51
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Abdollahi H. Radiotherapy dose painting by circadian rhythm based radiomics. Med Hypotheses 2019; 133:109415. [PMID: 31586813 DOI: 10.1016/j.mehy.2019.109415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/29/2019] [Indexed: 12/12/2022]
Abstract
Radiotherapy dose painting is a new dose delivery technique to achieve higher treatment outcome. In this approach, does is escalated to high progressive regions which are heterogeneous and determined by advanced medical imaging. Radiomics is issued as a feasible image quantification method to reveal tumor heterogeneity by extraction of high throughput mineable texture features. On the other hand, circadian rhythm is a given biological process that studied as a critical factor to obtain more effective treatment outcome. In this study, we hypothesized that radiotherapy dose painting could be enhanced by using circadian rhythm that is determined on the radiomics maps obtained from medical images. This hypothesis is based on the idea which circadian rhythm could change the tumor heterogeneity and therefore image features.
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Affiliation(s)
- Hamid Abdollahi
- Department of Radiologic Sciences and Medical Physics, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran; Student Research Committee, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
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52
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De Los Santos H, Bennett KP, Hurley JM. ENCORE: A Visualization Tool for Insight into Circadian Omics. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:5-14. [PMID: 31754663 PMCID: PMC6868525 DOI: 10.1145/3307339.3342137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Circadian rhythms are 24-hour biological cycles that control daily molecular rhythms in many organisms. The cellular elements that fall under the regulation of the clock are often studied through the use of omics-scale data sets gathered over time to determine how circadian regulation impacts cellular physiology. Previously, we created the ECHO (Extended Circadian Harmonic Oscillator) tool to identify rhythms in these data sets. Using ECHO, we found that circadian oscillations widely undergo a change in amplitude over time and that these amplitude changes have a biological function in the cell. However, ECHO does not align gene ontologies with the identified oscillating genes to give functional context. Thus, we created ENCORE (ECHO Native Circadian Ontological Rhythmicity Explorer), a novel visualization tool which combines the disparate databases of Gene Ontologies, protein-protein interactions, and auxiliary information to uncover the meaning of circadianly-regulated genes. This freely-available tool performs automatic enrichment and creates publication-worthy visualizations which we used to extend previously-gathered data on circadian regulation of physiology from published omics-scale studies in three circadian model organisms: mouse, fruit fly, and Neurospora crassa.
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Affiliation(s)
- Hannah De Los Santos
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Kristin P Bennett
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Jennifer M Hurley
- Department of Biological Sciences/Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY
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53
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Angptl8 mediates food-driven resetting of hepatic circadian clock in mice. Nat Commun 2019; 10:3518. [PMID: 31388006 PMCID: PMC6684615 DOI: 10.1038/s41467-019-11513-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 07/18/2019] [Indexed: 12/12/2022] Open
Abstract
Diurnal light-dark cycle resets the master clock, while timed food intake is another potent synchronizer of peripheral clocks in mammals. As the largest metabolic organ, the liver sensitively responds to the food signals and secretes hepatokines, leading to the robust regulation of metabolic and clock processes. However, it remains unknown which hepatokine mediates the food-driven resetting of the liver clock independent of the master clock. Here, we identify Angptl8 as a hepatokine that resets diurnal rhythms of hepatic clock and metabolic genes in mice. Mechanistically, the resetting function of Angptl8 is dependent on the signal relay of the membrane receptor PirB, phosphorylation of kinases and transcriptional factors, and consequently transient activation of the central clock gene Per1. Importantly, inhibition of Angptl8 signaling partially blocks food-entrained resetting of liver clock in mice. We have thus identified Angptl8 as a key regulator of the liver clock in response to food.
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54
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Pastore N, Vainshtein A, Herz NJ, Huynh T, Brunetti L, Klisch TJ, Mutarelli M, Annunziata P, Kinouchi K, Brunetti-Pierri N, Sassone-Corsi P, Ballabio A. Nutrient-sensitive transcription factors TFEB and TFE3 couple autophagy and metabolism to the peripheral clock. EMBO J 2019; 38:embj.2018101347. [PMID: 31126958 DOI: 10.15252/embj.2018101347] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
Autophagy and energy metabolism are known to follow a circadian pattern. However, it is unclear whether autophagy and the circadian clock are coordinated by common control mechanisms. Here, we show that the oscillation of autophagy genes is dependent on the nutrient-sensitive activation of TFEB and TFE3, key regulators of autophagy, lysosomal biogenesis, and cell homeostasis. TFEB and TFE3 display a circadian activation over the 24-h cycle and are responsible for the rhythmic induction of genes involved in autophagy during the light phase. Genetic ablation of TFEB and TFE3 in mice results in deregulated autophagy over the diurnal cycle and altered gene expression causing abnormal circadian wheel-running behavior. In addition, TFEB and TFE3 directly regulate the expression of Rev-erbα (Nr1d1), a transcriptional repressor component of the core clock machinery also involved in the regulation of whole-body metabolism and autophagy. Comparative analysis of the cistromes of TFEB/TFE3 and REV-ERBα showed an extensive overlap of their binding sites, particularly in genes involved in autophagy and metabolic functions. These data reveal a direct link between nutrient and clock-dependent regulation of gene expression shedding a new light on the crosstalk between autophagy, metabolism, and circadian cycles.
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Affiliation(s)
- Nunzia Pastore
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Anna Vainshtein
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Niculin J Herz
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tuong Huynh
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Tiemo J Klisch
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Kenichiro Kinouchi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Sciences, Medical Genetics, Federico II University, Naples, Italy
| | - Paolo Sassone-Corsi
- Department of Biological Chemistry, Center for Epigenetics and Metabolism, U1233 INSERM, School of Medicine, University of California Irvine (UCI), Irvine, CA, USA
| | - Andrea Ballabio
- Jan and Dan Duncan Neurological Research Institute, Texas Children Hospital, Houston, TX, USA .,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Sciences, Medical Genetics, Federico II University, Naples, Italy
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55
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Flis A, Mengin V, Ivakov AA, Mugford ST, Hubberten HM, Encke B, Krohn N, Höhne M, Feil R, Hoefgen R, Lunn JE, Millar AJ, Smith AM, Sulpice R, Stitt M. Multiple circadian clock outputs regulate diel turnover of carbon and nitrogen reserves. PLANT, CELL & ENVIRONMENT 2019; 42:549-573. [PMID: 30184255 DOI: 10.1111/pce.13440] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 08/27/2018] [Accepted: 08/31/2018] [Indexed: 05/09/2023]
Abstract
Plants accumulate reserves in the daytime to support growth at night. Circadian regulation of diel reserve turnover was investigated by profiling starch, sugars, glucose 6-phosphate, organic acids, and amino acids during a light-dark cycle and after transfer to continuous light in Arabidopsis wild types and in mutants lacking dawn (lhy cca1), morning (prr7 prr9), dusk (toc1, gi), or evening (elf3) clock components. The metabolite time series were integrated with published time series for circadian clock transcripts to identify circadian outputs that regulate central metabolism. (a) Starch accumulation was slower in elf3 and prr7 prr9. It is proposed that ELF3 positively regulates starch accumulation. (b) Reducing sugars were high early in the T-cycle in elf3, revealing that ELF3 negatively regulates sucrose recycling. (c) The pattern of starch mobilization was modified in all five mutants. A model is proposed in which dawn and dusk/evening components interact to pace degradation to anticipated dawn. (d) An endogenous oscillation of glucose 6-phosphate revealed that the clock buffers metabolism against the large influx of carbon from photosynthesis. (e) Low levels of organic and amino acids in lhy cca1 and high levels in prr7 prr9 provide evidence that the dawn components positively regulate the accumulation of amino acid reserves.
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Affiliation(s)
- Anna Flis
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Virginie Mengin
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alexander A Ivakov
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Beatrice Encke
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Nicole Krohn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Melanie Höhne
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - John E Lunn
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Andrew J Millar
- SynthSys and School of Biological Sciences, C.H. Waddington Building, University of Edinburgh, Edinburgh, UK
| | | | - Ronan Sulpice
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
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56
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Gil KE, Park CM. Thermal adaptation and plasticity of the plant circadian clock. THE NEW PHYTOLOGIST 2019; 221:1215-1229. [PMID: 30289568 DOI: 10.1111/nph.15518] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Contents Summary 1215 I. Introduction 1215 II. Molecular organization of the plant circadian clock 1216 III. Temperature compensation 1219 IV. Temperature regulation of circadian behaviors 1220 V. Thermal adaptation of the clock: evolutionary considerations 1223 VI. Light and temperature information for the clock function - synergic or individual? 1224 VII. Concluding remarks and future prospects 1225 Acknowledgements 1225 References 1225 SUMMARY: Plant growth and development is widely affected by diverse temperature conditions. Although studies have been focused mainly on the effects of stressful temperature extremes in recent decades, nonstressful ambient temperatures also influence an array of plant growth and morphogenic aspects, a process termed thermomorphogenesis. Notably, accumulating evidence indicates that both stressful and nonstressful temperatures modulate the functional process of the circadian clock, a molecular timer of biological rhythms in higher eukaryotes and photosynthetic prokaryotes. The circadian clock can sustain robust and precise timing over a range of physiological temperatures. Genes and molecular mechanisms governing the temperature compensation process have been explored in different plant species. In addition, a ZEITLUPE/HSP90-mediated protein quality control mechanism helps plants maintain the thermal stability of the clock under heat stress. The thermal adaptation capability and plasticity of the clock are of particular interest in view of the growing concern about global climate changes. Considering these circumstances in the field, we believe that it is timely to provide a provoking discussion on the current knowledge of temperature regulation of the clock function. The review also will discuss stimulating ideas on this topic along with ecosystem management and future agricultural innovation.
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Affiliation(s)
- Kyung-Eun Gil
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
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57
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Hirayama J, Alifu Y, Hamabe R, Yamaguchi S, Tomita J, Maruyama Y, Asaoka Y, Nakahama KI, Tamaru T, Takamatsu K, Takamatsu N, Hattori A, Nishina S, Azuma N, Kawahara A, Kume K, Nishina H. The clock components Period2, Cryptochrome1a, and Cryptochrome2a function in establishing light-dependent behavioral rhythms and/or total activity levels in zebrafish. Sci Rep 2019; 9:196. [PMID: 30655599 PMCID: PMC6336812 DOI: 10.1038/s41598-018-37879-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 12/03/2018] [Indexed: 11/09/2022] Open
Abstract
The circadian clock generates behavioral rhythms to maximize an organism’s physiological efficiency. Light induces the formation of these rhythms by synchronizing cellular clocks. In zebrafish, the circadian clock components Period2 (zPER2) and Cryptochrome1a (zCRY1a) are light-inducible, however their physiological functions are unclear. Here, we investigated the roles of zPER2 and zCRY1a in regulating locomotor activity and behavioral rhythms. zPer2/zCry1a double knockout (DKO) zebrafish displayed defects in total locomotor activity and in forming behavioral rhythms when briefly exposed to light for 3-h. Exposing DKO zebrafish to 12-h light improved behavioral rhythm formation, but not total activity. Our data suggest that the light-inducible circadian clock regulator zCRY2a supports rhythmicity in DKO animals exposed to 12-h light. Single cell imaging analysis revealed that zPER2, zCRY1a, and zCRY2a function in synchronizing cellular clocks. Furthermore, microarray analysis of DKO zebrafish showed aberrant expression of genes involved regulating cellular metabolism, including ATP production. Overall, our results suggest that zPER2, zCRY1a and zCRY2a help to synchronize cellular clocks in a light-dependent manner, thus contributing to behavioral rhythm formation in zebrafish. Further, zPER2 and zCRY1a regulate total physical activity, likely via regulating cellular energy metabolism. Therefore, these circadian clock components regulate the rhythmicity and amount of locomotor behavior.
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Affiliation(s)
- Jun Hirayama
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan. .,Department of Clinical Engineering, Faculty of Health Sciences, Komatsu University, Ishikawa, Japan.
| | - Yikelamu Alifu
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Rin Hamabe
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sho Yamaguchi
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Jun Tomita
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan
| | - Yusuke Maruyama
- Department of Biology, College of Liberal Arts and Sciences, Tokyo Medical and Dental University (TMDU), Ichikawa, Japan
| | - Yoichi Asaoka
- Department of Microbiology and Immunology, Yamaguchi University Graduate School of Medicine, Ube, Japan
| | - Ken-Ichi Nakahama
- Department of Cellular Physiological Chemistry, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Teruya Tamaru
- Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo, Japan
| | - Ken Takamatsu
- Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo, Japan
| | - Nobuhiko Takamatsu
- Department of Biosciences, School of Science, Kitasato University, Sagamihara, Japan
| | - Atsuhiko Hattori
- Department of Biology, College of Liberal Arts and Sciences, Tokyo Medical and Dental University (TMDU), Ichikawa, Japan
| | - Sachiko Nishina
- Department of Ophthalmology and Laboratory for Visual Science, National Center for Child Health and Development, Tokyo, Japan
| | - Noriyuki Azuma
- Department of Ophthalmology and Laboratory for Visual Science, National Center for Child Health and Development, Tokyo, Japan
| | - Atsuo Kawahara
- Laboratory for Developmental Biology, Center for Medical Education and Sciences, Graduate School of Medical Science, University of Yamanashi, Yamanashi, Japan
| | - Kazuhiko Kume
- Department of Neuropharmacology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan.
| | - Hiroshi Nishina
- Department of Developmental and Regenerative Biology, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo, Japan.
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58
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Johansson M, Köster T. On the move through time - a historical review of plant clock research. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21 Suppl 1:13-20. [PMID: 29607587 DOI: 10.1111/plb.12729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/27/2018] [Indexed: 06/08/2023]
Abstract
The circadian clock is an important regulator of growth and development that has evolved to help organisms to anticipate the predictably occurring events on the planet, such as light-dark transitions, and adapt growth and development to these. This review looks back in history on how knowledge about the endogenous biological clock has been acquired over the centuries, with a focus on discoveries in plants. Key findings at the physiological, genetic and molecular level are described and the role of the circadian clock in important molecular processes is reviewed.
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Affiliation(s)
- M Johansson
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - T Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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59
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Hajdu A, Dobos O, Domijan M, Bálint B, Nagy I, Nagy F, Kozma-Bognár L. ELONGATED HYPOCOTYL 5 mediates blue light signalling to the Arabidopsis circadian clock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1242-1254. [PMID: 30256479 DOI: 10.1111/tpj.14106] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 05/21/2023]
Abstract
Circadian clocks are gene networks producing 24-h oscillations at the level of clock gene expression that are synchronized to environmental cycles via light signals. The ELONGATED HYPOCOTYL 5 (HY5) transcription factor is a signalling hub acting downstream of several photoreceptors and is a key mediator of photomorphogenesis. Here we describe a mechanism by which light quality could modulate the pace of the circadian clock through governing abundance of HY5. We show that hy5 mutants display remarkably shorter period rhythms in blue but not in red light or darkness, and blue light is more efficient than red to induce accumulation of HY5 at transcriptional and post-transcriptional levels. We demonstrate that the pattern and level of HY5 accumulation modulates its binding to specific promoter elements of the majority of clock genes, but only a few of these show altered transcription in the hy5 mutant. Mathematical modelling suggests that the direct effect of HY5 on the apparently non-responsive clock genes could be masked by feedback from the clock gene network. We conclude that the information on the ratio of blue and red components of the white light spectrum is decoded and relayed to the circadian oscillator, at least partially, by HY5.
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Affiliation(s)
- Anita Hajdu
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
| | - Orsolya Dobos
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, Szeged, H-6726, Hungary
| | - Mirela Domijan
- Department of Mathematical Sciences, University of Liverpool, Liverpool, L69 7ZL, UK
| | | | - István Nagy
- SeqOmics Ltd, Mórahalom, H-6782, Hungary
- Institute of Biochemistry, Biological Research Centre, Szeged, H-6726, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - László Kozma-Bognár
- Institute of Plant Biology, Biological Research Centre, Szeged, H-6726, Hungary
- Department of Genetics, Faculty of Sciences and Informatics, University of Szeged, Szeged, H-6726, Hungary
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60
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Inoue K, Araki T, Endo M. Oscillator networks with tissue-specific circadian clocks in plants. Semin Cell Dev Biol 2018; 83:78-85. [DOI: 10.1016/j.semcdb.2017.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/31/2022]
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61
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Frøland Steindal IA, Beale AD, Yamamoto Y, Whitmore D. Development of the Astyanax mexicanus circadian clock and non-visual light responses. Dev Biol 2018; 441:345-354. [PMID: 29909064 PMCID: PMC6141809 DOI: 10.1016/j.ydbio.2018.06.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/06/2018] [Accepted: 06/13/2018] [Indexed: 12/25/2022]
Abstract
Most animals and plants live on the planet exposed to periods of rhythmic light and dark. As such, they have evolved endogenous circadian clocks to regulate their physiology rhythmically, and non-visual light detection mechanisms to set the clock to the environmental light-dark cycle. In the case of fish, circadian pacemakers are not only present in the majority of tissues and cells, but these tissues are themselves directly light-sensitive, expressing a wide range of opsin photopigments. This broad non-visual light sensitivity exists to set the clock, but also impacts a wide range of fundamental cell biological processes, such as DNA repair regulation. In this context, Astyanax mexicanus is a very intriguing model system with which to explore non-visual light detection and circadian clock function. Previous work has shown that surface fish possess the same directly light entrainable circadian clocks, described above. The same is true for cave strains of Astyanax in the laboratory, though no daily rhythms have been observed under natural dark conditions in Mexico. There are, however, clear alterations in the cave strain light response and changes to the circadian clock, with a difference in phase of peak gene expression and a reduction in amplitude. In this study, we expand these early observations by exploring the development of non-visual light sensitivity and clock function between surface and cave populations. When does the circadian pacemaker begin to oscillate during development, and are there differences between the various strains? Is the difference in acute light sensitivity, seen in adults, apparent from the earliest stages of development? Our results show that both cave and surface populations must experience daily light exposure to establish a larval gene expression rhythm. These oscillations begin early, around the third day of development in all strains, but gene expression rhythms show a significantly higher amplitude in surface fish larvae. In addition, the light induction of clock genes is developmentally delayed in cave populations. Zebrafish embryonic light sensitivity has been shown to be critical not only for clock entrainment, but also for transcriptional activation of DNA repair processes. Similar downstream transcriptional responses to light also occur in Astyanax. Interestingly, the establishment of the adult timing profile of clock gene expression takes several days to become apparent. This fact may provide mechanistic insight into the key differences between the cave and surface fish clock mechanisms. Non-visual light sensitivity is developmentally delayed in cave strains of Astyanax. Neither strains of Astyanax show clock gene oscillations in dark raised larvae. The timing of the circadian molecular clock rhythm is delayed by 6-h in Pachon. Expression CPD photolyase is raised in constant darkness in Pachon. The clock has gained greater regulation over light-responsive genes in cave strains.
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Affiliation(s)
- Inga A Frøland Steindal
- Department of Cell and Developmental Biology, University College London, 21 University Street, London WC1E 6DE, UK
| | - Andrew D Beale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yoshiyuki Yamamoto
- Department of Cell and Developmental Biology, University College London, 21 University Street, London WC1E 6DE, UK
| | - David Whitmore
- Department of Cell and Developmental Biology, University College London, 21 University Street, London WC1E 6DE, UK.
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62
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Epigenetics of Circadian Rhythms in Imprinted Neurodevelopmental Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:67-92. [PMID: 29933957 DOI: 10.1016/bs.pmbts.2017.11.023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA sequence information alone cannot account for the immense variability between chromosomal alleles within diverse cell types in the brain, whether these differences are observed across time, cell type, or parental origin. The complex control and maintenance of gene expression and modulation are regulated by a multitude of molecular and cellular mechanisms that layer on top of the genetic code. The integration of genetic and environmental signals required for regulating brain development and function is achieved in part by a dynamic epigenetic landscape that includes DNA methylation, histone modifications, and noncoding RNAs. These epigenetic mechanisms establish and maintain core biological processes, including genomic imprinting and entrainment of circadian rhythms. This chapter will focus on how the epigenetic layers of DNA methylation and long, noncoding RNAs interact with circadian rhythms at specific imprinted chromosomal loci associated with the human neurodevelopmental disorders Prader-Willi, Angelman, Kagami-Ogata, and Temple syndromes.
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63
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Chi-Castañeda D, Ortega A. Glial Cells in the Genesis and Regulation of Circadian Rhythms. Front Physiol 2018; 9:88. [PMID: 29483880 PMCID: PMC5816069 DOI: 10.3389/fphys.2018.00088] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/26/2018] [Indexed: 12/26/2022] Open
Abstract
Circadian rhythms are biological oscillations with a period of ~24 h. These rhythms are orchestrated by a circadian timekeeper in the suprachiasmatic nucleus of the hypothalamus, the circadian "master clock," which exactly adjusts clock outputs to solar time via photic synchronization. At the molecular level, circadian rhythms are generated by the interaction of positive and negative feedback loops of transcriptional and translational processes of the so-called "clock genes." A large number of clock genes encode numerous proteins that regulate their own transcription and that of other genes, collectively known as "clock-controlled genes." In addition to the sleep/wake cycle, many cellular processes are regulated by circadian rhythms, including synaptic plasticity in which an exquisite interplay between neurons and glial cells takes place. In particular, there is compelling evidence suggesting that glial cells participate in and regulate synaptic plasticity in a circadian fashion, possibly representing the missing cellular and physiological link between circadian rhythms with learning and cognition processes. Here we review recent studies in support of this hypothesis, focusing on the interplay between glial cells, synaptic plasticity, and circadian rhythmogenesis.
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Affiliation(s)
- Donají Chi-Castañeda
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, Mexico.,Soluciones para un México Verde S.A. de C.V., Ciudad de Mexico, Mexico
| | - Arturo Ortega
- Laboratorio de Neurotoxicología, Departamento de Toxicología, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, Mexico
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Torres M, Becquet D, Franc JL, François-Bellan AM. Circadian processes in the RNA life cycle. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1467. [PMID: 29424086 DOI: 10.1002/wrna.1467] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/24/2017] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
Abstract
The circadian clock drives daily rhythms of multiple physiological processes, allowing organisms to anticipate and adjust to periodic changes in environmental conditions. These physiological rhythms are associated with robust oscillations in the expression of at least 30% of expressed genes. While the ability for the endogenous timekeeping system to generate a 24-hr cycle is a cell-autonomous mechanism based on negative autoregulatory feedback loops of transcription and translation involving core-clock genes and their protein products, it is now increasingly evident that additional mechanisms also govern the circadian oscillations of clock-controlled genes. Such mechanisms can take place post-transcriptionally during the course of the RNA life cycle. It has been shown that many steps during RNA processing are regulated in a circadian manner, thus contributing to circadian gene expression. These steps include mRNA capping, alternative splicing, changes in splicing efficiency, and changes in RNA stability controlled by the tail length of polyadenylation or the use of alternative polyadenylation sites. RNA transport can also follow a circadian pattern, with a circadian nuclear retention driven by rhythmic expression within the nucleus of particular bodies (the paraspeckles) and circadian export to the cytoplasm driven by rhythmic proteins acting like cargo. Finally, RNA degradation may also follow a circadian pattern through the rhythmic involvement of miRNAs. In this review, we summarize the current knowledge of the post-transcriptional circadian mechanisms known to play a prominent role in shaping circadian gene expression in mammals. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > RNA Editing and Modification RNA Export and Localization > Nuclear Export/Import.
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Affiliation(s)
- Manon Torres
- CNRS, CRN2M-UMR7286, Faculté de Médecine Nord, Aix-Marseille Université, Marseille, France
| | - Denis Becquet
- CNRS, CRN2M-UMR7286, Faculté de Médecine Nord, Aix-Marseille Université, Marseille, France
| | - Jean-Louis Franc
- CNRS, CRN2M-UMR7286, Faculté de Médecine Nord, Aix-Marseille Université, Marseille, France
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CLOCKΔ19 mutation modifies the manner of synchrony among oscillation neurons in the suprachiasmatic nucleus. Sci Rep 2018; 8:854. [PMID: 29339832 PMCID: PMC5770461 DOI: 10.1038/s41598-018-19224-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 12/28/2017] [Indexed: 01/05/2023] Open
Abstract
In mammals, the principal circadian oscillator exists in the hypothalamic suprachiasmatic nucleus (SCN). In the SCN, CLOCK works as an essential component of molecular circadian oscillation, and ClockΔ19 mutant mice show unique characteristics of circadian rhythms such as extended free running periods, amplitude attenuation, and high-magnitude phase-resetting responses. Here we investigated what modifications occur in the spatiotemporal organization of clock gene expression in the SCN of ClockΔ19 mutants. The cultured SCN, sampled from neonatal homozygous ClockΔ19 mice on an ICR strain comprising PERIOD2::LUCIFERASE, demonstrated that the Clock gene mutation not only extends the circadian period, but also affects the spatial phase and period distribution of circadian oscillations in the SCN. In addition, disruption of the synchronization among neurons markedly attenuated the amplitude of the circadian rhythm of individual oscillating neurons in the mutant SCN. Further, with numerical simulations based on the present studies, the findings suggested that, in the SCN of the ClockΔ19 mutant mice, stable oscillation was preserved by the interaction among oscillating neurons, and that the orderly phase and period distribution that makes a phase wave are dependent on the functionality of CLOCK.
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66
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Chi-Castañeda D, Ortega A. Circadian Regulation of Glutamate Transporters. Front Endocrinol (Lausanne) 2018; 9:340. [PMID: 29977228 PMCID: PMC6021491 DOI: 10.3389/fendo.2018.00340] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 06/05/2018] [Indexed: 12/21/2022] Open
Abstract
L-glutamate is the major excitatory amino acid in the mammalian central nervous system (CNS). This neurotransmitter is essential for higher brain functions such as learning, cognition and memory. A tight regulation of extra-synaptic glutamate levels is needed to prevent a neurotoxic insult. Glutamate removal from the synaptic cleft is carried out by a family of sodium-dependent high-affinity transporters, collectively known as excitatory amino acid transporters. Dysfunction of glutamate transporters is generally involved in acute neuronal injury and neurodegenerative diseases, so characterizing and understanding the mechanisms that lead to the development of these disorders is an important goal in the design of novel treatments for the neurodegenerative diseases. Increasing evidence indicates glutamate transporters are controlled by the circadian system in direct and indirect manners, so in this contribution we focus on the mechanisms of circadian regulation (transcriptional, translational, post-translational and post-transcriptional regulation) of glutamate transport in neuronal and glial cells, and their consequence in brain function.
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67
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Inoue K, Araki T, Endo M. Circadian clock during plant development. JOURNAL OF PLANT RESEARCH 2018; 131:59-66. [PMID: 29134443 PMCID: PMC5897470 DOI: 10.1007/s10265-017-0991-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/06/2017] [Indexed: 05/14/2023]
Abstract
Plants have endogenous biological clocks that allow organisms to anticipate and prepare for daily and seasonal environmental changes and increase their fitness in changing environments. The circadian clock in plants, as in animals and insects, mainly consists of multiple interlocking transcriptional/translational feedback loops. The circadian clock can be entrained by environmental cues such as light, temperature and nutrient status to synchronize internal biological rhythms with surrounding environments. Output pathways link the circadian oscillator to various physiological, developmental, and reproductive processes for adjusting the timing of these biological processes to an appropriate time of day or a suitable season. Recent genomic studies have demonstrated that polymorphism in circadian clock genes may contribute to local adaptations over a wide range of latitudes in many plant species. In the present review, we summarize the circadian regulation of biological processes throughout the life cycle of plants, and describe the contribution of the circadian clock to local adaptation.
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Affiliation(s)
- Keisuke Inoue
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Takashi Araki
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
| | - Motomu Endo
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502 Japan
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68
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The Role of Mammalian Glial Cells in Circadian Rhythm Regulation. Neural Plast 2017; 2017:8140737. [PMID: 29435373 PMCID: PMC5757113 DOI: 10.1155/2017/8140737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/19/2017] [Indexed: 11/23/2022] Open
Abstract
Circadian rhythms are biological oscillations with a period of about 24 hours. These rhythms are maintained by an innate genetically determined time-keeping system called the circadian clock. A large number of the proteins involved in the regulation of this clock are transcription factors controlling rhythmic transcription of so-called clock-controlled genes, which participate in a plethora of physiological functions in the organism. In the brain, several areas, besides the suprachiasmatic nucleus, harbor functional clocks characterized by a well-defined time pattern of clock gene expression. This expression rhythm is not restricted to neurons but is also present in glia, suggesting that these cells are involved in circadian rhythmicity. However, only certain glial cells fulfill the criteria to be called glial clocks, namely, to display molecular oscillators based on the canonical clock protein PERIOD, which depends on the suprachiasmatic nucleus for their synchronization. In this contribution, we summarize the current information about activity of the clock genes in glial cells, their potential role as oscillators as well as clinical implications.
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69
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Colón W, Church J, Sen J, Thibeault J, Trasatti H, Xia K. Biological Roles of Protein Kinetic Stability. Biochemistry 2017; 56:6179-6186. [PMID: 29087706 DOI: 10.1021/acs.biochem.7b00942] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A protein's stability may range from nonexistent, as in the case of intrinsically disordered proteins, to very high, as indicated by a protein's resistance to degradation, even under relatively harsh conditions. The stability of this latter group is usually under kinetic control because of a high activation energy for unfolding that virtually traps the protein in a specific conformation, thereby conferring resistance to proteolytic degradation and misfolding aggregation. The usual outcome of kinetic stability is a longer protein half-life. Thus, the protective role of protein kinetic stability is often appreciated, but relatively little is known about the extent of biological roles related to this property. In this Perspective, we will discuss several known or putative biological roles of protein kinetic stability, including protection from stressors to avoid aggregation or premature degradation, achieving long-term phenotypic change, and regulating cellular processes by controlling the trigger and timing of molecular motion. The picture that emerges from this analysis is that protein kinetic stability is involved in a myriad of known and yet to be discovered biological functions via its ability to confer degradation resistance and control the timing, extent, and permanency of molecular motion.
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Affiliation(s)
- Wilfredo Colón
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jennifer Church
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jayeeta Sen
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Jane Thibeault
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Hannah Trasatti
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Ke Xia
- Department of Chemistry and Chemical Biology, ‡Center for Biotechnology and Interdisciplinary Studies, and §Biochemistry and Biophysics Graduate Program, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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70
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Agostinelli F, Ceglia N, Shahbaba B, Sassone-Corsi P, Baldi P. What time is it? Deep learning approaches for circadian rhythms. Bioinformatics 2017; 32:i8-i17. [PMID: 27307647 PMCID: PMC4908327 DOI: 10.1093/bioinformatics/btw243] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Motivation: Circadian rhythms date back to the origins of life, are found in virtually every species and every cell, and play fundamental roles in functions ranging from metabolism to cognition. Modern high-throughput technologies allow the measurement of concentrations of transcripts, metabolites and other species along the circadian cycle creating novel computational challenges and opportunities, including the problems of inferring whether a given species oscillate in circadian fashion or not, and inferring the time at which a set of measurements was taken. Results: We first curate several large synthetic and biological time series datasets containing labels for both periodic and aperiodic signals. We then use deep learning methods to develop and train BIO_CYCLE, a system to robustly estimate which signals are periodic in high-throughput circadian experiments, producing estimates of amplitudes, periods, phases, as well as several statistical significance measures. Using the curated data, BIO_CYCLE is compared to other approaches and shown to achieve state-of-the-art performance across multiple metrics. We then use deep learning methods to develop and train BIO_CLOCK to robustly estimate the time at which a particular single-time-point transcriptomic experiment was carried. In most cases, BIO_CLOCK can reliably predict time, within approximately 1 h, using the expression levels of only a small number of core clock genes. BIO_CLOCK is shown to work reasonably well across tissue types, and often with only small degradation across conditions. BIO_CLOCK is used to annotate most mouse experiments found in the GEO database with an inferred time stamp. Availability and Implementation: All data and software are publicly available on the CircadiOmics web portal: circadiomics.igb.uci.edu/. Contacts:fagostin@uci.edu or pfbaldi@uci.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | | | - Paolo Sassone-Corsi
- Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Pierre Baldi
- Department of Computer Science, Department of Biological Chemistry, University of California-Irvine, Irvine, CA 92697, USA
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71
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Fabbian F, Bhatia S, De Giorgi A, Maietti E, Bhatia S, Shanbhag A, Deshmukh A. Circadian Periodicity of Ischemic Heart Disease: A Systematic Review of the Literature. Heart Fail Clin 2017; 13:673-680. [PMID: 28865776 DOI: 10.1016/j.hfc.2017.05.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The authors performed a MEDLINE search to identify reports, published during the last 20 years, focused on circadian variation of acute myocardial infarction (AMI), and prevalence and the ratios between the number of events per hour during the morning and the other hours of the day were calculated. Despite the optimization of interventional and medical therapy of AMI since the first reports of circadian patterns in AMI occurrence, it was found that such a pattern still exists and that AMI happens most frequently in the morning hours.
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Affiliation(s)
- Fabio Fabbian
- Department of Medical Sciences, University of Ferrara, University Hospital St. Anna, Via Aldo Moro 8, I-44124, Cona, Ferrara, Italy.
| | - Subir Bhatia
- Department of Internal Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
| | - Afredo De Giorgi
- Department of Medical Sciences, University of Ferrara, University Hospital St. Anna, Via Aldo Moro 8, I-44124, Cona, Ferrara, Italy
| | - Elisa Maietti
- Department of Medical Sciences, University of Ferrara, Center for Clinical Epidemiology, 44121 Ferrara, Italy
| | - Sravya Bhatia
- School of Medicine, Duke University, 8 Duke University Medical Center Greenspace, Durham, NC 27703, USA
| | - Anusha Shanbhag
- Department of Internal Medicine, University of Arkansas for Medical Sciences, 4301 W. Markham Street, Little Rock, AR 72205, USA
| | - Abhishek Deshmukh
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, Minnesota, 200 First Street Southwest, Rochester, Minnesota 55905, USA
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Chew KS, Renna JM, McNeill DS, Fernandez DC, Keenan WT, Thomsen MB, Ecker JL, Loevinsohn GS, VanDunk C, Vicarel DC, Tufford A, Weng S, Gray PA, Cayouette M, Herzog ED, Zhao H, Berson DM, Hattar S. A subset of ipRGCs regulates both maturation of the circadian clock and segregation of retinogeniculate projections in mice. eLife 2017; 6:e22861. [PMID: 28617242 PMCID: PMC5513697 DOI: 10.7554/elife.22861] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 06/14/2017] [Indexed: 12/25/2022] Open
Abstract
The visual system consists of two major subsystems, image-forming circuits that drive conscious vision and non-image-forming circuits for behaviors such as circadian photoentrainment. While historically considered non-overlapping, recent evidence has uncovered crosstalk between these subsystems. Here, we investigated shared developmental mechanisms. We revealed an unprecedented role for light in the maturation of the circadian clock and discovered that intrinsically photosensitive retinal ganglion cells (ipRGCs) are critical for this refinement process. In addition, ipRGCs regulate retinal waves independent of light, and developmental ablation of a subset of ipRGCs disrupts eye-specific segregation of retinogeniculate projections. Specifically, a subset of ipRGCs, comprising ~200 cells and which project intraretinally and to circadian centers in the brain, are sufficient to mediate both of these developmental processes. Thus, this subset of ipRGCs constitute a shared node in the neural networks that mediate light-dependent maturation of the circadian clock and light-independent refinement of retinogeniculate projections.
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Affiliation(s)
- Kylie S Chew
- Department of Biology, Johns Hopkins University, Baltimore, United States
- Department of Biology, Stanford University, Stanford, United States
| | - Jordan M Renna
- Department of Biology, Program in Integrated Bioscience, The University of Akron, Akron, United States
| | - David S McNeill
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Diego C Fernandez
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - William T Keenan
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Michael B Thomsen
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - Jennifer L Ecker
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | | | - Cassandra VanDunk
- Department of Anatomy and Neurobiology, Washington University, St. Louis, United States
- Department of Neurobiology, Northwestern University, Evanston, United States
| | - Daniel C Vicarel
- Department of Biology, Program in Integrated Bioscience, The University of Akron, Akron, United States
| | - Adele Tufford
- Cellular Neurobiology Research Unit, Institut De Recherches Cliniques De Montréal, Montreal, Canada
| | - Shijun Weng
- Department of Neuroscience, Brown University, Providence, United States
| | - Paul A Gray
- Department of Anatomy and Neurobiology, Washington University, St. Louis, United States
- Indigo Agriculture, Charlestown, United States
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut De Recherches Cliniques De Montréal, Montreal, Canada
- Faculty of Medicine, Université De Montréal, Montreal, Canada
| | - Erik D Herzog
- Department of Biology, Washington University, St. Louis, United States
| | - Haiqing Zhao
- Department of Biology, Johns Hopkins University, Baltimore, United States
| | - David M Berson
- Department of Neuroscience, Brown University, Providence, United States
| | - Samer Hattar
- Department of Biology, Johns Hopkins University, Baltimore, United States
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Barberà M, Collantes-Alegre JM, Martínez-Torres D. Characterisation, analysis of expression and localisation of circadian clock genes from the perspective of photoperiodism in the aphid Acyrthosiphon pisum. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 83:54-67. [PMID: 28235563 DOI: 10.1016/j.ibmb.2017.02.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 02/17/2017] [Accepted: 02/20/2017] [Indexed: 06/06/2023]
Abstract
Aphids are typical photoperiodic insects that switch from viviparous parthenogenetic reproduction typical of long day seasons to oviparous sexual reproduction triggered by the shortening of photoperiod in autumn yielding an overwintering egg in which an embryonic diapause takes place. While the involvement of the circadian clock genes in photoperiodism in mammals is well established, there is still some controversy on their participation in insects. The availability of the genome of the pea aphid Acyrthosiphon pisum places this species as an excellent model to investigate the involvement of the circadian system in the aphid seasonal response. In the present report, we have advanced in the characterisation of the circadian clock genes and showed that these genes display extensive alternative splicing. Moreover, the expression of circadian clock genes, analysed at different moments of the day, showed a robust cycling of central clock genes period and timeless. Furthermore, the rhythmic expression of these genes was shown to be rapidly dampened under DD (continuous darkness conditions), thus supporting the model of a seasonal response based on a heavily dampened circadian oscillator. Additionally, increased expression of some of the circadian clock genes under short-day conditions suggest their involvement in the induction of the aphid seasonal response. Finally, in situ localisation of transcripts of genes period and timeless in the aphid brain revealed the site of clock neurons for the first time in aphids. Two groups of clock cells were identified: the Dorsal Neurons (DN) and the Lateral Neurons (LN), both in the protocerebrum.
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Affiliation(s)
- Miquel Barberà
- Institut de Biologia Integrativa de Sistemes & Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València, Spain
| | - Jorge Mariano Collantes-Alegre
- Institut de Biologia Integrativa de Sistemes & Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes & Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València, Spain.
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74
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Robust network topologies for generating oscillations with temperature-independent periods. PLoS One 2017; 12:e0171263. [PMID: 28152061 PMCID: PMC5289577 DOI: 10.1371/journal.pone.0171263] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/17/2017] [Indexed: 11/26/2022] Open
Abstract
Nearly all living systems feature a temperature-independent oscillation period in circadian clocks. This ubiquitous property occurs at the system level and is rooted in the network architecture of the clock machinery. To investigate the mechanism of this prominent property of the circadian clock and provide general guidance for generating robust genetic oscillators with temperature-compensated oscillations, we theoretically explored the design principle and core network topologies preferred by oscillations with a temperature-independent period. By enumerating all topologies of genetic regulatory circuits with three genes, we obtained four network motifs, namely, a delayed negative feedback oscillator, repressilator, activator-inhibitor oscillator and substrate-depletion oscillator; hybrids of these motifs constitute the vast majority of target network topologies. These motifs are biased in their capacities for achieving oscillations and the temperature sensitivity of the period. The delayed negative feedback oscillator and repressilator are more robust for oscillations, whereas the activator-inhibitor and substrate-depletion oscillators are superior for maintaining a temperature-independent oscillation period. These results suggest that thermally robust oscillation can be more plausibly achieved by hybridizing these two categories of network motifs. Antagonistic balance and temperature insulation mechanisms for achieving temperature compensation are typically found in these topologies with temperature robustness. In the temperature insulation approach, the oscillation period relies on very few parameters, and these parameters are influenced only slightly by temperature. This approach prevents the temperature from affecting the oscillation period and generates circadian rhythms that are robust against environmental perturbations.
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75
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Torres M, Becquet D, Blanchard MP, Guillen S, Boyer B, Moreno M, Franc JL, François-Bellan AM. Paraspeckles as rhythmic nuclear mRNA anchorages responsible for circadian gene expression. Nucleus 2017; 8:249-254. [PMID: 28060565 DOI: 10.1080/19491034.2016.1277304] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Circadian clocks regulate rhythmic gene expression levels by means of mRNA oscillations that are mainly driven by post-transcriptional regulation. We identified a new post-transcriptional mechanism, which involves nuclear bodies called paraspeckles. Major components of paraspeckles including the long noncoding RNA Neat1, which is the structural component, and its major protein partners, as well as the number of paraspeckles, follow a circadian pattern in pituitary cells. Paraspeckles are known to retain within the nucleus RNAs containing inverted repeats of Alu sequences. We showed that a reporter gene in which these RNA duplex elements were inserted in the 3'-UTR region displayed a circadian expression. Moreover, circadian endogenous mRNA associated with paraspeckles lost their circadian pattern when paraspeckles were disrupted. This work not only highlights a new paraspeckle-based post-transcriptional mechanism involved in circadian gene expression but also provides the list of all mRNA associated with paraspeckles in the nucleus of pituitary cells.
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Affiliation(s)
- Manon Torres
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Denis Becquet
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Marie-Pierre Blanchard
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Séverine Guillen
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Bénédicte Boyer
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Mathias Moreno
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
| | - Jean-Louis Franc
- a Aix Marseille Université, CNRS, CRN2M-UMR7286, Faculté de Médecine Nord , Marseille , France
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Qiao Q, Le Manach S, Huet H, Duvernois-Berthet E, Chaouch S, Duval C, Sotton B, Ponger L, Marie A, Mathéron L, Lennon S, Bolbach G, Djediat C, Bernard C, Edery M, Marie B. An integrated omic analysis of hepatic alteration in medaka fish chronically exposed to cyanotoxins with possible mechanisms of reproductive toxicity. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 219:119-131. [PMID: 27814527 DOI: 10.1016/j.envpol.2016.10.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/27/2016] [Accepted: 10/09/2016] [Indexed: 05/22/2023]
Abstract
Cyanobacterial blooms threaten human health as well as the population of other living organisms in the aquatic environment, particularly due to the production of natural toxic components, the cyanotoxin. So far, the most studied cyanotoxins are microcystins (MCs). In this study, the hepatic alterations at histological, proteome and transcriptome levels were evaluated in female and male medaka fish chronically exposed to 1 and 5 μg L-1 microcystin-LR (MC-LR) and to the extract of MC-producing Microcystis aeruginosa PCC 7820 (5 μg L-1 of equivalent MC-LR) by balneation for 28 days, aiming at enhancing our understanding of the potential reproductive toxicity of cyanotoxins in aquatic vertebrate models. Indeed, both MC and Microcystis extract adversely affect reproductive parameters including fecundity and egg hatchability. The liver of toxin treated female fish present glycogen storage loss and cellular damages. The quantitative proteomics analysis revealed that the quantities of 225 hepatic proteins are dysregulated. In particular, a notable decrease in protein quantities of vitellogenin and choriogenin was observed, which could explain the decrease in reproductive output. Liver transcriptome analysis through Illumina RNA-seq reveals that over 100-400 genes are differentially expressed under 5 μg L-1 MC-LR and Microcystis extract treatments, respectively. Ingenuity pathway analysis of the omic data attests that various metabolic pathways, such as energy production, protein biosynthesis and lipid metabolism, are disturbed by both MC-LR and the Microcystis extract, which could provoke the observed reproductive impairment. The transcriptomics analysis also constitutes the first report of the impairment of circadian rhythm-related gene induced by MCs. This study contributes to a better understanding of the potential consequences of chronic exposure of fish to environmental concentrations of cyanotoxins, suggesting that Microcystis extract could impact a wider range of biological pathways, compared with pure MC-LR, and even 1 μg L-1 MC-LR potentially induces a health risk for aquatic organisms.
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Affiliation(s)
- Qin Qiao
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France.
| | - Séverine Le Manach
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Hélène Huet
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France; Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, BioPôle Alfort, 94700 Maisons-Alfort, France
| | - Evelyne Duvernois-Berthet
- UMR 7221 CNRS/MNHN, Évolution des Régulations Endocriniennes, Sorbonne Universités, Muséum Nationale d'Histoire Naturelle, Paris, France
| | - Soraya Chaouch
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Charlotte Duval
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Benoit Sotton
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Loïc Ponger
- UMR 7196 MNHN/CNRS, INSERM U1154, Sorbonne Universités, Museum National d'Histoire Naturelle, Paris, France
| | - Arul Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Lucrèce Mathéron
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, 75005 Paris, France
| | | | - Gérard Bolbach
- Institut de Biologie Paris Seine/FR 3631, Plateforme Spectrométrie de masse et Protéomique, Institut de Biologie Intégrative IFR 83, Sorbonne Universités, Université Pierre et Marie Curie, 75005 Paris, France
| | - Chakib Djediat
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Cécile Bernard
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Marc Edery
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France
| | - Benjamin Marie
- UMR 7245 MNHN/CNRS Molécules de Communication et Adaptation des Micro-organismes, Sorbonne Universités, Muséum National d'Histoire Naturelle, CP 39, 12 Rue Buffon, 75005 Paris, France.
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77
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Goya ME, Romanowski A, Caldart CS, Bénard CY, Golombek DA. Circadian rhythms identified in Caenorhabditis elegans by in vivo long-term monitoring of a bioluminescent reporter. Proc Natl Acad Sci U S A 2016; 113:E7837-E7845. [PMID: 27849618 PMCID: PMC5137770 DOI: 10.1073/pnas.1605769113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Circadian rhythms are based on endogenous clocks that allow organisms to adjust their physiology and behavior by entrainment to the solar day and, in turn, to select the optimal times for most biological variables. Diverse model systems-including mice, flies, fungi, plants, and bacteria-have provided important insights into the mechanisms of circadian rhythmicity. However, the general principles that govern the circadian clock of Caenorhabditis elegans have remained largely elusive. Here we report robust molecular circadian rhythms in C elegans recorded with a bioluminescence assay in vivo and demonstrate the main features of the circadian system of the nematode. By constructing a luciferase-based reporter coupled to the promoter of the suppressor of activated let-60 Ras (sur-5) gene, we show in both population and single-nematode assays that C elegans expresses ∼24-h rhythms that can be entrained by light/dark and temperature cycles. We provide evidence that these rhythms are temperature-compensated and can be re-entrained after phase changes of the synchronizing agents. In addition, we demonstrate that light and temperature sensing requires the photoreceptors LITE and GUR-3, and the cyclic nucleotide-gated channel subunit TAX-2. Our results shed light on C elegans circadian biology and demonstrate evolutionarily conserved features in the circadian system of the nematode.
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Affiliation(s)
- María Eugenia Goya
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Buenos Aires B1876BXD, Argentina
| | - Andrés Romanowski
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Buenos Aires B1876BXD, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Ciudad Autónoma de Buenos Aires C1405BWE, Argentina
| | - Carlos S Caldart
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Buenos Aires B1876BXD, Argentina
| | - Claire Y Bénard
- Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605;
- Department of Biological Sciences University of Quebec at Montreal, Montreal, QC, Canada H2X 1Y4
| | - Diego A Golombek
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes/Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Buenos Aires B1876BXD, Argentina;
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78
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The Clock mutation reduces reproductive performance of mice by affecting the implantation capacity: Maternal Clock mutation is not the only factor affecting implantation. Theriogenology 2016; 86:1670-84. [PMID: 27520292 DOI: 10.1016/j.theriogenology.2016.05.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 05/04/2016] [Accepted: 05/20/2016] [Indexed: 11/21/2022]
Abstract
Here, we showed that the Clock gene was important for reproductive performance in mice. We compared outcomes from the four possible mating combinations between wild-type mice (WT) and mice homozygous for the Clock delta-19 mutation (CL). We found that the only significant differences were between the WT♂ × WT♀ and CL♂ × CL♀ mating groups; these groups differed with regard to elongation of the pregnancy period (19.3 vs. 20.5 days, respectively, P < 0.05) and the number of newborn pups (13.4 ± 0.8 vs. 8.6 ± 1.5, respectively, P < 0.05). Because CL dams impregnated by male CLs exhibited normal continuous increases in body weight during the entire gestation period and did not show any signs of spontaneous abortion from mid to late gestation, we reasoned that some embryos were lost before or at the time of implantation. Immediately before implantation (88 hours after fertilization), neither the number of embryos collected from uteri nor the percentage of the embryos that reached the blastocyst stage differed significantly among mating groups. In contrast, immediately after implantation (160 hours after fertilization), the average number of implantation sites was significantly lower for the CL♂ × CL♀ mating group than that for the WT♂ × WT♀ mating group (7.0 vs. 13.0, P < 0.05); this decrease was accompanied by a significant lowering of the positions of implantation sites in uteri, and this lowering of the implantation sites was more severe when mothers and embryos bore more CL alleles (WT♂ × WT♀ >CL♂ × WT♀ > WT♂ × CL♀ >CL♂ × CL♀), suggesting that the Clock mutation reduced the reproduction performance of the parents by affecting the implantation capacity via such as embryos' ability to implant.
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79
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Chi-Castañeda D, Ortega A. Clock Genes in Glia Cells: A Rhythmic History. ASN Neuro 2016; 8:8/5/1759091416670766. [PMID: 27666286 PMCID: PMC5037500 DOI: 10.1177/1759091416670766] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/22/2016] [Indexed: 11/17/2022] Open
Abstract
Circadian rhythms are periodic patterns in biological processes that allow the organisms to anticipate changes in the environment. These rhythms are driven by the suprachiasmatic nucleus (SCN), the master circadian clock in vertebrates. At a molecular level, circadian rhythms are regulated by the so-called clock genes, which oscillate in a periodic manner. The protein products of clock genes are transcription factors that control their own and other genes’ transcription, collectively known as “clock-controlled genes.” Several brain regions other than the SCN express circadian rhythms of clock genes, including the amygdala, the olfactory bulb, the retina, and the cerebellum. Glia cells in these structures are expected to participate in rhythmicity. However, only certain types of glia cells may be called “glial clocks,” since they express PER-based circadian oscillators, which depend of the SCN for their synchronization. This contribution summarizes the current information about clock genes in glia cells, their plausible role as oscillators and their medical implications.
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Affiliation(s)
- Donají Chi-Castañeda
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México Soluciones para un México Verde, S.A de C.V., Santa Fé Ciudad de México, México
| | - Arturo Ortega
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
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80
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Abstract
The circadian system in higher organisms temporally orchestrates rhythmic changes in a vast number of genes and gene products in different organs. Complex interactions between these components, both within and among cells, ultimately lead to rhythmic behavior and physiology. Identifying the plethora of circadian targets and mapping their interactions with one another is therefore essential to comprehend the molecular mechanisms of circadian regulation. The emergence of new technology for unbiased identification of biomolecules and for mapping interactions at the genome-wide scale is offering powerful tools to decipher the regulatory networks underpinning circadian rhythms. In this review, the authors discuss the potential application of these genome-wide approaches in the study of circadian rhythms.
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Affiliation(s)
- Luciano De Haro
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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81
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Comolli JC, Fagan T, Hastings JW. A Type-1 Phosphoprotein Phosphatase from a Dinoflagellate as a Possible Component of the Circadian Mechanism. J Biol Rhythms 2016; 18:367-76. [PMID: 14582853 DOI: 10.1177/0748730403254103] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Indicative of the importance of protein phosphorylation in the core circadian clock mechanism, chronically applied inhibitors of both protein kinases and phosphoprotein phosphatases have significant effects on the period, phase, and light-dependent regulation of circadian rhythms in the dinoflagellate Lingulodinium polyedrum. This study was aimed at identifying the presence of the affected phosphatase(s). Dephosphorylation of a PP1/PP2A-specific substrate by L. polyedrum extracts was inhibited by okadaic acid only at concentrations greater than 100 nM, as in vivo, by mammalian inhibitor-2 (I-2), and by an endogenous inhibitor with properties similar to I-2, indicating that a type-1 protein phosphatase (PP1) was predominant. A cDNA encoding a highly conserved PP1 was isolated, the 1st such signaling molecule identified in dinoflagellates. Anti-sera specific for this type of phosphatase recognized a 34 kDa protein in L. polyedrum extract, this being the same size as the PP1 encoded by the isolated cDNA. These findings are consistent with the suggestion that the L. polyedrum PP1 may be a part of the clock mechanism in this species.
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Affiliation(s)
- James C Comolli
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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82
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Xue T, Song C, Wang Q, Wang Y, Chen G. Investigations of the CLOCK and BMAL1 Proteins Binding to DNA: A Molecular Dynamics Simulation Study. PLoS One 2016; 11:e0155105. [PMID: 27153104 PMCID: PMC4859532 DOI: 10.1371/journal.pone.0155105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 04/25/2016] [Indexed: 11/18/2022] Open
Abstract
The circadian locomotor output cycles kaput (CLOCK), and brain and muscle ARNT-like 1 (BMAL1) proteins are important transcriptional factors of the endogenous circadian clock. The CLOCK and BMAL1 proteins can regulate the transcription-translation activities of the clock-related genes through the DNA binding. The hetero-/homo-dimerization and DNA combination of the CLOCK and BMAL1 proteins play a key role in the positive and negative transcriptional feedback processes. In the present work, we constructed a series of binary and ternary models for the bHLH/bHLH-PAS domains of the CLOCK and BMAL1 proteins, and the DNA molecule, and carried out molecular dynamics simulations, free energy calculations and conformational analysis to explore the interaction properties of the CLOCK and BMAL1 proteins with DNA. The results show that the bHLH domains of CLOCK and BMAL1 can favorably form the heterodimer of the bHLH domains of CLOCK and BMAL1 and the homodimer of the bHLH domains of BMAL1. And both dimers could respectively bind to DNA at its H1-H1 interface. The DNA bindings of the H1 helices in the hetero- and homo-bHLH dimers present the rectangular and diagonal binding modes, respectively. Due to the function of the α-helical forceps in these dimers, the tight gripping of the H1 helices to the major groove of DNA would cause the decrease of interactions at the H1-H2 interfaces in the CLOCK and BMAL1 proteins. The additional PAS domains in the CLOCK and BMAL1 proteins affect insignificantly the interactions of the CLOCK and BMAL1 proteins with the DNA molecule due to the flexible and long loop linkers located at the middle of the PAS and bHLH domains. The present work theoretically explains the interaction mechanisms of the bHLH domains of the CLOCK and BMAL1 proteins with DNA.
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Affiliation(s)
- Tuo Xue
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Chunnian Song
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Qing Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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83
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Salminen A, Kauppinen A, Kaarniranta K. AMPK/Snf1 signaling regulates histone acetylation: Impact on gene expression and epigenetic functions. Cell Signal 2016; 28:887-95. [PMID: 27010499 DOI: 10.1016/j.cellsig.2016.03.009] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/18/2016] [Indexed: 01/22/2023]
Abstract
AMP-activated protein kinase (AMPK) and its yeast homolog, Snf1, are critical regulators in the maintenance of energy metabolic balance not only stimulating energy production but also inhibiting energy-consuming processes. The AMPK/Snf1 signaling controls energy metabolism by specific phosphorylation of many metabolic enzymes and transcription factors, enhancing or suppressing their functions. The AMPK/Snf1 complexes can be translocated from cytoplasm into nuclei where they are involved in the regulation of transcription. Recent studies have indicated that AMPK/Snf1 activation can control histone acetylation through different mechanisms affecting not only gene transcription but also many other epigenetic functions. For instance, AMPK/Snf1 enzymes can phosphorylate the histone H3S10 (yeast) and H2BS36 (mammalian) sites which activate specific histone acetyltransferases (HAT), consequently enhancing histone acetylation. Moreover, nuclear AMPK can phosphorylate type 2A histone deacetylases (HDAC), e.g. HDAC4 and HDAC5, triggering their export from nuclei thus promoting histone acetylation reactions. AMPK activation can also increase the level of acetyl CoA, e.g. by inhibiting fatty acid and cholesterol syntheses. Acetyl CoA is a substrate for HATs, thus increasing their capacity for histone acetylation. On the other hand, AMPK can stimulate the activity of nicotinamide phosphoribosyltransferase (NAMPT) which increases the level of NAD(+). NAD(+) is a substrate for nuclear sirtuins, especially for SIRT1 and SIRT6, which deacetylate histones and transcription factors, e.g. those regulating ribosome synthesis and circadian clocks. Histone acetylation is an important epigenetic modification which subsequently can affect chromatin remodeling, e.g. via bromodomain proteins. We will review the signaling mechanisms of AMPK/Snf1 in the control of histone acetylation and subsequently clarify their role in the epigenetic regulation of ribosome synthesis and circadian clocks.
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Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland.
| | - Anu Kauppinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kai Kaarniranta
- Department of Ophthalmology, Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland; Department of Ophthalmology, Kuopio University Hospital, Kuopio, Finland
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84
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Ray S, Reddy AB. Cross-talk between circadian clocks, sleep-wake cycles, and metabolic networks: Dispelling the darkness. Bioessays 2016; 38:394-405. [PMID: 26866932 PMCID: PMC4817226 DOI: 10.1002/bies.201500056] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Integration of knowledge concerning circadian rhythms, metabolic networks, and sleep‐wake cycles is imperative for unraveling the mysteries of biological cycles and their underlying mechanisms. During the last decade, enormous progress in circadian biology research has provided a plethora of new insights into the molecular architecture of circadian clocks. However, the recent identification of autonomous redox oscillations in cells has expanded our view of the clockwork beyond conventional transcription/translation feedback loop models, which have been dominant since the first circadian period mutants were identified in fruit fly. Consequently, non‐transcriptional timekeeping mechanisms have been proposed, and the antioxidant peroxiredoxin proteins have been identified as conserved markers for 24‐hour rhythms. Here, we review recent advances in our understanding of interdependencies amongst circadian rhythms, sleep homeostasis, redox cycles, and other cellular metabolic networks. We speculate that systems‐level investigations implementing integrated multi‐omics approaches could provide novel mechanistic insights into the connectivity between daily cycles and metabolic systems.
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Affiliation(s)
- Sandipan Ray
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Akhilesh B Reddy
- Department of Clinical Neurosciences, University of Cambridge Metabolic Research Laboratories, National Institutes of Health Biomedical Research Centre, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
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85
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Yang G, Chen L, Grant GR, Paschos G, Song WL, Musiek ES, Lee V, McLoughlin SC, Grosser T, Cotsarelis G, FitzGerald GA. Timing of expression of the core clock gene Bmal1 influences its effects on aging and survival. Sci Transl Med 2016; 8:324ra16. [PMID: 26843191 PMCID: PMC4870001 DOI: 10.1126/scitranslmed.aad3305] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 12/29/2015] [Indexed: 12/11/2022]
Abstract
The absence of Bmal1, a core clock gene, results in a loss of circadian rhythms, an acceleration of aging, and a shortened life span in mice. To address the importance of circadian rhythms in the aging process, we generated conditional Bmal1 knockout mice that lacked the BMAL1 protein during adult life and found that wild-type circadian variations in wheel-running activity, heart rate, and blood pressure were abolished. Ocular abnormalities and brain astrogliosis were conserved irrespective of the timing of Bmal1 deletion. However, life span, fertility, body weight, blood glucose levels, and age-dependent arthropathy, which are altered in standard Bmal1 knockout mice, remained unaltered, whereas atherosclerosis and hair growth improved, in the conditional adult-life Bmal1 knockout mice, despite abolition of clock function. Hepatic RNA-Seq revealed that expression of oscillatory genes was dampened in the adult-life Bmal1 knockout mice, whereas overall gene expression was largely unchanged. Thus, many phenotypes in conventional Bmal1 knockout mice, hitherto attributed to disruption of circadian rhythms, reflect the loss of properties of BMAL1 that are independent of its role in the clock. These findings prompt reevaluation of the systemic consequences of disruption of the molecular clock.
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Affiliation(s)
- Guangrui Yang
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lihong Chen
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gregory R Grant
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Georgios Paschos
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wen-Liang Song
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Erik S Musiek
- Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Vivian Lee
- Department of Ophthalmology, University of Pennsylvania Scheie Eye Institute, Philadelphia, PA 19104, USA
| | - Sarah C McLoughlin
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tilo Grosser
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George Cotsarelis
- Department of Dermatology, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Garret A FitzGerald
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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86
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Foo M, Somers DE, Kim PJ. Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System. PLoS Comput Biol 2016; 12:e1004748. [PMID: 26828650 PMCID: PMC4734688 DOI: 10.1371/journal.pcbi.1004748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/11/2016] [Indexed: 02/03/2023] Open
Abstract
A wide range of organisms features molecular machines, circadian clocks, which generate endogenous oscillations with ~24 h periodicity and thereby synchronize biological processes to diurnal environmental fluctuations. Recently, it has become clear that plants harbor more complex gene regulatory circuits within the core circadian clocks than other organisms, inspiring a fundamental question: are all these regulatory interactions between clock genes equally crucial for the establishment and maintenance of circadian rhythms? Our mechanistic simulation for Arabidopsis thaliana demonstrates that at least half of the total regulatory interactions must be present to express the circadian molecular profiles observed in wild-type plants. A set of those essential interactions is called herein a kernel of the circadian system. The kernel structure unbiasedly reveals four interlocked negative feedback loops contributing to circadian rhythms, and three feedback loops among them drive the autonomous oscillation itself. Strikingly, the kernel structure, as well as the whole clock circuitry, is overwhelmingly composed of inhibitory, rather than activating, interactions between genes. We found that this tendency underlies plant circadian molecular profiles which often exhibit sharply-shaped, cuspidate waveforms. Through the generation of these cuspidate profiles, inhibitory interactions may facilitate the global coordination of temporally-distant clock events that are markedly peaked at very specific times of day. Our systematic approach resulting in experimentally-testable predictions provides insights into a design principle of biological clockwork, with implications for synthetic biology.
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Affiliation(s)
- Mathias Foo
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea
- School of Engineering, University of Warwick, Coventry, United Kingdom
| | - David E. Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Pan-Jun Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea
- Department of Physics, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
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87
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Choudhary MK, Nomura Y, Shi H, Nakagami H, Somers DE. Circadian Profiling of the Arabidopsis Proteome Using 2D-DIGE. FRONTIERS IN PLANT SCIENCE 2016; 7:1007. [PMID: 27462335 PMCID: PMC4940426 DOI: 10.3389/fpls.2016.01007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 06/27/2016] [Indexed: 05/18/2023]
Abstract
Clock-generated biological rhythms provide an adaptive advantage to an organism, resulting in increased fitness and survival. To better elucidate the plant response to the circadian system, we surveyed protein oscillations in Arabidopsis seedlings under constant light. Using large-scale two-dimensional difference in gel electrophoresis (2D-DIGE) the abundance of more than 1000 proteins spots was reproducibly resolved quantified and profiled across a circadian time series. A comparison between phenol-extracted samples and RuBisCO-depleted extracts identified 71 and 40 rhythmically-expressed proteins, respectively, and between 30 and 40% of these derive from non-rhythmic transcripts. These included proteins influencing transcriptional regulation, translation, metabolism, photosynthesis, protein chaperones, and stress-mediated responses. The phasing of maximum expression for the cyclic proteins was similar for both datasets, with a nearly even distribution of peak phases across the time series. STRING clustering analysis identified two interaction networks with a notable number of oscillating proteins: plastid-based and cytosolic chaperones and 10 proteins involved in photosynthesis. The oscillation of the ABA receptor, PYR1/RCAR11, with peak expression near dusk adds to a growing body of evidence that intimately ties ABA signaling to the circadian system. Taken together, this study provides new insights into the importance of post-transcriptional circadian control of plant physiology and metabolism.
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Affiliation(s)
- Mani K. Choudhary
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - Hua Shi
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource ScienceYokohama, Japan
| | - David E. Somers
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and TechnologyPohang, South Korea
- Department of Molecular Genetics, Ohio State UniversityColumbus, OH, USA
- *Correspondence: David E. Somers
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88
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Martins RST, Gomez A, Zanuy S, Carrillo M, Canário AVM. Photoperiodic Modulation of Circadian Clock and Reproductive Axis Gene Expression in the Pre-Pubertal European Sea Bass Brain. PLoS One 2015; 10:e0144158. [PMID: 26641263 PMCID: PMC4671726 DOI: 10.1371/journal.pone.0144158] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 11/14/2015] [Indexed: 12/19/2022] Open
Abstract
The acquisition of reproductive competence requires the activation of the brain-pituitary-gonad (BPG) axis, which in most vertebrates, including fishes, is initiated by changes in photoperiod. In the European sea bass long-term exposure to continuous light (LL) alters the rhythm of reproductive hormones, delays spermatogenesis and reduces the incidence of precocious males. In contrast, an early shift from long to short photoperiod (AP) accelerates spermatogenesis. However, how photoperiod affects key genes in the brain to trigger the onset of puberty is still largely unknown. Here, we investigated if the integration of the light stimulus by clock proteins is sufficient to activate key genes that trigger the BPG axis in the European sea bass. We found that the clock genes clock, npas2, bmal1 and the BPG genes gnrh, kiss and kissr share conserved transcription factor frameworks in their promoters, suggesting co-regulation. Other gene promoters of the BGP axis were also predicted to be co-regulated by the same frameworks. Co-regulation was confirmed through gene expression analysis of brains from males exposed to LL or AP photoperiod compared to natural conditions: LL fish had suppressed gnrh1, kiss2, galr1b and esr1, while AP fish had stimulated npas2, gnrh1, gnrh2, kiss2, kiss1rb and galr1b compared to NP. It is concluded that fish exposed to different photoperiods present significant expression differences in some clock and reproductive axis related genes well before the first detectable endocrine and morphological responses of the BPG axis.
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Affiliation(s)
- Rute S. T. Martins
- Comparative Endocrinology and Integrative Biology group, Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Ana Gomez
- Department of Fish Physiology and Biotechnology, Instituto de Acuicultura de Torre la Sal, Consejo Superior de Investigaciones Científicas (CSIC), Torre la Sal, Castellón, Spain
| | - Silvia Zanuy
- Department of Fish Physiology and Biotechnology, Instituto de Acuicultura de Torre la Sal, Consejo Superior de Investigaciones Científicas (CSIC), Torre la Sal, Castellón, Spain
| | - Manuel Carrillo
- Department of Fish Physiology and Biotechnology, Instituto de Acuicultura de Torre la Sal, Consejo Superior de Investigaciones Científicas (CSIC), Torre la Sal, Castellón, Spain
| | - Adelino V. M. Canário
- Comparative Endocrinology and Integrative Biology group, Centre of Marine Sciences (CCMAR), University of Algarve, Campus de Gambelas, Faro, Portugal
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89
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Adams S, Manfield I, Stockley P, Carré IA. Revised Morning Loops of the Arabidopsis Circadian Clock Based on Analyses of Direct Regulatory Interactions. PLoS One 2015; 10:e0143943. [PMID: 26625126 PMCID: PMC4666590 DOI: 10.1371/journal.pone.0143943] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/11/2015] [Indexed: 11/24/2022] Open
Abstract
The network structure of the plant circadian clock is complex and direct regulatory interactions between individual components have proven particularly difficult to predict from genetic analyses. Here, we systematically investigate in vivo binding interactions between the morning-specific transcription factor, LATE ELONGATED HYPOCOTYL (LHY) and the promoters of other components of the network. We then demonstrate the functionality of these interactions by testing the responsiveness of the target gene to an ethanol-induced change in expression level of the LHY protein. We uncover novel, negative autoregulatory feedback loops from LHY and the closely related CIRCADIAN CLOCK ASSOCIATED-1 (CCA1) onto their own and each other’s expression. Furthermore we show that LHY acts as a repressor of all other clock components, including PSEUDO-RESPONSE REGULATORs (PRRs) 9 and 7, which were previously thought to be positive regulatory targets. These experimental results lead to a substantial revision of the morning loops of the clock.
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Affiliation(s)
- Sally Adams
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian Manfield
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Peter Stockley
- Astbury Centre, University of Leeds, Leeds, United Kingdom
| | - Isabelle A. Carré
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- * E-mail:
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90
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A tunable artificial circadian clock in clock-defective mice. Nat Commun 2015; 6:8587. [PMID: 26617050 PMCID: PMC4674671 DOI: 10.1038/ncomms9587] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 09/09/2015] [Indexed: 12/17/2022] Open
Abstract
Self-sustaining oscillations are essential for diverse physiological functions such as the cell cycle, insulin secretion and circadian rhythms. Synthetic oscillators using biochemical feedback circuits have been generated in cell culture. These synthetic systems provide important insight into design principles for biological oscillators, but have limited similarity to physiological pathways. Here we report the generation of an artificial, mammalian circadian clock in vivo, capable of generating robust, tunable circadian rhythms. In mice deficient in Per1 and Per2 genes (thus lacking circadian rhythms), we artificially generate PER2 rhythms and restore circadian sleep/wake cycles with an inducible Per2 transgene. Our artificial clock is tunable as the period and phase of the rhythms can be modulated predictably. This feature, and other design principles of our work, might enhance the study and treatment of circadian dysfunction and broader aspects of physiology involving biological oscillators. Circadian rhythms are central to health and disease and there is renewed interest in chronotherapy. Here, the authors present a mouse with an artificial circadian clock that can be pharmacologically tuned, providing a tool for future studies of circadian biology and therapy.
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91
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A Hierarchical Multi-oscillator Network Orchestrates the Arabidopsis Circadian System. Cell 2015; 163:148-59. [DOI: 10.1016/j.cell.2015.08.062] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 07/01/2015] [Accepted: 08/06/2015] [Indexed: 11/23/2022]
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92
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de Bekker C, Ohm RA, Loreto RG, Sebastian A, Albert I, Merrow M, Brachmann A, Hughes DP. Gene expression during zombie ant biting behavior reflects the complexity underlying fungal parasitic behavioral manipulation. BMC Genomics 2015; 16:620. [PMID: 26285697 PMCID: PMC4545319 DOI: 10.1186/s12864-015-1812-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/03/2015] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Adaptive manipulation of animal behavior by parasites functions to increase parasite transmission through changes in host behavior. These changes can range from slight alterations in existing behaviors of the host to the establishment of wholly novel behaviors. The biting behavior observed in Carpenter ants infected by the specialized fungus Ophiocordyceps unilateralis s.l. is an example of the latter. Though parasitic manipulation of host behavior is generally assumed to be due to the parasite's gene expression, few studies have set out to test this. RESULTS We experimentally infected Carpenter ants to collect tissue from both parasite and host during the time period when manipulated biting behavior is experienced. Upon observation of synchronized biting, samples were collected and subjected to mixed RNA-Seq analysis. We also sequenced and annotated the O. unilateralis s.l. genome as a reference for the fungal sequencing reads. CONCLUSIONS Our mixed transcriptomics approach, together with a comparative genomics study, shows that the majority of the fungal genes that are up-regulated during manipulated biting behavior are unique to the O. unilateralis s.l. genome. This study furthermore reveals that the fungal parasite might be regulating immune- and neuronal stress responses in the host during manipulated biting, as well as impairing its chemosensory communication and causing apoptosis. Moreover, we found genes up-regulated during manipulation that putatively encode for proteins with reported effects on behavioral outputs, proteins involved in various neuropathologies and proteins involved in the biosynthesis of secondary metabolites such as alkaloids.
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Affiliation(s)
- Charissa de Bekker
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Goethestrasse 31, 80336, Munich, Germany.
- Department of Entomology and Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA.
| | - Robin A Ohm
- Microbiology, Faculty of Science, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands
| | - Raquel G Loreto
- Department of Entomology and Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, 70040-020, DF, Brazil
| | - Aswathy Sebastian
- Bioinformatics Consulting Center, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA
| | - Istvan Albert
- Bioinformatics Consulting Center, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA
| | - Martha Merrow
- Institute of Medical Psychology, Faculty of Medicine, Ludwig-Maximilians-University Munich, Goethestrasse 31, 80336, Munich, Germany
| | - Andreas Brachmann
- Faculty of Biology, Section Genetics, Ludwig-Maximilians-University Munich, Grosshaderner Strasse 2-4, 82152, Martinsried, Germany
| | - David P Hughes
- Department of Entomology and Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, State College, Pennsylvania, 16802, PA, USA.
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93
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Chen L, Yang G. Recent advances in circadian rhythms in cardiovascular system. Front Pharmacol 2015; 6:71. [PMID: 25883568 PMCID: PMC4381645 DOI: 10.3389/fphar.2015.00071] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/16/2015] [Indexed: 12/20/2022] Open
Abstract
Growing evidence shows that intrinsic circadian clocks are tightly related to cardiovascular functions. The diurnal changes in blood pressure and heart rate are well known circadian rhythms. Endothelial function, platelet aggregation and thrombus formation exhibit circadian changes as well. The onset of many cardiovascular diseases (CVDs) or events, such as myocardial infarction, stroke, arrhythmia, and sudden cardiac death, also exhibits temporal trends. Furthermore, there is strong evidence from animal models and epidemiological studies showing that disruption of circadian rhythms is a significant risk factor for many CVDs, and the intervention of CVDs may have a time dependent effect. In this mini review, we summarized recent advances in our understanding of the relationship between circadian rhythm and cardiovascular physiology and diseases including blood pressure regulation and myocardial infarction.
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Affiliation(s)
- Lihong Chen
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA ; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
| | - Guangrui Yang
- The Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA ; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, PA, USA
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94
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Circadian rhythms in liver metabolism and disease. Acta Pharm Sin B 2015; 5:113-22. [PMID: 26579436 PMCID: PMC4629216 DOI: 10.1016/j.apsb.2015.01.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/24/2014] [Accepted: 01/04/2015] [Indexed: 12/29/2022] Open
Abstract
Mounting research evidence demonstrates a significant negative impact of circadian disruption on human health. Shift work, chronic jet lag and sleep disturbances are associated with increased incidence of metabolic syndrome, and consequently result in obesity, type 2 diabetes and dyslipidemia. Here, these associations are reviewed with respect to liver metabolism and disease.
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Key Words
- ARC, arcuate nucleus
- BMAL1, brain and muscle ARNT-like 1
- CAR, constitutive androstane receptor
- CLOCK, circadian locomotor output cycles kaput
- CRY, cryptochrome
- CYP7A1, cholesterol 7α-hydroxylase
- CYPs, cytochrome P450 enzymes
- Circadian rhythm
- DBP, D-site binding protein
- E-box, enhance box
- EMT, emergency medical technician
- FAA, food anticipatory activity
- FASPS, familial advanced sleep-phase syndrome
- FEO, food entrainable oscillator
- FOXO3, forkhead box O3
- FXR, farnesoid-X receptor
- GLUT2, glucose transporter 2
- HDAC3, histone deacetylase 3
- HIP, hypoxia inducing protein
- HLF, hepatic leukemia factor
- LDL, low-density lipoprotein
- LRH1, liver receptor homolog 1
- Liver
- Metabolic syndrome
- NAD+, nicotinamide adenine dinucleotide
- PER, period
- RHT, retinohypothalamic tract
- RORE, ROR-response element
- RORα, retinoid-related orphan receptor α
- SCN, suprachiasmatic nucleus
- SHP, small heterodimer partner
- SIRT1, sirtuin 1
- TEF, thyrotroph embryonic factor
- TGR5, G protein-coupled bile acid receptor
- TTFL, transcriptional translational feedback loop
- Type 2 diabetes
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Bellemer A. Thermotaxis, circadian rhythms, and TRP channels in Drosophila. Temperature (Austin) 2015; 2:227-43. [PMID: 27227026 PMCID: PMC4843867 DOI: 10.1080/23328940.2015.1004972] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/31/2014] [Accepted: 01/01/2015] [Indexed: 01/24/2023] Open
Abstract
The fruit fly Drosophila melanogaster is a poikilothermic organism that must detect and respond to both fine and coarse changes in environmental temperature in order maintain optimal body temperature, synchronize behavior to daily temperature fluctuations, and to avoid potentially injurious environmental hazards. Members of the Transient Receptor Potential (TRP) family of cation channels are well known for their activation by changes in temperature and their essential roles in sensory transduction in both invertebrates and vertebrates. The Drosophila genome encodes 13 TRP channels, and several of these have key sensory transduction and modulatory functions in allowing larval and adult flies to make fine temperature discriminations to attain optimal body temperature, detect and avoid large environmental temperature fluctuations, and make rapid escape responses to acutely noxious stimuli. Drosophila use multiple, redundant signaling pathways and neural circuits to execute these behaviors in response to both increases and decreases in temperature of varying magnitudes and time scales. A plethora of powerful molecular and genetic tools and the fly's simple, well-characterized nervous system have given Drosophila neurobiologists a powerful platform to study the cellular and molecular mechanisms of TRP channel function and how these mechanisms are conserved in vertebrates, as well as how these channels function within sensorimotor circuits to generate both simple and complex thermosensory behaviors.
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Key Words
- A1, 1st Antennal Segment
- A2, 2nd Antennal Segment
- A3, 3rd Antennal Segment
- AC, Anterior Cell
- AL, Antennal Lobe
- AR, Arista
- Clk, Clock protein
- Cry, Cryptochrome
- Cyc, Cycle protein
- DN1, DN2, DN3, Dorsal Neuron group 1, 2, 3
- Dbt, Double Time protein
- Drosophila melanogaster
- GFP, Green Fluorescent Protein
- GPCR, G Protein-Coupled Receptor
- LN, Lateral Neuron
- LNd, Dorsal Lateral Neuron
- LNv, Ventral Lateral Neuron
- LPN, Lateral Posterior Neuron
- NEL, Nocifensive Escape Locomotion
- PAP, Proximal Antennal Protocerebrum
- PDF, Pigment Dispersing Factor
- PKD1, Polycistic Kidney Disease 1
- PLC, Phospholipase C
- Per, Period protein
- RNAi, RNA interference
- SAC, Sacculus
- SLPR, Superior Lateral Protocerebrum
- SOG, Suboesophageal Ganglion
- TRP channels
- TRP, Transient Receptor Potential
- TRPA, Transient Receptor Potential, group A (ankyrin repeat)
- TRPA1
- TRPC, Transient Receptor Potential, group C (canonical)
- TRPL, TRP-Like
- TRPM, Transient Receptor Potential, group M (melastatin)
- TRPP, Transient Receptor Potential, group P (polycystic)
- TRPV, Transient Receptor Potential, group V (vanilloid)
- Tim, Timeless protein
- VFP, Venus Fluorescent Protein
- circadian rhythms
- lLNv, Ventral Lateral Neuron, large cell body
- mdIV, Multidendritic Neuron, class IV
- nociception
- sLNv, Ventral Lateral Neuron, small cell body
- thermoTRP, thermosensitive TRP channel
- thermosensation
- thermotaxis
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Affiliation(s)
- Andrew Bellemer
- Department of Biology; Appalachian State University ; Boone, NC, USA
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97
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Virag JAI, Lust RM. Circadian influences on myocardial infarction. Front Physiol 2014; 5:422. [PMID: 25400588 PMCID: PMC4214187 DOI: 10.3389/fphys.2014.00422] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 10/12/2014] [Indexed: 11/13/2022] Open
Abstract
Components of circadian rhythm maintenance, or "clock genes," are endogenous entrainable oscillations of about 24 h that regulate biological processes and are found in the suprachaismatic nucleus (SCN) and many peripheral tissues, including the heart. They are influenced by external cues, or Zeitgebers, such as light and heat, and can influence such diverse phenomena as cytokine expression immune cells, metabolic activity of cardiac myocytes, and vasodilator regulation by vascular endothelial cells. While it is known that the central master clock in the SCN synchronizes peripheral physiologic rhythms, the mechanisms by which the information is transmitted are complex and may include hormonal, metabolic, and neuronal inputs. Whether circadian patterns are causally related to the observed periodicity of events, or whether they are simply epi-phenomena is not well established, but a few studies suggest that the circadian effects likely are real in their impact on myocardial infarct incidence. Cycle disturbances may be harbingers of predisposition and subsequent response to acute and chronic cardiac injury, and identifying the complex interactions of circadian rhythms and myocardial infarction may provide insights into possible preventative and therapeutic strategies for susceptible populations.
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Affiliation(s)
- Jitka A I Virag
- Department of Physiology, Brody School of Medicine, East Carolina University Greenville, NC, USA
| | - Robert M Lust
- Department of Physiology, Brody School of Medicine, East Carolina University Greenville, NC, USA
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Richter PR, Strauch SM, Ntefidou M, Schuster M, Daiker V, Nasir A, Haag FWM, Lebert M. Influence of different light-dark cycles on motility and photosynthesis of Euglena gracilis in closed bioreactors. ASTROBIOLOGY 2014; 14:848-858. [PMID: 25279932 PMCID: PMC4201281 DOI: 10.1089/ast.2014.1176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 09/03/2014] [Indexed: 06/03/2023]
Abstract
Abstract The unicellular photosynthetic freshwater flagellate Euglena gracilis is a promising candidate as an oxygen producer in biological life-support systems. In this study, the capacity of Euglena gracilis to cope with different light regimes was determined. Cultures of Euglena gracilis in closed bioreactors were exposed to different dark-light cycles (40 W/m(2) light intensity on the surface of the 20 L reactor; cool white fluorescent lamps in combination with a 100 W filament bulb): 1 h-1 h, 2 h-2 h, 4 h-4 h, 6 h-6 h, and 8 h-16 h, respectively. Motility and oxygen development in the reactors were measured constantly. It was found that, during exposure to light-dark cycles of 1 h-1 h, 2 h-2 h, 4 h-4 h, and 6 h-6 h, precision of gravitaxis as well as the number of motile cells increased during the dark phase, while velocity increased in the light phase. Oxygen concentration did not yet reach a plateau phase. During dark-light cycles of 8 h-16 h, fast changes of movement behavior in the cells were detected. The cells showed an initial decrease of graviorientation after onset of light and an increase after the start of the dark period. In the course of the light phase, graviorientation increased, while motility and velocity decreased after some hours of illumination. In all light profiles, Euglena gracilis was able to produce sufficient oxygen in the light phase to maintain the oxygen concentration above zero in the subsequent dark phase.
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Affiliation(s)
- Peter R Richter
- Cell Biology Division, Gravitational Biology, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen, Germany
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Kim JH, White SL, Devlin RH. Interaction of growth hormone overexpression and nutritional status on pituitary gland clock gene expression in coho salmon,Oncorhynchus kisutch. Chronobiol Int 2014; 32:113-27. [DOI: 10.3109/07420528.2014.958160] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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100
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Schirmer AE, Prete FR, Mantes ES, Urdiales AF, Bogue W. Circadian rhythms affect electroretinogram, compound eye color, striking behavior and locomotion of the praying mantis Hierodula patellifera. ACTA ACUST UNITED AC 2014; 217:3853-61. [PMID: 25214491 DOI: 10.1242/jeb.102947] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many behaviors and physiological processes oscillate with circadian rhythms that are synchronized to environmental cues (e.g. light onset), but persist with periods of ~24 h in the absence of such cues. We used a multilevel experimental approach to assess whether circadian rhythms modulate several aspects of the visual physiology and behavior of the praying mantis Hierodula patellifera. We used electroretinograms (ERGs) to assess compound eye sensitivity, colorimetric photographic analyses to assess compound eye color changes (screening pigment migration), behavioral assays of responsiveness to computer-generated prey-like visual stimuli and analyses of locomotor activity patterns on a modified treadmill apparatus. Our results indicate that circadian clocks control and/or modulate each of the target behaviors. Strong rhythms, persisting under constant conditions, with periods of ~24 h were evident in photoreceptor sensitivity to light, appetitive responsiveness to prey-like stimuli and gross locomotor activity. In the first two cases, responsiveness was highest during the subjective night and lowest during the subjective day. Locomotor activity was strongly clustered around the transition time from day to night. In addition, pigment migration and locomotor behavior responded strongly to light:dark cycles and anticipated the light-dark transition, suggesting that the circadian clocks modulating both were entrained to environmental light cues. Together, these data indicate that circadian rhythms operate at the cellular, cellular systems and organismal level in H. patellifera. Our results represent an intriguing first step in uncovering the complexities of circadian rhythms in the Mantodea.
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Affiliation(s)
- Aaron E Schirmer
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Frederick R Prete
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Edgar S Mantes
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Andrew F Urdiales
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
| | - Wil Bogue
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
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