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Abe S, Takahata Y, Miyakawa H. Daphnia uses its circadian clock for short-day recognition in environmental sex determination. Curr Biol 2024; 34:2002-2010.e3. [PMID: 38579713 DOI: 10.1016/j.cub.2024.03.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/12/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Some organisms have developed a mechanism called environmental sex determination (ESD), which allows environmental cues, rather than sex chromosomes or genes, to determine offspring sex.1,2,3,4 ESD is advantageous to optimize sex ratios according to environmental conditions, enhancing reproductive success.5,6 However, the process by which organisms perceive and translate diverse environmental signals into offspring sex remains unclear. Here, we analyzed the environmental perception mechanism in the crustacean, Daphnia pulex, a seasonal (photoperiodic) ESD arthropod, capable of producing females under long days and males under short days.7,8,9,10 Through breeding experiments, we found that their circadian clock likely contributes to perception of day length. To explore this further, we created a genetically modified daphnid by knocking out the clock gene, period, using genome editing. Knockout disrupted the daphnid's ability to sustain diel vertical migration (DVM) under constant darkness, driven by the circadian clock, and leading them to produce females regardless of day length. Additionally, when exposed to an analog of juvenile hormone (JH), an endocrine factor synthesized in mothers during male production, or subjected to unfavorable conditions of high density and low food availability, these knockout daphnids produced males regardless of day length, like wild-type daphnids. Based on these findings, we propose that recognizing short days via the circadian clock is the initial step in sex determination. This recognition subsequently triggers male production by signaling the endocrine system, specifically via the JH signal. Establishment of a connection between these two processes may be the crucial element in evolution of ESD in Daphnia.
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Affiliation(s)
- Shione Abe
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Yugo Takahata
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan
| | - Hitoshi Miyakawa
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi 321-8505, Japan.
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2
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Chawla S, Oster H, Duffield GE, Maronde E, Guido ME, Chabot C, Dkhissi-Benyahya O, Provencio I, Goel N, Youngstedt SD, Zi-Ching Mak N, Caba M, Nikhat A, Chakrabarti S, Wang L, Davis SJ. Reflections on Several Landmark Advances in Circadian Biology. J Circadian Rhythms 2024; 22:1. [PMID: 38617711 PMCID: PMC11011952 DOI: 10.5334/jcr.236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 04/16/2024] Open
Abstract
Circadian Biology intersects with diverse scientific domains, intricately woven into the fabric of organismal physiology and behavior. The rhythmic orchestration of life by the circadian clock serves as a focal point for researchers across disciplines. This retrospective examination delves into several of the scientific milestones that have fundamentally shaped our contemporary understanding of circadian rhythms. From deciphering the complexities of clock genes at a cellular level to exploring the nuances of coupled oscillators in whole organism responses to stimuli. The field has undergone significant evolution lately guided by genetics approaches. Our exploration here considers key moments in the circadian-research landscape, elucidating the trajectory of this discipline with a keen eye on scientific advancements and paradigm shifts.
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Affiliation(s)
| | - Henrik Oster
- Institute of Neurobiology, Center for Brain, Behavior & Metabolism (CBBM), University of Luebeck, 23562 Luebeck, DE
| | - Giles E. Duffield
- Department of Biological Sciences and Eck Institute for Global Health, Galvin Life Science Center, University of Notre Dame, Notre Dame, IN 46556, US
| | - Erik Maronde
- Institut für Anatomie II, Dr. Senckenbergische Anatomie, Goethe-Universität Frankfurt, Theodor-Stern-Kai-7, 60590 Frankfurt, DE
| | - Mario E. Guido
- CIQUIBIC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, AR
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, AR
| | - Christopher Chabot
- Department of Biological Sciences, Plymouth State University, Plymouth, NH 03264, US
| | - Ouria Dkhissi-Benyahya
- Inserm, Stem Cell and Brain Research Institute U1208, Univ Lyon, UniversitéClaude Bernard Lyon 1, 18 Avenue du Doyen Lépine, 69500, Bron, FR
| | - Ignacio Provencio
- Department of Biology and Department of Ophthalmology, University of Virginia, Charlottesville, VA, US
| | - Namni Goel
- Biological Rhythms Research Laboratory, Department of Psychiatry and Behavioral Sciences, Rush University Medical Center, Chicago, IL, US
| | - Shawn D. Youngstedt
- Edson College of Nursing and Health Innovation, Arizona State University, Phoenix, AZ, US
- Department of Medicine, University of Arizona, Tucson, AZ, US
| | | | - Mario Caba
- Centro de Investigaciones Biomédicas, Universidad Veracruzana, Xalapa, Ver., MX
| | - Anjoom Nikhat
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Shaon Chakrabarti
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Bangalore, Karnataka 560065, IN
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, China National Botanical Garden, Beijing 100093, CN
| | - Seth J. Davis
- Department of Biology, University of York, York YO105DD, UK
- State Key Laboratory of Crop Stress Biology, School of Life Sciences, Henan University, Kaifeng 475004, CN
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3
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Sorkin ML, Markham KK, Zorich S, Menon A, Edgeworth KN, Ricono A, Bryant D, Bart R, Nusinow DA, Greenham K. Assembly and operation of an imaging system for long-term monitoring of bioluminescent and fluorescent reporters in plants. PLANT METHODS 2023; 19:19. [PMID: 36859301 PMCID: PMC9976486 DOI: 10.1186/s13007-023-00997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Non-invasive reporter systems are powerful tools to query physiological and transcriptional responses in organisms. For example, fluorescent and bioluminescent reporters have revolutionized cellular and organismal assays and have been used to study plant responses to abiotic and biotic stressors. Integrated, cooled charge-coupled device (CCD) camera systems have been developed to image bioluminescent and fluorescent signals in a variety of organisms; however, these integrated long-term imaging systems are expensive. RESULTS We have developed self-assembled systems for both growing and monitoring plant fluorescence and bioluminescence for long-term experiments under controlled environmental conditions. This system combines environmental growth chambers with high-sensitivity CCD cameras, multi-wavelength LEDs, open-source software, and several options for coordinating lights with imaging. This easy-to-assemble system can be used for short and long-term imaging of bioluminescent reporters, acute light-response, circadian rhythms, delayed fluorescence, and fluorescent-protein-based assays in vivo. CONCLUSIONS We have developed two self-assembled imaging systems that will be useful to researchers interested in continuously monitoring in vivo reporter systems in various plant species.
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Affiliation(s)
- Maria L Sorkin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | | | | | | | - Kristen N Edgeworth
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- Department of Biological and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA
| | | | - Douglas Bryant
- Donald Danforth Plant Science Center, St. Louis, MO, USA
- NewLeaf Symbiotics, St Louis, MO, USA
| | - Rebecca Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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4
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Mather LM, Cholak ME, Morfoot CM, Curro KC, Love J, Cavanaugh DJ. Inducible Reporter Lines for Tissue-specific Monitoring of Drosophila Circadian Clock Transcriptional Activity. J Biol Rhythms 2023; 38:44-63. [PMID: 36495136 DOI: 10.1177/07487304221138946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Organisms track time of day through the function of cell-autonomous molecular clocks. In addition to a central clock located in the brain, molecular clocks are present in most peripheral tissues. Circadian clocks are coordinated within and across tissues, but the manner through which this coordination is achieved is not well understood. We reasoned that the ability to track in vivo molecular clock activity in specific tissues of the fruit fly, Drosophila melanogaster, would facilitate an investigation into the relationship between different clock-containing tissues. Previous efforts to monitor clock gene expression in single flies in vivo have used regulatory elements of several different clock genes to dictate expression of a luciferase reporter enzyme, the activity of which can be monitored using a luminometer. Although these reporter lines have been instrumental in our understanding of the circadian system, they generally lack cell specificity, making it difficult to compare molecular clock oscillations between different tissues. Here, we report the generation of several novel lines of flies that allow for inducible expression of a luciferase reporter construct for clock gene transcriptional activity. We find that these lines faithfully report circadian transcription, as they exhibit rhythmic luciferase activity that is dependent on a functional molecular clock. Furthermore, we take advantage of our reporter lines' tissue specificity to demonstrate that peripheral molecular clocks are able to retain rhythmicity for multiple days under constant environmental conditions.
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Affiliation(s)
- Lilyan M Mather
- Department of Biology, Loyola University Chicago, Chicago, Illinois
| | - Meghan E Cholak
- Department of Biology, Loyola University Chicago, Chicago, Illinois
| | - Connor M Morfoot
- Department of Biology, Loyola University Chicago, Chicago, Illinois
| | | | - Jacob Love
- Department of Biology, Loyola University Chicago, Chicago, Illinois
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5
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Giesecke A, Johnstone PS, Lamaze A, Landskron J, Atay E, Chen KF, Wolf E, Top D, Stanewsky R. A novel period mutation implicating nuclear export in temperature compensation of the Drosophila circadian clock. Curr Biol 2023; 33:336-350.e5. [PMID: 36584676 DOI: 10.1016/j.cub.2022.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/14/2022] [Accepted: 12/06/2022] [Indexed: 12/30/2022]
Abstract
Circadian clocks are self-sustained molecular oscillators controlling daily changes of behavioral activity and physiology. For functional reliability and precision, the frequency of these molecular oscillations must be stable at different environmental temperatures, known as "temperature compensation." Despite being an intrinsic property of all circadian clocks, this phenomenon is not well understood at the molecular level. Here, we use behavioral and molecular approaches to characterize a novel mutation in the period (per) clock gene of Drosophila melanogaster, which alters a predicted nuclear export signal (NES) of the PER protein and affects temperature compensation. We show that this new perI530A allele leads to progressively longer behavioral periods and clock oscillations with increasing temperature in both clock neurons and peripheral clock cells. While the mutant PERI530A protein shows normal circadian fluctuations and post-translational modifications at cool temperatures, increasing temperatures lead to both severe amplitude dampening and hypophosphorylation of PERI530A. We further show that PERI530A displays reduced repressor activity at warmer temperatures, presumably because it cannot inactivate the transcription factor CLOCK (CLK), indicated by temperature-dependent altered CLK post-translational modification in perI530A flies. With increasing temperatures, nuclear accumulation of PERI530A within clock neurons is increased, suggesting that wild-type PER is exported out of the nucleus at warm temperatures. Downregulating the nuclear export factor CRM1 also leads to temperature-dependent changes of behavioral rhythms, suggesting that the PER NES and the nuclear export of clock proteins play an important role in temperature compensation of the Drosophila circadian clock.
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Affiliation(s)
- Astrid Giesecke
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Peter S Johnstone
- Department of Biochemistry and Molecular Biology and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Angelique Lamaze
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Johannes Landskron
- Centre for Molecular Medicine Norway, University of Oslo, 0318 Oslo, Norway
| | - Ezgi Atay
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany
| | - Ko-Fan Chen
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Eva Wolf
- Johannes Gutenberg University (JGU) and Institute of Molecular Biology (IMB) Mainz, 55128 Mainz, Germany
| | - Deniz Top
- Department of Biochemistry and Molecular Biology and Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Ralf Stanewsky
- Institute of Neuro- and Behavioural Biology, Westfälische Wilhelms University, 48149 Münster, Germany.
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6
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Xiong X, Ma K. Methods to Monitor Circadian Clock Function in Skeletal Muscle. Methods Mol Biol 2023; 2640:249-257. [PMID: 36995600 DOI: 10.1007/978-1-0716-3036-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The circadian clock exerts temporal regulation in physiology and behavior. The skeletal muscle possesses cell-autonomous clock circuits that play key roles in diverse tissue growth, remodeling, and metabolic processes. Recent advances reveal the intrinsic properties, molecular regulations, and physiological functions of the molecular clock oscillators in progenitor and mature myocytes in muscle. While various approaches have been applied to examine clock functions in tissue explants or cell culture systems, defining the tissue-intrinsic circadian clock in muscle requires sensitive real-time monitoring using a Period2 promoter-driven luciferase reporter knock-in mouse model. This chapter describes the gold standard of applying the Per2::Luc reporter line to assess clock properties in skeletal muscle. This technique is suitable for the analysis of clock function in ex vivo muscle preps using intact muscle groups, dissected muscle strips, and cell culture systems using primary myoblasts or myotubes.
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Affiliation(s)
- Xuekai Xiong
- Department of Diabetes Complications & Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Ke Ma
- Department of Diabetes Complications & Metabolism, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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7
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Longitudinal monitoring of individual infection progression in Drosophila melanogaster. iScience 2022; 25:105378. [DOI: 10.1016/j.isci.2022.105378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/26/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022] Open
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8
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Smith CB, van der Vinne V, McCartney E, Stowie AC, Leise TL, Martin-Burgos B, Molyneux PC, Garbutt LA, Brodsky MH, Davidson AJ, Harrington ME, Dallmann R, Weaver DR. Cell-Type-Specific Circadian Bioluminescence Rhythms in Dbp Reporter Mice. J Biol Rhythms 2022; 37:53-77. [PMID: 35023384 DOI: 10.1177/07487304211069452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Circadian rhythms are endogenously generated physiological and molecular rhythms with a cycle length of about 24 h. Bioluminescent reporters have been exceptionally useful for studying circadian rhythms in numerous species. Here, we report development of a reporter mouse generated by modification of a widely expressed and highly rhythmic gene encoding D-site albumin promoter binding protein (Dbp). In this line of mice, firefly luciferase is expressed from the Dbp locus in a Cre recombinase-dependent manner, allowing assessment of bioluminescence rhythms in specific cellular populations. A mouse line in which luciferase expression was Cre-independent was also generated. The Dbp reporter alleles do not alter Dbp gene expression rhythms in liver or circadian locomotor activity rhythms. In vivo and ex vivo studies show the utility of the reporter alleles for monitoring rhythmicity. Our studies reveal cell-type-specific characteristics of rhythms among neuronal populations within the suprachiasmatic nuclei ex vivo. In vivo studies show Dbp-driven bioluminescence rhythms in the liver of Albumin-Cre;DbpKI/+ "liver reporter" mice. After a shift of the lighting schedule, locomotor activity achieved the proper phase relationship with the new lighting cycle more rapidly than hepatic bioluminescence did. As previously shown, restricting food access to the daytime altered the phase of hepatic rhythmicity. Our model allowed assessment of the rate of recovery from misalignment once animals were provided with food ad libitum. These studies confirm the previously demonstrated circadian misalignment following environmental perturbations and reveal the utility of this model for minimally invasive, longitudinal monitoring of rhythmicity from specific mouse tissues.
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Affiliation(s)
- Ciearra B Smith
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Vincent van der Vinne
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Department of Biology, Williams College, Williamstown, Massachusetts
| | | | - Adam C Stowie
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, Georgia
| | - Tanya L Leise
- Department of Mathematics & Statistics, Amherst College, Amherst, Massachusetts
| | | | | | - Lauren A Garbutt
- Division of Biomedical Sciences, Warwick Medical School, The University of Warwick, Coventry, UK
| | - Michael H Brodsky
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts
| | - Alec J Davidson
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, Georgia
| | | | - Robert Dallmann
- Division of Biomedical Sciences, Warwick Medical School, The University of Warwick, Coventry, UK
| | - David R Weaver
- Department of Neurobiology, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,Graduate Program in Neuroscience, University of Massachusetts Chan Medical School, Worcester, Massachusetts.,NeuroNexus Institute, University of Massachusetts Chan Medical School, Worcester, Massachusetts
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9
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Parasram K, Bachetti D, Carmona-Alcocer V, Karpowicz P. Fluorescent Reporters for Studying Circadian Rhythms in Drosophila melanogaster. Methods Mol Biol 2022; 2482:353-371. [PMID: 35610439 DOI: 10.1007/978-1-0716-2249-0_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Circadian rhythms are daily oscillations in physiology and gene expression that are governed by a molecular feedback loop known as the circadian clock. In Drosophila melanogaster, the core clock consists of transcription factors clock (Clk) and cycle (cyc) which form protein heterodimers that activate transcription of their repressors, period (per) and timeless (tim). Once produced, protein heterodimers of per/tim repress Clk/cyc activity. One cycle of activation and repression takes approximately ("circa") 24-h ("diem") and repeats even in the absence of external stimuli. The circadian clock is active in many cells throughout the body; however, tracking it dynamically represents a challenge. Traditional fluorescent reporters are slowly degraded and consequently cannot be used to assess dynamic temporal changes exhibited by the circadian clock. The use of rapidly degraded fluorescent protein reporters containing destabilized GFP (dGFP) that report transcriptional activity in vivo at a single-cell level with ~1-h temporal resolution can circumvent this problem. Here we describe the use of circadian clock reporter strains of Drosophila melanogaster, ClockPER and ClockTIM, to track clock transcriptional activity using the intestine as a tissue of interest. These methods may be extended to other tissues in the body.
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Affiliation(s)
- Kathyani Parasram
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Daniela Bachetti
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | | | - Phillip Karpowicz
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada.
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10
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Functional Imaging Using Bioluminescent Reporter Genes in Living Subjects. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00004-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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11
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van Alphen B, Semenza ER, Yap M, van Swinderen B, Allada R. A deep sleep stage in Drosophila with a functional role in waste clearance. SCIENCE ADVANCES 2021; 7:7/4/eabc2999. [PMID: 33523916 PMCID: PMC7817094 DOI: 10.1126/sciadv.abc2999] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Sleep is a highly conserved state, suggesting that sleep's benefits outweigh the increased vulnerability it brings. Yet, little is known about how sleep fulfills its functions. Here, we used video tracking in tethered flies to identify a discrete deep sleep stage in Drosophila, termed proboscis extension sleep, that is defined by repeated stereotyped proboscis extensions and retractions. Proboscis extension sleep is accompanied by highly elevated arousal thresholds and decreased brain activity, indicative of a deep sleep state. Preventing proboscis extensions increases injury-related mortality and reduces waste clearance. Sleep deprivation reduces waste clearance and during subsequent rebound sleep, sleep, proboscis extensions, and waste clearance are increased. Together, these results provide evidence of a discrete deep sleep stage that is linked to a specific function and suggest that waste clearance is a core and ancient function of deep sleep.
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Affiliation(s)
- Bart van Alphen
- The Department of Neurobiology, Northwestern University, 2205 Tech Drive, Hogan 2-160, Evanston, Illinois 60208, USA.
| | - Evan R Semenza
- The Department of Neurobiology, Northwestern University, 2205 Tech Drive, Hogan 2-160, Evanston, Illinois 60208, USA
| | - Melvyn Yap
- The Queensland Brain Institute, QBI Building, 79, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Bruno van Swinderen
- The Queensland Brain Institute, QBI Building, 79, The University of Queensland, St. Lucia QLD 4072, Australia
| | - Ravi Allada
- The Department of Neurobiology, Northwestern University, 2205 Tech Drive, Hogan 2-160, Evanston, Illinois 60208, USA.
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12
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Muranaka T, Oyama T. Application of Single-Cell Bioluminescent Imaging to Monitor Circadian Rhythms of Individual Plant Cells. Methods Mol Biol 2020; 2081:231-242. [PMID: 31721130 DOI: 10.1007/978-1-4939-9940-8_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
The bioluminescent reporter system is a powerful tool for the long-term monitoring of gene expression because of its noninvasive nature. Furthermore, in combination with high-sensitive imaging technology, spatiotemporal analysis on regulation and heterogeneity in gene expression is possible. We developed a single-cell bioluminescent imaging system for plants through a transient gene transfection by particle bombardment. By applying this system to a duckweed species, we succeeded in monitoring circadian rhythms of individual cells in an intact plant for over a week. Here we describe methods for gene transfection by particle bombardment and single-cell bioluminescence monitoring by a high-sensitive camera. This technique provides a platform for characterizing gene expression patterns of individual cells in the same tissue.
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Affiliation(s)
- Tomoaki Muranaka
- Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
| | - Tokitaka Oyama
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa-oiwake-cho, Kyoto, Japan.
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13
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A Robust and Self-Sustained Peripheral Circadian Oscillator Reveals Differences in Temperature Compensation Properties with Central Brain Clocks. iScience 2020; 23:101388. [PMID: 32798967 PMCID: PMC7452380 DOI: 10.1016/j.isci.2020.101388] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
Circadian clocks are characterized by three properties: they run in constant conditions with a period of ∼24 h, synchronize to the environmental cycles of light and temperature, and are temperature compensated, meaning they do not speed up with temperature. Central brain clocks regulate daily activity rhythms, whereas peripheral clocks are dispersed throughout the body of insects and vertebrates. Using a set of luciferase reporter genes, we show that Drosophila peripheral clocks are self-sustained but over-compensated, i.e., they slow down with increasing temperature. In contrast, central clock neurons in the fly brain, both in intact flies and in cultured brains, show accurate temperature compensation. Although this suggests that neural network properties contribute to temperature compensation, the circadian neuropeptide Pigment Dispersing Factor (PDF) is not required for temperature-compensated oscillations in brain clock neurons. Our findings reveal a fundamental difference between central and peripheral clocks, which likely also applies for vertebrate clocks. Drosophila halteres contain a robust circadian oscillator Circadian clocks of halteres and antennae are over-compensated The Drosophila central brain clock is temperature compensated The neuropeptide PDF is not required for temperature compensation of clock neurons
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14
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Wang Y, Yuan L, Su T, Wang Q, Gao Y, Zhang S, Jia Q, Yu G, Fu Y, Cheng Q, Liu B, Kong F, Zhang X, Song CP, Xu X, Xie Q. Light- and temperature-entrainable circadian clock in soybean development. PLANT, CELL & ENVIRONMENT 2020; 43:637-648. [PMID: 31724182 DOI: 10.1111/pce.13678] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 10/13/2019] [Accepted: 11/08/2019] [Indexed: 05/07/2023]
Abstract
In plants, the spatiotemporal expression of circadian oscillators provides adaptive advantages in diverse species. However, the molecular basis of circadian clock in soybean is not known. In this study, we used soybean hairy roots expression system to monitor endogenous circadian rhythms and the sensitivity of circadian clock to environmental stimuli. We discovered in experiments with constant light and temperature conditions that the promoters of clock genes GmLCLb2 and GmPRR9b1 drive a self-sustained, robust oscillation of about 24-h in soybean hairy roots. Moreover, we demonstrate that circadian clock is entrainable by ambient light/dark or temperature cycles. Specifically, we show that light and cold temperature pulses can induce phase shifts of circadian rhythm, and we found that the magnitude and direction of phase responses depends on the specific time of these two zeitgeber stimuli. We obtained a quadruple mutant lacking the soybean gene GmLCLa1, LCLa2, LCLb1, and LCLb2 using CRISPR, and found that loss-of-function of these four GmLCL orthologs leads to an extreme short-period circadian rhythm and late-flowering phenotype in transgenic soybean. Our study establishes that the morning-phased GmLCLs genes act constitutively to maintain circadian rhythmicity and demonstrates that their absence delays the transition from vegetative growth to reproductive development.
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Affiliation(s)
- Yu Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Li Yuan
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Tong Su
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiao Wang
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ya Gao
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Siyuan Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qian Jia
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Guolong Yu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfu Fu
- MOA Key Lab of Soybean Biology, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qun Cheng
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
- School of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xiao Zhang
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Chun-Peng Song
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaodong Xu
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiguang Xie
- Key Laboratory of Molecular and Cell Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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15
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Urquiza-García U, Millar AJ. Expanding the bioluminescent reporter toolkit for plant science with NanoLUC. PLANT METHODS 2019; 15:68. [PMID: 31316580 PMCID: PMC6613265 DOI: 10.1186/s13007-019-0454-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/28/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Protein data over circadian time scale is scarce for clock transcription factors. Further work in this direction is required for refining quantitative clock models. However, gathering highly resolved dynamics of low-abundance transcription factors has been a major challenge in the field. In this work we provide a new tool that could help this major issue. Bioluminescence is an important tool for gathering data on circadian gene expression. It allows data collection over extended time periods for low signal levels, thanks to a large signal-to-noise ratio. However, the main reporter so far used, firefly luciferase (FLUC), presents some disadvantages for reporting total protein levels. For example, the rapid, post-translational inactivation of this luciferase will result in underestimation of protein numbers. A more stable reporter protein could in principle tackle this issue. We noticed that NanoLUC might fill this gap, given its reported brightness and the stability of both enzyme and substrate. However, no data in plant systems on the circadian time scale had been reported. RESULTS We tested NanoLUC activity under different scenarios that will be important for generating highly quantitative data. These include enzyme purification for calibration curves, expression in transient plant systems, stable transgenic plants and in planta time series over circadian time scales. Furthermore, we show that the difference in substrate use between firefly luciferase and NanoLUC allows tracking of two different reporters from the same samples. We show this by exploring the impact of a BOAp:BOA-NanoLUC construct transformed into a Col-0 CCA1p:FLUC background. CONCLUSIONS We concluded that NanoLUC reporters are compatible with established instrumentation and protocols for firefly luciferase. Overall, our results provide guidelines for researchers gathering dynamic protein data over different time scales and experimental setups.
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Affiliation(s)
- Uriel Urquiza-García
- SynthSys and School of Biological Sciences, University of Edinburgh, C. H. Waddington Building, King’s Buildings, Max Born Crescent, Edinburgh, EH9 3BF Scotland, UK
- Institute for Molecular Plant Sciences, University of Edinburgh, D. Rutherford Building, King’s Buildings, Edinburgh, EH9 3BF UK
| | - Andrew J. Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, C. H. Waddington Building, King’s Buildings, Max Born Crescent, Edinburgh, EH9 3BF Scotland, UK
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16
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Sharp B, Paquet E, Naef F, Bafna A, Wijnen H. A new promoter element associated with daily time keeping in Drosophila. Nucleic Acids Res 2017; 45:6459-6470. [PMID: 28407113 PMCID: PMC5499816 DOI: 10.1093/nar/gkx268] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Circadian clocks are autonomous daily timekeeping mechanisms that allow organisms to adapt to environmental rhythms as well as temporally organize biological functions. Clock-controlled timekeeping involves extensive regulation of rhythmic gene expression. To date, relatively few clock-associated promoter elements have been identified and characterized. In an unbiased search of core clock gene promoters from 12 species of Drosophila, we discovered a 29-bp consensus sequence that we designated as the Clock-Associated Transcriptional Activation Cassette or 'CATAC'. To experimentally address the spatiotemporal expression information associated with this element, we generated constructs with four separate native CATAC elements upstream of a basal promoter driving expression of either the yeast Gal4 or firefly luciferase reporter genes. Reporter assays showed that presence of wild-type, but not mutated CATAC elements, imparted increased expression levels as well as rhythmic regulation. Part of the CATAC consensus sequence resembles the E-box binding site for the core circadian transcription factor CLOCK/CYCLE (CLK/CYC), and CATAC-mediated expression rhythms are lost in the presence of null mutations in either cyc or the gene encoding the CLK/CYC inhibitor, period (per). Nevertheless, our results indicate that CATAC's enhancer function persists in the absence of CLK/CYC. Thus, CATAC represents a novel cis-regulatory element encoding clock-controlled regulation.
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Affiliation(s)
- Brandi Sharp
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA
| | - Eric Paquet
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Felix Naef
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Akanksha Bafna
- Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Herman Wijnen
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA.,Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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17
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Chen X, Rahman R, Guo F, Rosbash M. Genome-wide identification of neuronal activity-regulated genes in Drosophila. eLife 2016; 5. [PMID: 27936378 PMCID: PMC5148613 DOI: 10.7554/elife.19942] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2016] [Accepted: 12/01/2016] [Indexed: 11/22/2022] Open
Abstract
Activity-regulated genes (ARGs) are important for neuronal functions like long-term memory and are well-characterized in mammals but poorly studied in other model organisms like Drosophila. Here we stimulated fly neurons with different paradigms and identified ARGs using high-throughput sequencing from brains as well as from sorted neurons: they included a narrow set of circadian neurons as well as dopaminergic neurons. Surprisingly, many ARGs are specific to the stimulation paradigm and very specific to neuron type. In addition and unlike mammalian immediate early genes (IEGs), fly ARGs do not have short gene lengths and are less enriched for transcription factor function. Chromatin assays using ATAC-sequencing show that the transcription start sites (TSS) of ARGs do not change with neural firing but are already accessible prior to stimulation. Lastly based on binding site enrichment in ARGs, we identified transcription factor mediators of firing and created neuronal activity reporters. DOI:http://dx.doi.org/10.7554/eLife.19942.001
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Affiliation(s)
- Xiao Chen
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Reazur Rahman
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Fang Guo
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
| | - Michael Rosbash
- Howard Hughes Medical Institute, Brandeis University, Waltham, United States.,National Center for Behavioral Genomics, Department of Biology, Brandeis University, Waltham, United States
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18
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Khabirova E, Chen KF, O'Neill JS, Crowther DC. Flyglow: Single-fly observations of simultaneous molecular and behavioural circadian oscillations in controls and an Alzheimer's model. Sci Rep 2016; 6:33759. [PMID: 27658441 PMCID: PMC5034315 DOI: 10.1038/srep33759] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/02/2016] [Indexed: 12/02/2022] Open
Abstract
Circadian rhythms are essential for health and are frequently disturbed in disease. A full understanding of the causal relationships between behavioural and molecular circadian rhythms requires simultaneous longitudinal observations over time in individual organisms. Current experimental paradigms require the measurement of each rhythm separately across distinct populations of experimental organisms, rendering the comparability of the resulting datasets uncertain. We therefore developed FLYGLOW, an assay using clock gene controlled luciferase expression detected by exquisitely sensitive EM-CCD imaging, to enable simultaneous quantification of parameters including locomotor, sleep consolidation and molecular rhythms in single flies over days/weeks. FLYGLOW combines all the strengths of existing techniques, and also allows powerful multiparametric paired statistics. We found the age-related transition from rhythmicity to arrhythmicity for each parameter occurs unpredictably, with some flies showing loss of one or more rhythms during middle-age. Using single-fly correlation analysis of rhythm robustness and period we demonstrated the independence of the peripheral clock from circadian behaviours in wild type flies as well as in an Alzheimer’s model. FLYGLOW is a useful tool for investigating the deterioration of behavioural and molecular rhythms in ageing and neurodegeneration. This approach may be applied more broadly within behavioural neurogenetics research.
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Affiliation(s)
- Eleonora Khabirova
- University of Cambridge, Department of Genetics, Downing Site, Cambridge, CB2 3EH, United Kingdom
| | - Ko-Fan Chen
- University of Cambridge, Department of Genetics, Downing Site, Cambridge, CB2 3EH, United Kingdom.,UCL Institute of Neurology, London WC1N 3BG, United Kingdom
| | - John S O'Neill
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Damian C Crowther
- University of Cambridge, Department of Genetics, Downing Site, Cambridge, CB2 3EH, United Kingdom.,AstraZeneca, Neuroscience, Sir Aaron Klug Building, Granta Park, Cambridge, CB21 6GH, United Kingdom
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19
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Fischer R, Helfrich-Förster C, Peschel N. GSK-3 Beta Does Not Stabilize Cryptochrome in the Circadian Clock of Drosophila. PLoS One 2016; 11:e0146571. [PMID: 26741981 PMCID: PMC4704813 DOI: 10.1371/journal.pone.0146571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 12/08/2015] [Indexed: 11/19/2022] Open
Abstract
Cryptochrome (CRY) is the primary photoreceptor of Drosophila’s circadian clock. It resets the circadian clock by promoting light-induced degradation of the clock protein Timeless (TIM) in the proteasome. Under constant light, the clock stops because TIM is absent, and the flies become arrhythmic. In addition to TIM degradation, light also induces CRY degradation. This depends on the interaction of CRY with several proteins such as the E3 ubiquitin ligases Jetlag (JET) and Ramshackle (BRWD3). However, CRY can seemingly also be stabilized by interaction with the kinase Shaggy (SGG), the GSK-3 beta fly orthologue. Consequently, flies with SGG overexpression in certain dorsal clock neurons are reported to remain rhythmic under constant light. We were interested in the interaction between CRY, Ramshackle and SGG and started to perform protein interaction studies in S2 cells. To our surprise, we were not able to replicate the results, that SGG overexpression does stabilize CRY, neither in S2 cells nor in the relevant clock neurons. SGG rather does the contrary. Furthermore, flies with SGG overexpression in the dorsal clock neurons became arrhythmic as did wild-type flies. Nevertheless, we could reproduce the published interaction of SGG with TIM, since flies with SGG overexpression in the lateral clock neurons shortened their free-running period. We conclude that SGG does not directly interact with CRY but rather with TIM. Furthermore we could demonstrate, that an unspecific antibody explains the observed stabilization effects on CRY.
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Affiliation(s)
- Robin Fischer
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | | | - Nicolai Peschel
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
- * E-mail:
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20
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Goda T, Sharp B, Wijnen H. Temperature-dependent resetting of the molecular circadian oscillator in Drosophila. Proc Biol Sci 2015; 281:rspb.2014.1714. [PMID: 25165772 DOI: 10.1098/rspb.2014.1714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Circadian clocks responsible for daily time keeping in a wide range of organisms synchronize to daily temperature cycles via pathways that remain poorly understood. To address this problem from the perspective of the molecular oscillator, we monitored temperature-dependent resetting of four of its core components in the fruitfly Drosophila melanogaster: the transcripts and proteins for the clock genes period (per) and timeless (tim). The molecular circadian cycle in adult heads exhibited parallel responses to temperature-mediated resetting at the levels of per transcript, tim transcript and TIM protein. Early phase adjustment specific to per transcript rhythms was explained by clock-independent temperature-driven transcription of per. The cold-induced expression of Drosophila per contrasts with the previously reported heat-induced regulation of mammalian Period 2. An altered and more readily re-entrainable temperature-synchronized circadian oscillator that featured temperature-driven per transcript rhythms and phase-shifted TIM and PER protein rhythms was found for flies of the 'Tim 4' genotype, which lacked daily tim transcript oscillations but maintained post-transcriptional temperature entrainment of tim expression. The accelerated molecular and behavioural temperature entrainment observed for Tim 4 flies indicates that clock-controlled tim expression constrains the rate of temperature cycle-mediated circadian resetting.
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Affiliation(s)
- Tadahiro Goda
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, USA
| | - Brandi Sharp
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, USA
| | - Herman Wijnen
- Department of Biology, University of Virginia, Charlottesville, VA 22904-4328, USA Centre for Biological Sciences and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
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21
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Automated monitoring and quantitative analysis of feeding behaviour in Drosophila. Nat Commun 2014; 5:4560. [PMID: 25087594 PMCID: PMC4143931 DOI: 10.1038/ncomms5560] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/30/2014] [Indexed: 11/08/2022] Open
Abstract
Food ingestion is one of the defining behaviours of all animals, but its quantification and analysis remain challenging. This is especially the case for feeding behaviour in small, genetically tractable animals such as Drosophila melanogaster. Here, we present a method based on capacitive measurements, which allows the detailed, automated and high-throughput quantification of feeding behaviour. Using this method, we were able to measure the volume ingested in single sips of an individual, and monitor the absorption of food with high temporal resolution. We demonstrate that flies ingest food by rhythmically extending their proboscis with a frequency that is not modulated by the internal state of the animal. Instead, hunger and satiety homeostatically modulate the microstructure of feeding. These results highlight similarities of food intake regulation between insects, rodents, and humans, pointing to a common strategy in how the nervous systems of different animals control food intake. Feeding is an important behaviour, but its quantification remains challenging, particularly in small animal models like Drosophila melanogaster. Here the authors describe a method which uses capacitive sensing for automated high-resolution measuring of feeding behaviour in individual flies.
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22
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Fropf R, Zhang J, Tanenhaus AK, Fropf WJ, Siefkes E, Yin JCP. Time of day influences memory formation and dCREB2 proteins in Drosophila. Front Syst Neurosci 2014; 8:43. [PMID: 24744705 PMCID: PMC3978337 DOI: 10.3389/fnsys.2014.00043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/11/2014] [Indexed: 11/15/2022] Open
Abstract
Many biological phenomena oscillate under the control of the circadian system, exhibiting peaks and troughs of activity across the day/night cycle. In most animal models, memory formation also exhibits this property, but the underlying neuronal and molecular mechanisms remain unclear. The dCREB2 transcription factor shows circadian regulated oscillations in its activity, and has been shown to be important for both circadian biology and memory formation. We show that the time-of-day (TOD) of behavioral training affects Drosophila memory formation. dCREB2 exhibits complex changes in protein levels across the daytime and nighttime, and these changes in protein abundance are likely to contribute to oscillations in dCREB2 activity and TOD effects on memory formation.
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Affiliation(s)
- Robin Fropf
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA ; Neuroscience Training Program, University of Wisconsin-Madison Madison, WI, USA
| | - Jiabin Zhang
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA ; Neuroscience Training Program, University of Wisconsin-Madison Madison, WI, USA
| | - Anne K Tanenhaus
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA ; Neuroscience Training Program, University of Wisconsin-Madison Madison, WI, USA
| | - Whitney J Fropf
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA
| | - Ellen Siefkes
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA
| | - Jerry C P Yin
- Departments of Genetics, University of Wisconsin-Madison Madison, WI, USA ; Department of Neurology, University of Wisconsin-Madison Madison, WI, USA
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23
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Tataroglu O, Emery P. Studying circadian rhythms in Drosophila melanogaster. Methods 2014; 68:140-50. [PMID: 24412370 DOI: 10.1016/j.ymeth.2014.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/02/2014] [Indexed: 11/25/2022] Open
Abstract
Circadian rhythms have a profound influence on most bodily functions: from metabolism to complex behaviors. They ensure that all these biological processes are optimized with the time-of-day. They are generated by endogenous molecular oscillators that have a period that closely, but not exactly, matches day length. These molecular clocks are synchronized by environmental cycles such as light intensity and temperature. Drosophila melanogaster has been a model organism of choice to understand genetically, molecularly and at the level of neural circuits how circadian rhythms are generated, how they are synchronized by environmental cues, and how they drive behavioral cycles such as locomotor rhythms. This review will cover a wide range of techniques that have been instrumental to our understanding of Drosophila circadian rhythms, and that are essential for current and future research.
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Affiliation(s)
- Ozgur Tataroglu
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, United States
| | - Patrick Emery
- Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, United States.
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24
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Light-dependent and circadian transcription dynamics in vivo recorded with a destabilized luciferase reporter in Neurospora. PLoS One 2013; 8:e83660. [PMID: 24391804 PMCID: PMC3877077 DOI: 10.1371/journal.pone.0083660] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 11/13/2013] [Indexed: 11/19/2022] Open
Abstract
We show that firefly luciferase is a stable protein when expressed at 25 °C in Neurospora, which limits its use as transcription reporter. We created a short-lived luciferase by fusing a PEST signal to its C-terminus (LUC-PEST) and applied the LUC-PEST reporter system to record in vivo transcription dynamics associated with the Neurospora circadian clock and its blue-light photosensory system over the course of several days. We show that the tool is suitable to faithfully monitor rapid, but also subtle changes in transcription in a medium to high throughput format.
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25
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Tanenhaus AK, Zhang J, Yin JCP. In vivo circadian oscillation of dCREB2 and NF-κB activity in the Drosophila nervous system. PLoS One 2012; 7:e45130. [PMID: 23077489 PMCID: PMC3471920 DOI: 10.1371/journal.pone.0045130] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 08/14/2012] [Indexed: 12/15/2022] Open
Abstract
cAMP response element-binding protein (CREB) and nuclear factor kappa-B (NF-κB) are two ubiquitous transcription factors involved in a wide number of cellular processes, including the circadian system. Many previous studies on these factors use cellular assays that provide limited information on circadian activity or anatomical specificity. The ability to study transcription factors in defined tissue within intact animals will help to bridge the gap between cellular and in vivo data. We have used the GAL4-UAS and FLP-FRT systems to gain spatial control over reporter gene expression. Using a luciferase-based reporter, we show in vivo that Drosophila dCREB2- and NF-κB-mediated transcription oscillates in neuronal cells, glia, and in the mushroom body, a higher-order brain center in flies. This oscillation is under circadian control, cycling with a 24-hour rhythm, under both light-dark and dark-dark conditions. In light-light conditions, dCREB2 and NF-κB reporter flies exhibit a suppression of rhythmic activity. Furthermore, neuronal cycling of dCREB2 and NF-κB activity are modulated in period mutant flies, indicating these oscillations are controlled through the central clock. This study shows for the first time region-specific circadian oscillation of dCREB2/NF-κB activity in the Drosophila nervous system.
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Affiliation(s)
- Anne K. Tanenhaus
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jiabin Zhang
- Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53706
| | - Jerry C. P. Yin
- Departments of Genetics and Neurology, University of Wisconsin-Madison, Madison, WI 53706
- * E-mail:
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26
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Abstract
Bioluminescence imaging of live cells has recently been recognized as an important alternative to fluorescence imaging. Fluorescent probes are much brighter than bioluminescent probes (luciferase enzymes) and, therefore, provide much better spatial and temporal resolution and much better contrast for delineating cell structure. However, with bioluminescence imaging there is virtually no background or toxicity. As a result, bioluminescence can be superior to fluorescence for detecting and quantifying molecules and their interactions in living cells, particularly in long-term studies. Structurally diverse luciferases from beetle and marine species have been used for a wide variety of applications, including tracking cells in vivo, detecting protein-protein interactions, measuring levels of calcium and other signaling molecules, detecting protease activity, and reporting circadian clock gene expression. Such applications can be optimized by the use of brighter and variously colored luciferases, brighter microscope optics, and ultrasensitive, low-noise cameras. This article presents a review of how bioluminescence differs from fluorescence, its applications to cellular imaging, and available probes, optics, and detectors. It also gives practical suggestions for optimal bioluminescence imaging of single cells.
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27
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Neuronal influence on peripheral circadian oscillators in pupal Drosophila prothoracic glands. Nat Commun 2012; 3:909. [PMID: 22713751 PMCID: PMC3621432 DOI: 10.1038/ncomms1922] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/22/2012] [Indexed: 11/08/2022] Open
Abstract
Rhythmic expression of period (per) and timeless (tim) genes in central circadian pacemaker neurons and prothoracic gland cells, part of the peripheral circadian oscillators in flies, may synergistically control eclosion rhythms, but their oscillatory profiles remain unclear. Here we show differences and interactions between peripheral and central oscillators using per-luciferase and cytosolic Ca2+ reporter (yellow cameleon) imaging in organotypic prothoracic gland cultures with or without the associated central nervous system. Isolated prothoracic gland cells exhibit light-insensitive synchronous per-transcriptional rhythms. In prothoracic gland cells associated with the central nervous system, however, per transcription is markedly amplified following 12-h light exposure, resulting in the manifestation of day–night rhythms in nuclear PER immunostaining levels and spontaneous Ca2+ spiking. Unlike PER expression, nuclear TIM expression is associated with day–night cycles that are independent of the central nervous system. These results demonstrate that photoreception and synaptic signal transduction in/from the central nervous system coordinate molecular 'gears' in endocrine oscillators to generate physiological rhythms. In the fruit fly Drosophila, changes in expression of circadian clock genes are believed to control eclosion. Morioka and colleagues show that transcriptional oscillations of the clock gene, period, in prothoracic gland cells are amplified by photic inputs from the central nervous system.
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28
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Pulit-Penaloza JA, Scherbik SV, Brinton MA. Activation of Oas1a gene expression by type I IFN requires both STAT1 and STAT2 while only STAT2 is required for Oas1b activation. Virology 2012; 425:71-81. [PMID: 22305621 DOI: 10.1016/j.virol.2011.11.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 09/15/2011] [Accepted: 11/29/2011] [Indexed: 12/24/2022]
Abstract
The murine 2'-5' oligoadenylate synthetase 1a (Oas1a) and Oas1b genes are type 1 IFN responsive genes. Oas1a is an active synthetase with broad antiviral activity mediated through RNase L. Oas1b is inactive but can inhibit Oas1a synthetase activity and mediate a flavivirus-specific antiviral activity through an unknown RNase L-independent mechanism. Analysis of promoter elements regulating gene transcription confirmed that an IFN-stimulated response element (ISRE) is required for IFN beta-activation but neither the overlapping IRF binding site present in both promoters nor the adjacent Oas1b NF-kappa B site is required. Mutation of the overlapping STAT site negatively affected IFN beta-induction of Oas1a but not of Oas1b. Also, IFN beta induction of Oas1a was STAT1- and STAT2-dependent, while induction of Oas1b was STAT1-independent but STAT2-dependent. The two promoters differ at a single nucleotide in the STAT site. The data indicate that these two duplicated genes can be differentially regulated by IFN beta.
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29
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Moschos SA, Frick M, Taylor B, Turnpenny P, Graves H, Spink KG, Brady K, Lamb D, Collins D, Rockel TD, Weber M, Lazari O, Perez-Tosar L, Fancy SA, Lapthorn C, Green MX, Evans S, Selby M, Jones G, Jones L, Kearney S, Mechiche H, Gikunju D, Subramanian R, Uhlmann E, Jurk M, Vollmer J, Ciaramella G, Yeadon M. Uptake, efficacy, and systemic distribution of naked, inhaled short interfering RNA (siRNA) and locked nucleic acid (LNA) antisense. Mol Ther 2011; 19:2163-8. [PMID: 21971426 PMCID: PMC3242665 DOI: 10.1038/mt.2011.206] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 08/30/2011] [Indexed: 12/20/2022] Open
Abstract
Antisense oligonucleotides (ASOs) and small interfering RNA (siRNA) promise specific correction of disease-causing gene expression. Therapeutic implementation, however, has been forestalled by poor delivery to the appropriate tissue, cell type, and subcellular compartment. Topical administration is considered to circumvent these issues. The availability of inhalation devices and unmet medical need in lung disease has focused efforts in this tissue. We report the development of a novel cell sorting method for quantitative, cell type-specific analysis of siRNA, and locked nucleic acid (LNA) ASO uptake and efficacy after intratracheal (i.t.) administration in mice. Through fluorescent dye labeling, we compare the utility of this approach to whole animal and whole tissue analysis, and examine the extent of tissue distribution. We detail rapid systemic access and renal clearance for both therapeutic classes and lack of efficacy at the protein level in lung macrophages, epithelia, or other cell types. We nevertheless observe efficient redirection of i.t. administered phosphorothioate (PS) LNA ASO to the liver and kidney leading to targeted gene knockdown. These data suggest delivery remains a key obstacle to topically administered, naked oligonucleotide efficacy in the lung and introduce inhalation as a potentially viable alternative to injection for antisense administration to the liver and kidneys.
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30
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Matsuo T, Ishiura M. Chlamydomonas reinhardtiias a new model system for studying the molecular basis of the circadian clock. FEBS Lett 2011; 585:1495-502. [DOI: 10.1016/j.febslet.2011.02.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2010] [Revised: 01/31/2011] [Accepted: 02/21/2011] [Indexed: 12/31/2022]
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Ryan PL, Christiansen DL, Hopper RM, Walters FK, Moulton K, Curbelo J, Greene JM, Willard ST. Horse species symposium: a novel approach to monitoring pathogen progression during uterine and placental infection in the mare using bioluminescence imaging technology and lux-modified bacteria. J Anim Sci 2011; 89:1541-51. [PMID: 21239661 DOI: 10.2527/jas.2010-3629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Uterine and placental infections are the leading cause of abortion, stillbirth, and preterm delivery in the mare. Whereas uterine and placental infections in women have been studied extensively, a comprehensive examination of the pathogenic processes leading to this unsatisfactory pregnancy outcome in the mare has yet to be completed. Most information in the literature relating to late-term pregnancy loss in mares is based on retrospective studies of clinical cases submitted for necropsy. Here we report the development and application of a novel approach, whereby transgenically modified bacteria transformed with lux genes of Xenorhabdus luminescens or Photorhabdus luminescens origin and biophotonic imaging are utilized to better understand pathogen-induced preterm birth in late-term pregnant mares. This technology uses highly sensitive bioluminescence imaging camera systems to localize and monitor pathogen progression during tissue invasion by measuring the bioluminescent signatures emitted by the lux-modified pathogens. This method has an important advantage in that it allows for the potential tracking of pathogens in vivo in real time and over time, which was hitherto impossible. Although the application of this technology in domestic animals is in its infancy, investigators were successful in identifying the fetal lungs, sinuses, nares, urinary, and gastrointestinal systems as primary tissues for pathogen invasion after experimental infection of pregnant mares with lux-modified Escherichia coli. It is important that pathogens were not detected in other vital organs, such as the liver, brain, and cardiac system. Such precision in localizing sites of pathogen invasion provides potential application for this novel approach in the development of more targeted therapeutic interventions for pathogen-related diseases in the equine and other domestic species.
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Affiliation(s)
- P L Ryan
- Department of Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MI 39762, USA.
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Robertson JB, Johnson CH. Luminescence as a continuous real-time reporter of promoter activity in yeast undergoing respiratory oscillations or cell division rhythms. Methods Mol Biol 2011; 734:63-79. [PMID: 21468985 DOI: 10.1007/978-1-61779-086-7_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This chapter describes a method for generating yeast respiratory oscillations in continuous culture and monitoring rhythmic promoter activity of the culture by automated real-time recording of luminescence. These techniques chiefly require the use of a strain of Saccharomyces cerevisiae that has been genetically modified to express firefly luciferase under the control of a promoter of interest and a continuous culture bioreactor that incorporates a photomultiplier apparatus for detecting light emission. Additionally, this chapter describes a method for observing rhythmic (cell cycle-related) promoter activity in small batch cultures of yeast through luminescence monitoring.
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Affiliation(s)
- J Brian Robertson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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Bioluminescence imaging of Arc expression enables detection of activity-dependent and plastic changes in the visual cortex of adult mice. Brain Struct Funct 2010; 216:91-104. [PMID: 21170725 DOI: 10.1007/s00429-010-0297-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Accepted: 12/06/2010] [Indexed: 02/04/2023]
Abstract
Induction of the activity-regulated cytoskeleton-associated protein gene (Arc), one of the immediate early genes, in the brain correlates with various sensory processes, natural behaviors, and pathological conditions. Arc is also involved in synaptic plasticity during development. Thus, in vivo monitoring of Arc expression is useful for the analysis of physiological and pathological conditions in the brain. Recently, in vivo imaging of Arc expression using various green fluorescent protein-based probes has been reported; however, these probes can only be applied for the detection of fluorescence signals from superficial layers of the cortex with some autofluorescence noise. Here, we generated a novel transgenic mouse strain to monitor the neuronal-activity-dependent Arc expression using bioluminescence signals in vivo. Because of the very high sensitivity with a high signal-to-noise ratio, we detected neuronal-activity-dependent plastic changes in the bioluminescence signal intensity in the mouse visual cortex after visual deprivation, suggesting structural plasticity after peripheral lesions in adults. We also detected drastic changes in bioluminescence signals after seizure induction with kainic acid. Our novel mouse strain will be valuable for the continuous monitoring of neuronal-activity-dependent Arc expression in the brain under physiological and pathological conditions.
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Zheng S, Eacker SM, Hong SJ, Gronostajski RM, Dawson TM, Dawson VL. NMDA-induced neuronal survival is mediated through nuclear factor I-A in mice. J Clin Invest 2010; 120:2446-56. [PMID: 20516644 DOI: 10.1172/jci33144] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 04/14/2010] [Indexed: 11/17/2022] Open
Abstract
Identification of the signaling pathways that mediate neuronal survival signaling could lead to new therapeutic targets for neurologic disorders and stroke. Sublethal doses of NMDA can induce robust endogenous protective mechanisms in neurons. Through differential analysis of primary library expression and microarray analyses, here we have shown that nuclear factor I, subtype A (NFI-A), a member of the NFI/CAAT-box transcription factor family, is induced in mouse neurons by NMDA receptor activation in a NOS- and ERK-dependent manner. Knockdown of NFI-A induction using siRNA substantially reduced the neuroprotective effects of sublethal doses of NMDA. Further analysis indicated that NFI-A transcriptional activity was required for the neuroprotective effects of NMDA receptor activation. Additional evidence of the neuroprotective effects of NFI-A was provided by the observations that Nfia(-/-) neurons were highly sensitive to NMDA-induced excitotoxicity and were more susceptible to developmental cell death than wild-type neurons and that Nfia(+/-) mice were more sensitive to NMDA-induced intrastriatal lesions than were wild-type animals. These results identify NFI-A as what we believe to be a novel neuroprotective transcription factor with implications in neuroprotection and neuronal plasticity following NMDA receptor activation.
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Affiliation(s)
- Sika Zheng
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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35
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New Insights into the Circadian Clock in Chlamydomonas. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 280:281-314. [DOI: 10.1016/s1937-6448(10)80006-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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36
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Martin JR. In VivoBrain Imaging: Fluorescence or Bioluminescence, Which to Choose? J Neurogenet 2009; 22:285-307. [DOI: 10.1080/01677060802298517] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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A role for the PERIOD:PERIOD homodimer in the Drosophila circadian clock. PLoS Biol 2009; 7:e3. [PMID: 19402744 PMCID: PMC2671555 DOI: 10.1371/journal.pbio.1000003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 11/12/2008] [Indexed: 01/13/2023] Open
Abstract
Circadian clocks in eukaryotes rely on transcriptional feedback loops, in which clock genes repress their own transcription resulting in molecular oscillations with a period of ∼24 h. In Drosophila, the clock proteins Period (PER) and Timeless (TIM) operate in such a feedback loop, whereby they first accumulate in the cytoplasm of clock cells as a heterodimer. Nuclear translocation of the complex or the individual PER and TIM proteins is followed by repression of per and tim transcription, whereby PER seems to act as the prime repressor. We found that in addition to PER:TIM complexes, functional PER:PER homodimers exist in flies. Specific disruption of PER homodimers results in drastically impaired behavioral and molecular rhythmicity, pointing the biological importance of this clock protein complex. Analysis of PER subcellular distribution and repressor competence in the PER dimer mutant revealed defects in PER nuclear translocation and a disruption of rhythmic period transcription. The striking similarity of these phenotypes with that of reduced CKII activity suggests that the formation or function of the PER dimer is closely linked to this kinase. Our results confirm a previous structural model for PER and provide strong evidence that PER homodimers are important for circadian clock function. The current models of circadian clocks in flies and mammals involve the formation of complexes between clock proteins in the cytoplasm. These complexes are usually heterodimers (that is, made up of two different clock proteins) and appear to enter the nucleus at certain times of the circadian day in order to shut down their own gene expression by deactivating specific transcription factors. After progressive phosphorylation the repressor proteins eventually are degraded so that a new cycle of transcription can begin. Here we present evidence that in addition to heterodimeric complexes, the clock protein PERIOD (PER) also forms homodimers (pairs of identical proteins). Based on a structural model a PER mutant was designed, which is not able to form homodimers but can still bind to its partner TIMELESS (TIM). Flies expressing this mutant PER protein show abnormal clock function in regard to PER nuclear translocation, repressor activity, and behavioral rhythms. The circadian clock model in flies therefore needs to be extended by adding the PER:PER homodimer as a functional unit. Recent structural studies with mammalian PER proteins suggest that homodimers between clock proteins are an important general feature of eukaryotic clocks. The circadian molecular clock model needs to be extended by adding the PERIOD:PERIOD homodimer as a functional unit in rhythm generation in Drosophila. Blocking this dimerization leads to faulty nuclear localization, reduced repressor activity, and impaired behavioral rhythms.
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Abstract
In mammals, AU-rich elements (AREs) are critical regulators of mRNA turnover. They recruit ARE-binding proteins that inhibit or stimulate rapid mRNA degradation in response to stress or developmental cues. Using a bioinformatics approach, we have identified AREs in Drosophila melanogaster 3' untranslated regions and validated their cross-species conservation in distant Drosophila genomes. We have generated a Drosophila ARE database (D-ARED) and established that about 16% of D. melanogaster genes contain the mammalian ARE signature, an AUUUA pentamer in an A/U-rich context. Using candidate ARE genes, we show that Drosophila AREs stimulate reporter mRNA decay in cultured cells and in the physiological context of the immune response in D. melanogaster. In addition, we found that the conserved ARE-binding protein Tis11 regulates temporal gene expression through ARE-mediated decay (AMD) in D. melanogaster. Our work reveals that AREs are conserved and functional cis regulators of mRNA decay in Drosophila and highlights this organism as a novel model system to unravel in vivo the contribution of AMD to various processes.
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Iijima-Ando K, Yin JCP. Transgenic cAMP response element reporter flies for monitoring circadian rhythms. Methods Enzymol 2008; 393:302-15. [PMID: 15817296 DOI: 10.1016/s0076-6879(05)93013-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The cAMP response Element (CRE)-binding protein (CREB) is involved in many adaptive behaviors, including circadian rhythms. In order to assess CREB activity in vivo, we made transgenic flies carrying a CRE-luciferase reporter and showed that this reporter is CRE and dCREB2 responsive. dCREB2 is the Drosophila homolog of mammalian CREB?CREM. The transgenic luciferase activity cycles with a 24-h periodicity, suggesting that dCREB2 and period are somehow linked. The CRE-luciferase reporter is a useful monitor of circadian activity, and mutations can be found that affect its periodicity, baseline activity, or amplitude. Analysis of such mutations should reveal information about how particular genes affect the molecular machinery of circadian cycling and how different genes affect the activity of dCREB2.
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Affiliation(s)
- Kanae Iijima-Ando
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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40
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Kivimäe S, Saez L, Young MW. Activating PER repressor through a DBT-directed phosphorylation switch. PLoS Biol 2008; 6:e183. [PMID: 18666831 PMCID: PMC2486307 DOI: 10.1371/journal.pbio.0060183] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Accepted: 06/17/2008] [Indexed: 11/18/2022] Open
Abstract
Protein phosphorylation plays an essential role in the generation of circadian rhythms, regulating the stability, activity, and subcellular localization of certain proteins that constitute the biological clock. This study examines the role of the protein kinase Doubletime (DBT), a Drosophila ortholog of human casein kinase I (CKI)ɛ/δ. An enzymatically active DBT protein is shown to directly phosphorylate the Drosophila clock protein Period (PER). DBT-dependent phosphorylation sites are identified within PER, and their functional significance is assessed in a cultured cell system and in vivo. The perS mutation, which is associated with short-period (19-h) circadian rhythms, alters a key phosphorylation target within PER. Inspection of this and neighboring sequence variants indicates that several DBT-directed phosphorylations regulate PER activity in an integrated fashion: Alternative phosphorylations of two adjoining sequence motifs appear to be associated with switch-like changes in PER stability and repressor function. Most proteins involved in circadian transcriptional feedback loops undergo reversible chemical modifications (called phosphorylation) that regulate their activity in a time-of-day–dependent manner. Doubletime (DBT), a Drosophila kinase, phosphorylates the circadian transcriptional repressor PERIOD (PER). Mutations of dbt shorten or lengthen the period of circadian behavioral rhythms, or abolish the rhythms altogether in flies. A mutation of the human ortholog of dbt, casein kinase I (CKI)δ, has been associated with certain forms of a heritable sleep disorder. The disorder may reflect altered activity of a human PER protein, as the syndrome can also be caused by mutation of a CKIɛ/δ phosphorylation site within PER2. In this study, we locate DBT-directed phosphorylation sites in the Drosophila PER protein, including a DBT target region of PER that was previously shown to regulate DBT activity. Two PER domains within this region appear to serve as alternative targets for DBT. Phosphorylation of the upstream domain seems to suppress phosphorylation elsewhere in the region, producing a stable PER protein with little activity as a transcriptional repressor. However, when phosphorylation of the upstream domain is blocked, downstream DBT targets appear to be phosphorylated, producing a highly active, but short-lived repressor. Our results suggest that ordered patterns of DBT-directed phosphorylation contribute to the timing of PER's function and disappearance, and thus influence the pace of the circadian clock. Two phosphorylation domains inDrosophila PERIOD protein interact in a switch-like fashion with each other and the kinase DOUBLETIME to regulate PER's stability and activity as a transcriptional repressor in the circadian transcriptional feedback loop.
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Affiliation(s)
- Saul Kivimäe
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Lino Saez
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
| | - Michael W Young
- Laboratory of Genetics, The Rockefeller University, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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41
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Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast. Proc Natl Acad Sci U S A 2008; 105:17988-93. [PMID: 19004762 DOI: 10.1073/pnas.0809482105] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The use of luciferase reporters has become a precise, noninvasive, high-throughput method for real-time monitoring of promoter activity in living cells, especially for rhythmic biological processes such as circadian rhythms. We developed a destabilized firefly luciferase as a reporter for rhythmic promoter activity in both the cell division and respiratory cycles of the budding yeast Saccharomyces cerevisiae in which real-time luminescence reporters have not been previously applied. The continuous output of light from luciferase reporters allowed us to explore the relationship between the cell division cycle and the yeast respiratory oscillation, including the observation of responses to chemicals that cause phase shifting of the respiratory oscillations. Destabilized firefly luciferase is a good reporter of cell cycle position in synchronized or partially synchronized yeast cultures, in both batch and continuous cultures. In addition, the oxygen dependence of luciferase can be used under certain conditions as a genetically encodable oxygen monitor. Finally, we use this reporter to show that there is a direct correlation between premature induction of cell division and phase resetting of the respiratory oscillation under the continuous culture conditions tested.
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42
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Lagido C, Pettitt J, Flett A, Glover LA. Bridging the phenotypic gap: real-time assessment of mitochondrial function and metabolism of the nematode Caenorhabditis elegans. BMC PHYSIOLOGY 2008; 8:7. [PMID: 18384668 PMCID: PMC2364618 DOI: 10.1186/1472-6793-8-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 04/02/2008] [Indexed: 12/21/2022]
Abstract
BACKGROUND The ATP levels of an organism are an important physiological parameter that is affected by genetic make up, ageing, stress and disease. RESULTS We have generated luminescent C. elegans through ubiquitous, constitutive expression of firefly luciferase, widely used for in vitro ATP determination. We hypothesise that whole animal luminescence reflects its intracellular ATP levels in vivo. To test this, we characterised the bioluminescence response of C. elegans during sublethal exposure to, and recovery from azide, a treatment that inhibits mitochondrial respiration reversibly, and causes ATP depletion. Consistent with our expectations, in vivo luminescence decreased with increasing sublethal azide levels, and recovered fully when worms were removed from azide. Firefly luciferase expression levels, stability and activity did not influence the final luminescence. Bioluminescence also reflected the lowered activity of the electron transport chain achieved with RNA interference (RNAi) of genes encoding respiratory chain components. CONCLUSION Results indicated that C. elegans luminescence reports on ATP levels in real-time. For the first time, we are able to directly assess the metabolism of a whole, living, multicellular organism by determination of the relative ATP levels. This will enable genetic analysis based on a readily quantifiable metabolic phenotype and will provide novel insights into mechanisms of fitness and disease that are likely to be of relevance for other organisms, as well as the worm.
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Affiliation(s)
- Cristina Lagido
- Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Jonathan Pettitt
- Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Aileen Flett
- Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - L Anne Glover
- Institute of Medical Sciences, School of Medical Sciences, University of Aberdeen, Aberdeen, UK
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43
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Gooch VD, Mehra A, Larrondo LF, Fox J, Touroutoutoudis M, Loros JJ, Dunlap JC. Fully codon-optimized luciferase uncovers novel temperature characteristics of the Neurospora clock. EUKARYOTIC CELL 2007; 7:28-37. [PMID: 17766461 PMCID: PMC2224151 DOI: 10.1128/ec.00257-07] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the complete reconstruction of the firefly luciferase gene, fully codon optimized for expression in Neurospora crassa. This reporter enhances light output by approximately 4 log orders over that with previously available versions, now producing light that is visible to the naked eye and sufficient for monitoring the activities of many poorly expressed genes. Time lapse photography of strains growing in race tubes, in which the frq or eas/ccg-2 promoter is used to drive luciferase, shows the highest levels of luciferase activity near the growth front and newly formed conidial bands. Further, we have established a sorbose medium colony assay that will facilitate luciferase-based screens. The signals from sorbose-grown colonies of strains in which the frq promoter drives luciferase exhibit the properties of circadian rhythms and can be tracked for many days to weeks. This reporter now makes it possible to follow the clock in real time, even in strains or under conditions in which the circadian rhythm in conidial banding is not expressed. This property has been used to discover short, ca. 15-h period rhythms at high temperatures, at which banding becomes difficult to observe in race tubes, and to generate a high-resolution temperature phase-response curve.
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Affiliation(s)
- Van D Gooch
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA
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44
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Okamoto K, Ishiura M, Torii T, Aoki S. A compact multi-channel apparatus for automated real-time monitoring of bioluminescence. ACTA ACUST UNITED AC 2007; 70:535-8. [PMID: 17300843 DOI: 10.1016/j.jbbm.2007.01.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 01/05/2007] [Accepted: 01/05/2007] [Indexed: 11/17/2022]
Abstract
We have developed a multi-channel apparatus for automated monitoring of bioluminescence in real time. We designed this apparatus to be compact (230 mm wide, 600 mm deep, and 227.5 mm high) so that it can be operated in a relatively small commercially-available incubator. The apparatus can process 20 samples at maximum in a single run, providing enough processibility in small-scale experiments. We verified the reliability and sensitivity of the apparatus by observing circadian bioluminescence rhythms over one week from a bioluminescent reporter strain (E9) of the cyanobacterium Synechococcus sp. strain PCC 7942 [Ishiura, M., Kutsuna, S., Aoki, S., Iwasaki, H., Andersson, C.R., Tanabe, A., Golden, S.S., Johnson, C.H., Kondo, T., Expression of a gene cluster kaiABC as a circadian feedback process in cyanobacteria, Science, 281 (1998) 1519-1523]. Our apparatus allows flexible experimental designs and will be effectively used for the studies of gene expression in various purposes.
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Affiliation(s)
- Kazuhisa Okamoto
- Gene Research Center, Nagoya University, Furo, Chikusa, Nagoya 464-8602, Japan
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45
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Yu W, Hardin PE. Use of firefly luciferase activity assays to monitor circadian molecular rhythms in vivo and in vitro. Methods Mol Biol 2007; 362:465-80. [PMID: 17417035 DOI: 10.1007/978-1-59745-257-1_38] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Circadian rhythms in metabolic, physiological, and behavioral processes are regulated by biological clocks. Many of these rhythmic processes can be measured over many days or weeks using automated recording devices, thus making it possible to precisely calculate period, phase, and amplitude values. With the advent of luciferase reporter genes and machines capable of quantifying luciferase-generated bioluminescence over long time frames, it is now possible to precisely monitor the rhythms in gene expression that underlie circadian clock function. These assays can be used to monitor gene expression in large numbers of individual plants and animals, and/or various cultured tissues and cells. After acquiring bioluminescence data, rhythm analysis programs are used to calculate the period, phase, amplitude, and overall levels of gene expression for individuals or groups, and to measure their statistical significance. Here we will describe how luciferase assays are performed and analyzed to measure gene expression rhythms in Drosophila.
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Affiliation(s)
- Wangjie Yu
- Department of Biology and Center for Research on Biological Rhythms, Texas A&M University, College Station, USA
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46
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Ceriani MF. Reporter assays. Methods Mol Biol 2007; 362:455-63. [PMID: 17417034 DOI: 10.1007/978-1-59745-257-1_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Transcriptional feedback loops are at the core of the molecular clockworks. As single clock genes were cloned it was compelling to develop an assay that allowed simple and direct functional testing of putative activators or repressors of transcription. This chapter includes a general description and guidelines to carry out transcriptional assays in transiently transfected Schneider's cells.
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Affiliation(s)
- M Fernanda Ceriani
- Department Behavioral Genetics, Fundación Instituto Leloir, Buenos Aires, Argentina
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47
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Hong HK, Chong JL, Song W, Song EJ, Jyawook AA, Schook AC, Ko CH, Takahashi JS. Inducible and reversible Clock gene expression in brain using the tTA system for the study of circadian behavior. PLoS Genet 2007; 3:e33. [PMID: 17319750 PMCID: PMC1802832 DOI: 10.1371/journal.pgen.0030033] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2006] [Accepted: 01/05/2007] [Indexed: 01/12/2023] Open
Abstract
The mechanism of circadian oscillations in mammals is cell autonomous and is generated by a set of genes that form a transcriptional autoregulatory feedback loop. While these “clock genes” are well conserved among animals, their specific functions remain to be fully understood and their roles in central versus peripheral circadian oscillators remain to be defined. We utilized the in vivo inducible tetracycline-controlled transactivator (tTA) system to regulate Clock gene expression conditionally in a tissue-specific and temporally controlled manner. Through the use of Secretogranin II to drive tTA expression, suprachiasmatic nucleus– and brain-directed expression of a tetO::ClockΔ19 dominant-negative transgene lengthened the period of circadian locomotor rhythms in mice, whereas overexpression of a tetO::Clockwt wild-type transgene shortened the period. Low doses (10 μg/ml) of doxycycline (Dox) in the drinking water efficiently inactivated the tTA protein to silence the tetO transgenes and caused the circadian periodicity to return to a wild-type state. Importantly, low, but not high, doses of Dox were completely reversible and led to a rapid reactivation of the tetO transgenes. The rapid time course of tTA-regulated transgene expression demonstrates that the CLOCK protein is an excellent indicator for the kinetics of Dox-dependent induction/repression in the brain. Interestingly, the daily readout of circadian period in this system provides a real-time readout of the tTA transactivation state in vivo. In summary, the tTA system can manipulate circadian clock gene expression in a tissue-specific, conditional, and reversible manner in the central nervous system. The specific methods developed here should have general applicability for the study of brain and behavior in the mouse. Although significant progress has been made in unraveling the molecular mechanism of circadian clocks in mammals, previous work has focused on germline mutations and in vitro methods for analysis. To address the function of clock genes, it is necessary to develop tools to manipulate circadian genes in a conditional and tissue-specific manner in vivo. We report such an approach using the tetracycline transactivator system. Despite the development of the “tet” system in transgenic mice over 10 y ago by Bujard and colleagues, there are still relatively few examples of the successful use of the tet system in the central nervous system. Transgenic expression of the Clock gene in the suprachiasmatic nucleus and brain of mice regulated the period length of circadian locomotor rhythms. These effects could be inhibited by low doses of doxycycline in the drinking water. Importantly, low, but not high, doses of doxycycline were completely reversible and led to a rapid reactivation of the Clock transgenes. In summary, the tetracycline-controlled transactivator system can manipulate circadian clock gene expression in a tissue-specific, conditional, and reversible manner in the central nervous system. The specific methods developed here should have general applicability for the study of brain and behavior in the mouse.
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Affiliation(s)
- Hee-Kyung Hong
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois, United States of America
- Center for Functional Genomics, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Jason L Chong
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Weimin Song
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Eun Joo Song
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Amira A Jyawook
- Center for Functional Genomics, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Andrew C Schook
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
| | - Caroline H Ko
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
| | - Joseph S Takahashi
- Howard Hughes Medical Institute, Northwestern University, Evanston, Illinois, United States of America
- Center for Functional Genomics, Northwestern University, Evanston, Illinois, United States of America
- Department of Neurobiology and Physiology, Northwestern University, Evanston, Illinois, United States of America
- * To whom correspondence should be addressed. E-mail:
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48
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Hall JC, Chang DC, Dolezelova E. Principles and problems revolving around rhythm-related genetic variants. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 72:215-232. [PMID: 18419279 DOI: 10.1101/sqb.2007.72.039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Much of what is known about the regulation of circadian rhythms has stemmed from the induction, recognition, or manufacture of genetic variants. Such investigations have been especially salient in chronobiological analyses of Drosophila. Many starting points for elucidation of rhythmic processes operating in this insect entailed the isolation of mutants or the design of engineered gene modifications. Various features of the principles and practices associated with the genetic approach toward understanding clock functions, and chronobiologically related ones, are discussed from perspectives that are largely genetic as such, although intertwined with certain neurogenetic and molecular-genetic concerns when appropriate. Key themes in this treatment connect with the power and problems associated with multiply mutant forms of rhythm-related genes, with the opportunistic or problematical aspects of multigenic variants that are in play (sometimes surprisingly), and with a question as to how forceful chronogenetic inferences have been in terms of elucidating the mechanisms of circadian pacemaking.
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Affiliation(s)
- J C Hall
- Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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Stanewsky R. Analysis of rhythmic gene expression in adult Drosophila using the firefly luciferase reporter gene. Methods Mol Biol 2007; 362:131-42. [PMID: 17417006 DOI: 10.1007/978-1-59745-257-1_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The study of circadian clock function in Drosophila relies heavily on the analysis of rhythmic gene expression. Typically, individuals or groups of flies collected during a specific time of the circadian day need to be sacrificed, followed by the extraction of clock gene products. This procedure makes it impossible to analyze molecular rhythms in an individual over time. To measure clock gene expression within the living animal, firefly luciferase can be used as real-time reporter gene. This chapter describes how rhythmic expression of clock or clock-controlled genes can be measured in living adult Drosophila. A survey of all existing clock-related luciferase transgenics is given.
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Affiliation(s)
- Ralf Stanewsky
- School of Biological and Chemical Sciences, Queen Mary University of London, UK
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Abstract
Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of mPer2, little is known about the other cis-elements of mPer2 oscillatory transcription. Here, we examined the contribution of E4BP4 to Per2 mRNA oscillation in the cell-autonomous clock. Knockdown experiments of E4BP4 in both Northern blots and real-time luciferase assays suggested that endogenous E4BP4 negatively regulates Per2 mRNA oscillation. Sequence analysis revealed two putative E4BP4-binding sites (termed A-site and B-site) on mammalian Per2 promoter regions. Luciferase assays with mutant constructs showed that a novel E4BP4-binding site (B-site) is responsible for E4BP4-mediated transcriptional repression of Per2. Furthermore, chromatin immunoprecipitation assays in vivo showed that the peak of E4BP4 binding to the B-site on the Per2 promoter almost matched the trough of Per2 mRNA expression. Importantly, real-time luciferase assays showed that the B-site in addition to the E2 enhancer is required for robust circadian expression of Per2 in the cell-autonomous clock. These findings indicated that E4BP4 is required for the negative regulation of mammalian circadian clocks.
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Affiliation(s)
- Tomoya Ohno
- Clock Cell Biology, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)Tsukuba 305-8566, Japan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukuba 305-8576, Japan
| | - Yoshiaki Onishi
- Clock Cell Biology, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)Tsukuba 305-8566, Japan
| | - Norio Ishida
- Clock Cell Biology, Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology (AIST)Tsukuba 305-8566, Japan
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukuba 305-8576, Japan
- To whom correspondence should be addressed at Clock Cell Biology, National Institute of Advanced Industrial Science and Technology, Central 6-5, 1-1-1 Higashi, Tsukuba 305-8566, Japan. Tel: +81 298 61 6053; Fax: +81 298 61 9499;
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