipative metabolic networks (DMN), and molecular rhythms. The second fundamental source of order is molecular information processing. Studies on effective connectivity based on transfer entropy (TE) have made possible the quantification in bits of biomolecular information flows in DMN. This information processing enables efficient self-regulatory control of metabolism. As a consequence of both main sources of order, systemic functional structures emerge in the cell; in fact, quantitative analyses with DMN have revealed that the basic units of life display a global enzymatic structure that seems to be an essential characteristic of the systemic functional metabolism. This global metabolic structure has been verified experimentally in both prokaryotic and eukaryotic cells. Here, we also discuss how the study of systemic DMN, using Artificial Intelligence and advanced tools of Statistic Mechanics, has shown the emergence of Hopfield-like dynamics characterized by exhibiting associative memory. We have recently confirmed this thesis by testing associative conditioning behavior in individual amoeba cells. In these Pavlovian-like experiments, several hundreds of cells could learn new systemic migratory behaviors and remember them over long periods relative to their cell cycle, forgetting them later. Such associative process seems to correspond to an epigenetic memory. The cellular capacity of learning new adaptive systemic behaviors represents a fundamental evolutionary mechanism for cell adaptation.

Elements of the cellular metabolic structure

A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.

Hepatocytes of cirrhotic rat liver accumulate glycogen more slowly than normal ones

PURPOSE

To investigate the accumulation of glycogen in cirrhotic rat liver at several time intervals after per os administration of glucose to fasted animals.

METHODS

Liver cirrhosis was produced by inhalation of the hepatotropic poison CCl4. Glycogen concentration in the liver was determined biochemically. Glycogen content in hepatocytes was measured cytofluorimetrically in the smears stained with a fluorescent PAS reaction. Glycogen content in the hepatocytes of the portal and the central zone of the liver lobule was determined by absorption cytophotometry.

RESULTS

Rats poisoned with CCl4 for 6 months developed typical liver cirrhosis characterized by a fourfold (p < 0.001) increase in the proportion of the connective tissue. In the cirrhotic rats fasted for 48 h, glycogen concentration in the liver and glycogen content in hepatocytes were lower as compared with the control by 36 and 27 % (p < 0.01), respectively. According to data obtained by different methods, the control animals accumulated glycogen at a high rate. In particular, the glycogen content in hepatocytes increased by 34 % after 10 min (p < 0.01). In the cirrhotic rats, glycogen content remained at the same level for 20 min. In both groups of animals, hepatocytes of the portal zone accumulated more glycogen than those of the central zone.

CONCLUSIONS

Glycogen accumulation in cirrhotic rats starts after a delay and proceeds at a lower rate than in the norm.

Rhythms of cell division of different periodicity in small intestinal cryptic epithelium and their contribution to circadian rhythm formation

We used an improved method of chronobiological information processing enabling not only to detect oscillations with different frequencies, but also to determine the significance of each harmonic. This has made it possible to identify significant high-power harmonics present in the majority of cell positions in the crypt. These harmonics make the major contribution to the formation of diurnal rhythm of cell division in the crypt and hence determine spatial and temporal organization of the proliferative system in the crypt.

No phylogeny without ontogeny: a comparative and developmental search for the sources of sleep-like neural and behavioral rhythms

A comprehensive review is presented of reported aspects and putative mechanisms of sleep-like motility rhythms throughout the animal kingdom. It is proposed that 'rapid eye movement (REM) sleep' be regarded as a special case of a distinct but much broader category of behavior, 'rapid body movement (RBM) sleep', defined by intrinsically-generated and apparently non-purposive movements. Such a classification completes a 2 × 2 matrix defined by the axes sleep versus waking and active versus quiet. Although 'paradoxical' arousal of forebrain electrical activity is restricted to warm-blooded vertebrates, we urge that juvenile or even infantile stages of development be investigated in cold-blooded animals, in view of the many reports of REM-like spontaneous motility (RBMs) in a wide range of species during sleep. The neurophysiological bases for motorically active sleep at the brainstem level and for slow-wave sleep in the forebrain appear to be remarkably similar, and to be subserved in both cases by a primitive diffuse mode of neuronal organization. Thus, the spontaneous synchronous burst discharges which are characteristics of the sleeping brain can be readily simulated even by highly unstructured neural network models. Neuromotor discharges during active sleep appear to reflect a hierarchy of simple relaxation oscillation mechanisms, spanning a wide range of spike-dependent relaxation times, whereas the periodic alternation of active and quiet sleep states more likely results from the entrainment of intrinsic cellular rhythms and/or from activity-dependent homeostatic changes in network excitability.

Melatonin modifies the rhythm of protein synthesis

Melatonin (5 nM) added to medium with primary hepatocyte cultures shifted the phase of circahoralian rhythm of protein synthesis and hence, can be a factor synchronizing fluctuations in protein synthesis and rhythm organizer in the hepatocyte population. Blockade of melatonin receptors with luzindole (20 nM) arrested rhythm organization of protein synthesis by melatonin. Prospects of studying biochemical mechanisms of protein synthesis rhythm organization with other drugs (calcium agonists, similarly to melatonin) are discussed.

Quantitative analysis of cellular metabolic dissipative, self-organized structures

One of the most important goals of the postgenomic era is understanding the metabolic dynamic processes and the functional structures generated by them. Extensive studies during the last three decades have shown that the dissipative self-organization of the functional enzymatic associations, the catalytic reactions produced during the metabolite channeling, the microcompartmentalization of these metabolic processes and the emergence of dissipative networks are the fundamental elements of the dynamical organization of cell metabolism. Here we present an overview of how mathematical models can be used to address the properties of dissipative metabolic structures at different organizational levels, both for individual enzymatic associations and for enzymatic networks. Recent analyses performed with dissipative metabolic networks have shown that unicellular organisms display a singular global enzymatic structure common to all living cellular organisms, which seems to be an intrinsic property of the functional metabolism as a whole. Mathematical models firmly based on experiments and their corresponding computational approaches are needed to fully grasp the molecular mechanisms of metabolic dynamical processes. They are necessary to enable the quantitative and qualitative analysis of the cellular catalytic reactions and also to help comprehend the conditions under which the structural dynamical phenomena and biological rhythms arise. Understanding the molecular mechanisms responsible for the metabolic dissipative structures is crucial for unraveling the dynamics of cellular life.

Body weight, metabolism and clock genes

Biological rhythms are present in the lives of almost all organisms ranging from plants to more evolved creatures. These oscillations allow the anticipation of many physiological and behavioral mechanisms thus enabling coordination of rhythms in a timely manner, adaption to environmental changes and more efficient organization of the cellular processes responsible for survival of both the individual and the species. Many components of energy homeostasis exhibit circadian rhythms, which are regulated by central (suprachiasmatic nucleus) and peripheral (located in other tissues) circadian clocks. Adipocyte plays an important role in the regulation of energy homeostasis, the signaling of satiety and cellular differentiation and proliferation. Also, the adipocyte circadian clock is probably involved in the control of many of these functions. Thus, circadian clocks are implicated in the control of energy balance, feeding behavior and consequently in the regulation of body weight. In this regard, alterations in clock genes and rhythms can interfere with the complex mechanism of metabolic and hormonal anticipation, contributing to multifactorial diseases such as obesity and diabetes. The aim of this review was to define circadian clocks by describing their functioning and role in the whole body and in adipocyte metabolism, as well as their influence on body weight control and the development of obesity.

Arrhythmic rats after SCN lesions and constant light differ in short time scale regulation of locomotor activity

Circadian rhythm disruption (i.e., arrhythmicity) in motor activity is an abnormal behavioral pattern. In rats, it can be caused by the lesion of the hypothalamic suprachiasmatic nucleus (SCN) and by prolonged exposure to constant light (LL). We carried out a comparative study of these arrhythmic phenotypes to assess the role of the SCN in the regulation of the motor output beyond circadian rhythmicity. Motor activity series were studied in rats that had become arrhythmic as a result of 1) LL exposure at 2 light intensities: 300 lux (LL(300)) and 1.3 lux (LL(1.3)), and 2) SCN lesion (SCNx). The Fourier spectra, the fractal Hurst coefficient (H) from the autocorrelation function, and the beta slope from the power spectral density were calculated in data sections at baseline, when the rats were still rhythmic, and later at stages with undetectable circadian rhythms. In the LL(300) group, high power content was detected at frequencies of 8 to 4 h (i.e., ultradian). Lower power content for these harmonics was found in the LL(1.3) group, whereas no dominant harmonics appeared in the SCNx group. Independently of the manifestation of circadian rhythm, H values were higher and more sustained in time in rats exposed to LL( 300) but gradually decreased in rats exposed to LL(1.3). Fractal correlation was found in control DD group but was absent in the SCNx group. We conclude that scale-invariant regulation of the motor pattern by SCN activity is dependent on light intensity but independent of the circadian rhythm output. Adjusting the light intensity by modifying the coupling degree between the population of oscillations could affect the dynamics of each individual oscillator in the SCN, making it less predictable.

Partial synchronization dynamics of coupled ultradian oscillators comprising an insect neurosecretory cell system

An insulin-related peptide, bombyxin, in the silkmoth Bombyx mori is secreted by four pairs of cerebral neurosecretory cells that form a weakly coupled oscillator system to produce a pulsatile pattern of hormone secretion. The activity of individual bombyxin-producing (BP) cells oscillated with different periods (20-70 min). The population of BP cells exhibited complex phase dynamics, including spontaneous synchronization and desynchronization of different combinations of cells. Statistical cross-correlation analyses of oscillation patterns between BP cells revealed that one cell usually correlated closely with a few particular cells of similar periodicity. Close investigation of the phase differences between individual active phases of the related cell pairs revealed that an inphase synchronous state was usually maintained for many cycles, whereas an antiphase state was transient, lasting for a few cycles. In contrast, antiphase synchronous states often occurred between several cell pairs when the brain containing the cerebral neurosecretory cell system was disconnected from the ventral nerve cord containing the neuronal mechanism that induced periodic heartbeat reversals at intervals of 80-110 min and exerted a periodic suppressive or phase-resetting effect on individual BP cells. These results suggest that the internal coupling mechanism in the BP cell system is not sufficient to maintain an in-phase synchronous state in the heterogeneous cell population, and that the external phase resetting mechanism may assist in-phase synchronization of many neurosecretory cells to generate an overall pulsatile pattern of bombyxin secretion.

Deterministic chaos and fractal complexity in the dynamics of cardiovascular behavior: perspectives on a new frontier

Physiological systems such as the cardiovascular system are capable of five kinds of behavior: equilibrium, periodicity, quasi-periodicity, deterministic chaos and random behavior. Systems adopt one or more these behaviors depending on the function they have evolved to perform. The emerging mathematical concepts of fractal mathematics and chaos theory are extending our ability to study physiological behavior. Fractal geometry is observed in the physical structure of pathways, networks and macroscopic structures such the vasculature and the His-Purkinje network of the heart. Fractal structure is also observed in processes in time, such as heart rate variability. Chaos theory describes the underlying dynamics of the system, and chaotic behavior is also observed at many levels, from effector molecules in the cell to heart function and blood pressure. This review discusses the role of fractal structure and chaos in the cardiovascular system at the level of the heart and blood vessels, and at the cellular level. Key functional consequences of these phenomena are highlighted, and a perspective provided on the possible evolutionary origins of chaotic behavior and fractal structure. The discussion is non-mathematical with an emphasis on the key underlying concepts.

Evolutionary roots of iodine and thyroid hormones in cell-cell signaling

In vertebrates, thyroid hormones (THs, thyroxine, and triiodothyronine) are critical cell signaling molecules. THs regulate and coordinate physiology within and between cells, tissues, and whole organisms, in addition to controlling embryonic growth and development, via dose-dependent regulatory effects on essential genes. While invertebrates and plants do not have thyroid glands, many utilize THs for development, while others store iodine as TH derivatives or TH precursor molecules (iodotyrosines)-or produce similar hormones that act in analogous ways. Such common developmental roles for iodotyrosines across kingdoms suggest that a common endocrine signaling mechanism may account for coordinated evolutionary change in all multi-cellular organisms. Here, I expand my earlier hypothesis for the role of THs in vertebrate evolution by proposing a critical evolutionary role for iodine, the essential ingredient in all iodotyrosines and THs. Iodine is known to be crucial for life in many unicellular organisms (including evolutionarily ancient cyanobacteria), in part, because it acts as a powerful antioxidant. I propose that during the last 3-4 billion years, the ease with which various iodine species become volatile, react with simple organic compounds, and catalyze biochemical reactions explains why iodine became an essential constituent of life and the Earth's atmosphere-and a potential marker for the origins of life. From an initial role as membrane antioxidant and biochemical catalyst, spontaneous coupling of iodine with tyrosine appears to have created a versatile, highly reactive and mobile molecule, which over time became integrated into the machinery of energy production, gene function, and DNA replication in mitochondria. Iodotyrosines later coupled together to form THs, the ubiquitous cell-signaling molecules used by all vertebrates. Thus, due to their evolutionary history, THs, and their derivative and precursors molecules not only became essential for communicating within and between cells, tissues and organs, and for coordinating development and whole-body physiology in vertebrates, but they can also be shared between organisms from different kingdoms.

Respiratory oscillations in yeasts

Respiratory oscillations in yeasts have been studied in three time domains with periods of (a) about a minute, (b) about 40 min, and (c) about a day. Reactive responses (damped oscillations), rhythms and temperature-compensated clocks have been described for (b) and (c), but a timekeeping clock has not yet been shown for (a). Synchronous populations reveal the time-structure that can only otherwise be studied in single organisms; this is because time-averaging through an asynchronous population conceals its fine structure. Early studies with synchronous cultures made by size selection methods indicated ultradian-clock driven oscillations in respiration, pools of adenylates, total protein, RNA synthesis and many enzyme activities (tau = 40 min in Schizosaccharomyces pombe, 30 min in Candida utilis), and more recently in self-synchronised continuous cultures of Saccharomyces cerevisiae (tau = 48 min). Most detailed understanding comes from the latter system, where continuous, noninvasive real-time monitoring (of 02 uptake, CO2 production, and NAD(P)H redox state) is combined with frequent discrete time samples (for other redox components, including H2S, GSH and cytochromes, metabolites, and mRNA levels). A redox switch lies at the heart of this ultradian clock and a plethora of outputs is optimized to a time-base that is genetically-determined and differs in different organisms. It is suggested that the entire temporal landscape of all eukaryotic organisms and the cells of higher plants and animals is constructed on this basis. A time frame for the coordination and coherence of all intracellular processes and the construction and assembly of cellular structures is provided by the ultradian clock The circadian clock matches these functions to the daily cycle of the external environment.

The scale-free dynamics of eukaryotic cells

Temporal organization of biological processes requires massively parallel processing on a synchronized time-base. We analyzed time-series data obtained from the bioenergetic oscillatory outputs of Saccharomyces cerevisiae and isolated cardiomyocytes utilizing Relative Dispersional (RDA) and Power Spectral (PSA) analyses. These analyses revealed broad frequency distributions and evidence for long-term memory in the observed dynamics. Moreover RDA and PSA showed that the bioenergetic dynamics in both systems show fractal scaling over at least 3 orders of magnitude, and that this scaling obeys an inverse power law. Therefore we conclude that in S. cerevisiae and cardiomyocytes the dynamics are scale-free in vivo. Applying RDA and PSA to data generated from an in silico model of mitochondrial function indicated that in yeast and cardiomyocytes the underlying mechanisms regulating the scale-free behavior are similar. We validated this finding in vivo using single cells, and attenuating the activity of the mitochondrial inner membrane anion channel with 4-chlorodiazepam to show that the oscillation of NAD(P)H and reactive oxygen species (ROS) can be abated in these two evolutionarily distant species. Taken together these data strongly support our hypothesis that the generation of ROS, coupled to redox cycling, driven by cytoplasmic and mitochondrial processes, are at the core of the observed rhythmicity and scale-free dynamics. We argue that the operation of scale-free bioenergetic dynamics plays a fundamental role to integrate cellular function, while providing a framework for robust, yet flexible, responses to the environment.

Spontaneous neuronal burst discharges as dependent and independent variables in the maturation of cerebral cortex tissue cultured in vitro: a review of activity-dependent studies in live 'model' systems for the development of intrinsically generated bioelectric slow-wave sleep patterns

A survey is presented of recent experiments which utilize spontaneous neuronal spike trains as dependent and/or independent variables in developing cerebral cortex cultures when synaptic transmission is interfered with for varying periods of time. Special attention is given to current difficulties in selecting suitable preparations for carrying out biologically relevant developmental studies, and in applying spike-train analysis methods with sufficient resolution to detect activity-dependent age and treatment effects. A hierarchy of synchronized nested burst discharges which approximate early slow-wave sleep patterns in the intact organism is established as a stable basis for isolated cortex function. The complexity of reported long- and short-term homeostatic responses to experimental interference with synaptic transmission is reviewed, and the crucial role played by intrinsically generated bioelectric activity in the maturation of cortical networks is emphasized.

Characterization of the conformational and orientational dynamics of ganglioside GM1 in a dipalmitoylphosphatidylcholine bilayer by molecular dynamics simulations

The structure and dynamics of a single GM1 (Gal5-beta1,3-GalNAc4-beta1,4-(NeuAc3-alpha2,3)-Gal2-beta1,4-Glc1-beta1,1-Cer) embedded in a DPPC bilayer have been studied by MD simulations. Eleven simulations, each of 10 ns productive run, were performed with different initial conformations of GM1. Simulations of GM1-Os in water and of a DPPC bilayer were also performed to delineate the effects of the bilayer and GM1 on the conformational and orientational dynamics of each other. The conformation of the GM1 headgroup observed in the simulations is in agreement with those reported in literature; but the headgroup is restricted when embedded in the bilayer. NeuAc3 is the outermost saccharide towards the water phase. Glc1 and Gal2 prefer a parallel, and NeuAc3, GalNac4 and Gal5 prefer a perpendicular, orientation with respect to the bilayer normal. The overall characteristics of the bilayer are not affected by the presence of GM1; however, GM1 does influence the DPPC molecules in its immediate vicinity. The implications of these observations on the specific recognition and binding of GM1 embedded in a lipid bilayer by exogenous proteins as well as proteins embedded in lipids have been discussed.

Redox rhythmicity: clocks at the core of temporal coherence

Ultradian rhythms are those that cycle many times in a day and are therefore measured in hours, minutes, seconds or even fractions of a second. In yeasts and protists, a temperature-compensated clock with a period of about an hour (30-90 minutes) provides the time base upon which all central processes are synchronized. A 40-minute clock in yeast times metabolic, respiratory and transcriptional processes, and controls cell division cycle progression. This system has at its core a redox cycle involving NAD(P)H and dithiol-disulfide interconversions. It provides an archetype for biological time keeping on longer time scales (e.g. the daily cycles driven by circadian clocks) and underpins these rhythms, which cannot be understood in isolation. Ultradian rhythms are the foundation upon which the coherent functioning of the organism depends.