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Lin MY, Kang YN, Apriliyasari RW, Tsai PS. Association Between Social Jetlag and Components of Metabolic Syndrome: A Systematic Review and Meta-Analysis. J Nurs Res 2024:00134372-990000000-00109. [PMID: 39158856 DOI: 10.1097/jnr.0000000000000628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
BACKGROUND A mismatch between biological and social time, often referred to as social jetlag (SJL), can lead to inadequate sleep and activities or taking meals at times that do not align with our biological rhythms, increasing the risk of metabolic abnormalities. Although the association between sleep and metabolic syndrome (MetS) is well established, the effects of SJL on MetS and the components of MetS in adults remain unclear. PURPOSE This study was designed to explore the relationship between SJL and MetS components in adults. METHODS A systematic review and meta-analysis was conducted on studies registered in PubMed, Cochrane, Web of Science, and Embase between the inception of each database until November 15, 2023. We focused on studies designed to evaluate the relationship between SJL and either MetS or its components. Only studies using cross-sectional, prospective, or retrospective designs were considered for inclusion. The relationship between SJL and MetS was depicted as an odds ratio with a corresponding 95% confidence interval (CI). We determined the mean differences and 95% CIs to estimate the associations between SJL and MetS components. The Joanna Briggs Institute Critical Appraisal Checklist was used to evaluate the methodological rigor of the selected studies. Data were analyzed using RevMan software Version 5.4. RESULTS The systematic review included 16 studies, with five analyzed via a meta-analysis covering four outcomes, each based on two to three studies. When comparing SJL of less than 1 hour with SJL of 2 hours or more, the latter showed a higher likelihood of MetS (pooled odds ratio: 1.52). Although a significant decrease in systolic blood pressure (pooled mean differences = -3.52 mmHg, 95% CI [-6.41, -0.64]) and a significant increase in waist circumference (pooled mean differences = 2.17 cm, 95% CI [0.61, 3.73]) were observed, the correlation between SJL and diastolic blood pressure failed to reach statistical significance. CONCLUSIONS/IMPLICATIONS FOR PRACTICE The meta-analysis conducted in this study found an association between SJL and MetS. Healthcare practitioners should prioritize the management of sleep quality and duration, especially for individuals exhibiting substantial SJL. Improving sleep can aid in controlling blood pressure and managing weight and should form part of MetS management strategies.
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Affiliation(s)
- Mei-Yu Lin
- PhD, RN, Assistant Professor, Department of Nursing, Tzu Chi University of Science and Technology, Hualien, Taiwan, ROC
| | - Yi-No Kang
- MS, Doctoral Student, Institute of Health Policy and Management, College of Public Health, National Taiwan University; Researcher, Cochrane Taiwan, Taipei Medical University; Consultant, Evidence-Based Medicine Center, Wan Fang Hospital, Taiwan, ROC
| | | | - Pei-Shan Tsai
- PhD, RN, Professor, School of Nursing, College of Nursing, Taipei Medical University; Department of Nursing and Center for Nursing and Healthcare Research in Clinical Practice Application, Wan Fang Hospital, Taipei Medical University; and Research Center of Sleep Medicine, Taipei Medical University Hospital, Taiwan, ROC
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2
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Helenek C, Krzysztoń R, Petreczky J, Wan Y, Cabral M, Coraci D, Balázsi G. Synthetic gene circuit evolution: Insights and opportunities at the mid-scale. Cell Chem Biol 2024; 31:1447-1459. [PMID: 38925113 PMCID: PMC11330362 DOI: 10.1016/j.chembiol.2024.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
Directed evolution focuses on optimizing single genetic components for predefined engineering goals by artificial mutagenesis and selection. In contrast, experimental evolution studies the adaptation of entire genomes in serially propagated cell populations, to provide an experimental basis for evolutionary theory. There is a relatively unexplored gap at the middle ground between these two techniques, to evolve in vivo entire synthetic gene circuits with nontrivial dynamic function instead of single parts or whole genomes. We discuss the requirements for such mid-scale evolution, with hypothetical examples for evolving synthetic gene circuits by appropriate selection and targeted shuffling of a seed set of genetic components in vivo. Implementing similar methods should aid the rapid generation, functionalization, and optimization of synthetic gene circuits in various organisms and environments, accelerating both the development of biomedical and technological applications and the understanding of principles guiding regulatory network evolution.
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Affiliation(s)
- Christopher Helenek
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Rafał Krzysztoń
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julia Petreczky
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
| | - Yiming Wan
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mariana Cabral
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA
| | - Damiano Coraci
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA.
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3
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Tan L, Wu H, Wang X, Liu Z, Hu J, Zheng X. Regulation of opsin and circadian clock genes on mate-finding behavior of the day-flying red moth, Phauda flammans (Walker). Chronobiol Int 2024:1-14. [PMID: 39046293 DOI: 10.1080/07420528.2024.2382315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/19/2024] [Accepted: 07/15/2024] [Indexed: 07/25/2024]
Abstract
First, significantly higher mate-finding success was found under light condition than under constant darkness condition in Phauda flammans, a typical diurnal moth. We speculate that mate-finding behavior in P. flammans may be influenced by the light-sensitive opsin genes Long wavelength opsin (PfLW), Ultraviolet opsin (PfUV) and Blue opsin (PfBL), which are potentially regulated by both light-cues and endogenous circadian rhythms. Second, the circadian clock genes Period (PfPer), Timeless (PfTim), Cryptochrome1 (PfCry1), Cryptochrome2 (PfCRY2), Cryptochrome3 (PfCry-like), Clock (PfClk), Cycle (PfCyc), Vrille (PfVri), and Slimb (PfSli) were identified in P. flammans. Third, circadian rhythms in the relative expression levels of opsin and circadian clock genes were demonstrated via quantitative real-time PCR analysis, with peak expression coinciding with the mate-finding peak. Notably, the relative expression of PfLW in males P. flammans was significantly higher than that in females P. flammans at the mate-finding peaks Zeitgeber time (ZT) 8 and ZT 10 under light, while the expression of the opsin gene PfBL showed a similar pattern at ZT 10 under light. Additionally, the expression of the clock gene PfCry-like was significantly higher in males than in females at ZT 8 and ZT 10 under light, while PfPer, PfTim, PfClk and PfCyc exhibited similar male-biased expression patterns at ZT 10 under light. Conversely, PfCry1 and PfVri expression was significantly higher in females than in male at ZT 8 under light. In conclusion, sex differences were detected in the expression of opsin and circadian clock genes, which indicated that light-mediated regulation of these genes may contribute to the daytime mate-finding behavior of P. flammans.
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Affiliation(s)
- Liusu Tan
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Haipan Wu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Xiaoyun Wang
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Zuojun Liu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Jin Hu
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Xialin Zheng
- Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, China
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4
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Savvidis C, Kallistrou E, Kouroglou E, Dionysopoulou S, Gavriiloglou G, Ragia D, Tsiama V, Proikaki S, Belis K, Ilias I. Circadian rhythm disruption and endocrine-related tumors. World J Clin Oncol 2024; 15:818-834. [PMID: 39071458 PMCID: PMC11271730 DOI: 10.5306/wjco.v15.i7.818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
This review delved into the intricate relationship between circadian clocks and physiological processes, emphasizing their critical role in maintaining homeostasis. Orchestrated by interlocked clock genes, the circadian timekeeping system regulates fundamental processes like the sleep-wake cycle, energy metabolism, immune function, and cell proliferation. The central oscillator in the hypothalamic suprachiasmatic nucleus synchronizes with light-dark cycles, while peripheral tissue clocks are influenced by cues such as feeding times. Circadian disruption, linked to modern lifestyle factors like night shift work, correlates with adverse health outcomes, including metabolic syndrome, cardiovascular diseases, infections, and cancer. We explored the molecular mechanisms of circadian clock genes and their impact on metabolic disorders and cancer pathogenesis. Specific associations between circadian disruption and endocrine tumors, spanning breast, ovarian, testicular, prostate, thyroid, pituitary, and adrenal gland cancers, are highlighted. Shift work is associated with increased breast cancer risk, with PER genes influencing tumor progression and drug resistance. CLOCK gene expression correlates with cisplatin resistance in ovarian cancer, while factors like aging and intermittent fasting affect prostate cancer. Our review underscored the intricate interplay between circadian rhythms and cancer, involving the regulation of the cell cycle, DNA repair, metabolism, immune function, and the tumor microenvironment. We advocated for integrating biological timing into clinical considerations for personalized healthcare, proposing that understanding these connections could lead to novel therapeutic approaches. Evidence supports circadian rhythm-focused therapies, particularly chronotherapy, for treating endocrine tumors. Our review called for further research to uncover detailed connections between circadian clocks and cancer, providing essential insights for targeted treatments. We emphasized the importance of public health interventions to mitigate lifestyle-related circadian disruptions and underscored the critical role of circadian rhythms in disease mechanisms and therapeutic interventions.
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Affiliation(s)
- Christos Savvidis
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Efthymia Kallistrou
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Eleni Kouroglou
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Sofia Dionysopoulou
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | | | - Dimitra Ragia
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Vasiliki Tsiama
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Stella Proikaki
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Konstantinos Belis
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
| | - Ioannis Ilias
- Department of Endocrinology, Hippocration General Hospital, Athens GR-11527, Greece
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Yu J, Wu M, Shi M, Gong Y, Gao F, Gu H, Dang B. Up-regulation of BMAL1 by epigallocatechin-3-gallate improves neurological damage in SBI rats. Brain Res Bull 2024; 215:111033. [PMID: 39032586 DOI: 10.1016/j.brainresbull.2024.111033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 07/14/2024] [Accepted: 07/18/2024] [Indexed: 07/23/2024]
Abstract
Brain Muscle ARNT-Like Protein 1 (BMAL1) suppresses oxidative stress in brain injury during surgery. Epigallocatechin-3-gallate (EGCG), a monomer in green tea, has been identified as an antioxidant and a potential agonist for BMAL1. In this work, the mechanism by which BMAL1 is regulated was investigated, as well as the therapeutic effect of EGCG on surgically injured rats. The pathological environment after brain injury during surgery was simulated by excising the right frontal lobe of rats. Rats received an intraperitoneal injection of EGCG immediately after surgery. Neurological scores and cerebral edema were recorded after surgery. Fluoro-Jade C staining, TUNEL staining, western blot, and lipid peroxidation analyses were conducted 3 days later. Here we show that the endogenous BMAL1 level decreased after brain injury. Postoperative administration of EGCG up-regulated the content of BMAL1 around the cerebral cortex, reduced the oxidative stress level, reduced neuronal apoptosis and the number of degenerated neurons, alleviated cerebral edema, and improved neurological scores in rats. This suggests that BMAL1 is an effective target for treating surgical brain injury, as well as that EGCG may be a promising agent for alleviating postoperative brain injury.
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Affiliation(s)
- Jiejie Yu
- Department of Emergency, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Muyao Wu
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Mengying Shi
- Department of Anesthesiology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Yating Gong
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Fan Gao
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Haiping Gu
- Department of Neurology, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China
| | - Baoqi Dang
- Department of Rehabilitation, Zhangjiagang TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Zhangjiagang 215600, China.
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Zhang Z, Howlett MG, Silvester E, Kukura P, Fletcher SP. A Chemical Reaction Network Drives Complex Population Dynamics in Oscillating Self-Reproducing Vesicles. J Am Chem Soc 2024; 146:18262-18269. [PMID: 38917079 PMCID: PMC11240260 DOI: 10.1021/jacs.4c00860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
We report chemically fueled oscillations of vesicles. The population cycling of vesicles is driven by their self-reproduction and collapse within a biphasic reaction network involving the interplay of molecular and supramolecular events. We studied the oscillations on the molecular and supramolecular scales and tracked vesicle populations in time by interferometric scattering microscopy and dynamic light scattering. Complex supramolecular events were observed during oscillations─including vesicle reproduction, growth, and decomposition─and differences in the number, size, and mass of aggregates can often be observed within and between pulses. This system's dynamic behavior is reminiscent of a reproductive cycle in living cells.
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Affiliation(s)
- Zhiheng Zhang
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Michael G. Howlett
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
| | - Emma Silvester
- The
Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K.
- Department
of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K.
| | - Philipp Kukura
- The
Kavli Institute for NanoScience Discovery, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K.
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K.
| | - Stephen P. Fletcher
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, U.K.
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7
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Dai M, Tan X, Ye Z, Chen X, Zhang Y, Ruan Y, Ma B, Kong D. Analysis of lettuce transcriptome reveals the mechanism of different light/dark cycle in promoting the growth and quality. FRONTIERS IN PLANT SCIENCE 2024; 15:1394434. [PMID: 39045594 PMCID: PMC11263018 DOI: 10.3389/fpls.2024.1394434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024]
Abstract
Light/dark (L/D) cycle plays a crucial role in controlling the production and quality of vegetables. However, the mechanism of L/D cycle on vegetable growth and quality is scarce studied. To investigate the impact of L/D cycle on lettuce growth and quality, we designed three diel scenarios, including 16 hours of light and 8 hours of darkness (L16/D8), 12 hours of light and 6 hours of darkness (L12/D6), and 8 hours of light and 4 hours of darkness (L8/D4). By phenotypic analysis, we found that lettuce grew taller under the L8/D4 scenario than under L16/D8 light cycle scenarios. The physiological indexes showed that the lettuce leaves grown in the L8/D4 scenario exhibited greater enhancements in the levels of soluble protein, soluble sugar, and carotenoid content compared to the other scenarios. By comparing the expression levels under different diel scenarios (L16/D8 vs L12/D6, L16/D8 vs L8/D4, and L12/D6 vs L8/D4), we identified 7,209 differentially expressed genes (DEGs). Additionally, 3 gene modules that were closely related to L/D cycle of lettuce were selected by WGCNA analysis. The eigengenes of three gene modules were enriched in plant hormone signal transduction, sphingolipid metabolism, and nucleocytoplasmic transport pathways. Through network analysis, we identified six hub genes (CIP1, SCL34, ROPGEF1, ACD6, CcmB, and Rps4) in the three gene modules, which were dominant in plant circadian rhythms and greatly affected lettuce growth. qRT-PCR analysis confirmed the diurnal response patterns of the 6 hub genes in different treatments were significant. This study intensively enhanced our comprehension of the L/D cycle in the growth morphology, nutritional quality, and metabolic pathways of lettuce.
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Affiliation(s)
- Mengdi Dai
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiangfeng Tan
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ziran Ye
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xuting Chen
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yi Zhang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (UCAS), Hangzhou, China
| | - Yunjie Ruan
- lnstitute of Agricultural Bio-Environmental Engineering, College of Bio-systems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Academy of Rural Development, Zhejiang University, Hangzhou, China
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Dedong Kong
- Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Schmal C. The seasons within: a theoretical perspective on photoperiodic entrainment and encoding. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:549-564. [PMID: 37659985 PMCID: PMC11226496 DOI: 10.1007/s00359-023-01669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/04/2023]
Abstract
Circadian clocks are internal timing devices that have evolved as an adaption to the omnipresent natural 24 h rhythmicity of daylight intensity. Properties of the circadian system are photoperiod dependent. The phase of entrainment varies systematically with season. Plastic photoperiod-dependent re-arrangements in the mammalian circadian core pacemaker yield an internal representation of season. Output pathways of the circadian clock regulate photoperiodic responses such as flowering time in plants or hibernation in mammals. Here, we review the concepts of seasonal entrainment and photoperiodic encoding. We introduce conceptual phase oscillator models as their high level of abstraction, but, yet, intuitive interpretation of underlying parameters allows for a straightforward analysis of principles that determine entrainment characteristics. Results from this class of models are related and discussed in the context of more complex conceptual amplitude-phase oscillators as well as contextual molecular models that take into account organism, tissue, and cell-type-specific details.
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany.
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9
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Wang B, Adamo ME, Zhou X, Wang Z, Gerber SA, Kettenbach AN, Dunlap JC. Acetylation of WCC is dispensable for the core circadian clock but differentially regulates acute light responses in Neurospora. J Biol Chem 2024; 300:107508. [PMID: 38944116 PMCID: PMC11325773 DOI: 10.1016/j.jbc.2024.107508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/01/2024] Open
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) formed by WC-1 and WC-2 drives expression of the frequency (frq) gene whose product FRQ feedbacks to inhibit transcriptional activity of WCC. Phosphorylation of WCC has been extensively studied, but the extent and significance of other post-translational modifications (PTM) have been poorly studied. To this end, we used mass-spectrometry to study alkylation sites on WCC, resulting in discovery of nine acetylation sites. Mutagenesis analysis showed most of the acetylation events individually do not play important roles in period determination. Moreover, mutating all the lysines falling in either half of WC-1 or all the lysine residues in WC-2 to arginines did not abolish circadian rhythms. In addition, we also found nine mono-methylation sites on WC-1, but like acetylation, individual ablation of most of the mono-methylation events did not result in a significant period change. Taken together, the data here suggest that acetylation or mono-methylation on WCC is not a determinant of the pace of the circadian feedback loop. The finding is consistent with a model in which repression of WCC's circadian activity is mainly controlled by phosphorylation. Interestingly, light-induced expression of some light-responsive genes has been modulated in certain wc-1 acetylation mutants, suggesting that WC-1 acetylation events differentially regulate light responses.
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Affiliation(s)
- Bin Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
| | - Mark E Adamo
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Xiaoying Zhou
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Ziyan Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Scott A Gerber
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA; Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Arminja N Kettenbach
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Jay C Dunlap
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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10
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Zhou M, Aziz M, Li J, Jha A, Ma G, Murao A, Wang P. BMAL2 promotes eCIRP-induced macrophage endotoxin tolerance. Front Immunol 2024; 15:1426682. [PMID: 38938563 PMCID: PMC11208452 DOI: 10.3389/fimmu.2024.1426682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Background The disruption of the circadian clock is associated with inflammatory and immunological disorders. BMAL2, a critical circadian protein, forms a dimer with CLOCK, activating transcription. Extracellular cold-inducible RNA-binding protein (eCIRP), released during sepsis, can induce macrophage endotoxin tolerance. We hypothesized that eCIRP induces BMAL2 expression and promotes macrophage endotoxin tolerance through triggering receptor expressed on myeloid cells-1 (TREM-1). Methods C57BL/6 wild-type (WT) male mice were subjected to sepsis by cecal ligation and puncture (CLP). Serum levels of eCIRP 20 h post-CLP were assessed by ELISA. Peritoneal macrophages (PerM) were treated with recombinant mouse (rm) CIRP (eCIRP) at various doses for 24 h. The cells were then stimulated with LPS for 5 h. The levels of TNF-α and IL-6 in the culture supernatants were assessed by ELISA. PerM were treated with eCIRP for 24 h, and the expression of PD-L1, IL-10, STAT3, TREM-1 and circadian genes such as BMAL2, CRY1, and PER2 was assessed by qPCR. Effect of TREM-1 on eCIRP-induced PerM endotoxin tolerance and PD-L1, IL-10, and STAT3 expression was determined by qPCR using PerM from TREM-1-/- mice. Circadian gene expression profiles in eCIRP-treated macrophages were determined by PCR array and confirmed by qPCR. Induction of BMAL2 activation in bone marrow-derived macrophages was performed by transfection of BMAL2 CRISPR activation plasmid. The interaction of BMAL2 in the PD-L1 promoter was determined by computational modeling and confirmed by the BIAcore assay. Results Serum levels of eCIRP were increased in septic mice compared to sham mice. Macrophages pre-treated with eCIRP exhibited reduced TNFα and IL-6 release upon LPS challenge, indicating macrophage endotoxin tolerance. Additionally, eCIRP increased the expression of PD-L1, IL-10, and STAT3, markers of immune tolerance. Interestingly, TREM-1 deficiency reversed eCIRP-induced macrophage endotoxin tolerance and significantly decreased PD-L1, IL-10, and STAT3 expression. PCR array screening of circadian clock genes in peritoneal macrophages treated with eCIRP revealed the elevated expression of BMAL2, CRY1, and PER2. In eCIRP-treated macrophages, TREM-1 deficiency prevented the upregulation of these circadian genes. In macrophages, inducible BMAL2 expression correlated with increased PD-L1 expression. In septic human patients, blood monocytes exhibited increased expression of BMAL2 and PD-L1 in comparison to healthy subjects. Computational modeling and BIAcore assay identified a putative binding region of BMAL2 in the PD-L1 promoter, suggesting BMAL2 positively regulates PD-L1 expression in macrophages. Conclusion eCIRP upregulates BMAL2 expression via TREM-1, leading to macrophage endotoxin tolerance in sepsis. Targeting eCIRP to maintain circadian rhythm may correct endotoxin tolerance and enhance host resistance to bacterial infection.
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Affiliation(s)
- Mian Zhou
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Monowar Aziz
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
| | - Jingsong Li
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Alok Jha
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Gaifeng Ma
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Atsushi Murao
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
| | - Ping Wang
- Center for Immunology and Inflammation, The Feinstein Institutes for Medical Research, Manhasset, NY, United States
- Departments of Surgery and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, United States
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Zhang W, Liu D, Yuan M, Zhu LQ. The mechanisms of mitochondrial abnormalities that contribute to sleep disorders and related neurodegenerative diseases. Ageing Res Rev 2024; 97:102307. [PMID: 38614368 DOI: 10.1016/j.arr.2024.102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Sleep is a highly intricate biological phenomenon, and its disorders play a pivotal role in numerous diseases. However, the specific regulatory mechanisms remain elusive. In recent years, the role of mitochondria in sleep disorders has gained considerable attention. Sleep deprivation not only impairs mitochondrial morphology but also decreases the number of mitochondria and triggers mitochondrial dysfunction. Furthermore, mitochondrial dysfunction has been implicated in the onset and progression of various sleep disorder-related neurological diseases, especially neurodegenerative conditions. Therefore, a greater understanding of the impact of sleep disorders on mitochondrial dysfunction may reveal new therapeutic targets for neurodegenerative diseases. In this review, we comprehensively summarize the recent key findings on the mechanisms underlying mitochondrial dysfunction caused by sleep disorders and their role in initiating or exacerbating common neurodegenerative diseases. In addition, we provide fresh insights into the diagnosis and treatment of sleep disorder-related diseases.
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Affiliation(s)
- Wentao Zhang
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Dan Liu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Mei Yuan
- The Second Affiliated Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China; Affiliated Nanhua Hospital, Department of Neurology, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Ling-Qiang Zhu
- Department of Pathophysiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China.
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12
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Boodaghian N, Park H, Cohen SE. Investigating the Roles for Essential Genes in the Regulation of the Circadian Clock in Synechococcus elongatus Using CRISPR Interference. J Biol Rhythms 2024; 39:308-317. [PMID: 38357890 DOI: 10.1177/07487304241228333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Circadian rhythms are found widely throughout nature where cyanobacteria are the simplest organisms, in which the molecular details of the clock have been elucidated. Circadian rhythmicity in cyanobacteria is carried out via the KaiA, KaiB, and KaiC core oscillator proteins that keep ~24 h time. A series of input and output proteins-CikA, SasA, and RpaA-regulate the clock by sensing environmental changes and timing rhythmic activities, including global rhythms of gene expression. Our previous work identified a novel set of KaiC-interacting proteins, some of which are encoded by genes that are essential for viability. To understand the relationship of these essential genes to the clock, we applied CRISPR interference (CRISPRi) which utilizes a deactivated Cas9 protein and single-guide RNA (sgRNA) to reduce the expression of target genes but not fully abolish their expression to allow for survival. Eight candidate genes were targeted, and strains were analyzed by quantitative real-time PCR (qRT-PCR) for reduction of gene expression, and rhythms of gene expression were monitored to analyze circadian phenotypes. Strains with reduced expression of SynPCC7942_0001, dnaN, which encodes for the β-clamp of the replicative DNA polymerase, or SynPCC7942_1081, which likely encodes for a KtrA homolog involved in K+ transport, displayed longer circadian rhythms of gene expression than the wild type. As neither of these proteins have been previously implicated in the circadian clock, these data suggest that diverse cellular processes, DNA replication and K+ transport, can influence the circadian clock and represent new avenues to understand clock function.
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Affiliation(s)
- Nouneh Boodaghian
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
| | - Hyunsook Park
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
| | - Susan E Cohen
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California
- Center for Circadian Biology, University of California, San Diego, San Diego, California
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13
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Xu H, Guo L, Hao T, Guo X, Huang M, Cen H, Chen M, Weng J, Huang M, Wu Z, Qin Z, Yang J, Wu B. Nasal solitary chemosensory cells govern daily rhythm in mouse model of allergic rhinitis. J Allergy Clin Immunol 2024:S0091-6749(24)00464-0. [PMID: 38734385 DOI: 10.1016/j.jaci.2024.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/29/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND While the daily rhythm of allergic rhinitis (AR) has long been recognized, the molecular mechanism underlying this phenomenon remains enigmatic. OBJECTIVE We aimed to investigate the role of circadian clock in AR development and to clarify the mechanism by which the daily rhythm of AR is generated. METHODS AR was induced in mice with ovalbumin. Toluidine blue staining, liquid chromatography-tandem mass spectrometry analysis, real-time quantitative PCR, and immunoblotting were performed with AR and control mice. RESULTS Ovalbumin-induced AR is diurnally rhythmic and associated with clock gene disruption in nasal mucosa. In particular, Rev-erbα is generally downregulated and its rhythm retained, but with a near-12-hour phase shift. Furthermore, global knockout of core clock gene Bmal1 or Rev-erbα increases the susceptibility of mice to AR and blunts AR rhythmicity. Importantly, nasal solitary chemosensory cells (SCCs) are rhythmically activated, and inhibition of the SCC pathway leads to attenuated AR and a loss of its rhythm. Moreover, rhythmic activation of SCCs is accounted for by diurnal expression of ChAT (an enzyme responsible for the synthesis of acetylcholine) and temporal generation of the neurotransmitter acetylcholine. Mechanistically, Rev-erbα trans-represses Chat through direct binding to a specific response element, generating a diurnal oscillation in this target gene. CONCLUSION SCCs, under the control of Rev-erbα, are a driver of AR rhythmicity; targeting SCCs should be considered as a new avenue for AR management.
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Affiliation(s)
- Haiman Xu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lianxia Guo
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Tingying Hao
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaocao Guo
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China; Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China
| | - Meiping Huang
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haobin Cen
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Min Chen
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Jiaxian Weng
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meixia Huang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zicong Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zifei Qin
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Jing Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
| | - Baojian Wu
- Institute of Molecular Rhythm and Metabolism, Guangzhou University of Chinese Medicine, Guangzhou, China.
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14
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Sharma D, Adnan D, Abdel-Reheem MK, Anafi RC, Leary DD, Bishehsari F. Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets. JCI Insight 2024; 9:e177697. [PMID: 38716727 PMCID: PMC11141942 DOI: 10.1172/jci.insight.177697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/03/2024] [Indexed: 06/02/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a lethal cancer characterized by a poor outcome and an increasing incidence. A significant majority (>80%) of newly diagnosed cases are deemed unresectable, leaving chemotherapy as the sole viable option, though with only moderate success. This necessitates the identification of improved therapeutic options for PDA. We hypothesized that there are temporal variations in cancer-relevant processes within PDA tumors, offering insights into the optimal timing of drug administration - a concept termed chronotherapy. In this study, we explored the presence of the circadian transcriptome in PDA using patient-derived organoids and validated these findings by comparing PDA data from The Cancer Genome Atlas with noncancerous healthy pancreas data from GTEx. Several PDA-associated pathways (cell cycle, stress response, Rho GTPase signaling) and cancer driver hub genes (EGFR and JUN) exhibited a cancer-specific rhythmic pattern intricately linked to the circadian clock. Through the integration of multiple functional measurements for rhythmic cancer driver genes, we identified top chronotherapy targets and validated key findings in molecularly divergent pancreatic cancer cell lines. Testing the chemotherapeutic efficacy of clinically relevant drugs further revealed temporal variations that correlated with drug-target cycling. Collectively, our study unravels the PDA circadian transcriptome and highlights a potential approach for optimizing chrono-chemotherapeutic efficacy.
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Affiliation(s)
- Deepak Sharma
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
| | - Darbaz Adnan
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
| | - Mostafa K. Abdel-Reheem
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
| | - Ron C. Anafi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel D. Leary
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
| | - Faraz Bishehsari
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush Medical College, Rush University Medical Center, Chicago, Illinois, USA
- Department of Internal Medicine, Division of Gastroenterology and
- Department of Anatomy and Cell Biology, Rush University Medical Center, Chicago, Illinois, USA
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15
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Yuan Y, Chen Q, Brovkina M, Clowney EJ, Yadlapalli S. Clock-dependent chromatin accessibility rhythms regulate circadian transcription. PLoS Genet 2024; 20:e1011278. [PMID: 38805552 PMCID: PMC11161047 DOI: 10.1371/journal.pgen.1011278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 06/07/2024] [Accepted: 04/29/2024] [Indexed: 05/30/2024] Open
Abstract
Chromatin organization plays a crucial role in gene regulation by controlling the accessibility of DNA to transcription machinery. While significant progress has been made in understanding the regulatory role of clock proteins in circadian rhythms, how chromatin organization affects circadian rhythms remains poorly understood. Here, we employed ATAC-seq (Assay for Transposase-Accessible Chromatin with Sequencing) on FAC-sorted Drosophila clock neurons to assess genome-wide chromatin accessibility at dawn and dusk over the circadian cycle. We observed significant oscillations in chromatin accessibility at promoter and enhancer regions of hundreds of genes, with enhanced accessibility either at dusk or dawn, which correlated with their peak transcriptional activity. Notably, genes with enhanced accessibility at dusk were enriched with E-box motifs, while those more accessible at dawn were enriched with VRI/PDP1-box motifs, indicating that they are regulated by the core circadian feedback loops, PER/CLK and VRI/PDP1, respectively. Further, we observed a complete loss of chromatin accessibility rhythms in per01 null mutants, with chromatin consistently accessible at both dawn and dusk, underscoring the critical role of Period protein in driving chromatin compaction during the repression phase at dawn. Together, this study demonstrates the significant role of chromatin organization in circadian regulation, revealing how the interplay between clock proteins and chromatin structure orchestrates the precise timing of biological processes throughout the day. This work further implies that variations in chromatin accessibility might play a central role in the generation of diverse circadian gene expression patterns in clock neurons.
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Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Qianqian Chen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Margarita Brovkina
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
| | - E Josephine Clowney
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
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16
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Yokomizo T, Takahashi Y. Plasticity of circadian and circatidal rhythms in activity and transcriptomic dynamics in a freshwater snail. Heredity (Edinb) 2024; 132:267-274. [PMID: 38538720 DOI: 10.1038/s41437-024-00680-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 05/08/2024] Open
Abstract
Organisms have diverse biological clocks synchronised with environmental cycles depending on their habitats. Anticipation of tidal changes has driven the evolution of circatidal rhythms in some marine species. In the freshwater snail, Semisulcospira reiniana, individuals in nontidal areas exhibit circadian rhythms, whereas those in tidal areas exhibit both circadian and circatidal rhythms. We investigated whether the circatidal rhythms are genetically determined or induced by environmental cycles. The exposure to a simulated tidal cycle did not change the intensity of circatidal rhythm in individuals in the nontidal population. However, snails in the tidal population showed different activity rhythms depending on the presence or absence of the exposure. Transcriptome analysis revealed that genes with circatidal oscillation increased due to entrainment to the tidal cycle in both populations and dominant rhythmicity was consistent with the environmental cycle. These results suggest plasticity in the endogenous rhythm in the gene expression in both populations. Note that circatidal oscillating genes were more abundant in the tidal population than in the nontidal population, suggesting that a greater number of genes are associated with circatidal clocks in the tidal population compared to the nontidal population. This increase of circatidal clock-controlled genes in the tidal population could be caused by genetic changes in the biological clock or the experience of tidal cycle in the early life stage. Our findings suggest that the plasticity of biological rhythms may have contributed to the adaptation to the tidal environment in S. reiniana.
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Affiliation(s)
- Takumi Yokomizo
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
| | - Yuma Takahashi
- Graduate School of Science, Chiba University, Chiba, 263-8522, Japan.
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17
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Del Olmo M, Legewie S, Brunner M, Höfer T, Kramer A, Blüthgen N, Herzel H. Network switches and their role in circadian clocks. J Biol Chem 2024; 300:107220. [PMID: 38522517 PMCID: PMC11044057 DOI: 10.1016/j.jbc.2024.107220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Michael Brunner
- Biochemistry Center, Universität Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Universität Heidelberg, Heidelberg, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
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18
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Aldrich JC, Scheinfeld AR, Lee SE, Dusenbery KJ, Mahach KM, Van de Veire BC, Fonken LK, Gaudet AD. Effects of dim light at night in C57BL/6 J mice on recovery after spinal cord injury. Exp Neurol 2024; 375:114725. [PMID: 38365132 PMCID: PMC10981559 DOI: 10.1016/j.expneurol.2024.114725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/09/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
Spinal cord injury (SCI) can cause long-lasting locomotor deficits, pain, and mood disorders. Anatomical and functional outcomes are exacerbated by inflammation after SCI, which causes secondary damage. One promising target after SCI is manipulating the circadian system, which optimizes biology and behavior for time of day - including neuroimmune responses and mood-related behaviors. Circadian disruption after SCI is likely worsened by a disruptive hospital environment, which typically includes dim light-at-night (dLAN). Here, we hypothesized that mice subjected to SCI, then placed in dLAN, would exhibit worsened locomotor deficits, pain-like behavior, and anxiety-depressive-like symptoms compared to mice maintained in light days with dark nights (LD). C57BL/6 J mice received sham surgery or moderate T9 contusion SCI, then were placed permanently in LD or dLAN. dLAN after SCI did not worsen locomotor deficits; rather, SCI-dLAN mice showed slight improvement in open-field locomotion at the final timepoint. Although dLAN did not alter SCI-induced heat hyperalgesia, SCI-dLAN mice exhibited an increase in mechanical allodynia at 13 days post-SCI compared to SCI-LD mice. SCI-LD and SCI-dLAN mice had similar outcomes using sucrose preference (depressive-like) and open-field (anxiety-like) tests. At 21 dpo, SCI-dLAN mice had reduced preference for a novel juvenile compared to SCI-LD, implying that dLAN combined with SCI may worsen this mood-related behavior. Finally, lesion size was similar between SCI-LD and SCI-dLAN mice. Therefore, newly placing C57BL/6 J mice in dLAN after SCI had modest effects on locomotor, pain-like, and mood-related behaviors. Future studies should consider whether clinically-relevant circadian disruptors, alone or in combination, could be ameliorated to enhance outcomes after SCI.
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Affiliation(s)
- John C Aldrich
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Ashley R Scheinfeld
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Sydney E Lee
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Kalina J Dusenbery
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Kathryn M Mahach
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Brigid C Van de Veire
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Laura K Fonken
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin
| | - Andrew D Gaudet
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin, USA; Department of Neurology, Dell Medical School, The University of Texas at Austin.
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19
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Prakash A, Gower DJ, Vengot R, Kotharambath R. Circadian rhythm and surface activity in soil-dwelling caecilians (Amphibia: Gymnophiona). Sci Rep 2024; 14:9950. [PMID: 38688941 PMCID: PMC11061191 DOI: 10.1038/s41598-024-60533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 04/23/2024] [Indexed: 05/02/2024] Open
Abstract
The degree to which burrowing, soil-dwelling caecilian amphibians spend time on the surface is little studied, and circadian rhythm has not been investigated in multiple species of this order or by manipulating light-dark cycles. We studied surface-activity rhythm of the Indian caecilians Ichthyophis cf. longicephalus and Uraeotyphlus cf. oxyurus (Ichthyophiidae) and Gegeneophis tejaswini (Grandisoniidae), under LD, DD and DL cycles. We examined daily surface activity and the role of light-dark cycles as a zeitgeber. All three species were strictly nocturnal and G. tejaswini displayed the least surface activity. Four out of thirteen individuals, two I. cf. longicephalus, one G. tejaswini and one U. cf. oxyurus, displayed a more or less distinct surface-activity rhythm in all three cycles, and for the nine other animals the activity patterns were not evident. An approximately 24 h free-run period was observed in the three species. When the light-dark cycle was inverted, surface activity in the three species shifted to the dark phase. The findings of this study suggest that caecilians have a weak circadian surface-activity rhythm, and that the absence of light can act as a prominent zeitgeber in these burrowing, limbless amphibians.
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Affiliation(s)
- Avanthika Prakash
- Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - David J Gower
- Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
- Natural History Museum, London, SW7 5BD, UK
| | - Ranjith Vengot
- Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India
| | - Ramachandran Kotharambath
- Department of Zoology, Central University of Kerala, Tejaswini Hills, Kasaragod, Kerala, India.
- Natural History Museum, London, SW7 5BD, UK.
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20
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Iima M. Optimal external forces of the lock-in phenomena for flow past an inclined plate in uniform flow. Phys Rev E 2024; 109:045102. [PMID: 38755879 DOI: 10.1103/physreve.109.045102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/04/2024] [Indexed: 05/18/2024]
Abstract
We theoretically studied the optimal control, frequency lock-in, and phase lock-in phenomena due to the spatially localized periodic forcing in flow past an inclined plate. Although frequency lock-in is evident in many fluid phenomena, especially fluid-structure interactions, not many researchers have investigated it using a theoretical approach based on flow details. We obtained detailed information on the lock-in phenomena to external periodic forcing using phase reduction theory, a mathematical method for extracting the dynamics near the limit cycle. Furthermore, the optimal forces applied to the velocity field were determined under the condition of the minimum forcing energy and maximum lock-in range. The study of uniform periodic forces applied within spatially confined regions led to the conclusion that the effective lock-in position, which includes both the upstream and downstream areas of the plate, depends on the principal frequency of the force. The frequency lock-in range of these forces was analyzed and compared with theoretical predictions.
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Affiliation(s)
- Makoto Iima
- Graduate School of Integrated Life Sciences, Hiroshima University, 1-7-1, Kagamiyama Higashihiroshima, Hiroshima 739-8521, Japan
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21
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Li T, Jiang Y, Bai Y, Jiang K, Du G, Chen P, Luo C, Li L, Qiao J, Shen J. A review for the impacts of circadian disturbance on urological cancers. Sleep Biol Rhythms 2024; 22:163-180. [PMID: 38524168 PMCID: PMC10959858 DOI: 10.1007/s41105-023-00500-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/18/2023] [Indexed: 03/26/2024]
Abstract
Circadian rhythm is an internal timing system and harmonizes a variety of cellular, behavioral, and physiological processes to daily environment. Circadian disturbance caused by altered life style or disrupted sleep patterns inevitably contributes to various disorders. As the rapidly increased cancer occurrences and subsequent tremendous financial burdens, more researches focus on reducing the morbidity rather than treating it. Recently, many epidemiologic studies demonstrated that circadian disturbance was tightly related to the occurrence and development of cancers. For urinary system, numerous clinical researches observed the incidence and progress of prostate cancer were influenced by nightshift work, sleep duration, chronotypes, light exposure, and meal timing, this was also proved by many genetic and fundamental findings. Although the epidemiological studies regarding the relationship between circadian disturbance and kidney/bladder cancers were relative limited, some basic researches still claimed circadian disruption was closely correlated to these two cancers. The role of circadian chemotherapy on cancers of prostate, kidney, and bladder were also explored, however, it has not been regularly recommended considering the limited evidence and poor standard protocols. Finally, the researches for the impacts of circadian disturbance on cancers of adrenal gland, penis, testis were not found at present. In general, a better understanding the relationship between circadian disturbance and urological cancers might help to provide more scientific work schedules and rational lifestyles which finally saving health resource by reducing urological tumorigenesis, however, the underlying mechanisms are complex which need further exploration.
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Affiliation(s)
- Tao Li
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Yiting Jiang
- Department of Otorhinolaryngology, The Ninth People’s Hospital of Chongqing, Chongqing, China
| | - Yunjin Bai
- Department of Urology and Institute of Urology, West China Hospital, Sichuan University, Chengdu, China
| | - Kehua Jiang
- Department of Urology, Guizhou Provincial People’s Hospital, Guiyang, China
| | - Guangshi Du
- Translational Medicine Research Center of Guizhou Medical University, Guiyang, China
| | - Peng Chen
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Chao Luo
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Lei Li
- Gastrointestinal Surgery Center, School of Medicine, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, University of Electronic Science and Technology of China, Chengdu, China
| | - Jun Qiao
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Jun Shen
- Department of Urology, Affiliated Hospital of Guizhou Medical University, Guiyang, China
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22
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Cavieres-Lepe J, Amini E, Zabel M, Nässel DR, Stanewsky R, Wegener C, Ewer J. Timed receptor tyrosine kinase signaling couples the central and a peripheral circadian clock in Drosophila. Proc Natl Acad Sci U S A 2024; 121:e2308067121. [PMID: 38442160 PMCID: PMC10945756 DOI: 10.1073/pnas.2308067121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 02/01/2024] [Indexed: 03/07/2024] Open
Abstract
Circadian clocks impose daily periodicities to behavior, physiology, and metabolism. This control is mediated by a central clock and by peripheral clocks, which are synchronized to provide the organism with a unified time through mechanisms that are not fully understood. Here, we characterized in Drosophila the cellular and molecular mechanisms involved in coupling the central clock and the peripheral clock located in the prothoracic gland (PG), which together control the circadian rhythm of emergence of adult flies. The time signal from central clock neurons is transmitted via small neuropeptide F (sNPF) to neurons that produce the neuropeptide Prothoracicotropic Hormone (PTTH), which is then translated into daily oscillations of Ca2+ concentration and PTTH levels. PTTH signaling is required at the end of metamorphosis and transmits time information to the PG through changes in the expression of the PTTH receptor tyrosine kinase (RTK), TORSO, and of ERK phosphorylation, a key component of PTTH transduction. In addition to PTTH, we demonstrate that signaling mediated by other RTKs contributes to the rhythmicity of emergence. Interestingly, the ligand to one of these receptors (Pvf2) plays an autocrine role in the PG, which may explain why both central brain and PG clocks are required for the circadian gating of emergence. Our findings show that the coupling between the central and the PG clock is unexpectedly complex and involves several RTKs that act in concert and could serve as a paradigm to understand how circadian clocks are coordinated.
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Affiliation(s)
- Javier Cavieres-Lepe
- Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso2360102, Chile
| | - Emad Amini
- Julius-Maximilians-Universität Würzburg, Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Am Hubland, Würzburg97074, Germany
| | - Maia Zabel
- Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso2360102, Chile
| | - Dick R. Nässel
- Department of Zoology, Stockholm University, 10691Stockholm, Sweden
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioral Biology, Multiscale Imaging Centre, University of Münster, 48149Münster, Germany
| | - Christian Wegener
- Julius-Maximilians-Universität Würzburg, Biocenter, Theodor-Boveri-Institute, Neurobiology and Genetics, Am Hubland, Würzburg97074, Germany
| | - John Ewer
- Centro Interdisciplinario de Neurociencias de Valparaíso, Universidad de Valparaíso, Valparaíso2360102, Chile
- Instituto de Neurociencias, Universidad de Valparaíso, Valparaíso2360102, Chile
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23
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Chavan A, Heisler J, Chang YG, Golden SS, Partch CL, LiWang A. Protocols for in vitro reconstitution of the cyanobacterial circadian clock. Biopolymers 2024; 115:e23559. [PMID: 37421636 PMCID: PMC10772220 DOI: 10.1002/bip.23559] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/26/2023] [Accepted: 06/16/2023] [Indexed: 07/10/2023]
Abstract
Circadian clocks are intracellular systems that orchestrate metabolic processes in anticipation of sunrise and sunset by providing an internal representation of local time. Because the ~24-h metabolic rhythms they produce are important to health across diverse life forms there is growing interest in their mechanisms. However, mechanistic studies are challenging in vivo due to the complex, that is, poorly defined, milieu of live cells. Recently, we reconstituted the intact circadian clock of cyanobacteria in vitro. It oscillates autonomously and remains phase coherent for many days with a fluorescence-based readout that enables real-time observation of individual clock proteins and promoter DNA simultaneously under defined conditions without user intervention. We found that reproducibility of the reactions required strict adherence to the quality of each recombinant clock protein purified from Escherichia coli. Here, we provide protocols for preparing in vitro clock samples so that other labs can ask questions about how changing environments, like temperature, metabolites, and protein levels are reflected in the core oscillator and propagated to regulation of transcription, providing deeper mechanistic insights into clock biology.
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Affiliation(s)
- Archana Chavan
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Joel Heisler
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Yong-Gang Chang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
| | - Susan S. Golden
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Molecular Biology, University of California – San Diego, La Jolla, CA 92093
| | - Carrie L. Partch
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- Department of Chemistry & Biochemistry, University of California – Santa Cruz, Santa Cruz, CA 95064
| | - Andy LiWang
- Center for Circadian Biology, University of California – San Diego, La Jolla, CA 92093
- School of Natural Sciences, University of California – Merced, Merced, CA 95343
- Department of Chemistry & Biochemistry, University of California – Merced, Merced, CA 95343
- Center for Cellular and Biomolecular Machines, University of California – Merced, Merced, CA 95343
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24
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Regmi P, Young M, Minigo G, Milic N, Gyawali P. Photoperiod and metabolic health: evidence, mechanism, and implications. Metabolism 2024; 152:155770. [PMID: 38160935 DOI: 10.1016/j.metabol.2023.155770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Circadian rhythms are evolutionarily programmed biological rhythms that are primarily entrained by the light cycle. Disruption of circadian rhythms is an important risk factor for several metabolic disorders. Photoperiod is defined as total duration of light exposure in a day. With the extended use of indoor/outdoor light, smartphones, television, computers, and social jetlag people are exposed to excessive artificial light at night increasing their photoperiod. Importantly long photoperiod is not limited to any geographical region, season, age, or socioeconomic group, it is pervasive. Long photoperiod is an established disrupter of the circadian rhythm and can induce a range of chronic health conditions including adiposity, altered hormonal signaling and metabolism, premature ageing, and poor psychological health. This review discusses the impact of exposure to long photoperiod on circadian rhythms, metabolic and mental health, hormonal signaling, and ageing and provides a perspective on possible preventive and therapeutic approaches for this pervasive challenge.
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Affiliation(s)
- Prashant Regmi
- Faculty of Health, Charles Darwin University, Australia.
| | - Morag Young
- Cardiovascular Endocrinology Laboratory, Baker IDI Heart and Diabetes Institute, Australia
| | | | - Natalie Milic
- Faculty of Health, Charles Darwin University, Australia
| | - Prajwal Gyawali
- Centre of Health Research and School of Health and Medical Sciences, University of Southern Queensland, Australia
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25
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Zhang H, Zhou Z, Guo J. The Function, Regulation, and Mechanism of Protein Turnover in Circadian Systems in Neurospora and Other Species. Int J Mol Sci 2024; 25:2574. [PMID: 38473819 DOI: 10.3390/ijms25052574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/18/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian clocks drive a large array of physiological and behavioral activities. At the molecular level, circadian clocks are composed of positive and negative elements that form core oscillators generating the basic circadian rhythms. Over the course of the circadian period, circadian negative proteins undergo progressive hyperphosphorylation and eventually degrade, and their stability is finely controlled by complex post-translational pathways, including protein modifications, genetic codon preference, protein-protein interactions, chaperon-dependent conformation maintenance, degradation, etc. The effects of phosphorylation on the stability of circadian clock proteins are crucial for precisely determining protein function and turnover, and it has been proposed that the phosphorylation of core circadian clock proteins is tightly correlated with the circadian period. Nonetheless, recent studies have challenged this view. In this review, we summarize the research progress regarding the function, regulation, and mechanism of protein stability in the circadian clock systems of multiple model organisms, with an emphasis on Neurospora crassa, in which circadian mechanisms have been extensively investigated. Elucidation of the highly complex and dynamic regulation of protein stability in circadian clock networks would greatly benefit the integrated understanding of the function, regulation, and mechanism of protein stability in a wide spectrum of other biological processes.
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Affiliation(s)
- Haoran Zhang
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Zengxuan Zhou
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jinhu Guo
- MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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26
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Yang Z, Zarbl H, Guo GL. Circadian Regulation of Endocrine Fibroblast Growth Factors on Systemic Energy Metabolism. Mol Pharmacol 2024; 105:179-193. [PMID: 38238100 PMCID: PMC10877735 DOI: 10.1124/molpharm.123.000831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/05/2024] [Indexed: 02/17/2024] Open
Abstract
The circadian clock is an endogenous biochemical timing system that coordinates the physiology and behavior of organisms to earth's ∼24-hour circadian day/night cycle. The central circadian clock synchronized by environmental cues hierarchically entrains peripheral clocks throughout the body. The circadian system modulates a wide variety of metabolic signaling pathways to maintain whole-body metabolic homeostasis in mammals under changing environmental conditions. Endocrine fibroblast growth factors (FGFs), namely FGF15/19, FGF21, and FGF23, play an important role in regulating systemic metabolism of bile acids, lipids, glucose, proteins, and minerals. Recent evidence indicates that endocrine FGFs function as nutrient sensors that mediate multifactorial interactions between peripheral clocks and energy homeostasis by regulating the expression of metabolic enzymes and hormones. Circadian disruption induced by environmental stressors or genetic ablation is associated with metabolic dysfunction and diurnal disturbances in FGF signaling pathways that contribute to the pathogenesis of metabolic diseases. Time-restricted feeding strengthens the circadian pattern of metabolic signals to improve metabolic health and prevent against metabolic diseases. Chronotherapy, the strategic timing of medication administration to maximize beneficial effects and minimize toxic effects, can provide novel insights into linking biologic rhythms to drug metabolism and toxicity within the therapeutical regimens of diseases. Here we review the circadian regulation of endocrine FGF signaling in whole-body metabolism and the potential effect of circadian dysfunction on the pathogenesis and development of metabolic diseases. We also discuss the potential of chrononutrition and chronotherapy for informing the development of timing interventions with endocrine FGFs to optimize whole-body metabolism in humans. SIGNIFICANCE STATEMENT: The circadian timing system governs physiological, metabolic, and behavioral functions in living organisms. The endocrine fibroblast growth factor (FGF) family (FGF15/19, FGF21, and FGF23) plays an important role in regulating energy and mineral metabolism. Endocrine FGFs function as nutrient sensors that mediate multifactorial interactions between circadian clocks and metabolic homeostasis. Chronic disruption of circadian rhythms increases the risk of metabolic diseases. Chronological interventions such as chrononutrition and chronotherapy provide insights into linking biological rhythms to disease prevention and treatment.
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Affiliation(s)
- Zhenning Yang
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy (Z.Y., G.L.G.), Environmental and Occupational Health Sciences Institute (Z.Y., H.Z., G.L.G.), Department of Environmental and Occupational Health Justice, School of Public Health (H.Z.), Rutgers Center for Lipid Research (G.L.G.), Rutgers, The State University of New Jersey, New Brunswick, New Jersey; and VA New Jersey Health Care System, Veterans Administration Medical Center, East Orange, New Jersey (G.L.G.)
| | - Helmut Zarbl
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy (Z.Y., G.L.G.), Environmental and Occupational Health Sciences Institute (Z.Y., H.Z., G.L.G.), Department of Environmental and Occupational Health Justice, School of Public Health (H.Z.), Rutgers Center for Lipid Research (G.L.G.), Rutgers, The State University of New Jersey, New Brunswick, New Jersey; and VA New Jersey Health Care System, Veterans Administration Medical Center, East Orange, New Jersey (G.L.G.)
| | - Grace L Guo
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy (Z.Y., G.L.G.), Environmental and Occupational Health Sciences Institute (Z.Y., H.Z., G.L.G.), Department of Environmental and Occupational Health Justice, School of Public Health (H.Z.), Rutgers Center for Lipid Research (G.L.G.), Rutgers, The State University of New Jersey, New Brunswick, New Jersey; and VA New Jersey Health Care System, Veterans Administration Medical Center, East Orange, New Jersey (G.L.G.)
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27
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Langebrake C, Manthey G, Frederiksen A, Lugo Ramos JS, Dutheil JY, Chetverikova R, Solov'yov IA, Mouritsen H, Liedvogel M. Adaptive evolution and loss of a putative magnetoreceptor in passerines. Proc Biol Sci 2024; 291:20232308. [PMID: 38320616 PMCID: PMC10846946 DOI: 10.1098/rspb.2023.2308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magnetic sensitivity in vitro compared to Cry4a from resident species. We investigate Cry and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes and identifies different selection regimes in passerines. We show that Cry4a is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that are likely to have facilitated the evolution of an optimized sensory protein for night-time orientation in songbirds. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines), and thus identified a gene deletion, which might facilitate testing the function of Cry4a in birds. In contrast, the other avian Cry (Cry1 and Cry2) were highly conserved across all species, indicating basal, non-sensory functions. Our results support a specialization or functional differentiation of Cry4 in songbirds which could be magnetosensation.
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Affiliation(s)
- Corinna Langebrake
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Georg Manthey
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Juan S. Lugo Ramos
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- The Francis Crick Institute, London NW1 1AT, UK
| | - Julien Y. Dutheil
- Research Group Molecular Systems Evolution, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Raisa Chetverikova
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Ilia A. Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Henrik Mouritsen
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Miriam Liedvogel
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
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28
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Jesse TG, Becer E, Kalkan R. Identification of the Relationship Between DNA Methylation of Circadian Rhythm Genes and Obesity. Biochem Genet 2024; 62:281-293. [PMID: 37329425 DOI: 10.1007/s10528-023-10415-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/06/2023] [Indexed: 06/19/2023]
Abstract
In children, teenagers, and young adults, environmental factors and genetic modifications have contributed to the development of obesity. There is a close relationship between obesity and circadian rhythm. To understand the role of CLOCK and BMAL1 in obesity, we analyzed the methylation status of CLOCK and BMAL1 in obese and control subjects. In this paper, we analyzed the methylation status of the CLOCK and BMAL1 genes by using MS-HRM in a total of 55 obese and 54 control subjects. In our study, we demonstrated that the level of fasting glucose and the level of HDL-cholesterol were associated with CLOCK methylation in obesity. We also showed a significant association between BMAL1 gene methylation and waist and hip circumference in obese subjects. This is the first study that shows the methylation of BMAL1 is associated with the obese phenotype. However, we could not show a direct association between CLOCK methylation and the obese phenotype. In this paper, a novel epigenetic interaction between circadian clock genes and obesity was demonstrated.
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Affiliation(s)
- Tirah Galaya Jesse
- Department of Medical Genetics, Faculty of Medicine, Near East University, Mersin 10, Nicosia, 99138, Turkey
| | - Eda Becer
- Faculty of Pharmacy, Eastern Mediterranean University, Mersin 10, Famagusta, 99628, Turkey
| | - Rasime Kalkan
- Department of Medical Genetics, Faculty of Medicine, Near East University, Mersin 10, Nicosia, 99138, Turkey.
- Department of Medical Genetics, Faculty of Medicine, Cyprus Health and Social Sciences University, Mersin 10, Guzelyurt, 99138, Turkey.
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29
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Sutton LB, Hurley JM. Circadian regulation of physiology by disordered protein-protein interactions. Curr Opin Struct Biol 2024; 84:102743. [PMID: 38091925 PMCID: PMC10922814 DOI: 10.1016/j.sbi.2023.102743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Cellular circadian clocks, the molecular timers that coordinate physiology to the day/night cycle across the domains of life, are widely regulated by disordereddisordered protein interactions. Here, we review the disordered-disordered protein interactions in the circadian clock of Neurospora crassa (N. crassa), a filamentous fungus which is a model organism for clocks in higher eukaryotes. We focus on what is known about the interactions between the intrinsically disordered core negative arm protein FREQUENCEY (FRQ), the other proteins comprising the transcription-translation feedback loop, and the proteins that control output. We compare and contrast this model with other models of eukaryotic clocks, illustrating that protein disorder is a conserved and essential mechanism in the maintenance of circadian clock across species.
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Affiliation(s)
- Lucas B Sutton
- Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, 110 8th St. Troy, NY, 12180, USA; Biological Sciences Department, Rensselaer Polytechnic Institute, 110 8th St. Troy, NY, 12180, USA
| | - Jennifer M Hurley
- Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute, 110 8th St. Troy, NY, 12180, USA; Biological Sciences Department, Rensselaer Polytechnic Institute, 110 8th St. Troy, NY, 12180, USA.
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30
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Naveed M, Chao OY, Hill JW, Yang YM, Huston JP, Cao R. Circadian neurogenetics and its implications in neurophysiology, behavior, and chronomedicine. Neurosci Biobehav Rev 2024; 157:105523. [PMID: 38142983 PMCID: PMC10872425 DOI: 10.1016/j.neubiorev.2023.105523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
The circadian rhythm affects multiple physiological processes, and disruption of the circadian system can be involved in a range of disease-related pathways. The genetic underpinnings of the circadian rhythm have been well-studied in model organisms. Significant progress has been made in understanding how clock genes affect the physiological functions of the nervous system. In addition, circadian timing is becoming a key factor in improving drug efficacy and reducing drug toxicity. The circadian biology of the target cell determines how the organ responds to the drug at a specific time of day, thus regulating pharmacodynamics. The current review brings together recent advances that have begun to unravel the molecular mechanisms of how the circadian clock affects neurophysiological and behavioral processes associated with human brain diseases. We start with a brief description of how the ubiquitous circadian rhythms are regulated at the genetic, cellular, and neural circuit levels, based on knowledge derived from extensive research on model organisms. We then summarize the latest findings from genetic studies of human brain disorders, focusing on the role of human clock gene variants in these diseases. Lastly, we discuss the impact of common dietary factors and medications on human circadian rhythms and advocate for a broader application of the concept of chronomedicine.
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Affiliation(s)
- Muhammad Naveed
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Department of Physiology and Pharmacology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Owen Y Chao
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA
| | - Jennifer W Hill
- Department of Physiology and Pharmacology, College of Medicine and Life Sciences, The University of Toledo, Toledo, OH 43614, USA
| | - Yi-Mei Yang
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812, USA; Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Joseph P Huston
- Center for Behavioral Neuroscience, Institute of Experimental Psychology, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Ruifeng Cao
- Department of Neuroscience and Cell Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA; Department of Neurology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
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31
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Yuan Y, Yadlapalli S. Regulation of circadian rhythms by clock protein nuclear bodies. Proc Natl Acad Sci U S A 2024; 121:e2321334121. [PMID: 38232300 PMCID: PMC10835046 DOI: 10.1073/pnas.2321334121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024] Open
Affiliation(s)
- Ye Yuan
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI48109
| | - Swathi Yadlapalli
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI48109
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI48109
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI48109
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32
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Del Olmo M, Kalashnikov A, Schmal C, Kramer A, Herzel H. Coupling allows robust mammalian redox circadian rhythms despite heterogeneity and noise. Heliyon 2024; 10:e24773. [PMID: 38312577 PMCID: PMC10835301 DOI: 10.1016/j.heliyon.2024.e24773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/06/2023] [Accepted: 01/14/2024] [Indexed: 02/06/2024] Open
Abstract
Circadian clocks are endogenous oscillators present in almost all cells that drive daily rhythms in physiology and behavior. There are two mechanisms that have been proposed to explain how circadian rhythms are generated in mammalian cells: through a transcription-translation feedback loop (TTFL) and based on oxidation/reduction reactions, both of which are intrinsically stochastic and heterogeneous at the single cell level. In order to explore the emerging properties of stochastic and heterogeneous redox oscillators, we simplify a recently developed kinetic model of redox oscillations to an amplitude-phase oscillator with 'twist' (period-amplitude correlation) and subject to Gaussian noise. We show that noise and heterogeneity alone lead to fast desynchronization, and that coupling between noisy oscillators can establish robust and synchronized rhythms with amplitude expansions and tuning of the period due to twist. Coupling a network of redox oscillators to a simple model of the TTFL also contributes to synchronization, large amplitudes and fine-tuning of the period for appropriate interaction strengths. These results provide insights into how the circadian clock compensates randomness from intracellular sources and highlight the importance of noise, heterogeneity and coupling in the context of circadian oscillators.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology - Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Anton Kalashnikov
- Institute for Theoretical Biology - Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Christoph Schmal
- Institute for Theoretical Biology - Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Philippstraße 13, 10115 Berlin, Germany
| | - Achim Kramer
- Institute for Medical Immunology - Laboratory of Chronobiology, Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology - Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Philippstraße 13, 10115 Berlin, Germany
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33
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Aldrich JC, Scheinfeld AR, Lee SE, Dusenbery KJ, Mahach KM, Van de Veire BC, Fonken LK, Gaudet AD. Effects of dim light at night in C57BL/6J mice on recovery after spinal cord injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.15.557980. [PMID: 37745393 PMCID: PMC10516041 DOI: 10.1101/2023.09.15.557980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Spinal cord injury (SCI) can cause long-lasting locomotor deficits, pain, and mood disorders. Anatomical and functional outcomes are exacerbated by inflammation after SCI, which causes secondary damage. One promising target after SCI is manipulating the circadian system, which optimizes biology and behavior for time of day - including neuroimmune responses and mood-related behaviors. Circadian disruption after SCI is likely worsened by a disruptive hospital environment, which typically includes dim light-at-night (dLAN). Here, we hypothesized that mice subjected to SCI, then placed in dLAN, would exhibit worsened locomotor deficits, pain-like behavior, and anxiety-depressive-like symptoms compared to mice maintained in light days with dark nights (LD). C57BL/6J mice received sham surgery or moderate T9 contusion SCI, then were placed permanently in LD or dLAN. dLAN after SCI did not worsen locomotor deficits; rather, SCI-dLAN mice showed slight improvement in open-field locomotion at the final timepoint. Although dLAN did not alter SCI-induced heat hyperalgesia, SCI-dLAN mice exhibited an increase in mechanical allodynia at 13 days post-SCI compared to SCI-LD mice. SCI-LD and SCI-dLAN mice had similar outcomes using sucrose preference (depressive-like) and open-field (anxiety-like) tests. At 21 dpo, SCI-dLAN mice had reduced preference for a novel juvenile compared to SCI-LD, implying that dLAN combined with SCI may worsen this mood-related behavior. Finally, lesion size was similar between SCI-LD and SCI-dLAN mice. Therefore, newly placing C57BL/6J mice in dLAN after SCI had modest effects on locomotor, pain-like, and mood-related behaviors. Future studies should consider whether clinically-relevant circadian disruptors, alone or in combination, could be ameliorated to enhance outcomes after SCI.
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Affiliation(s)
- John C Aldrich
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Ashley R Scheinfeld
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Sydney E Lee
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Kalina J Dusenbery
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Kathryn M Mahach
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Brigid C Van de Veire
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
| | - Laura K Fonken
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin
| | - Andrew D Gaudet
- Department of Psychology, College of Liberal Arts, The University of Texas at Austin
- Department of Neurology, Dell Medical School, The University of Texas at Austin
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Stengl M, Schneider AC. Contribution of membrane-associated oscillators to biological timing at different timescales. Front Physiol 2024; 14:1243455. [PMID: 38264332 PMCID: PMC10803594 DOI: 10.3389/fphys.2023.1243455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024] Open
Abstract
Environmental rhythms such as the daily light-dark cycle selected for endogenous clocks. These clocks predict regular environmental changes and provide the basis for well-timed adaptive homeostasis in physiology and behavior of organisms. Endogenous clocks are oscillators that are based on positive feedforward and negative feedback loops. They generate stable rhythms even under constant conditions. Since even weak interactions between oscillators allow for autonomous synchronization, coupling/synchronization of oscillators provides the basis of self-organized physiological timing. Amongst the most thoroughly researched clocks are the endogenous circadian clock neurons in mammals and insects. They comprise nuclear clockworks of transcriptional/translational feedback loops (TTFL) that generate ∼24 h rhythms in clock gene expression entrained to the environmental day-night cycle. It is generally assumed that this TTFL clockwork drives all circadian oscillations within and between clock cells, being the basis of any circadian rhythm in physiology and behavior of organisms. Instead of the current gene-based hierarchical clock model we provide here a systems view of timing. We suggest that a coupled system of autonomous TTFL and posttranslational feedback loop (PTFL) oscillators/clocks that run at multiple timescales governs adaptive, dynamic homeostasis of physiology and behavior. We focus on mammalian and insect neurons as endogenous oscillators at multiple timescales. We suggest that neuronal plasma membrane-associated signalosomes constitute specific autonomous PTFL clocks that generate localized but interlinked oscillations of membrane potential and intracellular messengers with specific endogenous frequencies. In each clock neuron multiscale interactions of TTFL and PTFL oscillators/clocks form a temporally structured oscillatory network with a common complex frequency-band comprising superimposed multiscale oscillations. Coupling between oscillator/clock neurons provides the next level of complexity of an oscillatory network. This systemic dynamic network of molecular and cellular oscillators/clocks is suggested to form the basis of any physiological homeostasis that cycles through dynamic homeostatic setpoints with a characteristic frequency-band as hallmark. We propose that mechanisms of homeostatic plasticity maintain the stability of these dynamic setpoints, whereas Hebbian plasticity enables switching between setpoints via coupling factors, like biogenic amines and/or neuropeptides. They reprogram the network to a new common frequency, a new dynamic setpoint. Our novel hypothesis is up for experimental challenge.
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Affiliation(s)
- Monika Stengl
- Department of Biology, Animal Physiology/Neuroethology, University of Kassel, Kassel, Germany
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Wang S, Chen Y, Zhou H, Ning Z, Hu T, Ye C, Mu W. Cloning, tissue distribution, and effects of different circadian rhythms on the mRNA expression levels of circadian clock genes Per1a and Per1b in Phoxinus lagowskii. Int J Biol Macromol 2024; 256:128310. [PMID: 38007023 DOI: 10.1016/j.ijbiomac.2023.128310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/10/2023] [Accepted: 11/19/2023] [Indexed: 11/27/2023]
Abstract
This study describes the cloning and characterization of Period 1a and Period 1b genes and the analysis of their mRNA and protein expression in Amur minnow (Phoxinus lagowskii) after exposure to different light cycles. The full-length P. lagowskii Per1a and Per1b genes encode proteins consisting of 1393 and 1409 amino acids, and share high homology with the per1 genes of other freshwater fish species. The Per1a and Per1b genes were widely expressed within the brain, eye, and peripheral tissues. The acrophase of the Per1a gene in the pituitary gland occurred during the dark phase at ZT15 (zeitgeber time 15, 12 L: 12 D) and ZT18 (8 L, 16 D), whereas the acrophase of the Per1b gene in the pituitary gland was observed during the light phase. Our study suggests that the expression of Per1a and Per1b in P. lagowskii varied depending on differences in circadian rhythm patterns. The results of our dual-luciferase reporter assays demonstrated that the P. lagowskii Per1b gene enhances the activation of NF-κB. This study is the first to examine the circadian clock gene Per1a and Per1b in the high-latitude fish P. lagowskii, offering valuable insights into the effects of different light periods on this fish species.
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Affiliation(s)
- Sihan Wang
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Yingqiao Chen
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Haishui Zhou
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Zhaoyang Ning
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Tingting Hu
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Cunrun Ye
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China
| | - Weijie Mu
- Key Laboratory of Biodiversity of Aquatic Organisms, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China.
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Kügler A, Lammers MO, Pack AA, Tenorio-Hallé L, Thode AM. Diel spatio-temporal patterns of humpback whale singing on a high-density breeding ground. ROYAL SOCIETY OPEN SCIENCE 2024; 11:230279. [PMID: 38269074 PMCID: PMC10805604 DOI: 10.1098/rsos.230279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 12/20/2023] [Indexed: 01/26/2024]
Abstract
Humpback whale song chorusing dominates the marine soundscape in Hawai'i during winter months, yet little is known about spatio-temporal habitat use patterns of singers. We analysed passive acoustic monitoring data from five sites off Maui and found that ambient noise levels associated with song chorusing decreased during daytime hours nearshore but increased offshore. To resolve whether these changes reflect a diel offshore-onshore movement or a temporal difference in singing activity, data from 71 concurrently conducted land-based theodolite surveys were analysed. Non-calf pods (n = 3082), presumably including the majority of singers, were found further offshore with increasing time of the day. Separately, we acoustically localized 217 nearshore singers using vector-sensors. During the day, distances to shore and minimum distances among singers increased, and singers switched more between being stationary and singing while travelling. Together, these findings suggest that the observed diel trends in humpback whale chorusing off Maui represent a pattern of active onshore-offshore movement of singers. We hypothesize that this may result from singers attempting to reduce intraspecific acoustic masking when densities are high nearshore and avoidance of a loud, non-humpback, biological evening chorus offshore, creating a dynamic of movement of singers aimed at increasing the efficiency of their acoustic display.
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Affiliation(s)
- Anke Kügler
- University of Hawai‘i at Mānoa, Honolulu, HI, USA
- Bioacoustics and Behavioral Ecology Lab, Syracuse University, Syracuse, NY, USA
- Oceanwide Science Institute, Honolulu, HI, USA
| | - Marc O. Lammers
- Oceanwide Science Institute, Honolulu, HI, USA
- Hawaiian Islands Humpback Whale National Marine Sanctuary, Kīhei, HI, USA
| | - Adam A. Pack
- University of Hawai‘i at Hilo, Hilo, HI, USA
- The Dolphin Institute, Hilo, HI, USA
| | - Ludovic Tenorio-Hallé
- Marine Physical Laboratory, Scripps Institute of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Aaron M. Thode
- Marine Physical Laboratory, Scripps Institute of Oceanography, University of California, San Diego, La Jolla, CA, USA
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Coughlan K, Sadowska ET, Bauchinger U. Repeat Sampling of Female Passerines During Reproduction Reveals Surprising Higher Plasma Oxidative Damage During Resting Compared to Active State. Integr Comp Biol 2023; 63:1197-1208. [PMID: 37698890 PMCID: PMC10755187 DOI: 10.1093/icb/icad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023] Open
Abstract
Traditional models of oxidative stress predict accumulation of damage caused by reactive oxygen species (ROS) production as highly correlated with aerobic metabolism, a prediction under increasing scrutiny. Here, we repeat sampled female great tits (Parus major) at two opposite levels of energy use during the period of maximum food provisioning to nestlings, once at rest and once during activity. Our results were in contrast to the above prediction, namely significantly higher levels of oxidative damage during rest opposed to active phase. This discrepancy could not be explained neither using levels of "first line" antioxidant enzymes activity measured from erythrocytes, nor from total nonenzymatic antioxidant capacity measured from plasma, as no differences were found between states. Significantly higher levels of uric acid, a potent antioxidant, were seen in the plasma during the active phase than in rest phase, which may explain the lower levels of oxidative damage despite high levels of physical activity. Our results challenge the hypothesis that oxidative stress is elevated during times with high energy use and call for more profound understanding of potential drivers of the modulation of oxidative stress such as metabolic state of the animal, and thus also the time of sampling in general.
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Affiliation(s)
- Kyle Coughlan
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Edyta T Sadowska
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
| | - Ulf Bauchinger
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteura St., 02-093 Warsaw, Poland
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Botté A, Payton L, Lefeuvre E, Tran D. Is part-night lighting a suitable mitigation strategy to limit Artificial Light at Night effects on the biological rhythm at the behavioral and molecular scales of the oyster Crassostrea gigas? THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167052. [PMID: 37714354 DOI: 10.1016/j.scitotenv.2023.167052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023]
Abstract
Artificial Light at Night (ALAN) is a fast-spreading threat to organisms, especially in coastal environments, where night lighting is increasing due to constant anthropization. Considering that ALAN affects a large diversity of coastal organisms, finding efficient solutions to limit these effects is of great importance but poorly investigated. The potential benefit of one strategy, in particular, should be studied since its use is growing: part-night lighting (PNL), which consists in switching off the lights for a few hours during nighttime. The aim of this study is to investigate the positive potential of the PNL strategy on the daily rhythm of the oyster Crassostrea gigas, a key species of coastal areas of ecological and commercial interest. Oysters were exposed to a control condition and three different ALAN modalities. A realistic PNL condition is applied, recreating a strategy of city policy in a coastal city boarding an urbanized bay (Lanton, Arcachon Bay, France). The PNL modality consists in switching off ALAN direct sources (5 lx) for 4 h (23-3 h) during which oysters are in darkness. Then, a PNL + skyglow (PNL + S) modality reproduces the previous one mimicking a skyglow (0.1 lx), an indirect ALAN source, during the direct lighting switch off, to get as close as possible to realistic conditions. Finally, the third ALAN condition mimics full-night direct lighting (FNL). Results revealed that PNL reduces some adverse effects of FNL on the behavioral daily rhythm. But, counterintuitively, PNL + S appears more harmful than FNL for some parameters of the behavioral daily rhythm. PNL + S modality is also the only one that affect oysters' clock and melatonin synthesis gene expression, suggesting physiological consequences. Thus, in realistic conditions, the PNL mitigation strategy might not be beneficial in the presence of skyglow, seeing worse for a coastal organism such as the oysters.
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Affiliation(s)
- Audrey Botté
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120 Arcachon, France
| | - Laura Payton
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120 Arcachon, France
| | - Elisa Lefeuvre
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120 Arcachon, France
| | - Damien Tran
- Univ. Bordeaux, CNRS, Bordeaux INP, EPOC, UMR 5805, F-33120 Arcachon, France.
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Dhungana P, Wei X, Meuti M, Sim C. Identification of CYCLE targets that contribute diverse features of circadian rhythms in the mosquito Culex pipiens. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 48:101140. [PMID: 37690215 PMCID: PMC10841209 DOI: 10.1016/j.cbd.2023.101140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Culex pipiens demonstrates robust circadian rhythms in adult eclosion, flight activity, mating, and development. These rhythmic patterns are believed to be controlled by the endogenous light-entrainable circadian clock that consists of positive and negative regulators working in a transcription-translation feedback loop. Moreover, these mosquitoes undergo seasonal diapause in exposure to the short photoperiod of late summer or early fall. However, the exact genetic and cellular mechanism behind the clock gene-mediated activity pattern, seasonal time measurement, and subsequent diapause initiation still need to be unraveled. To determine the possible linkage between clock genes and downstream processes, here we employed ChIP-sequencing to identify the direct targets of one of the core clock proteins, Cycle (CYC). The nearest genes with peaks mapping to their 1Kb upstream region of the transcription start site were extracted and scanned for consensus E box sequences, resulting in a dataset comprising the target genes possibly regulated by CYC. Based on the highest fold enrichment and functional relevance, we identified genes relating to five gene categories of potential interest, including peptide/receptors, neurotransmission, olfaction, immunity, and reproductive growth. Of these, we validated fourteen genes with ChIP-qPCR and qRT-PCR. These genes showed a significantly high expression in dusk compared to dawn in concert with the activity level of the CYC transcription factor and are thus strong candidates for mediating circadian rhythmicity and possibly regulating seasonal shifts in mosquito reproductive activity.
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Affiliation(s)
- Prabin Dhungana
- Department of Biology, Baylor University, Waco, TX 76798, USA. https://twitter.com/@Prabin_988
| | - Xueyan Wei
- Department of Biology, Baylor University, Waco, TX 76798, USA
| | - Megan Meuti
- Department of Entomology, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Columbus, OH 43210, USA. https://twitter.com/@MeganMeuti
| | - Cheolho Sim
- Department of Biology, Baylor University, Waco, TX 76798, USA.
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Rabinovich-Nikitin I, Kirshenbaum E, Kirshenbaum LA. Autophagy, Clock Genes, and Cardiovascular Disease. Can J Cardiol 2023; 39:1772-1780. [PMID: 37652255 DOI: 10.1016/j.cjca.2023.08.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/11/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023] Open
Abstract
Circadian rhythms are 24-hour cycles that regulate physical, mental, and behavioural changes of most living organisms. In the heart, circadian rhythms regulate processes such as heart rate, blood pressure, blood coagulability, and vascular tone. However, in addition to regulating physiologic processes, circadian rhythms regulate pathophysiologic processes in the heart. In this regard, circadian rhythms regulate the onset, severity, and outcome of many cardiovascular diseases (CVDs), including myocardial infarction, diabetic cardiomyopathy, doxorubicin (Dox)-induced cardiotoxicity, and heart failure. Notably, the underlying mechanism of many of these diseases is linked to impaired cellular quality control processes, such as autophagy. Autophagy is a homeostatic cellular process that regulates the removal of damaged cellular components, allowing their degradation and recycling into their basic constituents for production of cellular energy. Many studies from recent years point to a regulatory link between autophagy and circadian machinery in the control of CVDs. In this review, we highlight the recent discoveries in the field of circadian-induced autophagy in the heart and provide the molecular mechanisms and signalling pathways that underlie the crosstalk between autophagy and clock gene control in response to cardiac injury. Understanding the mechanisms that underlie circadian-induced autophagy in response to cardiac stress may prove to be beneficial in developing novel therapeutic approaches to treat cardiac disease.
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Affiliation(s)
- Inna Rabinovich-Nikitin
- Department of Physiology and Pathophysiology, Institute of Cardiovascular Sciences, St Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Eryn Kirshenbaum
- Department of Physiology and Pathophysiology, Institute of Cardiovascular Sciences, St Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada
| | - Lorrie A Kirshenbaum
- Department of Physiology and Pathophysiology, Institute of Cardiovascular Sciences, St Boniface Hospital Albrechtsen Research Centre, Winnipeg, Manitoba, Canada; Department of Pharmacology and Therapeutics, Rady College of Medicine, Max Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada.
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Wang B, Edamo ME, Zhou X, Wang Z, Gerber SA, Kettenbach AN, Dunlap JC. Acetylation of WCC is dispensable for the core circadian clock but differentially regulates acute light responses in Neurospora. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569266. [PMID: 38076981 PMCID: PMC10705461 DOI: 10.1101/2023.11.29.569266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
In the Neurospora circadian system, the White Collar Complex (WCC) formed by WC-1 and WC-2 drives expression of the frequency ( frq ) gene whose product FRQ feedbacks to inhibit transcriptional activity of WCC. Phosphorylation of WCC has been extensively studied, but the extent and significance of other post-translational modifications (PTM) has been poorly studied. To this end, we used mass-spectrometry to study alkylation sites on WCC, resulting in discovery of nine acetylation sites. Mutagenesis analysis showed most of the acetylation events individually do not play important roles in period determination. Moreover, mutating all the lysines falling in either half of WC-1 or all the lysine residues in WC-2 to arginines did not abolish circadian rhythms. In addition, we also found nine mono-methylation sites on WC-1, but like acetylation, individual ablation of most of the mono-methylation events did not result in a significant period change. Taken together, the data here suggest that acetylation or mono-methylation on WCC is not a determinant of the pace of the circadian feedback loop. The finding is consistent with a model in which repression of WCC's circadian activity is controlled mainly by phosphorylation. Interestingly, light-induced expression of some light-responsive genes has been modulated in certain wc-1 acetylation mutants, suggesting that WC-1 acetylation events differentially regulate light responses.
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42
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Li Z, Huang L, Luo Y, Yu B, Tian G. Effects and possible mechanisms of intermittent fasting on health and disease: a narrative review. Nutr Rev 2023; 81:1626-1635. [PMID: 36940184 DOI: 10.1093/nutrit/nuad026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
The imbalance between energy intake and expenditure in an environment of continuous food availability can lead to metabolic disturbances in the body and increase the risk of obesity and a range of chronic noncommunicable diseases. Intermittent fasting (IF) is one of the most popular nonpharmacological interventions to combat obesity and chronic noncommunicable diseases. The 3 most widely studied IF regimens are alternate-day fasting, time-restricted feeding, and the 5:2 diet. In rodents, IF helps optimize energy metabolism, prevent obesity, promote brain health, improve immune and reproductive function, and delay aging. In humans, IF's benefits are relevant for the aging global population and for increasing human life expectancy. However, the optimal model of IF remains unclear. In this review, the possible mechanisms of IF are summarized and its possible drawbacks are discussed on the basis of the results of existing research, which provide a new idea for nonpharmaceutical dietary intervention of chronic noncommunicable diseases.
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Affiliation(s)
- Zimei Li
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Liansu Huang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Yuheng Luo
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Bing Yu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
| | - Gang Tian
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, Sichuan, P. R. China
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Xie B, Yuan H, Zou X, Lu M, Zhang Y, Xu D, Peng X, Wang D, Zhao M, Wen X. p75NTR promotes tooth rhythmic mineralization via upregulation of BMAL1/CLOCK. Front Cell Dev Biol 2023; 11:1283878. [PMID: 38020910 PMCID: PMC10662321 DOI: 10.3389/fcell.2023.1283878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
The circadian clock plays a critical role in dentomaxillofacial development. Tooth biomineralization is characterized by the circadian clock; however, the mechanisms underlying the coordination of circadian rhythms with tooth development and biomineralization remain unclear. The p75 neurotrophin receptor (p75NTR) is a clock factor that regulates the oscillatory components of the circadian rhythm. This study aims to investigate the impact of p75NTR on the rhythmic mineralization of teeth and elucidate its underlying molecular mechanisms. We generated p75NTR knockout mice to examine the effects of p75NTR deficiency on tooth mineralization. Ectomesenchymal stem cells (EMSCs), derived from mouse tooth germs, were used for in vitro experiments. Results showed a reduction in tooth mineral density and daily mineralization rate in p75NTR knockout mice. Deletion of p75NTR decreased the expression of DMP1, DSPP, RUNX2, and ALP in tooth germ. Odontogenic differentiation and mineralization of EMSCs were activated by p75NTR. Histological results demonstrated predominant detection of p75NTR protein in odontoblasts and stratum intermedium cells during rapid formation phases of dental hard tissue. The mRNA expression of p75NTR exhibited circadian variations in tooth germs and EMSCs, consistent with the expression patterns of the core clock genes Bmal1 and Clock. The upregulation of BMAL1/CLOCK expression by p75NTR positively regulated the mineralization ability of EMSCs, whereas BMAL1 and CLOCK exerted a negative feedback regulation on p75NTR by inhibiting its promoter activity. Our findings suggest that p75NTR is necessary to maintain normal tooth biomineralization. Odontogenic differentiation and mineralization of EMSCs is regulated by the p75NTR-BMAL1/CLOCK signaling axis. These findings offer valuable insights into the associations between circadian rhythms, tooth development, and biomineralization.
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Affiliation(s)
- Bo Xie
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Hongyan Yuan
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Xuqiang Zou
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Mingjie Lu
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Yixin Zhang
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Dan Xu
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xuelian Peng
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
| | - Di Wang
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Manzhu Zhao
- Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, College of Stomatology, Chongqing Medical University, Chongqing, China
| | - Xiujie Wen
- Department of Orthodontics, School of Stomatology, Southwest Medical University, Luzhou, China
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Murgo E, Colangelo T, Bellet MM, Malatesta F, Mazzoccoli G. Role of the Circadian Gas-Responsive Hemeprotein NPAS2 in Physiology and Pathology. BIOLOGY 2023; 12:1354. [PMID: 37887064 PMCID: PMC10603908 DOI: 10.3390/biology12101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/14/2023] [Accepted: 10/20/2023] [Indexed: 10/28/2023]
Abstract
Neuronal PAS domain protein 2 (NPAS2) is a hemeprotein comprising a basic helix-loop-helix domain (bHLH) and two heme-binding sites, the PAS-A and PAS-B domains. This protein acts as a pyridine nucleotide-dependent and gas-responsive CO-dependent transcription factor and is encoded by a gene whose expression fluctuates with circadian rhythmicity. NPAS2 is a core cog of the molecular clockwork and plays a regulatory role on metabolic pathways, is important for the function of the central nervous system in mammals, and is involved in carcinogenesis as well as in normal biological functions and processes, such as cardiovascular function and wound healing. We reviewed the scientific literature addressing the various facets of NPAS2 and framing this gene/protein in several and very different research and clinical fields.
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Affiliation(s)
- Emanuele Murgo
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy;
| | - Tommaso Colangelo
- Department of Medical and Surgical Sciences, University of Foggia, Viale Pinto 1, 71100 Foggia, Italy;
- Cancer Cell Signaling Unit, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy
| | - Maria Marina Bellet
- Department of Medicine and Surgery, University of Perugia, P.le L. Severi 1, 06132 Perugia, Italy;
| | - Francesco Malatesta
- Department of Biochemical Sciences “Alessandro Rossi Fanelli”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Gianluigi Mazzoccoli
- Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Fondazione IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy;
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45
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Kaji H, Mori F, Ito H. Enhanced precision of circadian rhythm by output system. J Theor Biol 2023; 574:111621. [PMID: 37717817 DOI: 10.1016/j.jtbi.2023.111621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 09/19/2023]
Abstract
Circadian rhythms are biological rhythms with a period of approximately 24 h that persist even under constant conditions without daily environmental cues. The molecular circadian clock machinery generates physiological rhythms, which can be transmitted into the downstream output system. Owing to the stochastic nature of the biochemical reactions and the extracellular environment, the oscillation period of circadian rhythms exhibited by individual organisms or cells is not constant on a daily basis with variations as high as 10%, as reflected by the coefficient of variation. Although the fluctuations in the circadian rhythm are measured through a reporter system such as bioluminescence or fluorescence, which is an example of output systems, experimentally confirming whether the fluctuations found in the reporter system are the same as those in the circadian clock is challenging. This study investigated a coupled system of a circadian clock and its output system numerically and analytically, and then compared the fluctuations in the oscillation period of the two systems. We found that the amount of fluctuations in the output system is smaller than that in the circadian clock, assuming the degradation rate of the molecules responsible for the output system is a typical value for protein degradation. The results indicate that the output system can improve the accuracy of the circadian rhythm without the need for any denoising processes.
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Affiliation(s)
- Hotaka Kaji
- Faculty of Design, Kyushu University, 4-9-1, Shiobaru, Fukuoka, 815-8540, Japan
| | - Fumito Mori
- Faculty of Design, Kyushu University, 4-9-1, Shiobaru, Fukuoka, 815-8540, Japan; Education and Research Center for Mathematical and Data Science, Kyushu University, 744, Motoka, Fukuoka, 819-0395, Japan
| | - Hiroshi Ito
- Faculty of Design, Kyushu University, 4-9-1, Shiobaru, Fukuoka, 815-8540, Japan.
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46
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Savageau MA. Phenotype Design Space Provides a Mechanistic Framework Relating Molecular Parameters to Phenotype Diversity Available for Selection. J Mol Evol 2023; 91:687-710. [PMID: 37620617 PMCID: PMC10598110 DOI: 10.1007/s00239-023-10127-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023]
Abstract
Two long-standing challenges in theoretical population genetics and evolution are predicting the distribution of phenotype diversity generated by mutation and available for selection, and determining the interaction of mutation, selection and drift to characterize evolutionary equilibria and dynamics. More fundamental for enabling such predictions is the current inability to causally link genotype to phenotype. There are three major mechanistic mappings required for such a linking - genetic sequence to kinetic parameters of the molecular processes, kinetic parameters to biochemical system phenotypes, and biochemical phenotypes to organismal phenotypes. This article introduces a theoretical framework, the Phenotype Design Space (PDS) framework, for addressing these challenges by focusing on the mapping of kinetic parameters to biochemical system phenotypes. It provides a quantitative theory whose key features include (1) a mathematically rigorous definition of phenotype based on biochemical kinetics, (2) enumeration of the full phenotypic repertoire, and (3) functional characterization of each phenotype independent of its context-dependent selection or fitness contributions. This framework is built on Design Space methods that relate system phenotypes to genetically determined parameters and environmentally determined variables. It also has the potential to automate prediction of phenotype-specific mutation rate constants and equilibrium distributions of phenotype diversity in microbial populations undergoing steady-state exponential growth, which provides an ideal reference to which more realistic cases can be compared. Although the framework is quite general and flexible, the details will undoubtedly differ for different functions, organisms and contexts. Here a hypothetical case study involving a small molecular system, a primordial circadian clock, is used to introduce this framework and to illustrate its use in a particular case. The framework is built on fundamental biochemical kinetics. Thus, the foundation is based on linear algebra and reasonable physical assumptions, which provide numerous opportunities for experimental testing and further elaboration to deal with complex multicellular organisms that are currently beyond its scope. The discussion provides a comparison of results from the PDS framework with those from other approaches in theoretical population genetics.
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Affiliation(s)
- Michael A Savageau
- Department of Microbiology & Molecular Genetics, University of California, 228 Briggs, Davis, CA, 95616, USA.
- Department of Biomedical Engineering, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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47
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McKnight BM, Kang S, Le TH, Fang M, Carbonel G, Rodriguez E, Govindarajan S, Albocher-Kedem N, Tran AL, Duncan NR, Amster-Choder O, Golden SS, Cohen SE. Roles for the Synechococcus elongatus RNA-Binding Protein Rbp2 in Regulating the Circadian Clock. J Biol Rhythms 2023; 38:447-460. [PMID: 37515350 PMCID: PMC10528358 DOI: 10.1177/07487304231188761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
The cyanobacterial circadian oscillator, consisting of KaiA, KaiB, and KaiC proteins, drives global rhythms of gene expression and compaction of the chromosome and regulates the timing of cell division and natural transformation. While the KaiABC posttranslational oscillator can be reconstituted in vitro, the Kai-based oscillator is subject to several layers of regulation in vivo. Specifically, the oscillator proteins undergo changes in their subcellular localization patterns, where KaiA and KaiC are diffuse throughout the cell during the day and localized as a focus at or near the pole of the cell at night. Here, we report that the CI domain of KaiC, when in a hexameric state, is sufficient to target KaiC to the pole. Moreover, increased ATPase activity of KaiC correlates with enhanced polar localization. We identified proteins associated with KaiC in either a localized or diffuse state. We found that loss of Rbp2, found to be associated with localized KaiC, results in decreased incidence of KaiC localization and long-period circadian phenotypes. Rbp2 is an RNA-binding protein, and it appears that RNA-binding activity of Rbp2 is required to execute clock functions. These findings uncover previously unrecognized roles for Rbp2 in regulating the circadian clock and suggest that the proper localization of KaiC is required for a fully functional clock in vivo.
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Affiliation(s)
- Briana M. McKnight
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Shannon Kang
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Tam H. Le
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Mingxu Fang
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Genelyn Carbonel
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Esbeydi Rodriguez
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Sutharsan Govindarajan
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
- Department of Biological Sciences, SRM University AP, Amaravati, India
| | - Nitsan Albocher-Kedem
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Amanda L. Tran
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Nicholas R. Duncan
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
| | - Orna Amster-Choder
- Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University Faculty of Medicine, Jerusalem 91120, Israel
| | - Susan S. Golden
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
| | - Susan E. Cohen
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, CA 90032
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48
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Han X, Zhang D, Hong L, Yu D, Wu Z, Yang T, Rust M, Tu Y, Ouyang Q. Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex. Nat Commun 2023; 14:5907. [PMID: 37737245 PMCID: PMC10516925 DOI: 10.1038/s41467-023-41575-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level.
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Affiliation(s)
- Xu Han
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Dongliang Zhang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Lu Hong
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Daqi Yu
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Zhaolong Wu
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Tian Yang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China
| | - Michael Rust
- Departments of Molecular Genetics and Cell Biology and of Physics, University of Chicago, Chicago, IL, 60637, USA.
| | - Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, NY, 10598, USA.
| | - Qi Ouyang
- State Key Laboratory of Artificial Microstructure and Mesoscopic Physics, School of Physics, Peking University, Beijing, 100871, China.
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, AAIC, Peking University, Beijing, 100871, China.
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Cheng Y, Chi Y, Sun L, Wang GZ. Dominant constraints on the evolution of rhythmic gene expression. Comput Struct Biotechnol J 2023; 21:4301-4311. [PMID: 37692081 PMCID: PMC10492206 DOI: 10.1016/j.csbj.2023.08.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/21/2023] [Accepted: 08/31/2023] [Indexed: 09/12/2023] Open
Abstract
Although the individual transcriptional regulators of the core circadian clock are distinct among different organisms, the autoregulatory feedback loops they form are conserved. This unified design principle explains how daily physiological activities oscillate across species. However, it is unknown whether analogous design principles govern the gene expression output of circadian clocks. In this study, we performed a comparative analysis of rhythmic gene expression in eight diverse species and identified four common distribution patterns of cycling gene expression across these species. We hypothesized that the maintenance of reduced energetic costs constrains the evolution of rhythmic gene expression. Our large-scale computational simulations support this hypothesis by showing that selection against high-energy expenditure completely regenerates all cycling gene patterns. Moreover, we find that the peaks of rhythmic expression have been subjected to this type of selective pressure. The results suggest that selective pressure from circadian regulation efficiently removes unnecessary gene products from the transcriptome, thereby significantly impacting its evolutionary path.
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Affiliation(s)
| | | | | | - Guang-Zhong Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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50
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Olivares-Yañez C, Alessandri MP, Salas L, Larrondo LF. Methylxanthines Modulate Circadian Period Length Independently of the Action of Phosphodiesterase. Microbiol Spectr 2023; 11:e0372722. [PMID: 37272789 PMCID: PMC10434132 DOI: 10.1128/spectrum.03727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 05/22/2023] [Indexed: 06/06/2023] Open
Abstract
In Neurospora crassa, caffeine and other methylxanthines are known to inhibit phosphodiesterase (PDE) activity, leading to augmented cAMP levels. In this organism, it has also been shown that the addition of these drugs significantly lengthens the circadian period, as seen by conidiation rhythms. Utilizing in vivo bioluminescence reporters, pharmacological inhibitors, and cAMP analogs, we revisited the effect of methylxanthines and the role of cAMP signaling in the Neurospora clockworks. We observed that caffeine, like all tested methylxanthines, led to significant period lengthening, visualized with both core-clock transcriptional and translational reporters. Remarkably, this phenotype is still observed when phosphodiesterase (PDE) activity is genetically or chemically (via 3-isobutyl-1-methylxanthine) abrogated. Likewise, methylxanthines still exert a period effect in several cAMP signaling pathway mutants, including adenylate cyclase (cr-1) and protein kinase A (PKA) (Δpkac-1) mutants, suggesting that these drugs lead to circadian phenotypes through mechanisms different from the canonical PDE-cAMP-PKA signaling axis. Thus, this study highlights the strong impact of methylxanthines on circadian period in Neurospora, albeit the exact mechanisms somehow remain elusive. IMPORTANCE Evidence from diverse organisms show that caffeine causes changes in the circadian clock, causing period lengthening. The fungus Neurospora crassa is no exception; here, several methylxanthines such as caffeine, theophylline, and aminophylline cause period lengthening in a concentration-dependent manner. Although methylxanthines are expected to inhibit phosphodiesterase activity, we were able to show by genetic and pharmacological means that these drugs exert their effects through a different mechanism. Moreover, our results indicate that increases in cAMP levels and changes in PKA activity do not impact the circadian period and therefore are not part of underlying effects of methylxanthine. These results set the stage for future analyses dissecting the molecular mechanisms by which these drugs dramatically modify the circadian period.
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Affiliation(s)
- Consuelo Olivares-Yañez
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - María P. Alessandri
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto Salas
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F. Larrondo
- ANID-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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