Origins of circadian rhythmicity

A multiscale inflammatory map: linking individual stress to societal dysfunction

As populations worldwide show increasing levels of stress, understanding emerging links among stress, inflammation, cognition, and behavior is vital to human and planetary health. We hypothesize that inflammation is a multiscale driver connecting stressors that affect individuals to large-scale societal dysfunction and, ultimately, to planetary-scale environmental impacts. We propose a 'central inflammation map' hypothesis to explain how the brain regulates inflammation and how inflammation impairs cognition, emotion, and action. According to our hypothesis, these interdependent inflammatory and neural processes, and the inter-individual transmission of environmental, infectious, and behavioral stressors - amplified via high-throughput digital global communications - can culminate in a multiscale, runaway, feed-forward process that could detrimentally affect human decision-making and behavior at scale, ultimately impairing the ability to address these same stressors. This perspective could provide non-intuitive explanations for behaviors and relationships among cells, organisms, and communities of organisms, potentially including population-level responses to stressors as diverse as global climate change, conflicts, and the COVID-19 pandemic. To illustrate our hypothesis and elucidate its mechanistic underpinnings, we present a mathematical model applicable to the individual and societal levels to test the links among stress, inflammation, control, and healing, including the implications of transmission, intervention (e.g., via lifestyle modification or medication), and resilience. Future research is needed to validate the model's assumptions, expand the factors/variables employed, and validate it against empirical benchmarks. Our model illustrates the need for multilayered, multiscale stress mitigation interventions, including lifestyle measures, precision therapeutics, and human ecosystem design. Our analysis shows the need for a coordinated, interdisciplinary, international research effort to understand the multiscale nature of stress. Doing so would inform the creation of interventions that improve individuals' lives and communities' resilience to stress and mitigate its adverse effects on the world.

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.

Microbial gene expression in Guaymas Basin subsurface sediments responds to hydrothermal stress and energy limitation

Analyses of gene expression of subsurface bacteria and archaea provide insights into their physiological adaptations to in situ subsurface conditions. We examined patterns of expressed genes in hydrothermally heated subseafloor sediments with distinct geochemical and thermal regimes in Guaymas Basin, Gulf of California, Mexico. RNA recovery and cell counts declined with sediment depth, however, we obtained metatranscriptomes from eight sites at depths spanning between 0.8 and 101.9 m below seafloor. We describe the metabolic potential of sediment microorganisms, and discuss expressed genes involved in tRNA, mRNA, and rRNA modifications that enable physiological flexibility of bacteria and archaea in the hydrothermal subsurface. Microbial taxa in hydrothermally influenced settings like Guaymas Basin may particularly depend on these catalytic RNA functions since they modulate the activity of cells under elevated temperatures and steep geochemical gradients. Expressed genes for DNA repair, protein maintenance and circadian rhythm were also identified. The concerted interaction of many of these genes may be crucial for microorganisms to survive and to thrive in the Guaymas Basin subsurface biosphere.

The role of circadian clock genes in tumors

Circadian rhythms are generated via variations in the expression of clock genes that are organized into a complex transcriptional–translational autoregulatory network and regulate the diverse physiological and behavioral activities that are required to adapt to periodic environmental changes. Aberrant clock gene expression is associated with a heightened risk of diseases that affect all aspects of human health, including cancers. Within the past several years, a number of studies have indicated that clock genes contribute to carcinogenesis by altering the expression of clock-controlled and tumor-related genes downstream of many cellular pathways. This review comprehensively summarizes how clock genes affect the development of tumors and their prognosis. In addition, the review provides a full description of the current state of oral cancer research that aims to optimize cancer diagnosis and treatment modalities.

Circadian clock and oral cancer

The circadian clock is comprised of a master component situated in the hypothalamic suprachiasmatic nucleus and subordinate clock genes in almost every cell of the body. The circadian clock genes and their encoded proteins govern the organism to follow the natural signals of time, and adapt to external changes in the environment. The majority of physiological processes in mammals exhibit variable circadian rhythms, which are generated and coordinated by an oscillation in the expression of the clock genes. A number of studies have reported that alteration in the expression level of clock genes is correlated with several pathological conditions, including cancer. However, little is known about the role of clock genes in homeostasis of the oral epithelium and their disturbances in oral carcinogenesis. The present review summarizes the current state of knowledge of the implications of clock genes in oral cancer. It has been demonstrated that the development of oral squamous cell carcinoma undergoes circadian oscillation in relation to tumor volume and proliferation rate. The circadian clock gene period (PER)1 has been associated with oral cancer pathogenesis and it is suggested that changes in the expression of PER1 may exhibit an important role in the development, invasion, and metastasis of oral squamous cell carcinoma. However, its role remains elusive and there is a need for further research in order to understand the underlying mechanisms of the clock genes in oral cancer pathogenesis.

Light-dependent expression of four cryptic archaeal circadian gene homologs

Circadian rhythms are important biological signals that have been found in almost all major groups of life from bacteria to man, yet it remains unclear if any members of the second major prokaryotic domain of life, the Archaea, also possess a biological clock. As an initial investigation of this question, we examined the regulation of four cyanobacterial-like circadian gene homologs present in the genome of the haloarchaeon Haloferax volcanii. These genes, designated cirA, cirB, cirC, and cirD, display similarity to the KaiC-family of cyanobacterial clock proteins, which act to regulate rhythmic gene expression and to control the timing of cell division. Quantitative RT-PCR analysis was used to examine the expression of each of the four cir genes in response to 12 h light/12 h dark cycles (LD 12:12) in H. volcanii during balanced growth. Our data reveal that there is an approximately two to sixteen-fold increase in cir gene expression when cells are shifted from light to constant darkness, and this pattern of gene expression oscillates with the light conditions in a rhythmic manner. Targeted single- and double-gene knockouts in the H. volcanii cir genes result in disruption of light-dependent, rhythmic gene expression, although it does not lead to any significant effect on growth under these conditions. Restoration of light-dependent, rhythmic gene expression was demonstrated by introducing, in trans, a wild-type copy of individual cir genes into knockout strains. These results are noteworthy as this is the first attempt to characterize the transcriptional expression and regulation of the ubiquitous kaiC homologs found among archaeal genomes.

PER1 and CLOCK: potential circulating biomarkers for head and neck squamous cell carcinoma

BACKGROUND

Circadian clock regulates daily rhythms in various physiologic processes and deregulated circadian clock are linked to cancers. We have previously demonstrated the association between altered circadian clock genes (CCGs) and head and neck squamous cell carcinoma (HNSCC). The purpose of this study was to investigate whether the CCGs were also altered in peripheral blood (PB) of patients with HNSCC.

METHODS

The 9 CCGs expression profiles of PB leukocytes from 94 patients with HNSCC and 56 healthy individuals were investigated using real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) and immunocytochemistry.

RESULTS

All the 9 CCGs were significantly downregulated in the PB of preoperative patients (p < .0001). Recovery of PER1 and CLOCK expression was observed in postoperative patients with good prognosis but not in patients that died within 1 year after surgery.

CONCLUSION

CCGs were also altered in PB leukocytes of patients with HNSCC and PER1 and CLOCK are potential circulating prognostic markers for HNSCC.

Circadian rhythms and cancer

The circadian clock is an endogenous time keeping system shared by most organisms. In mammals, a master pacemaker in the hypothalamus orchestrates temporal alignment of behavior and physiology by transmitting daily signals to multiple clocks in peripheral tissues. Disruption of this communication has a profound affect on human health and has been linked to diverse pathogenic conditions, including cancer. At the center of the molecular circadian machinery is a set of clock genes, generating rhythmic oscillations on a cellular level. In the past several years, research from different fields has revealed the complexity and ubiquitous nature of circadian regulation, uncovering intriguing associations between clock components and cellular pathways implicated in tumorigenesis. In this review, we discuss the emerging role of circadian genes in hematological and hormone-related malignancies. These new insights suggest that manipulating circadian biology as a way to fight cancer, as well as, other life threatening diseases is within the realm of possibility.

Mammalian circadian biology: elucidating genome-wide levels of temporal organization

During the past decade, the molecular mechanisms underlying the mammalian circadian clock have been defined. A core set of circadian clock genes common to most cells throughout the body code for proteins that feed back to regulate not only their own expression, but also that of clock output genes and pathways throughout the genome. The circadian system represents a complex multioscillatory temporal network in which an ensemble of coupled neurons comprising the principal circadian pacemaker in the suprachiasmatic nucleus of the hypothalamus is entrained to the daily light/dark cycle and subsequently transmits synchronizing signals to local circadian oscillators in peripheral tissues. Only recently has the importance of this system to the regulation of such fundamental biological processes as the cell cycle and metabolism become apparent. A convergence of data from microarray studies, quantitative trait locus analysis, and mutagenesis screens demonstrates the pervasiveness of circadian regulation in biological systems. The importance of maintaining the internal temporal homeostasis conferred by the circadian system is revealed by animal models in which mutations in genes coding for core components of the clock result in disease, including cancer and disturbances to the sleep/wake cycle.