Glycolytic oscillations in isolated rabbit ventricular myocytes

On the coupling of intracellular K + ${{\rm{K}}}^{+}$ to glycolytic oscillations in yeast

We have investigated the interplay between glycolytic oscillations and intracellularK + ${{\rm{K}}}^{+}$ concentration in the yeast Saccharomyces cerevisiae. IntracellularK + ${{\rm{K}}}^{+}$ concentration was measured using the fluorophore potassium-binding benzofuranisophthalate (PBFI). We found thatK + ${{\rm{K}}}^{+}$ is an essential ion for the occurrence of glycolytic oscillations and that intracellularK + ${{\rm{K}}}^{+}$ concentration oscillates synchronously with other variables such as nicotinamide adenine dinucleotide hydride (NADH), intracellular adenosine triphosphate (ATP), and mitochondrial membrane potential. We also investigated if glycolysis and intracellularK + ${{\rm{K}}}^{+}$ concentration oscillate in a number of yeast strains with mutations inK + ${{\rm{K}}}^{+}$ transporters in the plasma membrane, mitochondrial membrane and in the vacuolar membrane. Most of these strains are still capable of showing glycolytic oscillations, but two strains are not: (i) a strain with a deletion in the mitochondrial Mdm38pK + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ transporter and (ii) a strain with deletion of the late endosomal Nhx1pK + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ (Na + ∕ H + ${\text{Na}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ ) transporter. In these two mutant strains intracellularK + ${{\rm{K}}}^{+}$ concentration seems to be low, indicating that the two transporters may be involved in transport ofK + ${{\rm{K}}}^{+}$ into the cytosol. In the strain, Mdm38pΔ ${\rm{\Delta }}$ oscillations in glycolysis could be restored by addition of theK + ∕ H + ${{\rm{K}}}^{+}\unicode{x02215}{{\rm{H}}}^{+}$ exchange ionophore nigericin. Furthermore, in two nonoscillating mutant strains with a defective V-ATPase and deletion of the Arp1p protein the intracellularK + ${{\rm{K}}}^{+}$ is relatively high, suggesting that the V-ATPase is essential for transport ofK + ${{\rm{K}}}^{+}$ out of the cytosol and that the cytoskeleton may be involved in bindingK + ${{\rm{K}}}^{+}$ to reduce the concentration of free ion in the cytosol. Analyses of the time series of oscillations of NADH, ATP, mitochondrial membrane potential, and potassium concentration using data-driven modeling corroborate the conjecture thatK + ${{\rm{K}}}^{+}$ ion is essential for the emergence of oscillations and support the experimental findings using mutant strains.

Kinetic modelling of glycolytic oscillations

Glycolytic oscillations have been studied for well over 60 years, but aspects of their function, and mechanisms of regulation and synchronisation remain unclear. Glycolysis is amenable to mechanistic mathematical modelling, as its components have been well characterised, and the system can be studied at many organisational levels: in vitro reconstituted enzymes, cell free extracts, individual cells, and cell populations. In recent years, the emergence of individual cell analysis has opened new ways of studying this intriguing system.

Are physiological oscillations physiological?

Despite widespread and striking examples of physiological oscillations, their functional role is often unclear. Even glycolysis, the paradigm example of oscillatory biochemistry, has seen questions about its oscillatory function. Here, we take a systems approach to argue that oscillations play critical physiological roles, such as enabling systems to avoid desensitization, to avoid chronically high and therefore toxic levels of chemicals, and to become more resistant to noise. Oscillation also enables complex physiological systems to reconcile incompatible conditions such as oxidation and reduction, by cycling between them, and to synchronize the oscillations of many small units into one large effect. In pancreatic β-cells, glycolytic oscillations synchronize with calcium and mitochondrial oscillations to drive pulsatile insulin release, critical for liver regulation of glucose. In addition, oscillation can keep biological time, essential for embryonic development in promoting cell diversity and pattern formation. The functional importance of oscillatory processes requires a re-thinking of the traditional doctrine of homeostasis, holding that physiological quantities are maintained at constant equilibrium values, a view that has largely failed in the clinic. A more dynamic approach will initiate a paradigm shift in our view of health and disease. A deeper look into the mechanisms that create, sustain and abolish oscillatory processes requires the language of nonlinear dynamics, well beyond the linearization techniques of equilibrium control theory. Nonlinear dynamics enables us to identify oscillatory ('pacemaking') mechanisms at the cellular, tissue and system levels.

Amplitude response and singularity behavior of circadian clock to external stimuli

Amplitude changes caused by environmental cues are universal in the circadian clock and associated with various diseases. Singularity behavior, characterized by the disruption of circadian rhythms due to critical stimuli, has been observed across various species. Several mathematical models of the circadian clock have replicated this phenomenon. A comprehensive understanding of the amplitude response remains elusive due to experimental limitations. In this study, we address this question by utilizing a simple normal form model that accurately fits previous experimental data, thereby presenting a general mechanism. We employ a geometric framework to illustrate the dynamics in different stimuli of light-induced transcription (LIT) and light-induced degradation (LID), highlighting the core role of invisible instability in amplitude response. Our model systematically elucidates how stimulus mode, phase, and strength determine amplitude responses. The results show that external stimuli induce alterations in both the amplitudes of individual oscillators and the synchronization among oscillators, collectively influencing the overall amplitude response. While experimental methods impose constraints resulting in limited outcomes under specific conditions, our model provides a comprehensive and three-dimensional mechanistic explanation. A comparison with existing experimental findings demonstrates the consistency of our proposed mechanism. Considering the response direction, the framework enables the identification of phases that lead to increased circadian amplitude. Based on this mechanism derived from the framework, stimulus strategies for resetting circadian rhythms with reduced side effects could be designed. Our results demonstrate that the framework has great potential for understanding and applying stimulus responses in the circadian clock and other limit cycle oscillations.

Synchronisation of glycolytic activity in yeast cells

Glycolysis is the central metabolic pathway of almost every cell and organism. Under appropriate conditions, glycolytic oscillations may occur in individual cells as well as in entire cell populations or tissues. In many biological systems, glycolytic oscillations drive coherent oscillations of other metabolites, for instance in cardiomyocytes near anorexia, or in pancreas where they lead to a pulsatile release of insulin. Oscillations at the population or tissue level require the cells to synchronize their metabolism. We review the progress achieved in studying a model organism for glycolytic oscillations, namely yeast. Oscillations may occur on the level of individual cells as well as on the level of the cell population. In yeast, the cell-to-cell interaction is realized by diffusion-mediated intercellular communication via a messenger molecule. The present mini-review focuses on the synchronisation of glycolytic oscillations in yeast. Synchronisation is a quorum-sensing phenomenon because the collective oscillatory behaviour of a yeast cell population ceases when the cell density falls below a threshold. We review the question, under which conditions individual cells in a sparse population continue or cease to oscillate. Furthermore, we provide an overview of the pathway leading to the onset of synchronized oscillations. We also address the effects of spatial inhomogeneities (e.g., the formation of spatial clusters) on the collective dynamics, and also review the emergence of travelling waves of glycolytic activity. Finally, we briefly review the approaches used in numerical modelling of synchronized cell populations.

Metabolic buffer analysis reveals the simultaneous, independent control of ATP and adenylate energy ratios

Determining the underlying principles behind biological regulation is important for understanding the principles of life, treating complex diseases and creating de novo synthetic biology. Buffering-the use of reservoirs of molecules to maintain molecular concentrations-is a widespread and important mechanism for biological regulation. However, a lack of theory has limited our understanding of its roles and quantified effects. Here, we study buffering in energy metabolism using control theory and novel buffer analysis. We find that buffering can enable the simultaneous, independent control of multiple coupled outputs. In metabolism, adenylate kinase and AMP deaminase enable simultaneous control of ATP and adenylate energy ratios, while feedback on metabolic pathways is fundamentally limited to controlling one of these outputs. We also quantify the regulatory effects of the phosphagen system-the above buffers and creatine kinase-revealing which mechanisms regulate which outputs. The results are supported by human muscle and mouse adipocyte data. Together, these results illustrate the synergy of feedback and buffering in molecular biology to simultaneously control multiple outputs.

Partial synchronisation of glycolytic oscillations in yeast cell populations

The transition between synchronized and asynchronous behaviour of immobilized yeast cells of the strain Saccharomyces carlsbergensis was investigated by monitoring the autofluorescence of the coenzyme NADH. In populations of intermediate cell densities the individual cells remained oscillatory, whereas on the level of the cell population both a partially synchronized and an asynchronous state were accessible for experimental studies. In the partially synchronized state, the mean oscillatory frequency was larger than that of the cells in the asynchronous state. This suggests that synchronisation occurred due to entrainment by the cells that oscillated more rapidly. This is typical for synchronisation due to phase advancement. Furthermore, the synchronisation of the frequency of the glycolytic oscillations preceded the synchronisation of their phases. However, the cells did not synchronize completely, as the distribution of the oscillatory frequencies only narrowed but did not collapse to a unique frequency. Cells belonging to spatially denser clusters showed a slightly enhanced local synchronisation during the episode of partial synchronisation. Neither the clusters nor a transition from partially synchronized glycolytic oscillations to travelling glycolytic waves did substantially affect the degree of partial synchronisation. Chimera states, i.e., the coexistence of a synchronized and an asynchronous part of the population, could not be found.

Evidence for rate-dependent filtering of global extrinsic noise by biochemical reactions in mammalian cells

Recent studies have revealed that global extrinsic noise arising from stochasticity in the intracellular biochemical environment plays a critical role in heterogeneous cell physiologies. However, it remains largely unclear how such extrinsic noise dynamically influences downstream reactions and whether it could be neutralized by cellular reactions. Here, using fluorescent protein (FP) maturation as a model biochemical reaction, we explored how cellular reactions might combat global extrinsic noise in mammalian cells. We developed a novel single-cell assay to systematically quantify the maturation rate and the associated noise for over a dozen FPs. By exploiting the variation in the maturation rate for different FPs, we inferred that global extrinsic noise could be temporally filtered by maturation reactions, and as a result, the noise levels for slow-maturing FPs are lower compared to fast-maturing FPs. This mechanism is validated by directly perturbing the maturation rates of specific FPs and measuring the resulting noise levels. Together, our results revealed a potentially general principle governing extrinsic noise propagation, where timescale separation allows cellular reactions to cope with dynamic global extrinsic noise.

A Spatiotemporal Ventricular Myocyte Model Incorporating Mitochondrial Calcium Cycling

Intracellular calcium (Ca2+) cycling dynamics in cardiac myocytes are spatiotemporally generated by stochastic events arising from a spatially distributed network of coupled Ca2+ release units that interact with an intertwined mitochondrial network. In this study, we developed a spatiotemporal ventricular myocyte model that integrates mitochondria-related Ca2+ cycling components into our previously developed ventricular myocyte model consisting of a three-dimensional Ca2+ release unit network. Mathematical formulations of mitochondrial membrane potential, mitochondrial Ca2+ cycling, mitochondrial permeability transition pore stochastic opening and closing, intracellular reactive oxygen species signaling, and oxidized Ca2+/calmodulin-dependent protein kinase II signaling were incorporated into the model. We then used the model to simulate the effects of mitochondrial depolarization on mitochondrial Ca2+ cycling, Ca2+ spark frequency, and Ca2+ amplitude, which agree well with experimental data. We also simulated the effects of the strength of mitochondrial Ca2+ uniporters and their spatial localization on intracellular Ca2+ cycling properties, which substantially affected diastolic and systolic Ca2+ levels in the mitochondria but exhibited only a small effect on sarcoplasmic reticulum and cytosolic Ca2+ levels under normal conditions. We show that mitochondrial depolarization can cause Ca2+ waves and Ca2+ alternans, which agrees with previous experimental observations. We propose that this new, to our knowledge, spatiotemporal ventricular myocyte model, incorporating properties of mitochondrial Ca2+ cycling and reactive-oxygen-species-dependent signaling, will be useful for investigating the effects of mitochondria on intracellular Ca2+ cycling and action potential dynamics in ventricular myocytes.

Discrimination of leukemic Jurkat cells from normal lymphocytes via novo label-free cytometry based on fluctuation of image gray values

We introduce a simple, label-free cytometry technique, based on the spatio-temporal fluctuation analysis of pixel gray levels of a cell image utilizing the Gray Level Information Entropy (GLIE) function. In this study, the difference in GLIE random fluctuations and its biophysical etiology in a comparison cell model of leukemic Jurkat cells and human healthy donor lymphocytes was explored. A combination of common bright field microscopy and a unique imaging dish wherein cells are individually held untethered in a picoliter volume matrix of optical chambers was used. Random GLIE fluctuations were found to be greater in malignant Jurkat cells than in benign lymphocytes, while these fluctuations correlate with intracellular vesicle Mean Square Displacement (MSD) values and are inhibited by myosin-2 and adenosine triphosphate (ATP) inhibitors. These results suggest that the incoherent active forces acting on the cytoskeleton which cause mechanical dissipative fluctuation of the cytoskeletal and related intracellular content are the biophysical cellular mechanism behind the GLIE random fluctuation results. Analysis of the results in Jurkat cells and normal lymphocytes suggests the possible potential of this simple and automated label-free cytometry to identify malignancy, particularly in a diagnostic setup of multiple cell examination.

The Ca2+ transient as a feedback sensor controlling cardiomyocyte ionic conductances in mouse populations

Conductances of ion channels and transporters controlling cardiac excitation may vary in a population of subjects with different cardiac gene expression patterns. However, the amount of variability and its origin are not quantitatively known. We propose a new conceptual approach to predict this variability that consists of finding combinations of conductances generating a normal intracellular Ca²⁺ transient without any constraint on the action potential. Furthermore, we validate experimentally its predictions using the Hybrid Mouse Diversity Panel, a model system of genetically diverse mouse strains that allows us to quantify inter-subject versus intra-subject variability. The method predicts that conductances of inward Ca²⁺ and outward K⁺ currents compensate each other to generate a normal Ca²⁺ transient in good quantitative agreement with current measurements in ventricular myocytes from hearts of different isogenic strains. Our results suggest that a feedback mechanism sensing the aggregate Ca²⁺ transient of the heart suffices to regulate ionic conductances.

Effect of Indolic-Amide Melatonin on Blood Cell Population: A Biophysical Gaussian Statistical Analysis

The problem of the correlation of indolic molecules with special regard to melatonin and immune processes has been widely investigated. However, there are only few studies focusing on circadian variation of peripheral blood leukocytes. The purpose of this study is thus to understand the influence of MLT on leukocyte populations and its correlation with leukocyte distribution. This is accomplished by administrating placebo and melatonin to different groups of individuals and by performing a biophysical Gaussian analysis on the number of leukocytes by means of a comparison of their p.m. vs. a.m. variations under the effect of placebo and of melatonin and via a comparison in the morning between leukocytes population of untreated group and MLT group. It is shown that: (a) melatonin has the effect of narrowing the normal distribution concentrating most of the individuals towards the mean value of the observed variation of leukocytes population and (b) the individuals who have not received either placebo or supplement have a leukocyte population that follows a normal distribution. These results confirm the crucial role played by melatonin, as the most representative of indolic amide in biological systems, in the circadian peripheral variations of leukocyte numbers because counts of white blood cells are essential in medical urgency and differential diagnosis situations. Hence, further studies are suggested to account for these physiological variations and for the evaluation of the full involvement of the action of MLT on leukocytes distribution.

Promotion and inhibition of synchronous glycolytic oscillations in yeast by chitosan

Synchronous rhythmic activities play crucial roles in diverse biological systems. Glycolytic oscillations in yeast cells have been studied for 50 years with the aim of elucidating the mechanisms underlying the intracellular oscillations and their synchronization. We investigated the effects of chemical disturbances on the individual and collective glycolytic oscillations in yeast cells encapsulated in alginate microparticles, and demonstrated that the addition of chitosan, an antimicrobial agent, decreased the duration of these oscillations. In contrast, the periods and the synchronicity states showed two different responses to the chitosan treatments. The periods were shown to be prolonged following the treatment with 5-50 mg·L^-1 and shortened at 75 mg·L^-1 of chitosan. Collective oscillations became more synchronized at 5 mg·L^-1 of chitosan, and desynchronized at 25-75 mg·L^-1 of this compound. These findings can be explained by the balance between two chitosan features, increasing cell membrane permeability and acetaldehyde scavenging. At low concentrations, chitosan presumably acts as a synchronization promoter that does not mediate the synchronization itself but induces an increase in intercellular coupling. We believe that our findings may provide new insights into the synchronous rhythmic activities in biological systems.

Akt regulation of glycolysis mediates bioenergetic stability in epithelial cells

Cells use multiple feedback controls to regulate metabolism in response to nutrient and signaling inputs. However, feedback creates the potential for unstable network responses. We examined how concentrations of key metabolites and signaling pathways interact to maintain homeostasis in proliferating human cells, using fluorescent reporters for AMPK activity, Akt activity, and cytosolic NADH/NAD⁺ redox. Across various conditions, including glycolytic or mitochondrial inhibition or cell proliferation, we observed distinct patterns of AMPK activity, including both stable adaptation and highly dynamic behaviors such as periodic oscillations and irregular fluctuations that indicate a failure to reach a steady state. Fluctuations in AMPK activity, Akt activity, and cytosolic NADH/NAD⁺ redox state were temporally linked in individual cells adapting to metabolic perturbations. By monitoring single-cell dynamics in each of these contexts, we identified PI3K/Akt regulation of glycolysis as a multifaceted modulator of single-cell metabolic dynamics that is required to maintain metabolic stability in proliferating cells.

The Interplay between Feedback and Buffering in Cellular Homeostasis

Buffering, the use of reservoirs of molecules to maintain concentrations of key molecular species, and negative feedback are the primary known mechanisms for robust homeostatic regulation. To our knowledge, however, the fundamental principles behind their combined effect have not been elucidated. Here, we study the interplay between buffering and negative feedback in the context of cellular homeostasis. We show that negative feedback counteracts slow-changing disturbances, whereas buffering counteracts fast-changing disturbances. Furthermore, feedback and buffering have limitations that create trade-offs for regulation: instability in the case of feedback and molecular noise in the case of buffering. However, because buffering stabilizes feedback and feedback attenuates noise from slower-acting buffering, their combined effect on homeostasis can be synergistic. These effects can be explained within a traditional control theory framework and are consistent with experimental observations of both ATP homeostasis and pH regulation in vivo. These principles are critical for studying robustness and homeostasis in biology and biotechnology.

Primordial oscillations in life: Direct observation of glycolytic oscillations in individual HeLa cervical cancer cells

We report the first direct observation of glycolytic oscillations in HeLa cervical cancer cells, which we regard as primordial oscillations preserved in living cells. HeLa cells starved of glucose or both glucose and serum exhibited glycolytic oscillations in nicotinamide adenine dinucleotide (NADH), exhibiting asynchronous intercellular behaviors. Also found were spatially homogeneous and inhomogeneous intracellular NADH oscillations in the individual cells. Our results demonstrate that starved HeLa cells may be induced to exhibit glycolytic oscillations by either high-uptake of glucose or the enhancement of a glycolytic pathway (Crabtree effect or the Warburg effect), or both. Their asynchronous collective behaviors in the oscillations were probably due to a weak intercellular coupling. Elucidation of the relationship between the mechanism of glycolytic dynamics in cancer cells and their pathophysiological characteristics remains a challenge in future.

Cardiovascular KATP channels and advanced aging

With advanced aging, there is a decline in innate cardiovascular function. This decline is not general in nature. Instead, specific changes occur that impact the basic cardiovascular function, which include alterations in biochemical pathways and ion channel function. This review focuses on a particular ion channel that couple the latter two processes, namely the K_ATP channel, which opening is promoted by alterations in intracellular energy metabolism. We show that the intrinsic properties of the K_ATP channel changes with advanced aging and argue that the channel can be further modulated by biochemical changes. The importance is widespread, given the ubiquitous nature of the K_ATP channel in the cardiovascular system where it can regulate processes as diverse as cardiac function, blood flow and protection mechanisms against superimposed stress, such as cardiac ischemia. We highlight questions that remain to be answered before the K_ATP channel can be considered as a viable target for therapeutic intervention.

Decline of Phosphotransfer and Substrate Supply Metabolic Circuits Hinders ATP Cycling in Aging Myocardium

Integration of mitochondria with cytosolic ATP-consuming/ATP-sensing and substrate supply processes is critical for muscle bioenergetics and electrical activity. Whether age-dependent muscle weakness and increased electrical instability depends on perturbations in cellular energetic circuits is unknown. To define energetic remodeling of aged atrial myocardium we tracked dynamics of ATP synthesis-utilization, substrate supply, and phosphotransfer circuits through adenylate kinase (AK), creatine kinase (CK), and glycolytic/glycogenolytic pathways using ¹⁸O stable isotope-based phosphometabolomic technology. Samples of intact atrial myocardium from adult and aged rats were subjected to ¹⁸O-labeling procedure at resting basal state, and analyzed using the ¹⁸O-assisted HPLC-GC/MS technique. Characteristics for aging atria were lower inorganic phosphate Pi[¹⁸O], γ-ATP[¹⁸O], β-ADP[¹⁸O], and creatine phosphate CrP[¹⁸O] ¹⁸O-labeling rates indicating diminished ATP utilization-synthesis and AK and CK phosphotransfer fluxes. Shift in dynamics of glycolytic phosphotransfer was reflected in the diminished G6P[¹⁸O] turnover with relatively constant glycogenolytic flux or G1P[¹⁸O] ¹⁸O-labeling. Labeling of G3P[¹⁸O], an indicator of G3P-shuttle activity and substrate supply to mitochondria, was depressed in aged myocardium. Aged atrial myocardium displayed reduced incorporation of ¹⁸O into second (¹⁸O₂), third (¹⁸O₃), and fourth (¹⁸O₄) positions of Pi[¹⁸O] and a lower Pi[¹⁸O]/γ-ATP[¹⁸ O]-labeling ratio, indicating delayed energetic communication and ATP cycling between mitochondria and cellular ATPases. Adrenergic stress alleviated diminished CK flux, AK catalyzed β-ATP turnover and energetic communication in aging atria. Thus, ¹⁸O-assisted phosphometabolomics uncovered simultaneous phosphotransfer through AK, CK, and glycolytic pathways and G3P substrate shuttle deficits hindering energetic communication and ATP cycling, which may underlie energetic vulnerability of aging atrial myocardium.

Collective and individual glycolytic oscillations in yeast cells encapsulated in alginate microparticles

Yeast cells were encapsulated into alginate microparticles of a few hundred micrometers diameter using a centrifuge-based droplet shooting device. We demonstrate the first experimental results of glycolytic oscillations in individual yeast cells immobilized in this way. We investigated both the individual and collective oscillatory behaviors at different cell densities. As the cell density increased, the amplitude of the individual oscillations increased while their period decreased, and the collective oscillations became more synchronized, with an order parameter close to 1 (indicating high synchrony). We also synthesized biphasic-Janus microparticles encapsulating yeast cells of different densities in each hemisphere. The cellular oscillations between the two hemispheres were entrained at both the individual and population levels. Such systems of cells encapsulated into microparticles are useful for investigating how cell-to-cell communication depends on the density and spatial distribution of cells.

On the dynamics of the adenylate energy system: homeorhesis vs homeostasis

Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.

Cancer stem cell theory and the warburg effect, two sides of the same coin?

Over the last 100 years, many studies have been performed to determine the biochemical and histopathological phenomena that mark the origin of neoplasms. At the end of the last century, the leading paradigm, which is currently well rooted, considered the origin of neoplasms to be a set of genetic and/or epigenetic mutations, stochastic and independent in a single cell, or rather, a stochastic monoclonal pattern. However, in the last 20 years, two important areas of research have underlined numerous limitations and incongruities of this pattern, the hypothesis of the so-called cancer stem cell theory and a revaluation of several alterations in metabolic networks that are typical of the neoplastic cell, the so-called Warburg effect. Even if this specific “metabolic sign” has been known for more than 85 years, only in the last few years has it been given more attention; therefore, the so-called Warburg hypothesis has been used in multiple and independent surveys. Based on an accurate analysis of a series of considerations and of biophysical thermodynamic events in the literature, we will demonstrate a homogeneous pattern of the cancer stem cell theory, of the Warburg hypothesis and of the stochastic monoclonal pattern; this pattern could contribute considerably as the first basis of the development of a new uniform theory on the origin of neoplasms. Thus, a new possible epistemological paradigm is represented; this paradigm considers the Warburg effect as a specific “metabolic sign” reflecting the stem origin of the neoplastic cell, where, in this specific metabolic order, an essential reason for the genetic instability that is intrinsic to the neoplastic cell is defined.

Kir6.2 limits Ca(2+) overload and mitochondrial oscillations of ventricular myocytes in response to metabolic stress

ATP-sensitive K(+) (KATP) channels are abundant membrane proteins in cardiac myocytes that are directly gated by intracellular ATP and form a signaling complex with metabolic enzymes, such as creatine kinase. KATP channels are known to be essential for adaption to cardiac stress, such as ischemia; however, how all the molecular components of the stress response interact is not fully understood. We examined the effects of decreasing the KATP current density on Ca(2+) and mitochondrial homeostasis and ischemic preconditioning. Acute knockdown of the pore-forming subunit, Kir6.2, was achieved using adenoviral delivery of short hairpin RNA targeted to Kir6.2. The acute nature of the knockdown of Kir6.2 accurately shows the effects of Kir6.2 depletion without any compensatory effects that may arise in transgenic studies. We also investigated the effect of reducing the KATP current while maintaining KATP channel protein in the sarcolemmal membrane using a nonconducting Kir6.2 construct. Only 50% KATP current remained after Kir6.2 knockdown, yet there were profound effects on myocyte responses to metabolic stress. Kir6.2 was essential for cardiac myocyte Ca(2+) homeostasis under both baseline conditions before any metabolic stress and after metabolic stress. Expression of nonconducting Kir6.2 also resulted in increased Ca(2+) overload, showing the importance of K(+) conductance in the protective response. Both ischemic preconditioning and protection during ischemia were lost when Kir6.2 was knocked down. KATP current density was also important for the mitochondrial membrane potential at rest and prevented mitochondrial membrane potential oscillations during oxidative stress. KATP channel density is important for adaption to metabolic stress.

An integrated multidisciplinary model describing initiation of cancer and the Warburg hypothesis

Background

In this paper we propose a chemical physics mechanism for the initiation of the glycolytic switch commonly known as the Warburg hypothesis, whereby glycolytic activity terminating in lactate continues even in well-oxygenated cells. We show that this may result in cancer via mitotic failure, recasting the current conception of the Warburg effect as a metabolic dysregulation consequent to cancer, to a biophysical defect that may contribute to cancer initiation.

Model

Our model is based on analogs of thermodynamic concepts that tie non-equilibrium fluid dynamics ultimately to metabolic imbalance, disrupted microtubule dynamics, and finally, genomic instability, from which cancers can arise. Specifically, we discuss how an analog of non-equilibrium Rayleigh-Benard convection can result in glycolytic oscillations and cause a cell to become locked into a higher-entropy state characteristic of cancer.

Conclusions

A quantitative model is presented that attributes the well-known Warburg effect to a biophysical mechanism driven by a convective disturbance in the cell. Contrary to current understanding, this effect may precipitate cancer development, rather than follow from it, providing new insights into carcinogenesis, cancer treatment, and prevention.

Ultrasensitive response motifs: basic amplifiers in molecular signalling networks

Multi-component signal transduction pathways and gene regulatory circuits underpin integrated cellular responses to perturbations. A recurring set of network motifs serve as the basic building blocks of these molecular signalling networks. This review focuses on ultrasensitive response motifs (URMs) that amplify small percentage changes in the input signal into larger percentage changes in the output response. URMs generally possess a sigmoid input–output relationship that is steeper than the Michaelis–Menten type of response and is often approximated by the Hill function. Six types of URMs can be commonly found in intracellular molecular networks and each has a distinct kinetic mechanism for signal amplification. These URMs are: (i) positive cooperative binding, (ii) homo-multimerization, (iii) multistep signalling, (iv) molecular titration, (v) zero-order covalent modification cycle and (vi) positive feedback. Multiple URMs can be combined to generate highly switch-like responses. Serving as basic signal amplifiers, these URMs are essential for molecular circuits to produce complex nonlinear dynamics, including multistability, robust adaptation and oscillation. These dynamic properties are in turn responsible for higher-level cellular behaviours, such as cell fate determination, homeostasis and biological rhythm.

Mitochondrial network energetics in the heart

At the core of eukaryotic aerobic life, mitochondrial function like 'hubs' in the web of energetic and redox processes in cells. In the heart, these networks-extending beyond the complex connectivity of biochemical circuit diagrams and apparent morphology-exhibit collective dynamics spanning several spatiotemporal levels of organization, from the cell, to the tissue, and the organ. The network function of mitochondria, i.e., mitochondrial network energetics, represents an advantageous behavior. Its coordinated action, under normal physiology, provides robustness despite failure in a few nodes, and improves energy supply toward a swiftly changing demand. Extensive diffuse loops, encompassing mitochondrial-cytoplasmic reaction/transport networks, control and regulate energy supply and demand in the heart. Under severe energy crises, the network behavior of mitochondria and associated glycolytic and other metabolic networks collapse, thereby triggering fatal arrhythmias.

Metabolic synchronization by traveling waves in yeast cell layers

The coordination of cellular behavior is a prerequisite of functionality of tissues and organs. Generally, this coordination occurs by signal transduction, neuronal control, or exchange of messenger molecules. The extent to which metabolic processes are involved in intercellular communication is less understood. Here, we address this question in layers of resting yeast cells and report for the first time the observation of intercellular glycolytic waves. We use a combined experimental and theoretical approach and explain the radial velocity of the waves to arise from the substrate gradient due to local substrate addition. Our results show that metabolic processes introduce an additional level of local intercellular coordination.

Periodic orbits in glycolytic oscillators: from elliptic orbits to relaxation oscillations

We consider the Sel'kov model of glycolytic oscillator for a quantitative study of the limit cycle oscillations in the system. We identify a region of parameter space where perturbation theory holds and use both Linstedt Poincaré technique and harmonic balance to obtain the shape and frequency of the limit cycle. The agreement with the numerically obtained result is excellent. We also find a different extreme, where the limit cycle is of the relaxation oscillator variety, has a large time period and it is seen that, as a particular parameter in the model is varied, the time period increases indefinitely. We characterize this divergence numerically. A calculational method is devised to capture the divergence approximately.

Nitric oxide/reactive oxygen species generation and nitroso/redox imbalance in heart failure: from molecular mechanisms to therapeutic implications

Adaptation of the heart to intrinsic and external stress involves complex modifications at the molecular and cellular levels that lead to tissue remodeling, functional and metabolic alterations, and finally to failure depending upon the nature, intensity, and chronicity of the stress. Reactive oxygen species (ROS) have long been considered as merely harmful entities, but their role as second messengers has gradually emerged. At the same time, our comprehension of the multifaceted role of nitric oxide (NO) and the related reactive nitrogen species (RNS) has been upgraded. The tight interlay between ROS and RNS suggests that their imbalance may implicate the impairment in physiological NO/redox-based signaling that contributes to the failing of the cardiovascular system. This review initially provides basic concepts on the role of nitroso/oxidative stress in the pathophysiology of heart failure with a particular focus on sources of ROS/RNS, their downstream targets, and endogenous modulators. Then, the role of NO/redox regulation of cardiomyocyte function, including calcium homeostasis, electrogenesis, and insulin signaling pathways, is described. Finally, an overview of old and emerging therapeutic opportunities in heart failure is presented, focusing on modulation of NO/redox mechanisms and discussing benefits and limitations.

Muscle KATP channels: recent insights to energy sensing and myoprotection

ATP-sensitive potassium (K(ATP)) channels are present in the surface and internal membranes of cardiac, skeletal, and smooth muscle cells and provide a unique feedback between muscle cell metabolism and electrical activity. In so doing, they can play an important role in the control of contractility, particularly when cellular energetics are compromised, protecting the tissue against calcium overload and fiber damage, but the cost of this protection may be enhanced arrhythmic activity. Generated as complexes of Kir6.1 or Kir6.2 pore-forming subunits with regulatory sulfonylurea receptor subunits, SUR1 or SUR2, the differential assembly of K(ATP) channels in different tissues gives rise to tissue-specific physiological and pharmacological regulation, and hence to the tissue-specific pharmacological control of contractility. The last 10 years have provided insights into the regulation and role of muscle K(ATP) channels, in large part driven by studies of mice in which the protein determinants of channel activity have been deleted or modified. As yet, few human diseases have been correlated with altered muscle K(ATP) activity, but genetically modified animals give important insights to likely pathological roles of aberrant channel activity in different muscle types.

Mitochondrial oscillations and waves in cardiac myocytes: insights from computational models

Periodic cellwide depolarizations of mitochondrial membrane potential (PsiM) which are triggered by reactive oxygen species (ROS) and propagated by ROS-induced ROS release (RIRR) have been postulated to contribute to cardiac arrhythmogenesis and injury during ischemia/reperfusion. Two different modes of RIRR have been described: PsiM oscillations involving ROS-sensitive mitochondrial inner membrane anion channels (IMAC), and slow depolarization waves related to mitochondrial permeability transition pore (MPTP) opening. In this study, we developed a computational model of mitochondria exhibiting both IMAC-mediated RIRR and MPTP-mediated RIRR, diffusively coupled in a spatially extended network, to study the spatiotemporal dynamics of RIRR on PsiM. Our major findings are: 1), as the rate of ROS production increases, mitochondria can exhibit either oscillatory dynamics facilitated by IMAC opening, or bistable dynamics facilitated by MPTP opening; 2), in a diffusively-coupled mitochondrial network, the oscillatory dynamics of IMAC-mediated RIRR results in rapidly propagating (approximately 25 microm/s) cellwide PsiM oscillations, whereas the bistable dynamics of MPTP-mediated RIRR results in slow (0.1-2 microm/s) PsiM depolarization waves; and 3), the slow velocity of the MPTP-mediated depolarization wave is related to competition between ROS scavenging systems and ROS diffusion. Our observations provide mechanistic insights into the spatiotemporal dynamics underlying RIRR-induced PsiM oscillations and waves observed experimentally in cardiac myocytes.

Glycolytic oscillations in single ischemic cardiomyocytes at near anoxia

Previous studies have shown that oscillations of the metabolism can occur in cardiomyocytes under conditions simulating ischemia/reperfusion. It is not known whether they can also occur during real ischemia with near-anoxic oxygen tension. Here, using oxygen clamp in on-chip picochambers, we exposed single resting cardiomyocytes to near anoxia (pO₂ < 0.1 mm Hg). We show that at near anoxia, the mitochondrial membrane potential (ΔΨ) was kept by the F₁F₀-ATPase reversal, using glycolytic adenosine triphosphate (ATP). In many cells, activation of current through sarcolemmal K_ATP channels (I_KATP) started after a delay with one or several oscillations (frequency of 0.044 ± 0.002 Hz). These oscillations were time correlated with oscillations of ΔΨ. Metabolic oscillations at near anoxia are driven by glycolysis because (a) they were inhibited when glycolysis was blocked, (b) they persisted in cells treated with cytoplasmic reactive oxygen species scavengers, and (c) the highest rate of ATP synthesis during an oscillation cycle was associated with the generation of reducing equivalents. Glycolytic oscillations could be initiated upon rapid, but not slow, transition to near anoxia, indicating that the speed of ATP/ADP ratio drop is a determinant of their occurrence. At enhanced oxidative stress, the rate of ATP consumption was increased as indicated by rapid I_KATP activation with large-scale oscillations. These results show that metabolic oscillations occur in cardiomyocytes at near anoxia and are driven by glycolysis and modulated by mitochondria through the rate of ATP hydrolysis, which, in turn, can be accelerated by oxidative stress.

Oscillatory growth in lily pollen tubes does not require aerobic energy metabolism

Oscillatory tip growth in pollen tubes depends on prodigious amounts of energy. We have tested the hypothesis that oscillations in the electron transport chain lead to growth oscillations in lily (Lilium formosanum). Using three respiratory inhibitors, oligomycin, antimycin A, and cyanide, we find that pollen tube growth is much less sensitive to respiratory inhibition than respiration is. All three block respiration at concentrations severalfold lower than necessary to inhibit growth. Mitochondrial NAD(P)H and potentiometric JC-1 fluorescence, employed as markers for electron transport chain activity, rise rapidly in response to oligomycin, as expected. Pollen tube growth stops for several minutes before resuming. Subsequent growth has a lower mean rate, but continues to oscillate, albeit with a longer period. NAD(P)H fluorescence no longer exhibits coherent oscillations, and mitochondria no longer congregate directly behind the apex: they distribute evenly throughout the cell. Postinhibition growth relies on aerobic fermentation for energy production as revealed by an increase in ethanol in the media. These data suggest that oscillatory growth depends not on a single oscillatory pacemaker but rather is an emergent property arising from a number of stable limit cycles.

Matching ATP supply and demand in mammalian heart: in vivo, in vitro, and in silico perspectives

Although the heart rapidly adapts cardiac output to match the body's circulatory demands, the regulatory mechanisms ensuring that sufficient ATP is available to perform the required cardiac work are not completely understood. Two mechanisms have been suggested to serve as key regulators: (1) ADP and Pi concentrations--ATP utilization/hydrolysis in the cytosol increases ADP and Pi fluxes to mitochondria and hence the amount of available substrates for ATP production increases; and (2) Ca2+ concentration--ATP utilization/hydrolysis is coupled to changes in free cytosolic calcium and mitochondrial calcium, the latter controlling Ca2+-dependent activation of mitochondrial enzymes taking part in ATP production. Here we discuss the evolving perspectives of each of the putative regulatory mechanisms and the precise molecular targets (dehydrogenase enzymes, ATP synthase) based on existing experimental and theoretical evidence. The data synthesis can generate novel hypotheses and experimental designs to solve the ongoing enigma of energy supply-demand matching in the heart.

Alternative oxidase: a defence against metabolic fluctuations?

An increasing number of oscillating or fluctuating cellular systems have been recently described following the adaptation of fluorescent technology. In diverse organisms, these variously involve signalling factors, heat production, central metabolism and reactive oxygen species (ROS). In response to many plant stresses and primarily via the influence of ROS, changes in mRNA and protein levels or in vivo activity of alternative oxidase are often observed. However, in several investigations, a lack of correlation between the mRNA, protein and in vivo activity has been evident. This discrepancy has made it questionable whether the induction of alternative oxidase has importance in regulating alternative pathway activity in vivo, or being diagnostic for a role of alternative oxidase in stress tolerance and ROS avoidance. Here, we suggest a role of alternative oxidase in counteracting deleterious short-term metabolic fluctuations, especially under stress conditions. This model emphasizes the importance of peak activity for establishing protein levels and allows an amalgamation of the present status of physiological, cellular and molecular knowledge.