Metabolic cycles as an underlying basis of biological oscillations

Design patterns of biological cells

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

Behavior and physiology in female Cricetulus barabensis are associated with the expression of circadian genes

The circadian clock regulates the behavior, physiology, and metabolism of mammals, and these characteristics, such as sleep-wake cycles, exercise capacity, and hormone levels, exhibit circadian rhythms. Light signaling is the main stimulator of the mammalian circadian system. The photoperiod regulates the reproductive cycle of seasonal breeding animals, and the circadian clock plays a pivotal role in this process. However, the role of the clock in coordinating animal behavior and physiology in response to photoperiodic changes needs further investigation. The present study investigated the changes and correlation of behavioral activities, physiological indicators, and gene expression in female striped hamsters (Cricetulus barabensis) within 24 h under a 12L:12D photoperiod. We found that the daily rhythms of sleep-wake and open field were significant in hamsters. The expression of clock genes, melatonin receptor genes, and genes involved in general metabolism oscillated significantly in central and peripheral tissues (brain, hypothalamus, liver, ovary, and thymus) and was significantly associated with behavior and physiology. Our results revealed that the neuroendocrine system regulated the rhythmicity of behavior and physiology, and central and peripheral clock genes (Bmal1, Clock, Per1, Per2, Cry1, and Cry2), melatonin receptor genes (MT1, MT2, and GPR50), and metabolizing genes (SIRT1, FGF21, and PPARα) played important roles. Our results suggest that central and peripheral circadian clocks, melatonin receptors, and genes involved in general metabolism may play key roles in maintaining circadian behavior and metabolic homeostasis in striped hamsters. Our results may have important implication for rodent pest control.

Sleep and circadian rhythmicity as entangled processes serving homeostasis

Sleep is considered essential for the brain and body. A predominant concept is that sleep is regulated by circadian rhythmicity and sleep homeostasis, processes that were posited to be functionally and mechanistically separate. Here we review and re-evaluate this concept and its assumptions using findings from recent human and rodent studies. Alterations in genes that are central to circadian rhythmicity affect not only sleep timing but also putative markers of sleep homeostasis such as electroencephalogram slow-wave activity (SWA). Perturbations of sleep change the rhythmicity in the expression of core clock genes in tissues outside the central clock. The dynamics of recovery from sleep loss vary across sleep variables: SWA and immediate early genes show an early response, but the recovery of non-rapid eye movement and rapid eye movement sleep follows slower time courses. Changes in the expression of many genes in response to sleep perturbations outlast the effects on SWA and time spent asleep. These findings are difficult to reconcile with the notion that circadian- and sleep-wake-driven processes are mutually independent and that the dynamics of sleep homeostasis are reflected in a single variable. Further understanding of how both sleep and circadian rhythmicity contribute to the homeostasis of essential physiological variables may benefit from the assessment of multiple sleep and molecular variables over longer time scales.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

Reverse genetic screening during L1 arrest reveals a role of the diacylglycerol kinase 1 gene dgk-1 and sphingolipid metabolism genes in sleep regulation

Sleep is a fundamental state of behavioral quiescence and physiological restoration. Sleep is controlled by environmental conditions, indicating a complex regulation of sleep by multiple processes. Our knowledge of the genes and mechanisms that control sleep during various conditions is, however, still incomplete. In Caenorhabditis elegans, sleep is increased when development is arrested upon starvation. Here, we performed a reverse genetic sleep screen in arrested L1 larvae for genes that are associated with metabolism. We found over 100 genes that are associated with a reduced sleep phenotype. Enrichment analysis revealed sphingolipid metabolism as a key pathway that controls sleep. A strong sleep loss was caused by the loss of function of the diacylglycerol kinase 1 gene, dgk-1, a negative regulator of synaptic transmission. Rescue experiments indicated that dgk-1 is required for sleep in cholinergic and tyraminergic neurons. The Ring Interneuron S (RIS) neuron is crucial for sleep in C. elegans and activates to induce sleep. RIS activation transients were abolished in dgk-1 mutant animals. Calcium transients were partially rescued by a reduction-of-function mutation of unc-13, suggesting that dgk-1 might be required for RIS activation by limiting synaptic vesicle release. dgk-1 mutant animals had impaired L1 arrest survival and dampened expression of the protective heat shock factor gene hsp-12.6. These data suggest that dgk-1 impairment causes broad physiological deficits. Microcalorimetry and metabolomic analyses of larvae with impaired RIS showed that RIS is broadly required for energy conservation and metabolic control, including for the presence of sphingolipids. Our data support the notion that metabolism broadly influences sleep and that sleep is associated with profound metabolic changes. We thus provide novel insights into the interplay of lipids and sleep and provide a rich resource of mutants and metabolic pathways for future sleep studies.

Mitochondrial control of sleep

The function of sleep remains one of biology's biggest mysteries. A solution to this problem is likely to come from a better understanding of sleep homeostasis, and in particular of the cellular and molecular processes that sense sleep need and settle sleep debt. Here, we highlight recent work in the fruit fly showing that changes in the mitochondrial redox state of sleep-promoting neurons lie at the heart of a homeostatic sleep-regulatory mechanism. Since the function of homeostatically controlled behaviours is often linked to the regulated variable itself, these findings corroborate with the hypothesis that sleep serves a metabolic function.

Seizure occurrence is linked to multiday cycles in diverse physiological signals

OBJECTIVE

The factors that influence seizure timing are poorly understood, and seizure unpredictability remains a major cause of disability. Work in chronobiology has shown that cyclical physiological phenomena are ubiquitous, with daily and multiday cycles evident in immune, endocrine, metabolic, neurological, and cardiovascular function. Additionally, work with chronic brain recordings has identified that seizure risk is linked to daily and multiday cycles in brain activity. Here, we provide the first characterization of the relationships between the cyclical modulation of a diverse set of physiological signals, brain activity, and seizure timing.

METHODS

In this cohort study, 14 subjects underwent chronic ambulatory monitoring with a multimodal wrist-worn sensor (recording heart rate, accelerometry, electrodermal activity, and temperature) and an implanted responsive neurostimulation system (recording interictal epileptiform abnormalities and electrographic seizures). Wavelet and filter-Hilbert spectral analyses characterized circadian and multiday cycles in brain and wearable recordings. Circular statistics assessed electrographic seizure timing and cycles in physiology.

RESULTS

Ten subjects met inclusion criteria. The mean recording duration was 232 days. Seven subjects had reliable electroencephalographic seizure detections (mean = 76 seizures). Multiday cycles were present in all wearable device signals across all subjects. Seizure timing was phase locked to multiday cycles in five (temperature), four (heart rate, phasic electrodermal activity), and three (accelerometry, heart rate variability, tonic electrodermal activity) subjects. Notably, after regression of behavioral covariates from heart rate, six of seven subjects had seizure phase locking to the residual heart rate signal.

SIGNIFICANCE

Seizure timing is associated with daily and multiday cycles in multiple physiological processes. Chronic multimodal wearable device recordings can situate rare paroxysmal events, like seizures, within a broader chronobiology context of the individual. Wearable devices may advance the understanding of factors that influence seizure risk and enable personalized time-varying approaches to epilepsy care.

Understanding Sleep Regulation in Normal and Pathological Conditions, and Why It Matters

Sleep occupies a peculiar place in our lives and in science, being both eminently familiar and profoundly enigmatic. Historically, philosophers, scientists and artists questioned the meaning and purpose of sleep. If Shakespeare's verses from MacBeth depicting "Sleep that soothes away all our worries" and "relieves the weary laborer and heals hurt minds" perfectly epitomize the alleviating benefits of sleep, it is only during the last two decades that the growing understanding of the sophisticated sleep regulatory mechanisms allows us to glimpse putative biological functions of sleep. Sleep control brings into play various brain-wide processes occurring at the molecular, cellular, circuit, and system levels, some of them overlapping with a number of disease-signaling pathways. Pathogenic processes, including mood disorders (e.g., major depression) and neurodegenerative illnesses such Huntington's or Alzheimer's diseases, can therefore affect sleep-modulating networks which disrupt the sleep-wake architecture, whereas sleep disturbances may also trigger various brain disorders. In this review, we describe the mechanisms underlying sleep regulation and the main hypotheses drawn about its functions. Comprehending sleep physiological orchestration and functions could ultimately help deliver better treatments for people living with neurodegenerative diseases.

The circadian rhythm regulates branched-chain amino acids metabolism in fast muscle of Chinese perch (Siniperca chuatsi) during short-term fasting by Clock-KLF15-Bcat2 pathway

As an internal time-keeping mechanism, circadian rhythm plays crucial role in maintaining homoeostasis when in response to nutrition change; meanwhile, branched-chain amino acids (BCAA) in skeletal muscle play an important role in preserving energy homoeostasis during fasting. Previous results from our laboratory suggested that fasting can influence peripheral circadian rhythm and BCAA metabolism in fish, but the relationship between circadian rhythm and BCAA metabolism, and whether circadian rhythm regulates BCAA metabolism to maintain physiological homoeostasis during fasting remains unclear. This study shows that the expression of fifteen core clock genes as well as KLF15 and Bcat2 is highly responsive to short-term fasting in fast muscle of Siniperca chuatsi, and the correlation coefficient between Clock and KLF15 expression is enhanced after fasting treatment. Furthermore, we demonstrate that the transcriptional expression of KLF15 is regulated by Clock, and the transcriptional expression of Bcat2 is regulated by KLF15 by using dual-luciferase reporter gene assay and Vivo-morpholinos-mediated gene knockdown technique. Therefore, fasting imposes a dynamic coordination of transcription between the circadian rhythm and BCAA metabolic pathways. The findings highlight the interaction between circadian rhythm and BCAA metabolism and suggest that fasting induces a switch in KLF15 expression through affecting the rhythmic expression of Clock, and then KLF15 promotes the transcription of Bcat2 to enhance the metabolism of BCAA, thus maintaining energy homoeostasis and providing energy for skeletal muscle as well as other tissues.

Investigation of the multi-targeted protection potential of tannic acid against doxorubicin-induced kidney damage in rats

Doxorubicin (DOX) is an antitumor drug that is powerful but can cause worse outcomes, including nephrotoxicity, and therefore has limited clinical use. Therefore, it is necessary to identify safer agents that can minimize the damage caused by the drug without shifting the treatment performance, in addition to clarifying the underlying mechanisms of DOX-induced aberrant in vivo renal activation. In this study, we tested the prophylactic capacity and mechanisms of action of tannic acid (TA) against DOX-mediated kidney damage in rats and evaluated the nephrotoxic activity of DOX when used with TA. Rats were treated during the two weeks with cumulative (18 mg/kg with six different injections) DOX, daily TA (50 mg/kg), and the DOX + TA combination. Changes in major metabolites and components involved in antioxidant metabolism were evaluated in the kidney tissues of all animals. Further, the gene expression levels of regulatory factors that have critical importance in cell metabolism, inflammation, and apoptosis were investigated. Both biochemical and molecular examinations showed that TA improved DOX-induced dysregulations at both protein and gene levels in the kidneys. Increased lipid peroxidation and decreased glutathione levels were reversed. Consistent with oxidative stress marker metabolites, suppressed antioxidant enzyme activities and transcript levels of antioxidant system members were restored. Of note, combination treatment with TA could overcome doxorubicin-induced gene expressions markedly altered by DOX, suggesting that nephroprotection conferred by TA involved the remodeling of stress resistance, cell metabolism, inflammation, and apoptosis. Collectively, the present in vivo study suggests that TA could be used as a multitarget and effective agent for the mitigation of doxorubicin-induced nephrotoxicity without changing the therapeutic efficacy of the drug.

Environmental light exposure and mealtime regularity: Implications for human health

Light exposure and mealtime act as cues to the human circadian rhythm, which subsequently regulates various physiological functions in the body. However, modernization alters lifestyles, with changes to social and work-related activities independent of the natural light-dark cycle. This review summarizes the role of light exposure and regular mealtime on bodily processes and, ultimately, metabolic health. Various aspects of light are reviewed, including the type of light (natural/artificial), intensity (lux), spectral composition, time of exposure (night/day), and exposure duration. Further, the possible relationship between light exposure and mealtime irregularity is discussed as a function affecting metabolic health. In essence, research evidence suggests that mealtime regularity and light exposure habits based on the natural occurring light-dark cycle are essential for metabolic health in relation to an aligned circadian rhythm.

Prereplication complex proteins get caught moonlighting

In this issue of PLOS Biology, Lattmann and colleagues report a new function for proteins of the DNA prereplication complex promoting the anchor cell to invade through the basement membrane and initiate vulval development in Caenorhabditis elegans.

The Fractal Tapestry of Life: II Entailment of Fractional Oncology by Physiology Networks

This is an essay advocating the efficacy of using the (noninteger) fractional calculus (FC) for the modeling of complex dynamical systems, specifically those pertaining to biomedical phenomena in general and oncological phenomena in particular. Herein we describe how the integer calculus (IC) is often incapable of describing what were historically thought to be simple linear phenomena such as Newton's law of cooling and Brownian motion. We demonstrate that even linear dynamical systems may be more accurately described by fractional rate equations (FREs) when the experimental datasets are inconsistent with models based on the IC. The Network Effect is introduced to explain how the collective dynamics of a complex network can transform a many-body noninear dynamical system modeled using the IC into a set of independent single-body fractional stochastic rate equations (FSREs). Note that this is not a mathematics paper, but rather a discussion focusing on the kinds of phenomena that have historically been approximately and improperly modeled using the IC and how a FC replacement of the model better explains the experimental results. This may be due to hidden effects that were not anticapated in the IC model, or to an effect that was acknowledged as possibly significant, but beyond the mathematical skills of the investigator to Incorporate into the original model. Whatever the reason we introduce the FRE used to describe mathematical oncology (MO) and review the quality of fit of such models to tumor growth data. The analytic results entailed in MO using ordinary diffusion as well as fractional diffusion are also briefly discussed. A connection is made between a time-dependent fractional-order derivative, technically called a distributed-order parameter, and the multifractality of time series, such that an observed multifractal time series can be modeled using a FRE with a distributed fractional-order derivative. This equivalence between multifractality and distributed fractional derivatives has not received the recognition in the applications literature we believe it warrants.

Recognition of acetylated histone by Yaf9 regulates metabolic cycling of transcription initiation and chromatin regulatory factors

How transcription programs rapidly adjust to changing metabolic and cellular cues remains poorly defined. Here, we reveal a function for the Yaf9 component of the SWR1-C and NuA4 chromatin regulatory complexes in maintaining timely transcription of metabolic genes across the yeast metabolic cycle (YMC). By reading histone acetylation during the oxidative and respiratory phase of the YMC, Yaf9 recruits SWR1-C and NuA4 complexes to deposit H2A.Z and acetylate H4, respectively. Increased H2A.Z and H4 acetylation during the oxidative phase promotes transcriptional initiation and chromatin machinery occupancy and is associated with reduced RNA polymerase II levels at genes-a pattern reversed during transition from oxidative to reductive metabolism. Prevention of Yaf9-H3 acetyl reading disrupted this pattern of transcriptional and chromatin regulator recruitment and impaired the timely transcription of metabolic genes. Together, these findings reveal that Yaf9 contributes to a dynamic chromatin and transcription initiation factor signature that is necessary for the proper regulation of metabolic gene transcription during the YMC. They also suggest that unique regulatory mechanisms of transcription exist at distinct metabolic states.

The mesoscale order of nacreous pearls

A pearl's distinguished beauty and toughness are attributable to the periodic stacking of aragonite tablets known as nacre. Nacre has naturally occurring mesoscale periodicity that remarkably arises in the absence of discrete translational symmetry. Gleaning the inspiring biomineral design of a pearl requires quantifying its structural coherence and understanding the stochastic processes that influence formation. By characterizing the entire structure of pearls (∼3 mm) in a cross-section at high resolution, we show that nacre has medium-range mesoscale periodicity. Self-correcting growth mechanisms actively remedy disorder and topological defects of the tablets and act as a countervailing process to long-range disorder. Nacre has a correlation length of roughly 16 tablets (∼5.5 µm) despite persistent fluctuations and topological defects. For longer distances (>25 tablets , ∼8.5 µm), the frequency spectrum of nacre tablets follows [Formula: see text] behavior, suggesting that growth is coupled to external stochastic processes-a universality found across disparate natural phenomena, which now includes pearls.

Diurnal regulation of oxidative phosphorylation restricts hepatocyte proliferation and inflammation

The principles guiding the diurnal organization of biological pathways remain to be fully elucidated. Here, we perturb the hepatic transcriptome through nutrient regulators (high-fat diet and mTOR signaling components) to identify enduring properties of pathway organization. Temporal separation and counter-regulation between pathways of energy metabolism and inflammation/proliferation emerge as persistent transcriptome features across animal models, and network analysis identifies the G0s2 and Rgs16 genes as potential mediators at the metabolism-inflammation interface. Mechanistically, G0s2 and Rgs16 are sequentially induced during the light phase, promoting amino acid oxidation and suppressing overall mitochondrial respiration. In their absence, sphingolipids and diacylglycerides accumulate, accompanied by hepatic inflammation and hepatocyte proliferation. Notably, the expression of G0s2 and Rgs16 is further induced in obese mouse livers, and silencing of their expression accentuates hepatic fibrosis. Therefore, diurnal regulation of energy metabolism alleviates inflammatory and proliferative stresses under physiological and pathological conditions.

Maximizing average throughput in oscillatory biochemical synthesis systems: an optimal control approach

A dynamical system entrains to a periodic input if its state converges globally to an attractor with the same period. In particular, for a constant input, the state converges to a unique equilibrium point for any initial condition. We consider the problem of maximizing a weighted average of the system's output along the periodic attractor. The gain of entrainment is the benefit achieved by using a non-constant periodic input relative to a constant input with the same time average. Such a problem amounts to optimal allocation of resources in a periodic manner. We formulate this problem as a periodic optimal control problem, which can be analysed by means of the Pontryagin maximum principle or solved numerically via powerful software packages. We then apply our framework to a class of nonlinear occupancy models that appear frequently in biological synthesis systems and other applications. We show that, perhaps surprisingly, constant inputs are optimal for various architectures. This suggests that the presence of non-constant periodic signals, which frequently appear in biological occupancy systems, is a signature of an underlying time-varying objective functional being optimized.

GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme

How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GIDSR4, which resembles an organometallic supramolecular chelate. The Chelator-GIDSR4 assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.

Modeling Cell Energy Metabolism as Weighted Networks of Non-autonomous Oscillators

Networks of oscillating processes are a common occurrence in living systems. This is as true as anywhere in the energy metabolism of individual cells. Exchanges of molecules and common regulation operate throughout the metabolic processes of glycolysis and oxidative phosphorylation, making the consideration of each of these as a network a natural step. Oscillations are similarly ubiquitous within these processes, and the frequencies of these oscillations are never truly constant. These features make this system an ideal example with which to discuss an alternative approach to modeling living systems, which focuses on their thermodynamically open, oscillating, non-linear and non-autonomous nature. We implement this approach in developing a model of non-autonomous Kuramoto oscillators in two all-to-all weighted networks coupled to one another, and themselves driven by non-autonomous oscillators. Each component represents a metabolic process, the networks acting as the glycolytic and oxidative phosphorylative processes, and the drivers as glucose and oxygen supply. We analyse the effect of these features on the synchronization dynamics within the model, and present a comparison between this model, experimental data on the glycolysis of HeLa cells, and a comparatively mainstream model of this experiment. In the former, we find that the introduction of oscillator networks significantly increases the proportion of the model's parameter space that features some form of synchronization, indicating a greater ability of the processes to resist external perturbations, a crucial behavior in biological settings. For the latter, we analyse the oscillations of the experiment, finding a characteristic frequency of 0.01–0.02 Hz. We further demonstrate that an output of the model comparable to the measurements of the experiment oscillates in a manner similar to the measured data, achieving this with fewer parameters and greater flexibility than the comparable model.

ROS and hypoxia signaling regulate periodic metabolic arousal during insect dormancy to coordinate glucose, amino acid, and lipid metabolism

Metabolic suppression is a hallmark of animal dormancy that promotes overall energy savings. Some diapausing insects and some mammalian hibernators have regular cyclic patterns of substantial metabolic depression alternating with periodic arousal where metabolic rates increase dramatically. Previous studies, largely in mammalian hibernators, have shown that periodic arousal is driven by an increase in aerobic mitochondrial metabolism and that many molecules related to energy metabolism fluctuate predictably across periodic arousal cycles. However, it is still not clear how these rapid metabolic shifts are regulated. We first found that diapausing flesh fly pupae primarily use anaerobic glycolysis during metabolic depression but engage in aerobic respiration through the tricarboxylic acid cycle during periodic arousal. Diapausing pupae also clear anaerobic by-products and regenerate many metabolic intermediates depleted in metabolic depression during arousal, consistent with patterns in mammalian hibernators. We found that decreased levels of reactive oxygen species (ROS) induced metabolic arousal and elevated ROS extended the duration of metabolic depression. Our data suggest ROS regulates the timing of metabolic arousal by changing the activity of two critical metabolic enzymes, pyruvate dehydrogenase and carnitine palmitoyltransferase I by modulating the levels of hypoxia inducible transcription factor (HIF) and phosphorylation of adenosine 5'-monophosphate-activated protein kinase (AMPK). Our study shows that ROS signaling regulates periodic arousal in our insect diapasue system, suggesting the possible importance ROS for regulating other types of of metabolic cycles in dormancy as well.

Characterizing glucose, illumination, and nitrogen-deprivation phenotypes of Synechocystis PCC6803 with Raman spectroscopy

Background

Synechocystis sp. PCC6803 is a model cyanobacterium that has been studied widely and is considered for metabolic engineering applications. Here, Raman spectroscopy and Raman chemometrics (Rametrix™) were used to (i) study broad phenotypic changes in response to growth conditions, (ii) identify phenotypic changes associated with its circadian rhythm, and (iii) correlate individual Raman bands with biomolecules and verify these with more accepted analytical methods.

Methods

Synechocystis cultures were grown under various conditions, exploring dependencies on light and/or external carbon and nitrogen sources. The Rametrix™ LITE Toolbox for MATLAB® was used to process Raman spectra and perform principal component analysis (PCA) and discriminant analysis of principal components (DAPC). The Rametrix™ PRO Toolbox was used to validate these models through leave-one-out routines that classified a Raman spectrum when growth conditions were withheld from the model. Performance was measured by classification accuracy, sensitivity, and specificity. Raman spectra were also subjected to statistical tests (ANOVA and pairwise comparisons) to identify statistically relevant changes in Synechocystis phenotypes. Finally, experimental methods, including widely used analytical and spectroscopic assays were used to quantify the levels of glycogen, fatty acids, amino acids, and chlorophyll a for correlations with Raman data.

Results

PCA and DAPC models produced distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on (i) growth in the presence of 5 mM glucose, (ii) illumination (dark, light/dark [12 h/12 h], and continuous light at 20 µE), (iii) nitrogen deprivation (0–100% NaNO₃ of native BG-11 medium in continuous light), and (iv) throughout a 24 h light/dark (12 h/12 h) circadian rhythm growth cycle. Rametrix™ PRO was successful in identifying glucose-induced phenotypes with 95.3% accuracy, 93.4% sensitivity, and 96.9% specificity. Prediction accuracy was above random chance values for all other studies. Circadian rhythm analysis showed a return to the initial phenotype after 24 hours for cultures grown in light/dark (12 h/12 h) cycles; this did not occur for cultures grown in the dark. Finally, correlation coefficients (R > 0.7) were found for glycogen, all amino acids, and chlorophyll a when comparing specific Raman bands to other experimental results.

Quorum sensing for population-level control of bacteria and potential therapeutic applications

Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.

Chromatin-remodeling links metabolic signaling to gene expression

BACKGROUND

ATP-dependent chromatin remodelers are evolutionarily conserved complexes that alter nucleosome positioning to influence many DNA-templated processes, such as replication, repair, and transcription. In particular, chromatin remodeling can dynamically regulate gene expression by altering accessibility of chromatin to transcription factors.

SCOPE OF REVIEW

This review provides an overview of the importance of chromatin remodelers in the regulation of metabolic gene expression. Particular emphasis is placed on the INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers in both yeast and mammals. This review details discoveries from the initial identification of chromatin remodelers in Saccharomyces cerevisiae to recent discoveries in the metabolic requirements of developing embryonic tissues in mammals.

MAJOR CONCLUSIONS

INO80 and SWI/SNF (BAF/PBAF) chromatin remodelers regulate the expression of energy metabolism pathways in S. cerevisiae and mammals in response to diverse nutrient environments. In particular, the INO80 complex organizes the temporal expression of gene expression in the metabolically synchronized S. cerevisiae system. INO80-mediated chromatin remodeling is also needed to constrain cell division during metabolically favorable conditions. Conversely, the BAF/PBAF remodeler regulates tissue-specific glycolytic metabolism and is disrupted in cancers that are dependent on glycolysis for proliferation. The role of chromatin remodeling in metabolic gene expression is downstream of the metabolic signaling pathways, such as the TOR pathway, a critical regulator of metabolic homeostasis. Furthermore, the INO80 and BAF/PBAF chromatin remodelers have both been shown to regulate heart development, the tissues of which have unique requirements for energy metabolism during development. Collectively, these results demonstrate that chromatin remodelers communicate metabolic status to chromatin and are a central component of homeostasis pathways that optimize cell fitness, organismal development, and prevent disease.

Is Neuronal Histamine Signaling Involved in Cancer Cachexia? Implications and Perspectives

In this paper, we present evidence in support of our hypothesis that the neuronal histaminergic system might be involved in cancer cachexia¹. To build our premise, we present the research and the reasonable inferences that can be drawn from it in a section by section approach starting from one of the key issues related to cachexia, increased resting energy expenditure (REE), and progressing to the other, anorexia. Based on an extensive survey of the literature and our own deliberations on the abovementioned topics, we investigate whether histamine signaling might be the mechanism used by a tumor to hijack the body's thermogenic machinery. Our hypothesis in short is that hypothalamic histaminergic neurons are stimulated by inputs from the parasympathetic nervous system (PSNS), which senses tumor traits early in cancer development. Histamine release in the preoptic area of the hypothalamus primarily activates brown adipose tissue (BAT), triggering a highly energy demanding mechanism. Chronic activation of BAT, which, in this context, refers to intermittent and/or low grade activation by the sympathetic nervous system, leads to browning of white adipose tissue and further enhances thermogenic potential. Aberrant histamine signaling not only triggers energy-consuming processes, but also anorexia. Moreover, since functions such as taste, smell, and sleep are governed by discrete structures of the brain, which are targeted by distinct histaminergic neuron populations even relatively minor symptoms of cachexia, such as sleep disturbances and taste and smell distortions, also might be ascribed to aberrant histamine signaling. In late stage cachexia, the sympathetic tone in skeletal muscle breaks down, which we hypothesize might be caused by a reduction in histamine signaling or by the interference of other cachexia related mechanisms. Histamine signaling thus might delineate distinct stages of cachexia progression, with the early phase marked by a PSNS-mediated increase in histamine signaling, increased sympathetic tone and symptomatic adipose tissue depletion, and the late phase characterized by reduced histamine signaling, decreased sympathetic tone and symptomatic muscle wasting. To support our hypothesis, we review the literature from across disciplines and highlight the many commonalities between the mechanisms underlying cancer cachexia and current research findings on the regulation of energy homeostasis (particularly as it relates to hypothalamic histamine signaling). Extrapolating from the current body of knowledge, we develop our hypothetical framework (based on experimentally falsifiable assumptions) about the role of a distinct neuron population in the pathophysiology of cancer cachexia. Our hope is that presenting our ideas will spark discussion about the pathophysiology of cachexia, cancer's devastating and intractable syndrome.

Exploring phylogeny to find the function of sleep

During sleep, animals do not eat, reproduce or forage. Sleeping animals are vulnerable to predation. Yet, the persistence of sleep despite evolutionary pressures, and the deleterious effects of sleep deprivation, indicate that sleep serves a function or functions that cannot easily be bypassed. Recent research demonstrates sleep to be phylogenetically far more pervasive than previously appreciated; it is possible that the very first animals slept. Here, we give an overview of sleep across various species, with the aim of determining its original purpose. Sleep exists in animals without cephalized nervous systems and can be influenced by non-neuronal signals, including those associated with metabolic rhythms. Together, these observations support the notion that sleep serves metabolic functions in neural and non-neural tissues.

XRCC2 Regulates Replication Fork Progression during dNTP Alterations

RAD51 paralogs are essential for maintenance of genomic integrity through protection of stalled replication forks and homology-directed repair (HDR) of double-strand breaks. Here, we find that a subset of RAD51 paralogs, XRCC2 (FANCU) and its binding partner RAD51D, restrain active DNA synthesis during dinucleotide triphosphate (dNTP) alterations in a manner independent of HDR. The absence of XRCC2 is associated with increased levels of RRM2, the regulatory subunit of ribonucleotide reductase (RNR), and concomitantly high nucleotide pools, leading to unrestrained fork progression and accumulation of DNA damage during dNTP alterations. Mechanistically, this function is independent of redox signaling and RAD51-mediated fork reversal and is regulated by ataxia-telangiectasia and Rad3-related (ATR) signaling through phosphorylation of XRCC2 (Ser247). Together, these findings identify roles of RAD51 paralogs in the control of replication fork progression and maintenance of genome stability during nucleotide pool alterations.

Recognition of Histone Crotonylation by Taf14 Links Metabolic State to Gene Expression

Metabolic signaling to chromatin often underlies how adaptive transcriptional responses are controlled. While intermediary metabolites serve as co-factors for histone-modifying enzymes during metabolic flux, how these modifications contribute to transcriptional responses is poorly understood. Here, we utilize the highly synchronized yeast metabolic cycle (YMC) and find that fatty acid β-oxidation genes are periodically expressed coincident with the β-oxidation byproduct histone crotonylation. Specifically, we found that H3K9 crotonylation peaks when H3K9 acetylation declines and energy resources become limited. During this metabolic state, pro-growth gene expression is dampened; however, mutation of the Taf14 YEATS domain, a H3K9 crotonylation reader, results in de-repression of these genes. Conversely, exogenous addition of crotonic acid results in increased histone crotonylation, constitutive repression of pro-growth genes, and disrupted YMC oscillations. Together, our findings expose an unexpected link between metabolic flux and transcription and demonstrate that histone crotonylation and Taf14 participate in the repression of energy-demanding gene expression.

Blood plasma metabolic profiling of pregnant women with antenatal depressive symptoms

Antenatal depression affects ~9-19% of pregnant women and can exert persistent adverse effects on both mother and child. There is a need for a deeper understanding of antenatal depression mechanisms and the development of tools for reliable diagnosis and early identification of women at high risk. As the use of untargeted blood metabolomics in the investigation of psychiatric and neurological diseases has increased substantially, the main objective of this study was to investigate whether untargeted gas chromatography-mass spectrometry (GC-MS) plasma metabolomics in 45 women in late pregnancy, residing in Uppsala, Sweden, could indicate metabolic differences between women with and without depressive symptoms. Furthermore, seasonal differences in the metabolic profiles were explored. When comparing the profiles of cases with controls, independently of season, no differences were observed. However, seasonal differences were observed in the metabolic profiles of control samples, suggesting a favorable cardiometabolic profile in the summer vs. winter, as indicated by lower glucose and sugar acid concentrations and lactate to pyruvate ratio, and higher abundance of arginine and phosphate. Similar differences were identified between cases and controls among summer pregnancies, indicating an association between a stressed metabolism and depressive symptoms. No depression-specific differences were apparent among depressed and non-depressed women, in the winter pregnancies; this could be attributed to an already stressed metabolism due to the winter living conditions. Our results provide new insights into the pathophysiology of antenatal depression, and warrant further investigation of the use of metabolomics in antenatal depression in larger cohorts.

Quantum biological tunnel junction for electron transfer imaging in live cells

Quantum biological electron transfer (ET) essentially involves in virtually all important biological processes such as photosynthesis, cellular respiration, DNA repair, cellular homeostasis, and cell death. However, there is no real-time imaging method to capture biological electron tunnelling in live cells to date. Here, we report a quantum biological electron tunnelling (QBET) junction and its application in real-time optical detection of QBET and the dynamics of ET in mitochondrial cytochrome c during cell life and death process. QBET junctions permit to see the behaviours of electron tunnelling through barrier molecules with different barrier widths. Using QBET spectroscopy, we optically capture real-time ET in cytochrome c redox dynamics during cellular apoptosis and necrosis in living cells. The non-invasive real-time QBET spectroscopic imaging of ET in live cell open a new era in life sciences and medicine by providing a way to capture spatiotemporal ET dynamics and to reveal the quantum biological mechanisms.

Although quantum biological electron transfer is important in many biological processes, imaging of the events in live cells has remained challenging. Here, the authors demonstrate real-time optical detection of quantum biological electron tunnelling between nanoparticles and cytochrome c inside living cells.

Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes

Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. However, most methods are designed to predict TF binding sites only. We present a computational method, dynamic motif occupancy analysis (DynaMO), to infer important TFs and their spatiotemporal binding activities in dynamic biological processes using chromatin profiling data from multiple biological conditions such as time-course histone modification ChIP-seq data. In the first step, DynaMO predicts TF binding sites with a random forests approach. Next and uniquely, DynaMO infers dynamic TF binding activities at predicted binding sites using their local chromatin profiles from multiple biological conditions. Another landmark of DynaMO is to identify key TFs in a dynamic process using a clustering and enrichment analysis of dynamic TF binding patterns. Application of DynaMO to the yeast ultradian cycle, mouse circadian clock and human neural differentiation exhibits its accuracy and versatility. We anticipate DynaMO will be generally useful for elucidating transcriptional programs in dynamic processes.

Atlas of Circadian Metabolism Reveals System-wide Coordination and Communication between Clocks

Metabolic diseases are often characterized by circadian misalignment in different tissues, yet how altered coordination and communication among tissue clocks relate to specific pathogenic mechanisms remains largely unknown. Applying an integrated systems biology approach, we performed 24-hr metabolomics profiling of eight mouse tissues simultaneously. We present a temporal and spatial atlas of circadian metabolism in the context of systemic energy balance and under chronic nutrient stress (high-fat diet [HFD]). Comparative analysis reveals how the repertoires of tissue metabolism are linked and gated to specific temporal windows and how this highly specialized communication and coherence among tissue clocks is rewired by nutrient challenge. Overall, we illustrate how dynamic metabolic relationships can be reconstructed across time and space and how integration of circadian metabolomics data from multiple tissues can improve our understanding of health and disease.

Genetic sleep deprivation: using sleep mutants to study sleep functions

Sleep is a fundamental conserved physiological state in animals and humans. It may serve multiple functions, ranging from energy conservation to higher brain operation. Understanding sleep functions and the underlying mechanisms requires the study of sleeplessness and its consequences. The traditional approach to remove sleep is sleep deprivation (SD) by sensory stimulation. However, stimulation-induced SD can be stressful and can cause non-specific side effects. An emerging alternative method is "genetic SD", which removes sleep using genetics or optogenetics. Sleep requires sleep-active neurons and their regulators. Thus, genetic impairment of sleep circuits might lead to more specific and comprehensive sleep loss. Here, I discuss the advantages and limits of genetic SD in key genetic sleep model animals: rodents, zebrafish, fruit flies and roundworms, and how the study of genetic SD alters our view of sleep functions. Genetic SD typically causes less severe phenotypes compared with stimulation-induced SD, suggesting that sensory stimulation-induced SD may have overestimated the role of sleep, calling for a re-investigation of sleep functions.

Metabolic rhythms: A framework for coordinating cellular function

Circadian clocks are widespread among eukaryotes and generally involve feedback loops coupled with metabolic processes and redox balance. The organising power of these oscillations has not only allowed organisms to anticipate day-night cycles, but also acts to temporally compartmentalise otherwise incompatible processes, enhance metabolic efficiency, make the system more robust to noise and propagate signals among cells. While daily rhythms and the function of the circadian transcription-translation loop have been the subject of extensive research over the past four decades, cycles of shorter period and respiratory oscillations, with which they are intertwined, have received less attention. Here, we describe features of yeast respiratory oscillations, which share many features with daily and 12 hr cellular oscillations in animal cells. This relatively simple system enables the analysis of dynamic rhythmic changes in metabolism, independent of cellular oscillations that are a product of the circadian transcription-translation feedback loop. Knowledge gained from studying ultradian oscillations in yeast will lead to a better understanding of the basic mechanistic principles and evolutionary origins of oscillatory behaviour among eukaryotes.

Flavin-based metabolic cycles are integral features of growth and division in single yeast cells

The yeast metabolic cycle (YMC) is a fascinating example of biological organization, in which cells constrain the function of specific genetic, protein and metabolic networks to precise temporal windows as they grow and divide. However, understanding the intracellular origins of the YMC remains a challenging goal, as measuring the oxygen oscillations traditionally associated with it requires the use of synchronized cultures growing in nutrient-limited chemostat environments. To address these limitations, we used custom-built microfluidic devices and time-lapse fluorescence microscopy to search for metabolic cycling in the form of endogenous flavin fluorescence in unsynchronized single yeast cells. We uncovered robust and pervasive metabolic cycles that were synchronized with the cell division cycle (CDC) and oscillated across four different nutrient conditions. We then studied the response of these metabolic cycles to chemical and genetic perturbations, showing that their phase synchronization with the CDC can be altered through treatment with rapamycin, and that metabolic cycles continue even in respiratory deficient strains. These results provide a foundation for future studies of the physiological importance of metabolic cycles in processes such as CDC control, metabolic regulation and cell aging.

Sleep Counteracts Aging Phenotypes to Survive Starvation-Induced Developmental Arrest in C. elegans

Sleep is ancient and fulfills higher brain functions as well as basic vital processes. Little is known about how sleep emerged in evolution and what essential functions it was selected for. Here, we investigated sleep in Caenorhabditis elegans across developmental stages and physiological conditions to find out when and how sleep in a simple animal becomes essential for survival. We found that sleep in worms occurs during most stages and physiological conditions and is typically induced by the sleep-active RIS neuron. Food quality and availability determine sleep amount. Extended starvation, which induces developmental arrest in larvae, presents a major sleep trigger. Conserved nutrient-sensing regulators of longevity and developmental arrest, AMP-activated kinase and FoxO, act in parallel to induce sleep during extended food deprivation. These metabolic factors can act in multiple tissues to signal starvation to RIS. Although sleep does not appear to be essential for a normal adult lifespan, it is crucial for survival of starvation-induced developmental arrest in larvae. Rather than merely saving energy for later use, sleep counteracts the progression of aging phenotypes, perhaps by allocating resources. Thus, sleep presents a protective anti-aging program that is induced by nutrient-sensing longevity pathways to survive starvation-induced developmental arrest. All organisms are threatened with the possibility of experienced famine in their life, which suggests that the molecular coupling of starvation, development, aging, and sleep was selected for early in the evolution of nervous systems and may be conserved in other species, including humans.

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C. elegans sleep across most physiological conditions, including developmental arrest

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The sleep-active RIS neuron generally induces physiological sleep

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Insulin and sirtuin signaling control AMPK and FoxO to induce sleep during starvation

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Sleep is required to survive developmental arrest and counteracts aging phenotypes

Cellular Timekeeping: It's Redox o'Clock

Mounting evidence in recent years supports the extensive interaction between the circadian and redox systems. The existence of such a relationship is not surprising because most organisms, be they diurnal or nocturnal, display daily oscillations in energy intake, locomotor activity, and exposure to exogenous and internally generated oxidants. The transcriptional clock controls the levels of many antioxidant proteins and redox-active cofactors, and, conversely, the cellular redox poise has been shown to feed back to the transcriptional oscillator via redox-sensitive transcription factors and enzymes. However, the circadian cycles in the S-sulfinylation of the peroxiredoxin (PRDX) proteins constituted the first example of an autonomous circadian redox oscillation, which occurred independently of the transcriptional clock. Importantly, the high phylogenetic conservation of these rhythms suggests that they might predate the evolution of the transcriptional oscillator, and therefore could be a part of a primordial circadian redox/metabolic oscillator. This discovery forced the reappraisal of the dogmatic transcription-centered view of the clockwork and opened a new avenue of research. Indeed, the investigation into the links between the circadian and redox systems is still in its infancy, and many important questions remain to be addressed.

Coordination of cardiac rhythmic output and circadian metabolic regulation in the heart

Over the course of a 24-h day, demand on the heart rises and falls with the sleep/wake cycles of the organism. Cardiac metabolism oscillates appropriately, with the relative contributions of major energy sources changing in a circadian fashion. The cardiac peripheral clock is hypothesized to drive many of these changes, yet the precise mechanisms linking the cardiac clock to metabolism remain a source of intense investigation. Here we summarize the current understanding of circadian alterations in cardiac metabolism and physiology, with an emphasis on novel findings from unbiased transcriptomic studies. Additionally, we describe progress in elucidating the links between the cardiac peripheral clock outputs and cardiac metabolism, as well as their implications for cardiac physiology.

Seasonal pattern in bipolar disorders and cardio-vascular risk factors: A study from the FACE-BD cohort

Seasonal pattern (SP) and metabolic syndrome (MetS) are major contributors to poor outcome in bipolar disorders (BD). Patients with seasonal bipolar depression present increased appetite, carbohydrate cravings, weight gain, and hypersomnia, which can increase the development of MetS. MetS also appears to be associated with seasonal mood changes in the general population. This study examines whether a SP in BD is associated with an increased risk of MetS and its sub-components. One thousand four hundred and seventy-one outpatients with BD were systematically enrolled from 2009 to 2016. Inclusion required a disease duration of at least 5 years, with 486 (33%) patients with SP (SP+) and 985 (67%) without (SP-) according to the DSM IV-TR criteria. When using continuous measures of metabolic components, SP+ patients, as compared to SP-, suffered from higher levels for systolic blood pressure (p = 0.01), low-density lipoprotein cholesterol (p = 0.009), fasting glucose (p = 0.007), triglycerides levels (p = 0.03), a larger abdominal circumference (p = 0.02), and a higher body mass index (p = 0.07). In the covariance analysis, adjusted for gender, age, and bipolar subtype, as well as the number of depressive and hypomanic episode, SP+ patients had a significantly higher level of fasting glucose and higher systolic blood pressure. The frequency of MetS did not differ between groups (21.2% in SP- versus 23.9% in SP+). When using categorical definitions for abnormal metabolic components (International Diabetes Federation criteria), there were no differences between groups, except that SP+ patients were more overweight/obese as compared to SP- patients (55.03% versus 46.7%, respectively; p = 0.002) and tended to have more frequently high fasting glucose (18.2% versus 14.3%, respectively; p = 0.07). MetS was frequent in patients with BD, however not associated with SP. Patients with SP appeared more vulnerable to overweight/obesity and presented with higher levels of MetS subcomponents although these parameters were mainly in the normal range. All patients with BD should benefit from early screening and targeted management of cardio-vascular risk factors.

The molecular basis of metabolic cycles and their relationship to circadian rhythms

Metabolic cycles result from the partitioning of oxidative and reductive metabolism into rhythmic phases of gene expression and oscillating post-translational protein modifications. Relatively little is known about how these switches in gene expression are controlled, although recent studies have suggested that transcription itself may play a central role. This review explores the molecular basis of the metabolic and gene-expression oscillations in the yeast Saccharomyces cerevisiae, as well as how they relate to other biological time-keeping mechanisms, such as circadian rhythms.

Switching of metabolic programs in response to light availability is an essential function of the cyanobacterial circadian output pathway

The transcription factor RpaA is the master regulator of circadian transcription in cyanobacteria, driving genome-wide oscillations in mRNA abundance. Deletion of rpaA has no effect on viability in constant light conditions, but renders cells inviable in cycling conditions when light and dark periods alternate. We investigated the mechanisms underlying this viability defect, and demonstrate that the rpaA^- strain cannot maintain appropriate energy status at night, does not accumulate carbon reserves during the day, and is defective in transcription of genes crucial for utilization of carbohydrate stores at night. Reconstruction of carbon utilization pathways combined with provision of an external carbon source restores energy charge and viability of the rpaA^- strain in light/dark cycling conditions. Our observations highlight how a circadian output pathway controls and temporally coordinates essential pathways in carbon metabolism to maximize fitness of cells facing periodic energy limitations.

DOI:http://dx.doi.org/10.7554/eLife.23210.001

The cycle of day and night is one of the most recurrent and predictable environmental changes on our planet. Consequently, organisms have evolved mechanisms that allow them to measure time over 24 hours and prepare for the periodic changes between light and dark. These mechanisms, known as circadian clocks, alter the activity of some of the organism’s genes in a rhythmic way across the course of a day. This in turn causes certain behaviors and biological activities of the organism to follow a daily cycle.

The bacterium Synechococcus elongatus needs to be able to track the daily cycle of light and dark because it performs photosynthesis and depends on sunlight to form sugars, which can later be broken down to release energy. The time information encoded in the circadian clock of S. elongatus is transmitted to the protein RpaA, which drives the regular circadian changes in gene activity in the cell. If RpaA is removed from the cell or prevented from working, S. elongatus can no longer control rhythmic gene activity and is unable to survive the night.

To better understand how the circadian system schedules biological tasks to help an organism to survive, Puszynska and O'Shea studied S. elongatus cells. This revealed that the bacteria normally prepare for darkness by storing sugars during the day and activating several genes at dusk to make enzymes that are required to break down stored sugars. This provides the cells with energy that they need to survive the night. But mutant cells that lack the gene that produces RpaA do not prepare for darkness; they do not accumulate a store of sugars during the day or activate the vital genes at dusk. They have low internal energy levels in the dark and they cannot survive long periods of darkness.

Providing the mutant cells with sugar and restoring the activity of the genes responsible for breaking down sugar enabled the cells to maintain energy in darkness and survive the night. It therefore appears that one role of the circadian system of S. elongatus is to coordinate building up sugar reserves during the day with breaking down sugar stores to generate energy during the night.

Puszynska and O'Shea also found many other genes that are not activated at dusk in the mutant cells. It will therefore be important to study whether other pathways that help cells to survive and grow are defective in these mutant cells.

DOI:http://dx.doi.org/10.7554/eLife.23210.002

The Sleep in Caenorhabditis elegans: What We Know Until Now

Sleep, as one of the most important requirements of our brain, has a mystical nature. Despite long-standing studies, the molecular mechanisms and physiological properties of sleep have not been defined well as the complexity of the mammals' brain make it difficult to investigate the mechanisms and properties of sleep. Although some features of sleep have changed during evolution, its existence in such a simple animal, Caenorhabditis elegans, not only signifies the importance of sleep in even simple animals, but also allows the scientist to assess the core mechanism and biological events in an uncomplicated organism. This article reviews the information which exists about the characteristics of sleep in C. elegans, its circadian rhythm, the neurons and neurotransmitters responsible for each state, and the signaling molecules involved. Although much still remains to be resolved about the sleep of C. elegans, the available knowledge helps the scientists to recognize the properties better of this mysterious function of the brain.

Neural Signaling Metabolites May Modulate Energy Use in Hibernation

Despite an epidemic in obesity and metabolic syndrome limited means exist to effect adiposity or metabolic rate other than life style changes. Here we review evidence that neural signaling metabolites may modulate thermoregulatory pathways and offer novel means to fine tune energy use. We extend prior reviews on mechanisms that regulate thermogenesis and energy use in hibernation by focusing primarily on the neural signaling metabolites adenosine, AMP and glutamate.

Transcriptional architecture of the mammalian circadian clock

Circadian clocks are endogenous oscillators that control 24-hour physiological and behavioural processes in organisms. These cell-autonomous clocks are composed of a transcription-translation-based autoregulatory feedback loop. With the development of next-generation sequencing approaches, biochemical and genomic insights into circadian function have recently come into focus. Genome-wide analyses of the clock transcriptional feedback loop have revealed a global circadian regulation of processes such as transcription factor occupancy, RNA polymerase II recruitment and initiation, nascent transcription, and chromatin remodelling. The genomic targets of circadian clocks are pervasive and are intimately linked to the regulation of metabolism, cell growth and physiology.