This review summarizes current understanding of the interaction between circadian rhythms of gene expression and epigenetic clocks characterized by the specific profile of DNA methylation in CpG-islands which mirror the chronological age of individual cells and the entire organism. Basic mechanisms of regulation for circadian genes CLOCK- BMAL1 as well as downstream clock-controlled genes (ССG) are also discussed here. It has been shown that circadian rhythms operate by finely tuned regulation of transcription and rely on various epigenetic mechanisms including activation of enhancers / suppressors, acetylation / deacetylation of histones and other proteins as well as DNA methylation. Overall, up to 20% of all genes expressed by the cell are subject to expression oscillations associated with circadian rhythms. Also included in the review is a brief list of genes involved in the regulation of circadian rhythms, along with genes important for metabolic control, aging, and oncogenesis. Knocking out some of them (for example, Sirt1) accelerates the aging process, while overexpression of Sirt1, on the contrary, protects against age-related changes. Circadian regulators control a number of genes that activate the cell cycle (Wee1, c-Myc, p20, p21, and Cyclin D1) and regulate histone modification and DNA methylation. Approaches for determining the epigenetic age from methylation profiles across CpG islands in individual cells are described. DNA methylation, which characterizes the function of the epigenetic clock, appears to link together such key biological processes as regeneration and functioning of stem cells, aging and malignant transformation. Finally, main features of adult stem cell aging in stem cell niches and current possibilities for modulating the epigenetic clock as part of antiaging therapy are discussed.

Gliomas are solid tumors of the Central Nervous System (CNS) that originated from different glial cells. The World Health Organization (WHO) classified these tumors into four groups (I-IV) with increasing malignancy. Glioblastoma (GBM) is the most common and aggressive type of brain tumor classified as a grade IV. GBM are resistant to conventional therapies with poor prognosis after diagnosis even when the Stupp protocol that combines surgery and radiochemotherapy is applied. Nowadays, few novel therapeutic strategies have been used to improve GBM treatment, looking for higher efficiency and lower side effects, but with relatively modest results. The circadian timing system temporally organizes the physiology and behavior of most organisms and daily regulates several cellular processes in organs, tissues, and even in individual cells, including tumor cells. The potentiality of the function of the circadian clock on cancer cells modulation as a new target for novel treatments with a chronobiological basis offers a different challenge that needs to be considered in further detail. The present review will discuss state of the art regarding GBM biology, the role of the circadian clock in tumor progression, and new chrono-chemotherapeutic strategies applied for GBM treatment.

Huntington’s disease (HD) causes progressive movement disorders and cognitive deficits. Besides, sleep disturbances and emotional distress are prominent clinical signatures of HD. The experimental subjects and HD human brains display altered regenerative plasticity resulting from aberrant neurogenic and nonneurogenic areas. Sleep disorders, emotional disruption, and cognitive deficits have been linked to impaired cell cycle events of neural stem cells (NSC) in neurodegenerative disorders. In a physiological state, circadian clock gene pathways play important roles in the regulation of the proliferation and differentiation of NSC, whereas the irregular circadian clock pathway is attributed to impairment in the neurogenic process. The recent advancement of chemogenetic-based approaches represents a potential scientific tool to rectify the abnormal circadian clock which may aid in mitigating neurogenic failure in the brain. Notably, GABAergic vasoactive intestinal peptide (VIP)-expressing neurons in the brain plays a key role in the regulation of neuroplasticity and circadian rhythm. Thus, this conceptual review article addresses the potential link between sleep disorder and aberrant neurogenic events in HD and proposes chemogenetic kindling of vasoactive intestinal peptide (VIP) -expressing GABAergic neurons in the brain as a therapeutic strategy for reprogramming the clock gene pathways in mitigating the neurodegenerative failure in HD.

The Munich ChronoType Questionnaire (MCTQ) has now been available for more than 15 years; its original publication has been cited 1,240 times (Google Scholar, May 2019); its online version, which was available until July 2017, has produced almost 300,000 entries from all over the world (MCTQ database). The MCTQ has gone through several versions, has been translated into 13 languages and has been validated against other more objective measures of daily timing in several independent studies. Besides being used as a method to correlate circadian features of human biology with other factors – ranging from health issues to geographical factors – the MCTQ gave rise to quantifying old wisdoms, like “teenagers are late” and has produced new concepts, like social jetlag. Some like the MCTQ’s simplicity and some view it critically; it is time to have a self-critical view on the MCTQ, to address some misunderstandings and give some definitions about MCTQ-derived chronotype and the concept of social jetlag.

In this paper, we revisit the q-states clock model for small systems. We present results for the thermodynamics of the q-states clock model from $q=2$ to $q=20$ for small square lattices $L \times L$, with L ranging from $L=3$ to $L=64$ with free-boundary conditions. Energy, specific heat, entropy and magnetization are measured. We found that the Berezinskii-Kosterlitz-Thouless (BKT)-like transition appears for $q>5$ regardless of lattice size, while the transition at $q=5$ is lost for $L<10$; for $q\leq 4$ the BKT transition is never present. We report the phase diagram in terms of $q$ showing the transition from the ferromagnetic (FM) to the paramagnetic (PM) phases at a critical temperature T$_1$ for small systems which turns into a transition from the FM to the BKT phase for larger systems, while a second phase transition between the BKT and the PM phases occurs at T$_2$. We also show that the magnetic phases are well characterized by the two dimensional (2D) distribution of the magnetization values. We make use of this opportunity to do an information theory analysis of the time series obtained from the Monte Carlo simulations. In particular, we calculate the phenomenological mutability and diversity functions. Diversity characterizes the phase transitions, but the phases are less detectable as $q$ increases. Free boundary conditions are used to better mimic the reality of small systems (far from any thermodynamic limit). The role of size is discussed.

Beyond the usual ferromagnetic and paramagnetic phases present in spin systems, the usual q-state clock model, presents an intermediate vortex state when the number of possible orientations q for the system is equal to 5 or larger. Such vortex states give rise to the Berezinskii-Kosterlitz-Thouless (BKT) phase present up to the XY model in the limit q→∞. Based on information theory, we present here an analysis of the classical order parameters plus new short-range parameters defined here. Thus, we show that even using the first nearest neighbors spin-spin correlations only, it is possible to distinguish the two transitions presented by this system for q greater than or equal to 5. Moreover, the appearance at relatively low temperature and disappearance of the BKT phase at a rather fix higher temperature is univocally determined by the short-range interactions recognized by the information content of classical and new parameters.

An autonomous endogenous time-keeping is ubiquitous across many living organisms known as circadian clock when it has a period of about 24 hours. Interestingly, the fundamental design principle with a network of interconnected negative and positive feedback loops is conserved through evolution, although the molecular components differ. Filamentous fungus \textit{Neurospora crassa} is a well established chrono-genetics model organism to investigate the underlying mechanisms. The core negative feedback loop of the clock of \textit{Neurospora} is composed of the transcription activator White Collar Complex (WCC) (heterodimer of WC1 and WC2) and the inhibitory element called FFC complex which is made of FRQ (Frequency protein), FRH (Frequency interacting RNA Helicase) and CK1a (Casein kinase 1a). While exploring their temporal dynamics we investigate how limit cycle oscillations arise and how molecular switches support self-sustained rhythms. We develop a mathematical model of 10 variables with 26 parameters to understand the interactions and feedbacks among WC1 and FFC elements in nuclear and cytoplasmic compartments. We performed control and bifurcation analysis to show that our novel model produces robust oscillations with a wild-type period of 22.5 hrs. Our model reveals a switch between WC1 induced transcription and FFC assisted inactivation of WC1. Using the new model we also study possible mechanisms of glucose compensation. A fairly simple model with just 3 non-linearities helps to elucidate clock dynamics revealing a mechanism of rhythms production. The model can further be utilized to study entrainment and temperature compensation.

In Newtonian mechanics, time as well as space are perceived as absolute entities. In 2 Einstein’s special relativity, time is frame dependent. Time is also affected by gravitational field 3 and as the field varies in space, time also varies throughout space. In the present article, a 4 thermodynamic-based time is investigated. The entity is called "irreversibility", which is generated 5 when availability (also known as exergy) is destroyed. Since each thermodynamic system may 6 generate different amount of irreversibility, this quantity is system dependent. The time’s arrow is 7 automatically satisfied, since irreversibility generation always proceeds in one direction (toward 8 future). We have demonstrated that, like common time, irreversibility is frame dependent, and 9 affected by gravity in the similar manner as the common time. For this reason, we propose to 10 assign the entity irreversibility of the system as thermodynamic time. A possible application of the 11 thermodynamic time is an interpretation and managing of the aging of biological systems. The 12 metabolic efficiency is related to the irreversibility of the chemical processes and affect the aging of 13 the system. Our sensation of time-flow may be attributed to the flow of availability and destruction 14 of it through the living system. It is shown by other authors that entropy generation (equivalent to 15 irreversibility) is a parameter for the human life span. Since the thermodynamic time is based on a 16 concept of thermodynamics that is universal, further applications to other subjects, such as biological 17 clock, telomere, and cosmology are possible.

Restricted feeding is well known to affect expression profiles of both clock and metabolic genes. However, it is unknown whether these changes in metabolic gene expression result from changes in the molecular clock or in feeding behavior. Here we eliminated the daily rhythm in feeding behavior by providing 6-meals evenly distributed over the light/dark-cycle. Animals on this 6-meals-a-day feeding schedule retained the normal day/night difference in physiological parameters including body temperature and locomotor activity. The daily rhythm in respiratory exchange ratio (RER), however, was significantly phase-shifted through increased utilization of carbohydrates during the light phase and increased lipid oxidation during the dark phase. This 6-meals-a-day feeding schedule did not have a major impact on the clock gene expression rhythms in the master clock but did have mild effects on peripheral clocks. By contrast, genes involved in glucose and lipid metabolism showed differential expression. Concluding, eliminating the daily rhythm in feeding behavior in rats does not affect the master clock and only mildly affects peripheral clocks, but disturbs metabolic rhythms in liver, skeletal muscle and brown adipose tissue in a tissue-dependent manner. Thereby a clear daily rhythm in feeding behavior strongly regulates timing of peripheral metabolism, separately from circadian clocks.

This study investigates whether a chronotherapeutic treatment of hepatocellular carcinoma (HCC) may improve treatment efficacy and mitigate side effects on healthy liver (HL). HCC was induced in Per2::luc mice which were irradiated at four time points of the day. Proliferation and DNA-double strand breaks were investigated in irradiated and non-irradiated organotypic slice culture (OSC) and ex vivo samples by detection of Ki67 and γ-H2AX. OSC proved useful to determine dose-dependent effects on proliferation and DNA damage but appeared unsuited to test the chronotherapeutic approach. Irradiation of ex vivo samples was most effective at the proliferation peaks in HCC at ZT02 (early inactivity phase) and ZT20 (late activity phase). Irradiation effects on HL were minimal at ZT20. Ex vivo samples revealed disruption in daily variation and down-regulation of all investigated clock genes except Per1 in non-irradiated HCC as compared with HL. Irradiation affected rhythmic clock gene expression in HL and HCC at all ZTs except at ZT20. Irradiation at ZT20 had no effect on total leukocyte numbers. Our results indicate ZT20 as the optimal time point for irradiation of HCC in mice. Translational studies are now needed to evaluate whether the late activity phase is the optimal time point for irradiation of HCC in man.

Orbit and clock products are used in real-time GNSS precise point positioning without knowing their quality. This study develops a new approach to detect orbit and clock errors through comparing geometry-free and geometry-based wide-lane ambiguities in PPP model. The reparameterization and estimation procedures of the geometry-free and geometry-based ambiguities are described in detail. The effects of orbit and clock errors on ambiguities are given in analytical expressions. The numerical similarity and differences of geometry-free and geometry-based wide-lane ambiguities are analyzed using different orbit and clock products. Furthermore, two types of typical errors in orbit and clock are simulated and their effects on wide-lane ambiguities are numerically produced and analyzed. The contribution discloses that the geometry-free and geometry-based wide-lane ambiguities are equivalent in terms of their formal errors. Although they are very close in terms of their estimates when the used orbit and clock for geometry-based ambiguities are precise enough, they are not the same, in particular, in the case that the used orbit and clock, as a combination, contain significant errors. It is discovered that the discrepancies of geometry-free and geometry-based wide-lane ambiguities are coincided with the actual time-variant errors in the used orbit and clock at the line-of-sight direction. This provides a quality index for real-time users to detect the errors in real-time orbit and clock products, which potentially improves the accuracy of positioning.

Running at odds with the timing imposed by the circadian clock plays an important role in the process that leads to communicable and non communicable diseases. The primary objective of this study was to analyse whether early dinner eater children were at lower risks of acute respiratory infections than late dinner eater children, during the COVID-19 pandemic. Methods: This cross sectional study was conducted from July to December 2020 on children attending Majorcan emergency services. Clinical data collected included timing, symptoms, laboratory tests and imaging studies of current illness. Each diagnosis was validated by general paediatricians. Our survey on dinner time habits was carried out by using self-administered questionnaires. Results: A total of 669 children under age 18 were included in the study. The median of dinner time was 8:30 pm. Late dinner eaters accounted for a higher proportion of acute otitis media than early dinner eaters (7% vs 3%; P=0.028). Other infectious diseases were not associated with dinner time habits. Conclusions: We make a preliminary estimate of the link between late dinner habits and acute otitis media in children. However, no conclusions about causality can be established due to the observational design of the study.

Patients with degenerative diseases refer to feeling more pain during the night. However, it is unknown whether spinal nociception can be circadian and how is it controlled. We investigated whether the paw withdrawal threshold (PWT) could exhibit physiological circadian behavior as well as the contribution of the dopaminergic A11 nucleus and the spinal dopamine (DA) receptors (DRs) on the circadian PWT and the spinal clock gene transcription. Results revealed that control rats present a circadian PWT. Injecting 6-hydroxidopamine (6-OHDA) into the dopaminergic A11 nucleus reduced DA tissue content in the lumbar spinal cord, abolished the circadian PWT, induced allodynia, and reduced Period 1 and 2 (Per1 and 2), retinoid-related orphan receptor α (Rorα), Cryptochrome 1 (Cry1), and brain and muscle aryl-hydrocarbon receptor nuclear translocator-like protein (Bmal) mRNA. Likewise, administration of D1-like and D2-like DR antagonists blunted circadian PWT, producing allodynia, and altered the clock genes mRNA. In contrast, administration of D1-like or D2-like DR agonists blocked 6-OHDA-induced allodynia. This study shows that the spinal cord has physiological circadian PWT, which is modulated by the descending dopaminergic A11 through differential activation of the spinal DRs. Also, A11 nuclei and spinal DRs can regulate the clock gene transcription, which can likely modulate the circadian PWT.

This present work explores the performance of a thermal-magnetic engine of Otto type, considering as a working substance an effective interacting spin model corresponding to the q− state clock model. We obtain all the thermodynamic quantities for the q = 2, 4, 6, 8 cases in a small lattice size (3×3 with free boundary conditions) by using the exact partition function calculated from the energies of all the accessible microstates of the system. The extension to bigger lattices was performed using the mean-field approximation. Our results indicate that the total work extraction of the cycle is highest for the q=4 case, while the performance for the Ising model (q=2) is the lowest of all cases studied. These results are strongly linked with the phase diagram of the working substance and the location of the cycle in the different magnetic phases present, where we find that the transition from a ferromagnetic to a paramagnetic phase extracts more work than one of the Berezinskii–Kosterlitz–Thouless to paramagnetic type. Additionally, as the size of the lattice increases, the extraction work is lower than smaller lattices for all values of q presented in this study.

Clock Network Design (CDN) is a critical step while designing any Integrated-Circuits (ICs). It holds vital importance in the performance of entire circuit. Due to continuous scaling, 3D ICs stacked with TSV are gaining importance, with an objective to continue with the Moore's law. Through-Silicon-Via (TSV) provides the vertical interconnection between two die, which allows the electrical signal to flow through it. 3D ICs has many advantages over conventional 2D planar ICs like reduced power, area, cost, wire-length etc. The proposed work is mainly focused on power reduction and obstacle avoidance for 3D ICs. Various techniques have already been introduced for minimizing clock power within specified clock constraints of the 3D CND network. Proposed 3D Clock Tree Synthesis (CTS) is a combination of various algorithms with an objective to meet reduction in power as well as avoidance of obstacle or blockages while routing the clock signal from one sink to other sink. These blockages like RAM, ROM, PLL etc. are fixed during the placement process. The work is carried out mainly in three steps- first is Generation of 3D Clock tree avoiding the blockages, then Buffering and Embedding and finally validating the results by SPICE simulation. The experimental result shows that our CTS approach results in significant 9% reduction in power as compare to the existing work.

Circadian rhythms misalignment is associated with hypertension. The aim of the study was to evaluate the concentration of selected clock proteins- cryptochrome 1 (CRY1) and circadian locomotor output cycles kaput (CLOCK) and to determine their relationships with biochemical and anthropometric parameters and lifestyle elements (diet, physical activity, quality of sleep) in hypertensive patients. In 25 female with hypertension (HT) and 49 non-hypertensive women (NHT), the CRY1 and CLOCK concentrations, total antioxidant status (TAS), lipid profile and glycemia were conducted. Blood pressure and anthropometric measurements, nutritional, exercise and sleep analyses were performed. In HT the CRY1 level was 40.2% lower than in the NHT. No differences were noted in CLOCK concentration between groups. The study showed no relationship between CRY1 or CLOCK concentrations and glucose or lipids profile, amount of physical activity and sleep quality, although CRY1 was associated with some anthropometric parameters. There was a negative correlation between the CLOCK concentration and the amount of saturated fatty acids consumed (24h) in HT. That indicates the possible influence of the diet on the CLOCK level. In a detailed prognosis of the risk of hypertension, it is worth considering the measurement of the level of CRY1 in populations with abnormal anthropometric indices.

GIGANTEA (GI) is a gene involved in multiple biological functions, which were analysed and are partially conserved in a series of mono- and dicotyledonous plant species. The identified biological functions include control over the circadian rhythm, light signalling, cold tolerance, hormone signalling and photoperiodic flowering. The latter function is a central role of GI, as it involves a multitude of pathways, both dependent and independent of the gene CONSTANS(CO) as well as on the basis of interaction with miRNA. The complexity of gene function of GI increases due to the existence of paralogs showing changes in genome structure as well as incidences of sub- and neofunctionalization. We present an updated report of the biological function of GI, integrating late insights into its role in floral initiation, flower development and flower volatile production.

The severity and outcome of coronavirus disease 2019 (COVID-19) largely depends on a patient’s age. Over 80% of hospitalizations are of those over 65 years of age with a 23-fold greater risk of death. In the clinic, COVID-19 patients most commonly present with fever, cough and dyspnea. Particularly in those over 65, it can progress to pneumonia, lung consolidation, cytokine release syndrome, endotheliitis, coagulopathy, multiple organ failure and death. Comorbidities such as cardiovascular disease, diabetes, obesity and hypertension increase the chances of fatal disease, but they alone do not explain the variability in COVID-19 symptoms. Here, we present the molecular differences between the young, middle-aged and elderly that may determine whether COVID-19 is a mild or life-threatening illness. We also discuss several biological age clocks that could be used in conjunction with genetic tests to identify both the mechanisms of the disease and individuals most at risk. Finally, based on these mechanisms, we discuss treatments that could increase survival in the elderly, not simply by inhibiting the virus, but by restoring patients’ ability to clear the infection.

In this paper, we will revisit the derivation of Heisenberg's uncertainty principle. We will see how the Heisenberg principle collapses at the Planck scale by introducing a minor modification. The beauty of our suggested modification is that it does not change the main equations in quantum mechanics; it only gives them a Planck scale limit where uncertainty collapses. We suspect that Einstein could have been right after all, when he stated, ``God does not throw dice." His now-famous saying was an expression of his skepticism towards the concept that quantum randomness could be the ruling force, even at the deepest levels of reality. Here we will explore the quantum realm with a fresh perspective, by re-deriving the Heisenberg principle in relation to the Planck scale. We will show how this idea also leads to an upper boundary on uncertainty, in addition to the lower boundary. These upper and lower boundaries are identical for the Planck mass particle; in fact, they are zero, and this highlights the truly unique nature of the Planck mass particle. Further, there may be a close connection between light and the Planck mass particle: In our model, the standard relativistic energy momentum relation also seems to apply to light, while in modern physics light generally stands outside the standard relativistic momentum energy relation. We will also suggest a new way to look at elementary particles, where mass and time are closely related, consistent with some of the recent work in experimental physics. Our model leads to a new time operator that does not appear to be in conflict with the Pauli objection. This indicates that both mass and momentum come in quanta, which are perfectly correlated to an internal Compton `clock' frequency in elementary particles.

In humans, age-associated degrading changes are observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psy-chological abilities, and memory. Cross talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, ge-nome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirali-ty, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition of protein structure, makes them prone to multiple types of enzymatic and spontaneous PTMs, including racemization and isomerization. Spontaneous racemization leads to the loss of the balanced prevalent chirality. Advanced biological aging re-lated to irreversible PTMs SP has been associated with the nontrivial interplay between poor so-matic and mental health conditions. Through stress response systems (SRS), the environmental and psychological stressors contribute to the age-associated “collapse” of protein homochirality. The role of prevalent protein chirality and entropy of protein folding in biological aging is mainly overlooked. In a more generalized context, the time-dependent shift from enzymatic to the non-enzymatic transformation of biochirality might represent an important and yet un-der-appreciated hallmark of aging.