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Madhuri S, Lepetit B, Fürst AH, Kroth PG. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components. PLANTS (BASEL, SWITZERLAND) 2024; 13:1465. [PMID: 38891274 PMCID: PMC11174801 DOI: 10.3390/plants13111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.
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Affiliation(s)
| | | | | | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany; (S.M.); (B.L.); (A.H.F.)
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2
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Doležel D. Sociosexual interactions: A clock synchronized by smell. Curr Biol 2024; 34:R284-R286. [PMID: 38593773 DOI: 10.1016/j.cub.2024.02.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
While the daily rhythmicity of organisms is entrained by several cues, light is thought to be the strongest signal. Surprisingly, a new study in a moth shows that olfactory communication can be even more powerful for synchronization, and, at least to some extent, works across related species.
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Affiliation(s)
- David Doležel
- Biology Centre of the Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic.
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3
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Chawla S, O’Neill J, Knight MI, He Y, Wang L, Maronde E, Rodríguez SG, van Ooijen G, Garbarino-Pico E, Wolf E, Dkhissi-Benyahya O, Nikhat A, Chakrabarti S, Youngstedt SD, Zi-Ching Mak N, Provencio I, Oster H, Goel N, Caba M, Oosthuizen M, Duffield GE, Chabot C, Davis SJ. Timely Questions Emerging in Chronobiology: The Circadian Clock Keeps on Ticking. J Circadian Rhythms 2024; 22:2. [PMID: 38617710 PMCID: PMC11011957 DOI: 10.5334/jcr.237] [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: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 04/16/2024] Open
Abstract
Chronobiology investigations have revealed much about cellular and physiological clockworks but we are far from having a complete mechanistic understanding of the physiological and ecological implications. Here we present some unresolved questions in circadian biology research as posed by the editorial staff and guest contributors to the Journal of Circadian Rhythms. This collection of ideas is not meant to be comprehensive but does reveal the breadth of our observations on emerging trends in chronobiology and circadian biology. It is amazing what could be achieved with various expected innovations in technologies, techniques, and mathematical tools that are being developed. We fully expect strengthening mechanistic work will be linked to health care and environmental understandings of circadian function. Now that most clock genes are known, linking these to physiological, metabolic, and developmental traits requires investigations from the single molecule to the terrestrial ecological scales. Real answers are expected for these questions over the next decade. Where are the circadian clocks at a cellular level? How are clocks coupled cellularly to generate organism level outcomes? How do communities of circadian organisms rhythmically interact with each other? In what way does the natural genetic variation in populations sculpt community behaviors? How will methods development for circadian research be used in disparate academic and commercial endeavors? These and other questions make it a very exciting time to be working as a chronobiologist.
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Affiliation(s)
| | - John O’Neill
- MRC Laboratory of Molecular Biology Cambridge, UK
| | | | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Erik Maronde
- Institut für Anatomie II, Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, Theodor-Stern-Kai-7, 60590 Frankfurt, DE
| | - Sergio Gil Rodríguez
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Gerben van Ooijen
- School of Biological Sciences, University of Edinburgh, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Eduardo Garbarino-Pico
- Universidad Nacional de Córdoba (UNC), Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, AR
- CONICET-UNC, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, AR
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch- Weg 17, 55128 Mainz, DE
| | - Ouria Dkhissi-Benyahya
- Inserm, Stem Cell and Brain Research Institute U1208, Univ Lyon, UniversitéClaude Bernard Lyon 1, 18 Avenue du Doyen Lépine, 69500, Bron, FR
| | - Anjoom Nikhat
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shawn D. Youngstedt
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, US
- Department of Medicine, University of Arizona, Tucson, AZ, US
| | | | - Ignacio Provencio
- Department of Biology and Department of Ophthalmology, University of Virginia, Charlottesville, VA, US
| | - Henrik Oster
- Institute of Neurobiology, Center for Brain, Behavior & Metabolism (CBBM), University of Luebeck, 23562 Luebeck, DE
| | - Namni Goel
- Biological Rhythms Research Laboratory, Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, US
| | - Mario Caba
- Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa, Ver., MX
| | - Maria Oosthuizen
- Department of Zoology and Entomology, University of Pretoria, Pretoria, ZA
- Mammal Research Institute, University of Pretoria, Hatfield, ZA
| | - Giles E. Duffield
- Department of Biological Sciences, Galvin Life Science Center, University of Notre Dame, Notre Dame, US
| | - Christopher Chabot
- Department of Biological Sciences, Plymouth State University, Plymouth, NH 03264, US
| | - Seth J. Davis
- Department of Biology, University of York, York YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, CN
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4
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Matallana-Surget S, Geron A, Decroo C, Wattiez R. Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications. Int J Mol Sci 2024; 25:2934. [PMID: 38474181 DOI: 10.3390/ijms25052934] [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: 02/01/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Circadian rhythms, characterized by approximately 24 h cycles, play a pivotal role in enabling various organisms to synchronize their biological activities with daily variations. While ubiquitous in Eukaryotes, circadian clocks remain exclusively characterized in Cyanobacteria among Prokaryotes. These rhythms are regulated by a core oscillator, which is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Interestingly, recent studies revealed rhythmic activities, potentially tied to a circadian clock, in other Prokaryotes, including purple bacteria such as Rhodospirillum rubrum, known for its applications in fuel and plastic bioproduction. However, the pivotal question of how light and dark cycles influence protein dynamics and the expression of putative circadian clock genes remains unexplored in purple non-sulfur bacteria. Unraveling the regulation of these molecular clocks holds the key to unlocking optimal conditions for harnessing the biotechnological potential of R. rubrum. Understanding how its proteome responds to different light regimes-whether under continuous light or alternating light and dark cycles-could pave the way for precisely fine-tuning bioproduction processes. Here, we report for the first time the expressed proteome of R. rubrum grown under continuous light versus light and dark cycle conditions using a shotgun proteomic analysis. In addition, we measured the impact of light regimes on the expression of four putative circadian clock genes (kaiB1, kaiB2, kaiC1, kaiC2) at the transcriptional and translational levels using RT-qPCR and targeted proteomic (MRM-MS), respectively. The data revealed significant effects of light conditions on the overall differential regulation of the proteome, particularly during the early growth stages. Notably, several proteins were found to be differentially regulated during the light or dark period, thus impacting crucial biological processes such as energy conversion pathways and the general stress response. Furthermore, our study unveiled distinct regulation of the four kai genes at both the mRNA and protein levels in response to varying light conditions. Deciphering the impact of the diel cycle on purple bacteria not only enhances our understanding of their ecology but also holds promise for optimizing their applications in biotechnology, providing valuable insights into the origin and evolution of prokaryotic clock mechanisms.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Augustin Geron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Corentin Decroo
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, B-7000 Mons, Belgium
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5
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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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6
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Dwivedi SL, Quiroz LF, Spillane C, Wu R, Mattoo AK, Ortiz R. Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops. PLANTA 2024; 259:72. [PMID: 38386103 PMCID: PMC10884192 DOI: 10.1007/s00425-023-04324-8] [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: 10/30/2023] [Accepted: 12/24/2023] [Indexed: 02/23/2024]
Abstract
MAIN CONCLUSION Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.
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Affiliation(s)
| | - Luis Felipe Quiroz
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland.
| | - Rongling Wu
- Beijing Yanqi Lake Institute of Mathematical Sciences and Applications, Beijing, 101408, China
| | - Autar K Mattoo
- USDA-ARS, Sustainable Agricultural Systems Laboratory, Beltsville, MD, 20705-2350, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Sundsvagen, 10, Box 190, SE 23422, Lomma, Sweden.
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7
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Chen J, Wu W, Long J, Liu X, Hazlerigg D, Zhan X. The circannual clock: Empowering seasonal anticipation in organisms. Sci Bull (Beijing) 2024:S2095-9273(24)00104-X. [PMID: 38402031 DOI: 10.1016/j.scib.2024.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2024]
Affiliation(s)
- Junfeng Chen
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Long
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Liu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - David Hazlerigg
- Arctic Seasonal Timekeeping Initiative (ASTI), Department of Arctic and Marine Biology UiT, The Arctic University of Norway, Tromsø 9037, Norway
| | - Xiangjiang Zhan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Cardiff University - Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing 100101, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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8
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Gonzalez-Aponte MF, Damato AR, Trebucq LL, Simon T, Cárdenas-García SP, Cho K, Patti GJ, Golombek DA, Chiesa JJ, Rubin JB, Herzog ED. Circadian regulation of MGMT expression and promoter methylation underlies daily rhythms in TMZ sensitivity in glioblastoma. J Neurooncol 2024; 166:419-430. [PMID: 38277015 DOI: 10.1007/s11060-023-04535-9] [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: 09/13/2023] [Accepted: 12/07/2023] [Indexed: 01/27/2024]
Abstract
BACKGROUND Glioblastoma (GBM) is the most common primary brain tumor in adults. Despite extensive research and clinical trials, median survival post-treatment remains at 15 months. Thus, all opportunities to optimize current treatments and improve patient outcomes should be considered. A recent retrospective clinical study found that taking TMZ in the morning compared to the evening was associated with a 6-month increase in median survival in patients with MGMT-methylated GBM. Here, we hypothesized that TMZ efficacy depends on time-of-day and O6-Methylguanine-DNA Methyltransferase (MGMT) activity in murine and human models of GBM. METHODS AND RESULTS In vitro recordings using real-time bioluminescence reporters revealed that GBM cells have intrinsic circadian rhythms in the expression of the core circadian clock genes Bmal1 and Per2, as well as in the DNA repair enzyme, MGMT. Independent measures of MGMT transcript levels and promoter methylation also showed daily rhythms intrinsic to GBM cells. These cells were more susceptible to TMZ when delivered at the daily peak of Bmal1 transcription. We found that in vivo morning administration of TMZ also decreased tumor size and increased body weight compared to evening drug delivery in mice bearing GBM xenografts. Finally, inhibition of MGMT activity with O6-Benzylguanine abrogated the daily rhythm in sensitivity to TMZ in vitro by increasing sensitivity at both the peak and trough of Bmal1 expression. CONCLUSION We conclude that chemotherapy with TMZ can be dramatically enhanced by delivering at the daily maximum of tumor Bmal1 expression and minimum of MGMT activity and that scoring MGMT methylation status requires controlling for time of day of biopsy.
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Affiliation(s)
| | - Anna R Damato
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Laura Lucía Trebucq
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Tatiana Simon
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Kevin Cho
- Departments of Chemistry and Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J Patti
- Departments of Chemistry and Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
| | - Diego A Golombek
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés, B1644BID, Victoria, Buenos Aires, Argentina
| | - Juan José Chiesa
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, Buenos Aires, Argentina
| | - Joshua B Rubin
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO, USA
| | - Erik D Herzog
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
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9
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Wu Y, Zhong M, Yin J, Ou W, Zhuang Y, Zhang N, Lin S, Zhu Y. A novel small-animal locomotor activity recording device for biological clock research. Animal Model Exp Med 2024; 7:71-76. [PMID: 38375555 PMCID: PMC10961864 DOI: 10.1002/ame2.12381] [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: 09/03/2023] [Accepted: 12/14/2023] [Indexed: 02/21/2024] Open
Abstract
The rodent running-wheel recording apparatus is a reliable approach for studying circadian rhythm. This study demonstrated how to construct a simple and intelligent running-wheel recording system. The running wheel was attached to the cage's base, whereas the Hall sensor was attached to the cage's cover. Then, the RJ25 adaptor relayed the running signal to the main control board. Finally, the main control board was connected to the USB port of the computer with the USB connection. Data were collected using the online-accessible, self-created software Magturning. Through Magturning, generated data were saved and exported in real time. Afterward, the device was validated by collecting data on the locomotor activities of mice under different light conditions. In conclusion, this new device can record circadian activity of rodents. Our device is appropriate for interdisciplinary investigations related to biological clock research.
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Affiliation(s)
- Yi‐Long Wu
- Endoscopy CenterThe First Affiliated Hospital, Fujian Medical UniversityFuzhouChina
| | - Ming Zhong
- Department of EndocrinologyThe First Affiliated Hospital, Fujian Medical UniversityFuzhouChina
| | - Jun Yin
- Chuangke Workshop Technology Co., LtdShenzhenChina
| | - Wei‐Jie Ou
- Department of Digestive NutritionFujian Children's HospitalFuzhouChina
| | - Yu‐Bin Zhuang
- Experimental Animal CenterFujian Medical UniversityFuzhouChina
| | - Nan‐Wen Zhang
- Department of PharmacologyFujian Medical UniversityFuzhouChina
| | - Su Lin
- Department of Hepatology, Hepatology Research Institute, Clinical Research Center for Liver and Intestinal Diseases of Fujian ProvinceThe First Affiliated Hospital, Fujian Medical UniversityFuzhouChina
| | - Yue‐Yong Zhu
- Department of Hepatology, Hepatology Research Institute, Clinical Research Center for Liver and Intestinal Diseases of Fujian ProvinceThe First Affiliated Hospital, Fujian Medical UniversityFuzhouChina
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10
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Chen YC, Wang WS, Lewis SJG, Wu SL. Fighting Against the Clock: Circadian Disruption and Parkinson's Disease. J Mov Disord 2024; 17:1-14. [PMID: 37989149 PMCID: PMC10846969 DOI: 10.14802/jmd.23216] [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: 10/19/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 11/23/2023] Open
Abstract
Circadian disruption is being increasingly recognized as a critical factor in the development and progression of Parkinson's disease (PD). This review aims to provide an in-depth overview of the relationship between circadian disruption and PD by exploring the molecular, cellular, and behavioral aspects of this interaction. This review will include a comprehensive understanding of how the clock gene system and transcription-translation feedback loops function and how they are diminished in PD. The article also discusses the role of clock genes in the regulation of circadian rhythms, as well as the impact of clock gene dysregulation on mitochondrial function, oxidative stress, and neuroinflammation, including the microbiota-gut-brain axis, which have all been proposed as being crucial mechanisms in the pathophysiology of PD. Finally, this review highlights potential therapeutic strategies targeting the clock gene system and circadian rhythm for the treatment of PD.
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Affiliation(s)
- Yen-Chung Chen
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Wei-Sheng Wang
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Simon J G Lewis
- Brain and Mind Centre, School of Medical Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, National Changhua University of Education, Changhua, Taiwan
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11
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Maruko A, Iijima KM, Ando K. Dissecting the daily feeding pattern: Peripheral CLOCK/CYCLE generate the feeding/fasting episodes and neuronal molecular clocks synchronize them. iScience 2023; 26:108164. [PMID: 37915609 PMCID: PMC10616324 DOI: 10.1016/j.isci.2023.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 06/06/2023] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
A 24-h rhythm of feeding behavior, or synchronized feeding/fasting episodes during the day, is crucial for survival. Internal clocks and light input regulate rhythmic behaviors, but how they generate feeding rhythms is not fully understood. Here we aimed to dissect the molecular pathways that generate daily feeding patterns. By measuring the semidiurnal amount of food ingested by single flies, we demonstrate that the generation of feeding rhythms under light:dark conditions requires quasimodo (qsm) but not molecular clocks. Under constant darkness, rhythmic feeding patterns consist of two components: CLOCK (CLK) in digestive/metabolic tissues generating feeding/fasting episodes, and the molecular clock in neurons synchronizing them to subjective daytime. Although CLK is a part of the molecular clock, the generation of feeding/fasting episodes by CLK in metabolic tissues was independent of molecular clock machinery. Our results revealed novel functions of qsm and CLK in feeding rhythms in Drosophila.
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Affiliation(s)
- Akiko Maruko
- Department of Neuroscience, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Koichi M. Iijima
- Department of Neurogenetics, National Center for Geriatrics and Gerontology, Obu, Aichi 474-8511, Japan
- Department of Experimental Gerontology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi 467-8603, Japan
| | - Kanae Ando
- Department of Biological Sciences, School of Science, Graduate School of Science, Tokyo Metropolitan University, Tokyo 192-0397, Japan
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12
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Gonzalez-Aponte MF, Damato AR, Trebucq LL, Simon T, Cárdenas-García SP, Cho K, Patti GJ, Golombek DA, Chiesa JJ, Herzog ED. Circadian regulation of MGMT expression and promoter methylation underlies daily rhythms in TMZ sensitivity in glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557630. [PMID: 37745358 PMCID: PMC10515960 DOI: 10.1101/2023.09.13.557630] [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
Background Glioblastoma (GBM) is the most common primary brain tumor in adults. Despite extensive research and clinical trials, median survival post-treatment remains at 15 months. Thus, all opportunities to optimize current treatments and improve patient outcomes should be considered. A recent retrospective clinical study found that taking TMZ in the morning compared to the evening was associated with a 6-month increase in median survival in patients with MGMT-methylated GBM. Here, we hypothesized that TMZ efficacy depends on time-of-day and O6-Methylguanine-DNA Methyltransferase (MGMT) activity in murine and human models of GBM. Methods and Results In vitro recordings using real-time bioluminescence reporters revealed that GBM cells have intrinsic circadian rhythms in the expression of the core circadian clock genes Bmal1 and Per2, as well as in the DNA repair enzyme, MGMT. Independent measures of MGMT transcript levels and promoter methylation also showed daily rhythms intrinsic to GBM cells. These cells were more susceptible to TMZ when delivered at the daily peak of Bmal1 transcription. We found that in vivo morning administration of TMZ also decreased tumor size and increased body weight compared to evening drug delivery in mice bearing GBM xenografts. Finally, inhibition of MGMT activity with O6-Benzylguanine abrogated the daily rhythm in sensitivity to TMZ in vitro by increasing sensitivity at both the peak and trough of Bmal1 expression. Conclusion We conclude that chemotherapy with TMZ can be dramatically enhanced by delivering at the daily maximum of tumor Bmal1 expression and minimum of MGMT activity.
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Affiliation(s)
- Maria F. Gonzalez-Aponte
- Department of Biology, Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Anna R. Damato
- Department of Biology, Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Laura Lucía Trebucq
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Tatiana Simon
- Department of Biology, Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Sandra P. Cárdenas-García
- Department of Biology, Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | - Kevin Cho
- Departments of Chemistry and Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
| | - Gary J. Patti
- Departments of Chemistry and Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Center for Metabolomics and Isotope Tracing, Washington University in St. Louis, St. Louis, MO, USA
| | - Diego A. Golombek
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, B1876BXD, Bernal, Buenos Aires, Argentina
- Laboratorio Interdisciplinario del Tiempo (LITERA), Universidad de San Andrés, Victoria, B1644BID, Buenos Aires, Argentina
| | - Juan José Chiesa
- Laboratorio de Cronobiología, Universidad Nacional de Quilmes-CONICET, B1876BXD, Bernal, Buenos Aires, Argentina
| | - Erik D. Herzog
- Department of Biology, Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
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13
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Géron A, Werner J, Wattiez R, Matallana-Surget S. Towards the discovery of novel molecular clocks in Prokaryotes. Crit Rev Microbiol 2023:1-13. [PMID: 37330701 DOI: 10.1080/1040841x.2023.2220789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 01/17/2023] [Accepted: 02/15/2023] [Indexed: 06/19/2023]
Abstract
Diel cycle is of enormous biological importance as it imposes daily oscillation in environmental conditions, which temporally structures most ecosystems. Organisms developed biological time-keeping mechanisms - circadian clocks - that provide a significant fitness advantage over competitors by optimising the synchronisation of their biological activities. While circadian clocks are ubiquitous in Eukaryotes, they are so far only characterised in Cyanobacteria within Prokaryotes. However, growing evidence suggests that circadian clocks are widespread in the bacterial and archaeal domains. As Prokaryotes are at the heart of crucial environmental processes and are essential to human health, unravelling their time-keeping systems provides numerous applications in medical research, environmental sciences, and biotechnology. In this review, we elaborate on how novel circadian clocks in Prokaryotes offer research and development perspectives. We compare and contrast the different circadian systems in Cyanobacteria and discuss about their evolution and taxonomic distribution. We necessarily provide an updated phylogenetic analysis of bacterial and archaeal species that harbour homologs of the main cyanobacterial clock components. Finally, we elaborate on new potential clock-controlled microorganisms that represent opportunities of ecological and industrial relevance in prokaryotic groups such as anoxygenic photosynthetic bacteria, methanogenic archaea, methanotrophs or sulphate-reducing bacteria.
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Affiliation(s)
- Augustin Géron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), University of Tübingen, Tübingen, Germany
| | - Ruddy Wattiez
- Proteomic and Microbiology Department, University of Mons, Mons, Belgium
| | - Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
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14
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Häfker NS, Andreatta G, Manzotti A, Falciatore A, Raible F, Tessmar-Raible K. Rhythms and Clocks in Marine Organisms. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:509-538. [PMID: 36028229 DOI: 10.1146/annurev-marine-030422-113038] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.
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Affiliation(s)
- N Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Alessandro Manzotti
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Angela Falciatore
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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15
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Chrononutrition-When We Eat Is of the Essence in Tackling Obesity. Nutrients 2022; 14:nu14235080. [PMID: 36501110 PMCID: PMC9739590 DOI: 10.3390/nu14235080] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Obesity is a chronic and relapsing public health problem with an extensive list of associated comorbidities. The worldwide prevalence of obesity has nearly tripled over the last five decades and continues to pose a serious threat to wider society and the wellbeing of future generations. The pathogenesis of obesity is complex but diet plays a key role in the onset and progression of the disease. The human diet has changed drastically across the globe, with an estimate that approximately 72% of the calories consumed today come from foods that were not part of our ancestral diets and are not compatible with our metabolism. Additionally, multiple nutrient-independent factors, e.g., cost, accessibility, behaviours, culture, education, work commitments, knowledge and societal set-up, influence our food choices and eating patterns. Much research has been focused on 'what to eat' or 'how much to eat' to reduce the obesity burden, but increasingly evidence indicates that 'when to eat' is fundamental to human metabolism. Aligning feeding patterns to the 24-h circadian clock that regulates a wide range of physiological and behavioural processes has multiple health-promoting effects with anti-obesity being a major part. This article explores the current understanding of the interactions between the body clocks, bioactive dietary components and the less appreciated role of meal timings in energy homeostasis and obesity.
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16
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The wheat clock strikes a balance across subgenomes to regulate gene expression. PLoS Biol 2022; 20:e3001825. [PMID: 36240153 PMCID: PMC9565369 DOI: 10.1371/journal.pbio.3001825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Increasing crop yields is complicated by the polyploid nature of our major crops. This Primer explores the implications of a PLOS Biology study that provides a transcriptomic view of the influence of the circadian clock on agriculturally relevant traits in the polyploid bread wheat.
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17
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Oravec MW, Greenham K. The adaptive nature of the plant circadian clock in natural environments. PLANT PHYSIOLOGY 2022; 190:968-980. [PMID: 35894658 PMCID: PMC9516730 DOI: 10.1093/plphys/kiac337] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/27/2022] [Indexed: 05/10/2023]
Abstract
The plant circadian clock coordinates developmental, physiological, and metabolic processes with diel changes in light and temperature throughout the year. The balance between the persistence and plasticity of the clock in response to predictable and unpredictable environmental changes may be key to the clock's adaptive nature across temporal and spatial scales. Studies under controlled conditions have uncovered critical signaling pathways involved in light and temperature perception by the clock; however, they don't account for the natural lag of temperature behind photoperiod. Studies in natural environments provide key insights into the clock's adaptive advantage under more complex natural settings. Here, we discuss the role of the circadian clock in light and temperature perception and signaling, how the clock integrates these signals for a coordinated and adaptive response, and the adaptive advantage conferred by the clock across time and space in natural environments.
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Affiliation(s)
- Madeline W Oravec
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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18
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Pun TB, Phillips CL, Marshall NS, Comas M, Hoyos CM, D’Rozario AL, Bartlett DJ, Davis W, Hu W, Naismith SL, Cain S, Postnova S, Grunstein RR, Gordon CJ. The Effect of Light Therapy on Electroencephalographic Sleep in Sleep and Circadian Rhythm Disorders: A Scoping Review. Clocks Sleep 2022; 4:358-373. [PMID: 35997384 PMCID: PMC9397048 DOI: 10.3390/clockssleep4030030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/21/2022] [Accepted: 08/02/2022] [Indexed: 01/27/2023] Open
Abstract
Light therapy is used to treat sleep and circadian rhythm disorders, yet there are limited studies on whether light therapy impacts electroencephalographic (EEG) activity during sleep. Therefore, we aimed to provide an overview of research studies that examined the effects of light therapy on sleep macro- and micro-architecture in populations with sleep and circadian rhythm disorders. We searched for randomized controlled trials that used light therapy and included EEG sleep measures using MEDLINE, PubMed, CINAHL, PsycINFO and Cochrane Central Register of Controlled Trials databases. Five articles met the inclusion criteria of patients with either insomnia or delayed sleep−wake phase disorder (DSWPD). These trials reported sleep macro-architecture outcomes using EEG or polysomnography. Three insomnia trials showed no effect of the timing or intensity of light therapy on total sleep time, wake after sleep onset, sleep efficiency and sleep stage duration compared to controls. Only one insomnia trial reported significantly higher sleep efficiency after evening light therapy (>4000 lx between 21:00−23:00 h) compared with afternoon light therapy (>4000 lx between 15:00−17:00 h). In the only DSWPD trial, six multiple sleep latency tests were conducted across the day (09:00 and 19:00 h) and bright light (2500 lx) significantly lengthened sleep latency in the morning (09:00 and 11:00 h) compared to control light (300 lx). None of the five trials reported any sleep micro-architecture measures. Overall, there was limited research about the effect of light therapy on EEG sleep measures, and studies were confined to patients with insomnia and DSWPD only. More research is needed to better understand whether lighting interventions in clinical populations affect sleep macro- and micro-architecture and objective sleep timing and quality.
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Affiliation(s)
- Teha B. Pun
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Craig L. Phillips
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Nathaniel S. Marshall
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Maria Comas
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Camilla M. Hoyos
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Angela L. D’Rozario
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Delwyn J. Bartlett
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
| | - Wendy Davis
- School of Architecture, Design and Planning, The University of Sydney, Sydney, NSW 2008, Australia
| | - Wenye Hu
- School of Architecture, Design and Planning, The University of Sydney, Sydney, NSW 2008, Australia
| | - Sharon L. Naismith
- Healthy Brain Ageing Program, Brain and Mind Centre, The University of Sydney, Sydney, NSW 2050, Australia
- School of Psychology, Faculty of Science, The University of Sydney, Sydney, NSW 2050, Australia
| | - Sean Cain
- School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, VIC 3800, Australia
| | - Svetlana Postnova
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- School of Physics, Faculty of Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Ron R. Grunstein
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Sleep and Severe Mental Illness Clinic, CPC-RPA Clinic, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Christopher J. Gordon
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia
- CIRUS, Centre for Sleep and Chronobiology, Woolcock Institute of Medical Research, Sydney, NSW 2037, Australia
- Correspondence: ; Tel.: +61-2-9351-0586
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19
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Perez-Garcia P, Serrano-Ron L, Moreno-Risueno MA. The nature of the root clock at single cell resolution: Principles of communication and similarities with plant and animal pulsatile and circadian mechanisms. Curr Opin Cell Biol 2022; 77:102102. [DOI: 10.1016/j.ceb.2022.102102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/14/2022] [Accepted: 04/24/2022] [Indexed: 11/30/2022]
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20
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Muranaka T, Ito S, Kudoh H, Oyama T. Circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis. iScience 2022; 25:104634. [PMID: 35800759 PMCID: PMC9253726 DOI: 10.1016/j.isci.2022.104634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/27/2022] [Accepted: 06/13/2022] [Indexed: 11/29/2022] Open
Abstract
Phenotypic variation is the basis for trait adaptation via evolutionary selection. However, the driving forces behind quantitative trait variations remain unclear owing to their complexity at the molecular level. This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the phase phenotype of clock-dependent physiology. Lemna aequinoctialis in Japan is a paddy field duckweed that exhibits a latitudinal cline of critical day length (CDL) for short-day flowering. We collected 72 strains of L. aequinoctialis and found a significant correlation between FRPs and locally adaptive CDLs, confirming that variation in the FRP-dependent phase phenotype underlies photoperiodic adaptation. Diel transcriptome analysis revealed that the induction timing of an FT gene is key to connecting the clock phase to photoperiodism at the molecular level. This study highlights the importance of FRP as a variation resource for evolutionary adaptation. Natural variation of flowering/circadian traits in a paddy-field duckweed is studied. Critical day length for flowering of the duckweed in Japan shows a latitudinal cline. A negative correlation between critical day length and circadian period was found. An FT gene responding to lengthening of the dark period was isolated.
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21
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Nelson RJ, Bumgarner JR, Liu JA, Love JA, Meléndez-Fernández OH, Becker-Krail DD, Walker WH, Walton JC, DeVries AC, Prendergast BJ. Time of day as a critical variable in biology. BMC Biol 2022; 20:142. [PMID: 35705939 PMCID: PMC9202143 DOI: 10.1186/s12915-022-01333-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/17/2022] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Circadian rhythms are important for all aspects of biology; virtually every aspect of biological function varies according to time of day. Although this is well known, variation across the day is also often ignored in the design and reporting of research. For this review, we analyzed the top 50 cited papers across 10 major domains of the biological sciences in the calendar year 2015. We repeated this analysis for the year 2019, hypothesizing that the awarding of a Nobel Prize in 2017 for achievements in the field of circadian biology would highlight the importance of circadian rhythms for scientists across many disciplines, and improve time-of-day reporting. RESULTS Our analyses of these 1000 empirical papers, however, revealed that most failed to include sufficient temporal details when describing experimental methods and that few systematic differences in time-of-day reporting existed between 2015 and 2019. Overall, only 6.1% of reports included time-of-day information about experimental measures and manipulations sufficient to permit replication. CONCLUSIONS Circadian rhythms are a defining feature of biological systems, and knowing when in the circadian day these systems are evaluated is fundamentally important information. Failing to account for time of day hampers reproducibility across laboratories, complicates interpretation of results, and reduces the value of data based predominantly on nocturnal animals when extrapolating to diurnal humans.
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Affiliation(s)
- Randy J Nelson
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA.
| | - Jacob R Bumgarner
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - Jennifer A Liu
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - Jharnae A Love
- Department of Psychology, University of Chicago and Institute for Mind and Biology, IL, 60637, Chicago, USA
| | - O Hecmarie Meléndez-Fernández
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - Darius D Becker-Krail
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - William H Walker
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - James C Walton
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - A Courtney DeVries
- Department of Neuroscience, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
- Department of Medicine, Rockefeller Neuroscience Institute, West Virginia University, Morgantown, WV, 26505, USA
| | - Brian J Prendergast
- Department of Psychology, University of Chicago and Institute for Mind and Biology, IL, 60637, Chicago, USA
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Haj Darwich CM, Chrzanowski MM, Bernatowicz PP, Polanska MA, Joachimiak E, Bebas P. Molecular Oscillator Affects Susceptibility of Caterpillars to Insecticides: Studies on the Egyptian Cotton Leaf Worm- Spodoptera littoralis (Lepidoptera: Noctuidae). INSECTS 2022; 13:insects13050488. [PMID: 35621821 PMCID: PMC9147166 DOI: 10.3390/insects13050488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
The molecular oscillator is the core of the biological clock and is formed by genes and proteins whose cyclic expression is regulated in the transcriptional-translational feedback loops (TTFLs). Proteins of the TTFLs are regulators of both their own and executive genes involved in the control of many processes in insects (e.g., rhythmic metabolism of xenobiotics, including insecticides). We disrupted the clock operation in S. littoralis larvae by injecting the dsRNA of clock genes into their body cavity and culturing the larvae under continuous light. As a result, the daily susceptibility of larvae to insecticides was abolished and the susceptibility itself increased (in most cases). In the fat body, midgut, and Malpighian tubules (the main organs metabolizing xenobiotics) of the larvae treated with injected-dsRNA, the daily activity profiles of enzymes involved in detoxification-cytochrome P450 monooxygenases, Glutathione-S-transferase, and esterase-have changed significantly. The presented results prove the role of the molecular oscillator in the regulation of larvae responses to insecticides and provide grounds for rational use of these compounds (at suitable times of the day), and may indicate clock genes as potential targets of molecular manipulation to produce plant protection compounds based on the RNAi method.
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Affiliation(s)
- Choukri M. Haj Darwich
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (C.M.H.D.); (P.P.B.); (M.A.P.)
| | - Marcin M. Chrzanowski
- Biology Teaching Laboratory, Faculty’s Independent Centers, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Piotr P. Bernatowicz
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (C.M.H.D.); (P.P.B.); (M.A.P.)
| | - Marta A. Polanska
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (C.M.H.D.); (P.P.B.); (M.A.P.)
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology PAS, 02-093 Warsaw, Poland;
| | - Piotr Bebas
- Department of Animal Physiology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (C.M.H.D.); (P.P.B.); (M.A.P.)
- Correspondence: ; Tel.: +48-22-554-1030
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Lee S, Hong CI. Organoids as Model Systems to Investigate Circadian Clock-Related Diseases and Treatments. Front Genet 2022; 13:874288. [PMID: 35559029 PMCID: PMC9086274 DOI: 10.3389/fgene.2022.874288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Circadian rhythms exist in most cell types in mammals regulating temporal organization of numerous cellular and physiological processes ranging from cell cycle to metabolism. The master clock, suprachiasmatic nucleus (SCN) in the hypothalamus, processes light input and coordinates peripheral clocks optimizing organisms' survival and functions aligning with external conditions. Intriguingly, it was demonstrated that circadian rhythms in the mouse liver can be decoupled from the master clock under time-restricted feeding regimen when food was provided during their inactive phase. Furthermore, mouse liver showed clock-controlled gene expression even in the absence of the master clock demonstrating independent functions of peripheral clocks apart from the SCN. These findings suggest a dynamic relationship between the master and peripheral clocks and highlight potential functions of peripheral clocks independent of the master clock. Importantly, disruption of circadian rhythms correlates with numerous human ailments including cancer and metabolic diseases, suggesting that diseases may be exacerbated by disruption of circadian rhythms in the SCN and/or peripheral clocks. However, molecular mechanisms providing causative links between circadian rhythms and human diseases remain largely unknown. Recent technical advances highlighted PCS- and tissue-derived 3-dimensional organoids as in vitro organs that possess numerous applications ranging from disease modeling to drug screening. In this mini-review, we highlight recent findings on the importance and contributions of peripheral clocks and potential uses of 3D organoids investigating complex circadian clock-related diseases.
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Affiliation(s)
| | - Christian I. Hong
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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Venkat A, Muneer S. Role of Circadian Rhythms in Major Plant Metabolic and Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2022; 13:836244. [PMID: 35463437 PMCID: PMC9019581 DOI: 10.3389/fpls.2022.836244] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/23/2022] [Indexed: 05/10/2023]
Abstract
Plants require an endogenous regulatory network and mechanism to cope with diurnal environmental changes and compensate for their sessile nature. Plants use the circadian clock to anticipate diurnal changes. Circadian rhythm predicts a 24-h cycle with 16 h of light and 8 h of darkness in response to abiotic and biotic factors as well as the appropriate temperature. For a plant's fitness, proper growth, and development, these rhythms synchronize the diurnal photoperiodic changes. Input pathway, central oscillator, and output pathway are the three components that make up the endogenous clock. There are also transcriptional and translational feedback loops (TTFLs) in the clock, which are dependent on the results of gene expression. Several physiological processes, such as stress acclimatization, hormone signaling, morphogenesis, carbon metabolism, and defense response, are currently being investigated for their interactions with the circadian clock using phenotypic, genomic, and metabolic studies. This review examines the role of circadian rhythms in the regulation of plant metabolic pathways, such as photosynthesis and carbon metabolism, as well as developmental and degenerative processes, such as flowering and senescence. Furthermore, we summarized signaling pathways related to circadian rhythms, such as defense response and gene regulatory pathways.
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Affiliation(s)
- Ajila Venkat
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Sowbiya Muneer
- Horticulture and Molecular Physiology Lab, School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
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Yang C, Hwang C, Tsai N, Yang M. Expression of circadian clock genes in leukocytes of patients with Meniere's disease. Laryngoscope Investig Otolaryngol 2022; 7:584-591. [PMID: 35434324 PMCID: PMC9008173 DOI: 10.1002/lio2.757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
Objectives The underlying etiology of Meniere's disease (MD) is not completely clear, but the precipitated triggers may alter the circadian clock in patients with MD. This study aims to survey the expression of circadian clock genes in peripheral blood (PB) leukocytes of MD patients. Methods We investigated the expression of nine circadian clock genes in the PB leukocytes of patients with MD and normal controls using real‐time quantitative reverse transcriptase‐polymerase chain reaction (qRT‐PCR). Results We observed significantly lower expression of PER1 gene and higher expression of CLOCK gene in MD patients than those in normal controls (p < 0.05). PER1 did not associate with the degree of dizziness handicap in the patients with MD, but a lower expression of PER1 was significantly correlated with higher pure tone average (PTA) and speech reception threshold of the affected ear (p < 0.05). Patients with PTA > 30 dB had significantly lower PER1 expression than those with PTA ≤30 dB in the affected ear (p < 0.05). Our qRT‐PCR result was validated by fewer positively stained leukocytes for PER1 protein in the MD patients using the immunocytochemical study. Conclusion Our study implies the alteration of the circadian clock in patients with MD. In particular, the downregulation of PER1 correlated with the degree of hearing loss in the affected ear. PER1 in PB leukocytes may be a potential marker for the progression of hearing loss in MD.
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Affiliation(s)
- Chao‐Hui Yang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Chung‐Feng Hwang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Nai‐Wen Tsai
- Department of Neurology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
| | - Ming‐Yu Yang
- Department of Otolaryngology Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung Taiwan
- Graduate Institute of Clinical Medical Sciences College of Medicine, Chang Gung University Tao‐Yuan Taiwan
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26
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Menéndez-Velázquez A, Morales D, García-Delgado AB. Light Pollution and Circadian Misalignment: A Healthy, Blue-Free, White Light-Emitting Diode to Avoid Chronodisruption. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19031849. [PMID: 35162871 PMCID: PMC8835293 DOI: 10.3390/ijerph19031849] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 02/07/2023]
Abstract
Sunlight has participated in the development of all life forms on Earth. The micro-world and the daily rhythms of plants and animals are strongly regulated by the light-dark rhythm. Human beings have followed this pattern for thousands of years. The discovery and development of artificial light sources eliminated the workings of this physiological clock. The world's current external environment is full of light pollution. In many electrical light bulbs used today and considered "environmentally friendly," such as LED devices, electrical energy is converted into short-wavelength illumination that we have not experienced in the past. Such illumination effectively becomes "biological light pollution" and disrupts our pineal melatonin production. The suppression of melatonin at night alters our circadian rhythms (biological rhythms with a periodicity of 24 h). This alteration is known as chronodisruption and is associated with numerous diseases. In this article, we present a blue-free WLED (white light-emitting diode) that can avoid chronodisruption and preserve circadian rhythms. This WLED also maintains the spectral quality of light measured through parameters such as CRI (color reproduction index).
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27
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Tacad DKM, Tovar AP, Richardson CE, Horn WF, Keim NL, Krishnan GP, Krishnan S. Satiety Associated with Calorie Restriction and Time-Restricted Feeding: Central Neuroendocrine Integration. Adv Nutr 2022; 13:758-791. [PMID: 35134815 PMCID: PMC9156369 DOI: 10.1093/advances/nmac011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/08/2021] [Accepted: 02/02/2022] [Indexed: 02/06/2023] Open
Abstract
This review focuses on summarizing current knowledge on how time-restricted feeding (TRF) and continuous caloric restriction (CR) affect central neuroendocrine systems involved in regulating satiety. Several interconnected regions of the hypothalamus, brainstem, and cortical areas of the brain are involved in the regulation of satiety. Following CR and TRF, the increase in hunger and reduction in satiety signals of the melanocortin system [neuropeptide Y (NPY), proopiomelanocortin (POMC), and agouti-related peptide (AgRP)] appear similar between CR and TRF protocols, as do the dopaminergic responses in the mesocorticolimbic circuit. However, ghrelin and leptin signaling via the melanocortin system appears to improve energy balance signals and reduce hyperphagia following TRF, which has not been reported in CR. In addition to satiety systems, CR and TRF also influence circadian rhythms. CR influences the suprachiasmatic nucleus (SCN) or the primary circadian clock as seen by increased clock gene expression. In contrast, TRF appears to affect both the SCN and the peripheral clocks, as seen by phasic changes in the non-SCN (potentially the elusive food entrainable oscillator) and metabolic clocks. The peripheral clocks are influenced by the primary circadian clock but are also entrained by food timing, sleep timing, and other lifestyle parameters, which can supersede the metabolic processes that are regulated by the primary circadian clock. Taken together, TRF influences hunger/satiety, energy balance systems, and circadian rhythms, suggesting a role for adherence to CR in the long run if implemented using the TRF approach. However, these suggestions are based on only a few studies, and future investigations that use standardized protocols for the evaluation of the effect of these diet patterns (time, duration, meal composition, sufficiently powered) are necessary to verify these preliminary observations.
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Affiliation(s)
- Debra K M Tacad
- Obesity and Metabolism Research Unit, USDA–Western Human Nutrition Research Center, Davis, CA, USA,Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Ashley P Tovar
- Department of Nutrition, University of California, Davis, Davis, CA, USA
| | | | - William F Horn
- Obesity and Metabolism Research Unit, USDA–Western Human Nutrition Research Center, Davis, CA, USA
| | - Nancy L Keim
- Obesity and Metabolism Research Unit, USDA–Western Human Nutrition Research Center, Davis, CA, USA,Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Giri P Krishnan
- Department of Medicine, School of Medicine, University of California, San Diego, San Diego, CA, USA
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Rosi-Andersen A, Meister L, Graham B, Brown S, Bryant R, Ehlers A, Kleim B. Circadian influence on intrusive re-experiencing in trauma survivors' daily lives. Eur J Psychotraumatol 2022; 13:1899617. [PMID: 35295874 PMCID: PMC8920362 DOI: 10.1080/20008198.2021.1899617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The core clinical feature of posttraumatic stress disorder (PTSD) is recurrent re-experiencing in form of intrusive memories. While a great number of biological processes are regulated by sleep and internal biological clocks, the effect of 24-hour biological cycles, named circadian rhythm, has not been investigated in the context of intrusive memories. OBJECTIVE Here we examined effects of time of day on frequency and characteristics of intrusive re-experiencing. METHODS Fifty trauma survivors reported intrusive memories for 7 consecutive days using ecological momentary assessment in their daily life. We investigated (i) time-of-day dependent effects on frequency and distribution of intrusive re-experiencing in the overall sample as well as in PTSD versus non-PTSD and (ii) time-of-day dependent effects on the memory characteristics intrusiveness, vividness, nowness and fear. RESULTS Intrusive memories showed a curvilinear pattern that peaked at 2pm. Intrusive memories in the PTSD group showed a constant level of intrusive re-experiencing in the afternoon and evening, whereas a descending slope was present in the non-PTSD group. In PTSD, intrusive memories might thus be experienced in a more time-scattered fashion throughout the day, indicating chronodisruption. Intrusion characteristics did not follow this pattern. CONCLUSION Although preliminary and based on a small sample size, these findings contribute to a better understanding of the everyday occurrence and characteristics of intrusive memories, and point to the added value of examining time-dependent effects, which can directly inform prevention and intervention science.
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Affiliation(s)
- Alex Rosi-Andersen
- Department of Psychology, University of Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, Zurich, Switzerland.,Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Laura Meister
- Department of Psychology, University of Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, Zurich, Switzerland
| | - Belinda Graham
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - Steven Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Richard Bryant
- School of Psychology, University of New South Wales, Sydney, Australia
| | - Anke Ehlers
- Department of Experimental Psychology, University of Oxford, Oxford, UK
| | - Birgit Kleim
- Department of Psychology, University of Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, Psychiatric University Hospital Zurich, Zurich, Switzerland
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Simon D, Mukaiyama A, Furuike Y, Akiyama S. Slow and temperature-compensated autonomous disassembly of KaiB–KaiC complex. Biophys Physicobiol 2022; 19:1-11. [PMID: 35666689 PMCID: PMC9135616 DOI: 10.2142/biophysico.bppb-v19.0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Damien Simon
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences
| | - Atsushi Mukaiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences
| | - Yoshihiko Furuike
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences
| | - Shuji Akiyama
- Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences
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Rawlinson KA, Reid AJ, Lu Z, Driguez P, Wawer A, Coghlan A, Sankaranarayanan G, Buddenborg SK, Soria CD, McCarthy C, Holroyd N, Sanders M, Hoffmann KF, Wilcockson D, Rinaldi G, Berriman M. Daily rhythms in gene expression of the human parasite Schistosoma mansoni. BMC Biol 2021; 19:255. [PMID: 34852797 PMCID: PMC8638415 DOI: 10.1186/s12915-021-01189-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/10/2021] [Indexed: 12/13/2022] Open
Abstract
Background The consequences of the earth’s daily rotation have led to 24-h biological rhythms in most organisms. Even some parasites are known to have daily rhythms, which, when in synchrony with host rhythms, can optimise their fitness. Understanding these rhythms may enable the development of control strategies that take advantage of rhythmic vulnerabilities. Recent work on protozoan parasites has revealed 24-h rhythms in gene expression, drug sensitivity and the presence of an intrinsic circadian clock; however, similar studies on metazoan parasites are lacking. To address this, we investigated if a metazoan parasite has daily molecular oscillations, whether they reveal how these longer-lived organisms can survive host daily cycles over a lifespan of many years and if animal circadian clock genes are present and rhythmic. We addressed these questions using the human blood fluke Schistosoma mansoni that lives in the vasculature for decades and causes the tropical disease schistosomiasis. Results Using round-the-clock transcriptomics of male and female adult worms collected from experimentally infected mice, we discovered that ~ 2% of its genes followed a daily pattern of expression. Rhythmic processes included a stress response during the host’s active phase and a ‘peak in metabolic activity’ during the host’s resting phase. Transcriptional profiles in the female reproductive system were mirrored by daily patterns in egg laying (eggs are the main drivers of the host pathology). Genes cycling with the highest amplitudes include predicted drug targets and a vaccine candidate. These 24-h rhythms may be driven by host rhythms and/or generated by a circadian clock; however, orthologs of core clock genes are missing and secondary clock genes show no 24-h rhythmicity. Conclusions There are daily rhythms in the transcriptomes of adult S. mansoni, but they appear less pronounced than in other organisms. The rhythms reveal temporally compartmentalised internal processes and host interactions relevant to within-host survival and between-host transmission. Our findings suggest that if these daily rhythms are generated by an intrinsic circadian clock then the oscillatory mechanism must be distinct from that in other animals. We have shown which transcripts oscillate at this temporal scale and this will benefit the development and delivery of treatments against schistosomiasis. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01189-9.
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Affiliation(s)
| | - Adam J Reid
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Zhigang Lu
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick Driguez
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.,King Abdullah University of Science and Technology, Thuwal, Makkah, Saudi Arabia
| | - Anna Wawer
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Avril Coghlan
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | | | | | | | - Nancy Holroyd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Mandy Sanders
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Karl F Hoffmann
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - David Wilcockson
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Gabriel Rinaldi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
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Lin J, Yu Z, Ye C, Hong L, Chu Y, Shen Y, Li QQ. Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis. RNA Biol 2021; 18:2594-2604. [PMID: 34036876 PMCID: PMC8632115 DOI: 10.1080/15476286.2021.1933732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/03/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
Alternative polyadenylation (APA) is a widespread post-transcriptional modification method that changes the 3' ends of transcripts by altering poly(A) site usage. However, the longitudinal transcriptomic 3' end profile and its mechanism of action are poorly understood. We applied diurnal time-course poly(A) tag sequencing (PAT-seq) for Arabidopsis and identified 3284 genes that generated both rhythmic and arrhythmic transcripts. These two classes of transcripts appear to exhibit dramatic differences in expression and translation activisty. The asynchronized transcripts derived by APA are embedded with different poly(A) signals, especially for rhythmic transcripts, which contain higher AAUAAA and UGUA signal proportions. The Pol II occupancy maximum is reached upstream of rhythmic poly(A) sites, while it is present directly at arrhythmic poly(A) sites. Integrating H3K9ac and H3K4me3 time-course data analyses revealed that transcriptional activation of histone markers may be involved in the differentiation of rhythmic and arrhythmic APA transcripts. These results implicate an interplay between histone modification and RNA 3'-end processing, shedding light on the mechanism of transcription rhythm and alternative polyadenylation.
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Affiliation(s)
- Juncheng Lin
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yiru Chu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, USA
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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Shen X, Yan H, Jiang J, Li W, Xiong Y, Liu Q, Liu Y. Profile of gene expression changes during estrodiol-17β-induced feminization in the Takifugu rubripes brain. BMC Genomics 2021; 22:851. [PMID: 34819041 PMCID: PMC8614003 DOI: 10.1186/s12864-021-08158-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background As the critical tissue of the central nervous system, the brain has been found to be involved in gonad development. Previous studies have suggested that gonadal fate may be affected by the brain. Identifying brain-specific molecular changes that occur during estrodiol-17β (E2) -induced feminization is crucial to our understanding of the molecular control of sex differentiation by the brains of fish. Results In this study, the differential transcriptomic responses of the Takifugu rubripes larvae brain were compared after E2 treatment for 55 days. Our results showed that 514 genes were differentially expressed between E2-treated-XX (E-XX) and Control-XX (C-XX) T. rubripes, while 362 genes were differentially expressed between E2-treated-XY (E-XY) and Control-XY (C-XY). For example, the expression of cyp19a1b, gnrh1 and pgr was significantly up-regulated, while st, sl, tshβ, prl and pit-1, which belong to the growth hormone/prolactin family, were significantly down-regulated after E2 treatment, in both sexes. The arntl1, bhlbe, nr1d2, per1b, per3, cry1, cipc and ciart genes, which are involved in the circadian rhythm, were also found to be altered. Differentially expressed genes (DEGs), which were identified between E-XX and C-XX, were significantly enriched in neuroactive ligand-receptor interaction, arachidonic acid metabolism, cytokine-cytokine receptor interaction and the calcium signaling pathway. The DEGs that were identified between E-XY and C-XY were significantly enriched in tyrosine metabolism, phenylalanine metabolism, arachidonic acid metabolism and linoleic acid metabolism. Conclusion A number of genes and pathways were identified in the brain of E2-treated T. rubripes larvae by RNA-seq. It provided the opportunity for further study on the possible involvement of networks in the brain-pituitary-gonadal axis in sex differentiation in T. rubripes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08158-0.
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Affiliation(s)
- Xufang Shen
- College of Life Sciences, Liaoning Normal University, Dalian, 116029, Liaoning, China.,Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China
| | - Hongwei Yan
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China.
| | - Jieming Jiang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China.,College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Weiyuan Li
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Yuyu Xiong
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China.,College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, Liaoning, China
| | - Qi Liu
- College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, Liaoning, China.
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, Dalian, 116023, China.,College of Marine Science and Environment Engineering, Dalian Ocean University, Dalian, 116023, Liaoning, China
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Yan J, Li S, Kim YJ, Zeng Q, Radziejwoski A, Wang L, Nomura Y, Nakagami H, Somers DE. TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth. EMBO J 2021; 40:e108684. [PMID: 34726281 DOI: 10.15252/embj.2021108684] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/09/2022] Open
Abstract
Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.
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Affiliation(s)
- Jiapei Yan
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Shibai Li
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,Memorial Sloan Kettering Cancer Center, Molecular Biology Program, New York, NY, USA
| | - Yeon Jeong Kim
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | - Qingning Zeng
- Molecular Genetics, Ohio State University, Columbus, OH, USA
| | | | - Lei Wang
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,The Chinese Academy of Sciences, Institute of Botany, Beijing, China
| | - Yuko Nomura
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan
| | - Hirofumi Nakagami
- RIKEN Center for Sustainable Resource Science (CSRS), Plant Proteomics Research Unit, Yokohama, Japan.,Max Planck Institute for Plant Breeding Research, Protein Mass Spectrometry, Cologne, Germany
| | - David E Somers
- Molecular Genetics, Ohio State University, Columbus, OH, USA.,POSTECH, Division of Integrative Biosciences and Biotechnology, Pohang, South Korea
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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36
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Wang XL, Li L. Circadian Clock Regulates Inflammation and the Development of Neurodegeneration. Front Cell Infect Microbiol 2021; 11:696554. [PMID: 34595127 PMCID: PMC8476957 DOI: 10.3389/fcimb.2021.696554] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
The circadian clock regulates numerous key physiological processes and maintains cellular, tissue, and systemic homeostasis. Disruption of circadian clock machinery influences key activities involved in immune response and brain function. Moreover, Immune activation has been closely linked to neurodegeneration. Here, we review the molecular clock machinery and the diurnal variation of immune activity. We summarize the circadian control of immunity in both central and peripheral immune cells, as well as the circadian regulation of brain cells that are implicated in neurodegeneration. We explore the important role of systemic inflammation on neurodegeneration. The circadian clock modulates cellular metabolism, which could be a mechanism underlying circadian control. We also discuss the circadian interventions implicated in inflammation and neurodegeneration. Targeting circadian clocks could be a potential strategy for the prevention and treatment of inflammation and neurodegenerative diseases.
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Affiliation(s)
- Xiao-Lan Wang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lianjian Li
- Department of Surgery, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, China.,Hubei Province Academy of Traditional Chinese Medicine, Wuhan, China
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37
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Markham KK, Greenham K. Abiotic stress through time. THE NEW PHYTOLOGIST 2021; 231:40-46. [PMID: 33780004 DOI: 10.1111/nph.17367] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Throughout plant evolution the circadian clock has expanded into a complex signaling network, coordinating physiological and metabolic processes with the environment. Early land plants faced new environmental pressures that required energy-demanding stress responses. Integrating abiotic stress response into the circadian system provides control over daily energy expenditure. Here, we describe the evolution of the circadian clock in plants and the limited, yet compelling, evidence for conserved regulation of abiotic stress. The need to introduce abiotic stress tolerance into current crops has expanded research into wild accessions and revealed extensive variation in circadian clock parameters across monocot and eudicot species. We argue that research into the ancestral links between the clock and abiotic stress will benefit crop improvement efforts.
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Affiliation(s)
- Kathleen K Markham
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Kathleen Greenham
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, 55108, USA
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38
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Matchen TD, Moehlis J. Leveraging deep learning to control neural oscillators. BIOLOGICAL CYBERNETICS 2021; 115:219-235. [PMID: 33909165 DOI: 10.1007/s00422-021-00874-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Modulation of the firing times of neural oscillators has long been an important control objective, with applications including Parkinson's disease, Tourette's syndrome, epilepsy, and learning. One common goal for such modulation is desynchronization, wherein two or more oscillators are stimulated to transition from firing in phase with each other to firing out of phase. The optimization of such stimuli has been well studied, but this typically relies on either a reduction of the dimensionality of the system or complete knowledge of the parameters and state of the system. This limits the applicability of results to real problems in neural control. Here, we present a trained artificial neural network capable of accurately estimating the effects of square-wave stimuli on neurons using minimal output information from the neuron. We then apply the results of this network to solve several related control problems in desynchronization, including desynchronizing pairs of neurons and achieving clustered subpopulations of neurons in the presence of coupling and noise.
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Affiliation(s)
- Timothy D Matchen
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, 93106, USA.
| | - Jeff Moehlis
- Department of Mechanical Engineering, Program in Dynamical Neuroscience, University of California, Santa Barbara, CA, 93106, USA
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39
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Björk V. Aging of the Suprachiasmatic Nucleus, CIRCLONSA Syndrome, Implications for Regenerative Medicine and Restoration of the Master Body Clock. Rejuvenation Res 2021; 24:274-282. [PMID: 33573456 DOI: 10.1089/rej.2020.2388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The suprachiasmatic nucleus (SCN) in the brain is the master regulator of the circadian clocks throughout the human body. With increasing age the circadian clock in humans and other mammals becomes increasingly disorganized leading to a large number of more or less well-categorized problems. While a lot of aging research has focused on the peripheral clocks in tissues across organisms, it remains a paramount task to quantify aging of the most important master clock, the human SCN. Furthermore, a pipeline needs to be developed with therapies to mitigate the systemic cellular circadian dysfunction in the elderly and ultimately repair and reverse aging of the SCN itself. A disease classification for the aging SCN, Circadian Clock Neuronal Senile Atrophy (CIRCLONSA syndrome), would improve research funding and goal-oriented biotechnological entrepreneurship.
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40
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Parnell AA, De Nobrega AK, Lyons LC. Translating around the clock: Multi-level regulation of post-transcriptional processes by the circadian clock. Cell Signal 2021; 80:109904. [PMID: 33370580 PMCID: PMC8054296 DOI: 10.1016/j.cellsig.2020.109904] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022]
Abstract
The endogenous circadian clock functions to maintain optimal physiological health through the tissue specific coordination of gene expression and synchronization between tissues of metabolic processes throughout the 24 hour day. Individuals face numerous challenges to circadian function on a daily basis resulting in significant incidences of circadian disorders in the United States and worldwide. Dysfunction of the circadian clock has been implicated in numerous diseases including cancer, diabetes, obesity, cardiovascular and hepatic abnormalities, mood disorders and neurodegenerative diseases. The circadian clock regulates molecular, metabolic and physiological processes through rhythmic gene expression via transcriptional and post-transcriptional processes. Mounting evidence indicates that post-transcriptional regulation by the circadian clock plays a crucial role in maintaining tissue specific biological rhythms. Circadian regulation affecting RNA stability and localization through RNA processing, mRNA degradation, and RNA availability for translation can result in rhythmic protein synthesis, even when the mRNA transcripts themselves do not exhibit rhythms in abundance. The circadian clock also targets the initiation and elongation steps of translation through multiple pathways. In this review, the influence of the circadian clock across the levels of post-transcriptional, translation, and post-translational modifications are examined using examples from humans to cyanobacteria demonstrating the phylogenetic conservation of circadian regulation. Lastly, we briefly discuss chronotherapies and pharmacological treatments that target circadian function. Understanding the complexity and levels through which the circadian clock regulates molecular and physiological processes is important for future advancement of therapeutic outcomes.
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Affiliation(s)
- Amber A Parnell
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Aliza K De Nobrega
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Lisa C Lyons
- Department of Biological Science, Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
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The circadian machinery links metabolic disorders and depression: A review of pathways, proteins and potential pharmacological interventions. Life Sci 2020; 265:118809. [PMID: 33249097 DOI: 10.1016/j.lfs.2020.118809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Circadian rhythms are responsible for regulating a number of physiological processes. The central oscillator is located within the suprachiasmatic nucleus (SCN) of the hypothalamus and the SCN synchronises the circadian clocks that are found in our peripheral organs through neural and humoral signalling. At the molecular level, biological clocks consist of transcription-translation feedback loops (TTFLs) and these pathways are influenced by transcription factors, post-translational modifications, signalling pathways and epigenetic modifiers. When disruptions occur in the circadian machinery, the activities of the proteins implicated in this network and the expression of core clock or clock-controlled genes (CCGs) can be altered. Circadian misalignment can also arise when there is desychronisation between our internal clocks and environmental stimuli. There is evidence in the literature demonstrating that disturbances in the circadian rhythm contribute to the pathophysiology of several diseases and disorders. This includes the metabolic syndrome and recently, it has been suggested that the 'circadian syndrome' may be a more appropriate term to use to not only describe the cardio-metabolic risk factors but also the associated comorbidities. Here we overview the molecular architecture of circadian clocks in mammals and provide insight into the effects of shift work, exposure to artificial light, food intake and stress on the circadian rhythm. The relationship between circadian rhythms, metabolic disorders and depression is reviewed and this is a topic that requires further investigation. We also describe how particular proteins involved in the TTFLs can be potentially modulated by small molecules, including pharmacological interventions and dietary compounds.
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Falcón J, Torriglia A, Attia D, Viénot F, Gronfier C, Behar-Cohen F, Martinsons C, Hicks D. Exposure to Artificial Light at Night and the Consequences for Flora, Fauna, and Ecosystems. Front Neurosci 2020; 14:602796. [PMID: 33304237 PMCID: PMC7701298 DOI: 10.3389/fnins.2020.602796] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/22/2020] [Indexed: 12/22/2022] Open
Abstract
The present review draws together wide-ranging studies performed over the last decades that catalogue the effects of artificial-light-at-night (ALAN) upon living species and their environment. We provide an overview of the tremendous variety of light-detection strategies which have evolved in living organisms - unicellular, plants and animals, covering chloroplasts (plants), and the plethora of ocular and extra-ocular organs (animals). We describe the visual pigments which permit photo-detection, paying attention to their spectral characteristics, which extend from the ultraviolet into infrared. We discuss how organisms use light information in a way crucial for their development, growth and survival: phototropism, phototaxis, photoperiodism, and synchronization of circadian clocks. These aspects are treated in depth, as their perturbation underlies much of the disruptive effects of ALAN. The review goes into detail on circadian networks in living organisms, since these fundamental features are of critical importance in regulating the interface between environment and body. Especially, hormonal synthesis and secretion are often under circadian and circannual control, hence perturbation of the clock will lead to hormonal imbalance. The review addresses how the ubiquitous introduction of light-emitting diode technology may exacerbate, or in some cases reduce, the generalized ever-increasing light pollution. Numerous examples are given of how widespread exposure to ALAN is perturbing many aspects of plant and animal behaviour and survival: foraging, orientation, migration, seasonal reproduction, colonization and more. We examine the potential problems at the level of individual species and populations and extend the debate to the consequences for ecosystems. We stress, through a few examples, the synergistic harmful effects resulting from the impacts of ALAN combined with other anthropogenic pressures, which often impact the neuroendocrine loops in vertebrates. The article concludes by debating how these anthropogenic changes could be mitigated by more reasonable use of available technology - for example by restricting illumination to more essential areas and hours, directing lighting to avoid wasteful radiation and selecting spectral emissions, to reduce impact on circadian clocks. We end by discussing how society should take into account the potentially major consequences that ALAN has on the natural world and the repercussions for ongoing human health and welfare.
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Affiliation(s)
- Jack Falcón
- Laboratoire Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), MNHN, CNRS FRE 2030, SU, IRD 207, UCN, UA, Paris, France
| | - Alicia Torriglia
- Centre de Recherche des Cordeliers, INSERM U 1138, Ophtalmopole Hôpital Cochin, Assistance Publique - Hôpitaux de Paris, Université de Paris - SU, Paris, France
| | - Dina Attia
- ANSES, French Agency for Food, Environmental and Occupational Health & Safety, Maisons-Alfort, France
| | | | - Claude Gronfier
- Lyon Neuroscience Research Center (CRNL), Waking Team, Inserm UMRS 1028, CNRS UMR 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - Francine Behar-Cohen
- Centre de Recherche des Cordeliers, INSERM U 1138, Ophtalmopole Hôpital Cochin, Assistance Publique - Hôpitaux de Paris, Université de Paris - SU, Paris, France
| | | | - David Hicks
- Inserm, CNRS, Institut des Neurosciences Cellulaires et Intégratives, Université de Strasbourg, Strasbourg, France
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43
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Rijo-Ferreira F, Takahashi JS. Sleeping Sickness: A Tale of Two Clocks. Front Cell Infect Microbiol 2020; 10:525097. [PMID: 33134186 PMCID: PMC7562814 DOI: 10.3389/fcimb.2020.525097] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Sleeping sickness is caused by a eukaryotic unicellular parasite known to infect wild animals, cattle, and humans. It causes a fatal disease that disrupts many rhythmic physiological processes, including daily rhythms of hormonal secretion, temperature regulation, and sleep, all of which are under circadian (24-h) control. In this review, we summarize research on sleeping sickness parasite biology and the impact it has on host health. We also consider the possible evolutionary advantages of sleep and circadian deregulation for the parasite.
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Affiliation(s)
- Filipa Rijo-Ferreira
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, United States
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44
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Farré EM. The brown clock: circadian rhythms in stramenopiles. PHYSIOLOGIA PLANTARUM 2020; 169:430-441. [PMID: 32274814 DOI: 10.1111/ppl.13104] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/01/2020] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Circadian clocks allow organisms to anticipate environmental changes associated with the diurnal light/dark cycle. Circadian oscillators have been described in plants and green algae, cyanobacteria, animals and fungi, however, little is known about the circadian clocks of photosynthetic eukaryotes outside the green lineage. Stramenopiles are a diverse group of secondary endosymbionts whose plastid originated from a red alga. Photosynthetic stramenopiles, which include diatoms and brown algae, play key roles in biogeochemical cycles and are important components of marine ecosystems. Genome annotation efforts indicated the presence of a novel type of oscillator in these organisms and the first circadian clock component in a stramenopile has been recently discovered. This review summarizes the phenotypic characterization of circadian rhythms in stramenopiles and current efforts to determine the mechanisms of this 'brown clock'. The elucidation of this brown clock will enable a deeper understanding of the role of self-sustained oscillations in the adaptation to life in marine environments.
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Affiliation(s)
- Eva M Farré
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
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45
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Partch CL. Orchestration of Circadian Timing by Macromolecular Protein Assemblies. J Mol Biol 2020; 432:3426-3448. [DOI: 10.1016/j.jmb.2019.12.046] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 12/13/2019] [Accepted: 12/18/2019] [Indexed: 12/13/2022]
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