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Qin P, Li Y, Su Y, Wang Z, Wu R, Liang X, Zeng Y, Guo P, Yu Z, Huang X, Yang H, Zeng Z, Zhao X, Gong S, Han J, Chen Z, Xiao W, Chen A. Bifidobacterium adolescentis-derived hypaphorine alleviates acetaminophen hepatotoxicity by promoting hepatic Cry1 expression. J Transl Med 2024; 22:525. [PMID: 38822329 PMCID: PMC11143572 DOI: 10.1186/s12967-024-05312-6] [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: 01/09/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024] Open
Abstract
Acetaminophen (APAP)-induced liver injury (AILI) is a pressing public health concern. Although evidence suggests that Bifidobacterium adolescentis (B. adolescentis) can be used to treat liver disease, it is unclear if it can prevent AILI. In this report, we prove that B. adolescentis significantly attenuated AILI in mice, as demonstrated through biochemical analysis, histopathology, and enzyme-linked immunosorbent assays. Based on untargeted metabolomics and in vitro cultures, we found that B. adolescentis generates microbial metabolite hypaphorine. Functionally, hypaphorine inhibits the inflammatory response and hepatic oxidative stress to alleviate AILI in mice. Transcriptomic analysis indicates that Cry1 expression is increased in APAP-treated mice after hypaphorine treatment. Overexpression of Cry1 by its stabilizer KL001 effectively mitigates liver damage arising from oxidative stress in APAP-treated mice. Using the gene expression omnibus (GEO) database, we verified that Cry1 gene expression was also decreased in patients with APAP-induced acute liver failure. In conclusion, this study demonstrates that B. adolescentis inhibits APAP-induced liver injury by generating hypaphorine, which subsequently upregulates Cry1 to decrease inflammation and oxidative stress.
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Affiliation(s)
- Ping Qin
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Advanced Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 510006, China
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yanru Li
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- School of Nursing, Southern Medical University, Guangzhou, 510515, China
| | - Yangjing Su
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Advanced Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Ze Wang
- Department of Critical Care Medicine, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510665, China
| | - Rong Wu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoqi Liang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yunong Zeng
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Advanced Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Peiheng Guo
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhichao Yu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xintao Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Hong Yang
- Department of Critical Care Medicine, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510665, China
| | - Zhenhua Zeng
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoshan Zhao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Shenhai Gong
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jiaochan Han
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Zhongqing Chen
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Wei Xiao
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
| | - Ali Chen
- Center for Drug Research and Development, Guangdong Provincial Key Laboratory of Advanced Drug Delivery System, Guangdong Pharmaceutical University, Guangzhou, 510006, China.
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Schmal C, Maier B, Ashwal-Fluss R, Bartok O, Finger AM, Bange T, Koutsouli S, Robles MS, Kadener S, Herzel H, Kramer A. Alternative polyadenylation factor CPSF6 regulates temperature compensation of the mammalian circadian clock. PLoS Biol 2023; 21:e3002164. [PMID: 37379316 DOI: 10.1371/journal.pbio.3002164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/15/2023] [Indexed: 06/30/2023] Open
Abstract
A defining property of circadian clocks is temperature compensation, characterized by the resilience of their near 24-hour free-running periods against changes in environmental temperature within the physiological range. While temperature compensation is evolutionary conserved across different taxa of life and has been studied within many model organisms, its molecular underpinnings remain elusive. Posttranscriptional regulations such as temperature-sensitive alternative splicing or phosphorylation have been described as underlying reactions. Here, we show that knockdown of cleavage and polyadenylation specificity factor subunit 6 (CPSF6), a key regulator of 3'-end cleavage and polyadenylation, significantly alters circadian temperature compensation in human U-2 OS cells. We apply a combination of 3'-end-RNA-seq and mass spectrometry-based proteomics to globally quantify changes in 3' UTR length as well as gene and protein expression between wild-type and CPSF6 knockdown cells and their dependency on temperature. Since changes in temperature compensation behavior should be reflected in alterations of temperature responses within one or all of the 3 regulatory layers, we statistically assess differential responses upon changes in ambient temperature between wild-type and CPSF6 knockdown cells. By this means, we reveal candidate genes underlying circadian temperature compensation, including eukaryotic translation initiation factor 2 subunit 1 (EIF2S1).
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Affiliation(s)
- Christoph Schmal
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bert Maier
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Reut Ashwal-Fluss
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Osnat Bartok
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anna-Marie Finger
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Tanja Bange
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Stella Koutsouli
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Maria S Robles
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-Universität München, München, Germany
| | - Sebastian Kadener
- Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt-Universität zu Berlin and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
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3
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Almeida S, Chaves M, Delaunay F. Cell cycle period control through modulation of clock inputs. J Bioinform Comput Biol 2020; 18:2040006. [DOI: 10.1142/s0219720020400065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this work, we study period control of the mammalian cell cycle via coupling with the cellular clock. For this, we make use of the oscillators’ synchronization dynamics and investigate methods of slowing down the cell cycle with the use of clock inputs. Clock control of the cell cycle is well established via identified molecular mechanisms, such as the CLOCK:BMAL1-mediated induction of the wee1 gene, resulting in the WEE1 kinase that represses the active form of mitosis promoting factor (MPF), the essential cell cycle component. To investigate the coupling dynamics of these systems, we use previously developed models of the clock and cell cycle oscillators and center our studies on unidirectional clock [Formula: see text] cell cycle coupling. Moreover, we propose an hypothesis of a Growth Factor (GF)-responsive clock, involving a pathway of the non-essential cell cycle complex cyclin D/CDK4. We observe a variety of rational ratios of clock to cell cycle period, such as: 1:1, 3:2, 4:3, and 5:4. Finally, our protocols of period control are successful in effectively slowing down the cell cycle by the use of clock modulating inputs, some of which correspond to existing drugs.
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Affiliation(s)
- S. Almeida
- Inria, iBV, Université Côte d’Azur, Sophia Antipolis, France
| | - M. Chaves
- Inria, Université Côte d’Azur, INRA, CNRS, Sorbonne Université, Sophia Antipolis, France
| | - F. Delaunay
- iBV, Université Côte d’Azur, CNRS, INSERM, Sophia Antipolis, France
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4
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Rashid MM, Kurata H. Coupling protocol of interlocked feedback oscillators in circadian clocks. J R Soc Interface 2020; 17:20200287. [PMID: 32486952 DOI: 10.1098/rsif.2020.0287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Circadian rhythms (approx. 24 h) show the robustness of key oscillatory features such as phase, period and amplitude against external and internal variations. The robustness of Drosophila circadian clocks can be generated by interlocked transcriptional-translational feedback loops, where two negative feedback loops are coupled through mutual activations. The mechanisms by which such coupling protocols have survived out of many possible protocols remain to be revealed. To address this question, we investigated two distinct coupling protocols: activator-coupled oscillators (ACO) and repressor-coupled oscillators (RCO). We focused on the two coupling parameters: coupling dissociation constant and coupling time-delay. Interestingly, the ACO was able to produce anti-phase or morning-evening cycles, whereas the RCO produced in-phase ones. Deterministic and stochastic analyses demonstrated that the anti-phase ACO provided greater fluctuations in amplitude not only with respect to changes in coupling parameters but also to random parameter perturbations than the in-phase RCO. Moreover, the ACO deteriorated the entrainability to the day-night master clock, whereas the RCO produced high entrainability. Considering that the real, interlocked feedback loops have evolved as the ACO, instead of the RCO, we first proposed a hypothesis that the morning-evening or anti-phase cycle is more essential for Drosophila than achieving robustness and entrainability.
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Affiliation(s)
- Md Mamunur Rashid
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
| | - Hiroyuki Kurata
- Biomedical Informatics R&D Center, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502, Japan
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5
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Almeida S, Chaves M, Delaunay F. Transcription-based circadian mechanism controls the duration of molecular clock states in response to signaling inputs. J Theor Biol 2019; 484:110015. [PMID: 31539528 DOI: 10.1016/j.jtbi.2019.110015] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/10/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022]
Abstract
The molecular oscillator of the mammalian circadian clock consists in a dynamical network of genes and proteins whose main regulatory mechanisms occur at the transcriptional level. From a dynamical point of view, the mechanisms leading to an oscillatory solution with an orderly protein peak expression and a clear day/night phase distinction remain unclear. Our goal is to identify the essential interactions needed to generate phase opposition between the activating CLOCK:BMAL1 and the repressing PER:CRY complexes and to better distinguish these two main clock molecular phases relating to rest/activity and fast/feeding cycles. To do this, we develop a transcription-based mathematical model centered on linear combinations of the clock controlled elements (CCEs): E-box, R-box and D-box. Each CCE is responsive to activators and repressors. After model calibration with single-cell data, we explore entrainment and period tuning via interplay with metabolism. Variation of the PER degradation rate γp, relating to the tau mutation, results in asymmetric changes in the duration of the different clock molecular phases. Time spent at the state of high PER/PER:CRY decreases with γp, while time spent at the state of high BMAL1 and CRY1, both proteins with activity in promoting insulin sensitivity, remains constant. This result suggests a possible mechanism behind the altered metabolism of tau mutation animals. Furthermore, we expose the clock system to two regulatory inputs, one relating to the fast/feeding cycle and the other to the light-dependent synchronization signaling. We observe the phase difference between these signals to also affect the relative duration of molecular clock states. Simulated circadian misalignment, known to correlate with insulin resistance, leads to decreased duration of BMAL1 expression. Our results reveal a possible mechanism for clock-controlled metabolic homeostasis, whereby the circadian clock controls the relative duration of different molecular (and metabolic) states in response to signaling inputs.
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Affiliation(s)
- Sofia Almeida
- 1600 Université Côte d'Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France; Université Côte d'Azur, CNRS, INSERM, iBV, France.
| | - Madalena Chaves
- 1600 Université Côte d'Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France. http://www-sop.inria.fr/members/Madalena.Chaves/
| | - Franck Delaunay
- Université Côte d'Azur, CNRS, INSERM, iBV, France. http://www.ibv.unice.fr/research-team/delaunay/
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6
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Schmal C, Ono D, Myung J, Pett JP, Honma S, Honma KI, Herzel H, Tokuda IT. Weak coupling between intracellular feedback loops explains dissociation of clock gene dynamics. PLoS Comput Biol 2019; 15:e1007330. [PMID: 31513579 PMCID: PMC6759184 DOI: 10.1371/journal.pcbi.1007330] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 09/24/2019] [Accepted: 08/12/2019] [Indexed: 01/11/2023] Open
Abstract
Circadian rhythms are generated by interlocked transcriptional-translational negative feedback loops (TTFLs), the molecular process implemented within a cell. The contributions, weighting and balancing between the multiple feedback loops remain debated. Dissociated, free-running dynamics in the expression of distinct clock genes has been described in recent experimental studies that applied various perturbations such as slice preparations, light pulses, jet-lag, and culture medium exchange. In this paper, we provide evidence that this "presumably transient" dissociation of circadian gene expression oscillations may occur at the single-cell level. Conceptual and detailed mechanistic mathematical modeling suggests that such dissociation is due to a weak interaction between multiple feedback loops present within a single cell. The dissociable loops provide insights into underlying mechanisms and general design principles of the molecular circadian clock.
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Affiliation(s)
- Christoph Schmal
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Daisuke Ono
- Department of Neuroscience II, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Jihwan Myung
- Laboratory of Braintime, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Graduate Institute of Mind, Brain, and Consciousness, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Brain and Consciousness, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - J. Patrick Pett
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Institute for Theoretical Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Isao T. Tokuda
- Department of Mechanical Engineering, Ritsumeikan University, Kusatsu, Japan
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7
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Ashraf H, Ahmad J, Hassan A, Ali A. Computational modeling and analysis of the impacts of sleep deprivation on glucose stimulated insulin secretion. Biosystems 2019; 179:1-14. [PMID: 30790613 DOI: 10.1016/j.biosystems.2019.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 01/02/2019] [Accepted: 02/13/2019] [Indexed: 01/12/2023]
Abstract
Circadian clock is an exquisite internal biological clock functioning in all living organisms. Lifestyle changes such as shift work or frequent travelling might result in malfunctioning of the central and consequently the peripheral clocks leading to different metabolic disorders. Disruptions in β cell clock have been found to be a potential reason behind β cell failure that makes a person prone towards developing type 2 diabetes (T2DM). In this study, a Petri net model for β cell circadian clock has been developed, followed by analysis of the negative impacts of sleep deprivation conditions on the process of glucose stimulated insulin secretion (GSIS) through misalignment of circadian clock. The analysis of structural properties of the Petri net model reveals robustness of the circadian system. The simulation results predict that sleep loss negatively affects the expression of circadian genes which eventually leads to impaired GSIS and β cell failure. These results suggest that sleep/wake cycle is a vital contributor for the entrainment of the circadian clock and normal functioning of β cell.
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Affiliation(s)
- Hufsah Ashraf
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Jamil Ahmad
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan; Department of Computer Science and Information Technology, University of Malakand, Chakdara, Pakistan.
| | - Azka Hassan
- Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Amjad Ali
- Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Islamabad, Pakistan
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Deciphering the Dynamics of Interlocked Feedback Loops in a Model of the Mammalian Circadian Clock. Biophys J 2018; 115:2055-2066. [PMID: 30473017 DOI: 10.1016/j.bpj.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 09/29/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
Mathematical models of fundamental biological processes play an important role in consolidating theory and experiments, especially if they are systematically developed, thoroughly characterized, and well tested by experimental data. In this work, we report a detailed bifurcation analysis of a mathematical model of the mammalian circadian clock network developed by Relógio et al., noteworthy for its consistency with available data. Using one- and two-parameter bifurcation diagrams, we explore how oscillations in the model depend on the expression levels of its constituent genes and the activities of their encoded proteins. These bifurcation diagrams allow us to decipher the dynamics of interlocked feedback loops by parametric variation of genes and proteins in the model. Among other results, we find that REV-ERB, a member of a subfamily of orphan nuclear receptors, plays a critical role in the intertwined dynamics of Relógio's model. The bifurcation diagrams reported here can be used for predicting how the core clock network responds-in terms of period, amplitude and phases of oscillations-to different perturbations.
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9
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Kim JK. Protein sequestration versus Hill-type repression in circadian clock models. IET Syst Biol 2018; 10:125-35. [PMID: 27444022 DOI: 10.1049/iet-syb.2015.0090] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Circadian (∼24 h) clocks are self-sustained endogenous oscillators with which organisms keep track of daily and seasonal time. Circadian clocks frequently rely on interlocked transcriptional-translational feedback loops to generate rhythms that are robust against intrinsic and extrinsic perturbations. To investigate the dynamics and mechanisms of the intracellular feedback loops in circadian clocks, a number of mathematical models have been developed. The majority of the models use Hill functions to describe transcriptional repression in a way that is similar to the Goodwin model. Recently, a new class of models with protein sequestration-based repression has been introduced. Here, the author discusses how this new class of models differs dramatically from those based on Hill-type repression in several fundamental aspects: conditions for rhythm generation, robust network designs and the periods of coupled oscillators. Consistently, these fundamental properties of circadian clocks also differ among Neurospora, Drosophila, and mammals depending on their key transcriptional repression mechanisms (Hill-type repression or protein sequestration). Based on both theoretical and experimental studies, this review highlights the importance of careful modelling of transcriptional repression mechanisms in molecular circadian clocks.
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Affiliation(s)
- Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro Yuseong-gu, Daejeon, 34141, Korea.
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10
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Wang G, Peskin CS. Entrainment of a cellular circadian oscillator by light in the presence of molecular noise. Phys Rev E 2018; 97:062416. [PMID: 30011522 DOI: 10.1103/physreve.97.062416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 11/07/2022]
Abstract
In this paper, we consider a stochastic molecular circadian oscillator described by a sequence of biological reactions and its deterministic kinetics governed by a system of ordinary differential equations in the limit of large numbers of molecules. The oscillations in the model are generated by negative feedback regulation of a gene. The focus of this paper is the entrainment of the oscillator by a periodic light signal that affects the maximal transcription rate of the gene. We introduce two scalings of the model parameters that provide independent control over the natural frequency of the oscillator and the relative noise level. We study entrainment in two ways: by visualizing the stochastic limit cycle in various projections of the discrete phase space of the system and by evaluating the maximum of the normalized cross correlation of the light signal with the number of protein molecules in the cell. The visualization method ignores the phase of the oscillator, and we find in this way that entrainment has a subtle organizing effect on the limit cycle as a whole. The cross correlation results reveal an interval of natural frequencies of the oscillator surrounding the frequency of the light signal within which maximal entrainment occurs with rather sharp drops in entrainment at the edges of this interval. The width of the interval of maximal entrainment increases with the amplitude of the light signal. These statements are applicable both to the stochastic oscillator and to its deterministic limit, but the results are most clear-cut in the deterministic case and degrade from there as the relative noise level increases.
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Affiliation(s)
- Guanyu Wang
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Charles S Peskin
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
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11
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Wang Y, Ni X, Yan J, Yang L. Modeling transcriptional co-regulation of mammalian circadian clock. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2018; 14:1447-1462. [PMID: 29161870 DOI: 10.3934/mbe.2017075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The circadian clock is a self-sustaining oscillator that has a period of about 24 hours at the molecular level. The oscillator is a transcription-translation feedback loop system composed of several genes. In this paper, a scalar nonlinear differential equation with two delays, modeling the transcriptional co-regulation in mammalian circadian clock, is proposed and analyzed. Sufficient conditions are established for the asymptotic stability of the unique nontrivial positive equilibrium point of the model by studying an exponential polynomial characteristic equation with delay-dependent coefficients. The existence of the Hopf bifurcations can be also obtained. Numerical simulations of the model with proper parameter values coincide with the theoretical result.
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Affiliation(s)
- Yanqin Wang
- School of Mathematical Sciences, Soochow University, Suzhou 215006, Jiangsu, China
| | - Xin Ni
- School of Mathematical Sciences, Soochow University, Suzhou 215006, Jiangsu, China
| | - Jie Yan
- School of Mathematical Sciences, Soochow University, Suzhou 215006, Jiangsu, China
| | - Ling Yang
- School of Mathematical Sciences, Soochow University, Suzhou 215006, Jiangsu, China
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12
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Battogtokh D, Kojima S, Tyson JJ. Modeling the interactions of sense and antisense Period transcripts in the mammalian circadian clock network. PLoS Comput Biol 2018; 14:e1005957. [PMID: 29447160 PMCID: PMC5831635 DOI: 10.1371/journal.pcbi.1005957] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 02/28/2018] [Accepted: 01/04/2018] [Indexed: 12/28/2022] Open
Abstract
In recent years, it has become increasingly apparent that antisense transcription plays an important role in the regulation of gene expression. The circadian clock is no exception: an antisense transcript of the mammalian core-clock gene PERIOD2 (PER2), which we shall refer to as Per2AS RNA, oscillates with a circadian period and a nearly 12 h phase shift from the peak expression of Per2 mRNA. In this paper, we ask whether Per2AS plays a regulatory role in the mammalian circadian clock by studying in silico the potential effects of interactions between Per2 and Per2AS RNAs on circadian rhythms. Based on the antiphasic expression pattern, we consider two hypotheses about how Per2 and Per2AS mutually interfere with each other's expression. In our pre-transcriptional model, the transcription of Per2AS RNA from the non-coding strand represses the transcription of Per2 mRNA from the coding strand and vice versa. In our post-transcriptional model, Per2 and Per2AS transcripts form a double-stranded RNA duplex, which is rapidly degraded. To study these two possible mechanisms, we have added terms describing our alternative hypotheses to a published mathematical model of the molecular regulatory network of the mammalian circadian clock. Our pre-transcriptional model predicts that transcriptional interference between Per2 and Per2AS can generate alternative modes of circadian oscillations, which we characterize in terms of the amplitude and phase of oscillation of core clock genes. In our post-transcriptional model, Per2/Per2AS duplex formation dampens the circadian rhythm. In a model that combines pre- and post-transcriptional controls, the period, amplitude and phase of circadian proteins exhibit non-monotonic dependencies on the rate of expression of Per2AS. All three models provide potential explanations of the observed antiphasic, circadian oscillations of Per2 and Per2AS RNAs. They make discordant predictions that can be tested experimentally in order to distinguish among these alternative hypotheses.
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Affiliation(s)
- Dorjsuren Battogtokh
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail: (DB); (JJT)
| | - Shihoko Kojima
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Biocomplexity Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Division of Systems Biology, Academy of Integrated Science, Virginia Polytechnic Institute and State University, Blacksburg, United States of America
| | - John J. Tyson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Biocomplexity Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- Division of Systems Biology, Academy of Integrated Science, Virginia Polytechnic Institute and State University, Blacksburg, United States of America
- * E-mail: (DB); (JJT)
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13
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Ono D, Honma S, Nakajima Y, Kuroda S, Enoki R, Honma KI. Dissociation of Per1 and Bmal1 circadian rhythms in the suprachiasmatic nucleus in parallel with behavioral outputs. Proc Natl Acad Sci U S A 2017; 114:E3699-E3708. [PMID: 28416676 PMCID: PMC5422828 DOI: 10.1073/pnas.1613374114] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The temporal order of physiology and behavior in mammals is primarily regulated by the circadian pacemaker located in the hypothalamic suprachiasmatic nucleus (SCN). Taking advantage of bioluminescence reporters, we monitored the circadian rhythms of the expression of clock genes Per1 and Bmal1 in the SCN of freely moving mice and found that the rate of phase shifts induced by a single light pulse was different in the two rhythms. The Per1-luc rhythm was phase-delayed instantaneously by the light presented at the subjective evening in parallel with the activity onset of behavioral rhythm, whereas the Bmal1-ELuc rhythm was phase-delayed gradually, similar to the activity offset. The dissociation was confirmed in cultured SCN slices of mice carrying both Per1-luc and Bmal1-ELuc reporters. The two rhythms in a single SCN slice showed significantly different periods in a long-term (3 wk) culture and were internally desynchronized. Regional specificity in the SCN was not detected for the period of Per1-luc and Bmal1-ELuc rhythms. Furthermore, neither is synchronized with circadian intracellular Ca2+ rhythms monitored by a calcium indicator, GCaMP6s, or with firing rhythms monitored on a multielectrode array dish, although the coupling between the circadian firing and Ca2+ rhythms persisted during culture. These findings indicate that the expressions of two key clock genes, Per1 and Bmal1, in the SCN are regulated in such a way that they may adopt different phases and free-running periods relative to each other and are respectively associated with the expression of activity onset and offset.
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Affiliation(s)
- Daisuke Ono
- Photonic Bioimaging Section, Research Center for Cooperative Projects, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan;
| | - Sato Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan;
| | - Yoshihiro Nakajima
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Takamatsu, Kagawa 761-0395, Japan
| | - Shigeru Kuroda
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0020, Japan
| | - Ryosuke Enoki
- Photonic Bioimaging Section, Research Center for Cooperative Projects, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama 332-0012, Japan
| | - Ken-Ichi Honma
- Department of Chronomedicine, Hokkaido University Graduate School of Medicine, Sapporo, 060-8638, Japan
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Abstract
This review summarizes various mathematical models of cell-autonomous mammalian circadian clock. We present the basics necessary for understanding of the cell-autonomous mammalian circadian oscillator, modern experimental data essential for its reconstruction and some special problems related to the validation of mathematical circadian oscillator models. This work compares existing mathematical models of circadian oscillator and the results of the computational studies of the oscillating systems. Finally, we discuss applications of the mathematical models of mammalian circadian oscillator for solving specific problems in circadian rhythm biology.
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15
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Millius A, Ueda HR. Systems Biology-Derived Discoveries of Intrinsic Clocks. Front Neurol 2017; 8:25. [PMID: 28220104 PMCID: PMC5292584 DOI: 10.3389/fneur.2017.00025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/17/2017] [Indexed: 12/19/2022] Open
Abstract
A systems approach to studying biology uses a variety of mathematical, computational, and engineering tools to holistically understand and model properties of cells, tissues, and organisms. Building from early biochemical, genetic, and physiological studies, systems biology became established through the development of genome-wide methods, high-throughput procedures, modern computational processing power, and bioinformatics. Here, we highlight a variety of systems approaches to the study of biological rhythms that occur with a 24-h period-circadian rhythms. We review how systems methods have helped to elucidate complex behaviors of the circadian clock including temperature compensation, rhythmicity, and robustness. Finally, we explain the contribution of systems biology to the transcription-translation feedback loop and posttranslational oscillator models of circadian rhythms and describe new technologies and "-omics" approaches to understand circadian timekeeping and neurophysiology.
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Affiliation(s)
- Arthur Millius
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
| | - Hiroki R. Ueda
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Suita, Osaka, Japan
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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16
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Huang B, Tian X, Liu F, Wang W. Impact of time delays on oscillatory dynamics of interlinked positive and negative feedback loops. Phys Rev E 2016; 94:052413. [PMID: 27967134 DOI: 10.1103/physreve.94.052413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Interlinking a positive feedback loop (PFL) with a negative feedback loop (NFL) constitutes a typical motif in genetic networks, performing various functions in cell signaling. How time delay in feedback regulation affects the dynamics of such systems still remains unclear. Here, we investigate three systems of interlinked PFL and NFL with time delays: a synthetic genetic oscillator, a three-node circuit, and a simplified single-node model. The stability of steady states and the routes to oscillation in the single-node model are analyzed in detail. The amplitude and period of oscillations vary with a pointwise periodicity over a range of time delay. Larger-amplitude oscillations can be induced when the PFL has an appropriately long delay, in comparison with the PFL with no delay or short delay; this conclusion holds true for all the three systems. We unravel the underlying mechanism for the above effects via analytical derivation under a limiting condition. We also develop a stochastic algorithm for simulating a single reaction with two delays and show that robust oscillations can be maintained by the PFL with a properly long delay in the single-node system. This work presents an effective method for constructing robust large-amplitude oscillators and interprets why similar circuit architectures are engaged in timekeeping systems such as circadian clocks.
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Affiliation(s)
- Bo Huang
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Xinyu Tian
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Feng Liu
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructures, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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