1
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Shafer OT. 25 years of Drosophila "Sleep genes". Fly (Austin) 2025; 19:2502180. [PMID: 40326454 PMCID: PMC12064057 DOI: 10.1080/19336934.2025.2502180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Revised: 04/24/2025] [Accepted: 04/28/2025] [Indexed: 05/07/2025] Open
Abstract
The field of Drosophila sleep research, which began 25 years ago, has identified more than 200 genes influencing sleep. In this review, I summarize the foundation of the field and the growing list of genes implicated in sleep regulation. I compare the genetic methods used to identify genes governing sleep and circadian rhythms and the distinct outcomes of screens for genes regulating these two highly related processes. Finally, I discuss the ~ 200 sleep-regulating genes of Drosophila in the context of recent developments in the field and voice reasons for scepticism regarding the relevance of these genes to the homoeostatic regulation of sleep. Finally, I speculate on the future promise of the fly model system for revealing conserved molecular mechanisms of sleep homoeostasis.
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Affiliation(s)
- Orie Thomas Shafer
- Gill Institute for Neuroscience and Department of Biology, Indiana University in Bloomington, Bloomington, IN, USA
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2
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Keleş MF, Sapci AOB, Brody C, Palmer I, Mehta A, Ahmadi S, Le C, Taştan Ö, Keleş S, Wu MN. FlyVISTA, an integrated machine learning platform for deep phenotyping of sleep in Drosophila. SCIENCE ADVANCES 2025; 11:eadq8131. [PMID: 40073129 PMCID: PMC11900856 DOI: 10.1126/sciadv.adq8131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 02/03/2025] [Indexed: 03/14/2025]
Abstract
There is great interest in using genetically tractable organisms such as Drosophila to gain insights into the regulation and function of sleep. However, sleep phenotyping in Drosophila has largely relied on simple measures of locomotor inactivity. Here, we present FlyVISTA, a machine learning platform to perform deep phenotyping of sleep in flies. This platform comprises a high-resolution closed-loop video imaging system, coupled with a deep learning network to annotate 35 body parts, and a computational pipeline to extract behaviors from high-dimensional data. FlyVISTA reveals the distinct spatiotemporal dynamics of sleep and wake-associated microbehaviors at baseline, following administration of the sleep-inducing drug gaboxadol, and with dorsal fan-shaped body drivers. We identify a microbehavior ("haltere switch") exclusively seen during quiescence that indicates a deeper sleep stage. These results enable the rigorous analysis of sleep in Drosophila and set the stage for computational analyses of microbehaviors in quiescent animals.
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Affiliation(s)
- Mehmet F. Keleş
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ali Osman Berk Sapci
- Department of Computer Science, Sabanci University, Tuzla, Istanbul 34956, Turkey
| | - Casey Brody
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Isabelle Palmer
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anuradha Mehta
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Shahin Ahmadi
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christin Le
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Öznur Taştan
- Department of Computer Science, Sabanci University, Tuzla, Istanbul 34956, Turkey
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark N. Wu
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21287, USA
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3
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Sato DX, Okuyama T, Takahashi Y. Multifaceted and extensive behavioral trajectories of genomically diverse Drosophila lines. Sci Data 2025; 12:400. [PMID: 40055352 PMCID: PMC11889213 DOI: 10.1038/s41597-025-04724-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 02/27/2025] [Indexed: 05/13/2025] Open
Abstract
Detailed tracking data is essential to understanding the intricate mechanisms behind animal behavior. Here, we present a comprehensive dataset containing behavioral movies and trajectories from over 30,000 Drosophila melanogaster individuals across 105 genetically distinct strains, including 104 wild-type strains from the Drosophila Genetic Reference Panel, along with one visually impaired mutant. These data, categorized by genetic background, sex, and social context (isolated or in groups), were collected during 15-minute sessions that included five minutes of repeated looming stimuli to elicit fear responses. Additionally, our experimental design incorporated group experiments with randomly combined pairs of strains to investigate synergistic effects of group members on behavioral dynamics. Beyond enabling detailed analyses of genetic factors underlying locomotion, fear responses, and social interactions, this dataset provides a unique opportunity to examine individual behavioral variability within genetically identical flies. By capturing a broad spectrum of behaviors across different genetic and environmental contexts, these data serve as a valuable resource for advancing our understanding of how genetics, individuality, and group interactions shape animal behavior.
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Affiliation(s)
- Daiki X Sato
- Institute for Advanced Academic Research, Chiba University, Chiba, Japan.
- Graduate School of Science, Chiba University, Chiba, Japan.
| | - Takahira Okuyama
- Graduate School of Science and Engineering, Chiba University, Chiba, Japan
| | - Yuma Takahashi
- Graduate School of Science, Chiba University, Chiba, Japan.
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4
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Shekhar S, Tracy C, Lidsky PV, Andino R, Wert KJ, Krämer H. Sensory quiescence induces a cell-non-autonomous integrated stress response curbed by condensate formation of the ATF4 and XRP1 effectors. Nat Commun 2025; 16:252. [PMID: 39747204 PMCID: PMC11695831 DOI: 10.1038/s41467-024-55576-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 12/13/2024] [Indexed: 01/04/2025] Open
Abstract
Sensory disabilities have been identified as significant risk factors for dementia but underlying molecular mechanisms are unknown. In different Drosophila models with loss of sensory input, we observe non-autonomous induction of the integrated stress response (ISR) deep in the brain, as indicated by eIF2αS50 phosphorylation-dependent elevated levels of the ISR effectors ATF4 and XRP1. Unlike during canonical ISR, however, the ATF4 and XRP1 transcription factors are enriched in cytosolic granules that are positive for RNA and the stress granule markers Caprin, FMR1, and p62, and are reversible upon restoration of vision for blind flies. Cytosolic restraint of the ATF4 and XRP1 transcription factors dampens expression of their downstream targets including genes of cell death pathways activated during chronic cellular stress and thus constitutes a chronic stress protective response (CSPR). Cytosolic granules containing both p62 and ATF4 are also evident in the thalamus and hippocampus of mouse models of congenital or degenerative blindness. These data indicate a conserved link between loss of sensory input and curbed stress responses critical for protein quality control in the brain.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA
| | - Peter V Lidsky
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Katherine J Wert
- Department of Ophthalmology, Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
- O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX, USA.
- O'Donnell Brain Institute, UT Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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5
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Sitaraman D, Vecsey CG, Koochagian C. Activity Monitoring for Analysis of Sleep in Drosophila melanogaster. Cold Spring Harb Protoc 2024; 2024:pdb.top108095. [PMID: 38336390 PMCID: PMC11827337 DOI: 10.1101/pdb.top108095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Sleep is important for survival, and the need for sleep is conserved across species. In the past two decades, the fruit fly Drosophila melanogaster has emerged as a promising system in which to study the genetic, neural, and physiological bases of sleep. Through significant advances in our understanding of the regulation of sleep in flies, the field is poised to address several open questions about sleep, such as how the need for sleep is encoded, how molecular regulators of sleep are situated within brain networks, and what the functions of sleep are. Here, we describe key findings, open questions, and commonly used methods that have been used to inform existing theories and develop new ways of thinking about the function, regulation, and adaptability of sleep behavior.
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Affiliation(s)
- Divya Sitaraman
- Department of Psychology, College of Science, California State University, Hayward, California 94542, USA
| | | | - Casey Koochagian
- Neuroscience Program, Skidmore College, Saratoga Springs, New York 12866, USA
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6
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Decet M, Scott P, Kuenen S, Meftah D, Swerts J, Calatayud C, Gallego SF, Kaempf N, Nachman E, Praschberger R, Schoovaerts N, Tang CC, Eidelberg D, Al Adawi S, Al Asmi A, Nandhagopal R, Verstreken P. A candidate loss-of-function variant in SGIP1 causes synaptic dysfunction and recessive parkinsonism. Cell Rep Med 2024; 5:101749. [PMID: 39332416 PMCID: PMC11513836 DOI: 10.1016/j.xcrm.2024.101749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/14/2024] [Accepted: 08/31/2024] [Indexed: 09/29/2024]
Abstract
Synaptic dysfunction is recognized as an early step in the pathophysiology of parkinsonism. Several genetic mutations affecting the integrity of synaptic proteins cause or increase the risk of developing disease. We have identified a candidate causative mutation in synaptic "SH3GL2 Interacting Protein 1" (SGIP1), linked to early-onset parkinsonism in a consanguineous Arab family. Additionally, affected siblings display intellectual, cognitive, and behavioral dysfunction. Metabolic network analysis of [18F]-fluorodeoxyglucose positron emission tomography scans shows patterns very similar to those of idiopathic Parkinson's disease. We show that the identified SGIP1 mutation causes a loss of protein function, and analyses in newly created Drosophila models reveal movement defects, synaptic transmission dysfunction, and neurodegeneration, including dopaminergic synapse loss. Histology and correlative light and electron microscopy reveal the absence of synaptic multivesicular bodies and the accumulation of degradative organelles. This research delineates a putative form of recessive parkinsonism, converging on defective synaptic proteostasis and opening avenues for diagnosis, genetic counseling, and treatment.
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Affiliation(s)
- Marianna Decet
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Patrick Scott
- Laboratory of Molecular Biology, Sainte-Justine University Hospital Center, Montréal QC H3T 1C5, Canada
| | - Sabine Kuenen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Douja Meftah
- Laboratory of Pulmonary Physiology, Department of Pediatrics, Sainte-Justine University Hospital Center, Montréal QC H3T 1C5, Canada
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Carles Calatayud
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Sandra F Gallego
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Natalie Kaempf
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Eliana Nachman
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Chris C Tang
- Center for Neurosciences, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - David Eidelberg
- Center for Neurosciences, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Samir Al Adawi
- Department of Behavioral Medicine, College of Medicine & Health Sciences, Sultan Qaboos University, Al Khod 123, Muscat, Oman
| | - Abdullah Al Asmi
- Neurology Unit, Department of Medicine, College of Medicine and Health Sciences, Sultan Qaboos University, Al Khod 123, Muscat, Oman
| | - Ramachandiran Nandhagopal
- Neurology Unit, Department of Medicine, College of Medicine and Health Sciences, Sultan Qaboos University, Al Khod 123, Muscat, Oman.
| | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
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7
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Dos Santos E, Cochemé HM. How does a fly die? Insights into ageing from the pathophysiology of Drosophila mortality. GeroScience 2024; 46:4003-4015. [PMID: 38642259 PMCID: PMC11336040 DOI: 10.1007/s11357-024-01158-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 04/05/2024] [Indexed: 04/22/2024] Open
Abstract
The fruit fly Drosophila melanogaster is a common animal model in ageing research. Large populations of flies are used to study the impact of genetic, nutritional and pharmacological interventions on survival. However, the processes through which flies die and their relative prevalence in Drosophila populations are still comparatively unknown. Understanding the causes of death in an animal model is essential to dissect the lifespan-extending interventions that are organism- or disease-specific from those broadly applicable to ageing. Here, we review the pathophysiological processes that can lead to fly death and discuss their relation to ageing.
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Affiliation(s)
- Eliano Dos Santos
- MRC Laboratory of Medical Sciences (LMS), Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK
- Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College London, Du Cane Road, London, W12 0HS, UK
| | - Helena M Cochemé
- MRC Laboratory of Medical Sciences (LMS), Hammersmith Hospital Campus, Du Cane Road, London, W12 0HS, UK.
- Institute of Clinical Sciences, Hammersmith Hospital Campus, Imperial College London, Du Cane Road, London, W12 0HS, UK.
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8
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Gil-Martí B, Isidro-Mézcua J, Poza-Rodriguez A, Asti Tello GS, Treves G, Turiégano E, Beckwith EJ, Martin FA. Socialization causes long-lasting behavioral changes. Sci Rep 2024; 14:22302. [PMID: 39333212 PMCID: PMC11436997 DOI: 10.1038/s41598-024-73218-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
In modern human societies, social isolation acts as a negative factor for health and life quality. On the other hand, social interaction also has profound effects on animal and human, impacting aggressiveness, feeding and sleep, among many other behaviors. Here, we observe that in the fly Drosophila melanogaster these behavioral changes long-last even after social interaction has ceased, suggesting that the socialization experience triggers behavioral plasticity. These modified behaviors maintain similar levels for 24 h and persist up to 72 h, although showing a progressive decay. We also find that impairing long-term memory mechanisms either genetically or by anesthesia abolishes the expected behavioral changes in response to social interaction. Furthermore, we show that socialization increases CREB-dependent neuronal activity and synaptic plasticity in the mushroom body, the main insect memory center analogous to mammalian hippocampus. We propose that social interaction triggers socialization awareness, understood as long-lasting changes in behavior caused by experience with mechanistic similarities to long-term memory formation.
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Affiliation(s)
- Beatriz Gil-Martí
- Cajal Institute, Spanish National Research Council (CSIC), Av Dr Arce 37, 28002, Madrid, Spain
- Department of Biology, Autonomous University of Madrid, Madrid, Spain
| | - Julia Isidro-Mézcua
- Cajal Institute, Spanish National Research Council (CSIC), Av Dr Arce 37, 28002, Madrid, Spain
| | - Adriana Poza-Rodriguez
- Cajal Institute, Spanish National Research Council (CSIC), Av Dr Arce 37, 28002, Madrid, Spain
| | - Gerson S Asti Tello
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), UBA-CONICET, Buenos Aires, Argentina
| | - Gaia Treves
- Cajal Institute, Spanish National Research Council (CSIC), Av Dr Arce 37, 28002, Madrid, Spain
| | - Enrique Turiégano
- Department of Biology, Autonomous University of Madrid, Madrid, Spain
| | - Esteban J Beckwith
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), UBA-CONICET, Buenos Aires, Argentina.
| | - Francisco A Martin
- Cajal Institute, Spanish National Research Council (CSIC), Av Dr Arce 37, 28002, Madrid, Spain.
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9
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Woodling N. Sex- and strain-dependent effects of ageing on sleep and activity patterns in Drosophila. PLoS One 2024; 19:e0308652. [PMID: 39150918 PMCID: PMC11329114 DOI: 10.1371/journal.pone.0308652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 07/27/2024] [Indexed: 08/18/2024] Open
Abstract
The fruit fly Drosophila is a major discovery platform in the biology of ageing due to its balance of relatively short lifespan and relatively complex physiology and behaviour. Previous studies have suggested that some important phenotypes of ageing, for instance increasingly fragmented sleep, are shared from humans to Drosophila and can be useful measures of behavioural change with age: these phenotypes therefore hold potential as readouts of healthy ageing for genetic or pharmacological interventions aimed at the underpinning biology of ageing. However, some age-related phenotypes in Drosophila show differing results among studies, leading to questions regarding the source of discrepancies among experiments. In this study, I have tested females and males from three common laboratory strains of Drosophila to determine the extent to which sex and background strain influence age-related behavioural changes in sleep and activity patterns. Surprisingly, I find that some phenotypes-including age-related changes in total activity, total sleep, and sleep fragmentation-depend strongly on sex and strain, to the extent that some phenotypes show opposing age-related changes in different sexes or strains. Conversely, I identify other phenotypes, including age-related decreases in morning and evening anticipation, that are more uniform across sexes and strains. These results reinforce the importance of controlling for background strain in both behavioural and ageing experiments, and they imply that caution should be used when drawing conclusions from studies on a single sex or strain of Drosophila. At the same time, these findings also offer suggestions for behavioural measures that merit further investigation as potentially more consistent phenotypes of ageing.
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Affiliation(s)
- Nathan Woodling
- School of Molecular Biosciences, University of Glasgow, Glasgow, United Kingdom
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10
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Otto T, Rose J. The open toolbox for behavioral research. Behav Res Methods 2024; 56:4522-4529. [PMID: 37794209 PMCID: PMC11289225 DOI: 10.3758/s13428-023-02199-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2023] [Indexed: 10/06/2023]
Abstract
In this work, we describe a new open-source MATLAB toolbox for the control of behavioral experiments. The toolbox caters to very different types of experiments in different species, and with different underlying hardware. Typical examples are operant chambers in animals, with or without neurophysiology, behavioral experiments in human subjects, and neurophysiological recordings in humans such as EEG and fMRI. In addition, the toolbox supports communication via Ethernet to either control and monitor one or several experimental setups remotely or to implement distributed paradigms across different computers. This flexibility is possible, since the toolbox supports a wide range of hardware, some of which is custom developments. An example is a fast network-based digital-IO device for the communication with experimental hardware such as feeders or triggers in neurophysiological setups. We also included functions for online video analysis allowing paradigms to be contingent on responses to a screen, the head movement of a bird in an operant chamber, or the physical location of an animal in an open arena. While the toolbox is well tested and many components of it have been in use for many years, we do not see it as a finished product but rather a continuing development with a focus on easy extendibility and customization.
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Affiliation(s)
- Tobias Otto
- Cognitive Psychology, Faculty of Psychology, Ruhr University Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Jonas Rose
- Neural Basis of Learning, Faculty of Psychology, Ruhr University Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
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11
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Keleş MF, Sapci AOB, Brody C, Palmer I, Le C, Taştan Ö, Keleş S, Wu MN. FlyVISTA, an Integrated Machine Learning Platform for Deep Phenotyping of Sleep in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.30.564733. [PMID: 37961473 PMCID: PMC10635029 DOI: 10.1101/2023.10.30.564733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Animal behavior depends on internal state. While subtle movements can signify significant changes in internal state, computational methods for analyzing these "microbehaviors" are lacking. Here, we present FlyVISTA, a machine-learning platform to characterize microbehaviors in freely-moving flies, which we use to perform deep phenotyping of sleep. This platform comprises a high-resolution closed-loop video imaging system, coupled with a deep-learning network to annotate 35 body parts, and a computational pipeline to extract behaviors from high-dimensional data. FlyVISTA reveals the distinct spatiotemporal dynamics of sleep-associated microbehaviors in flies. We further show that stimulation of dorsal fan-shaped body neurons induces micromovements, not sleep, whereas activating R5 ring neurons triggers rhythmic proboscis extension followed by persistent sleep. Importantly, we identify a novel microbehavior ("haltere switch") exclusively seen during quiescence that indicates a deeper sleep stage. These findings enable the rigorous analysis of sleep in Drosophila and set the stage for computational analyses of microbehaviors.
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Affiliation(s)
- Mehmet F. Keleş
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ali Osman Berk Sapci
- Department of Computer Science, Sabanci University, Tuzla, Istanbul, 34956, Turkey
| | - Casey Brody
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Isabelle Palmer
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Christin Le
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Öznur Taştan
- Department of Computer Science, Sabanci University, Tuzla, Istanbul, 34956, Turkey
| | - Sündüz Keleş
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark N. Wu
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21287, USA
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12
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Joyce M, Falconio FA, Blackhurst L, Prieto-Godino L, French AS, Gilestro GF. Divergent evolution of sleep in Drosophila species. Nat Commun 2024; 15:5091. [PMID: 38876988 PMCID: PMC11178934 DOI: 10.1038/s41467-024-49501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 06/05/2024] [Indexed: 06/16/2024] Open
Abstract
Living organisms synchronize their biological activities with the earth's rotation through the circadian clock, a molecular mechanism that regulates biology and behavior daily. This synchronization factually maximizes positive activities (e.g., social interactions, feeding) during safe periods, and minimizes exposure to dangers (e.g., predation, darkness) typically at night. Beyond basic circadian regulation, some behaviors like sleep have an additional layer of homeostatic control, ensuring those essential activities are fulfilled. While sleep is predominantly governed by the circadian clock, a secondary homeostatic regulator, though not well-understood, ensures adherence to necessary sleep amounts and hints at a fundamental biological function of sleep beyond simple energy conservation and safety. Here we explore sleep regulation across seven Drosophila species with diverse ecological niches, revealing that while circadian-driven sleep aspects are consistent, homeostatic regulation varies significantly. The findings suggest that in Drosophilids, sleep evolved primarily for circadian purposes. The more complex, homeostatically regulated functions of sleep appear to have evolved independently in a species-specific manner, and are not universally conserved. This laboratory model may reproduce and recapitulate primordial sleep evolution.
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Affiliation(s)
- Michaela Joyce
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Research Institute, London, UK
| | | | | | | | - Alice S French
- Department of Life Sciences, Imperial College London, London, UK.
- The Francis Crick Research Institute, London, UK.
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.
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13
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Dopp J, Ortega A, Davie K, Poovathingal S, Baz ES, Liu S. Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep-wake cycles. Nat Neurosci 2024; 27:359-372. [PMID: 38263460 PMCID: PMC10849968 DOI: 10.1038/s41593-023-01549-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 12/07/2023] [Indexed: 01/25/2024]
Abstract
The sleep-wake cycle is determined by circadian and sleep homeostatic processes. However, the molecular impact of these processes and their interaction in different brain cell populations are unknown. To fill this gap, we profiled the single-cell transcriptome of adult Drosophila brains across the sleep-wake cycle and four circadian times. We show cell type-specific transcriptomic changes, with glia displaying the largest variation. Glia are also among the few cell types whose gene expression correlates with both sleep homeostat and circadian clock. The sleep-wake cycle and sleep drive level affect the expression of clock gene regulators in glia, and disrupting clock genes specifically in glia impairs homeostatic sleep rebound after sleep deprivation. These findings provide a comprehensive view of the effects of sleep homeostatic and circadian processes on distinct cell types in an entire animal brain and reveal glia as an interaction site of these two processes to determine sleep-wake dynamics.
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Affiliation(s)
- Joana Dopp
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Antonio Ortega
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Kristofer Davie
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Suresh Poovathingal
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - El-Sayed Baz
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Leuven Brain Institute, KU Leuven, Leuven, Belgium
- Zoology Department, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Sha Liu
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium.
- Department of Neurosciences, KU Leuven, Leuven, Belgium.
- Leuven Brain Institute, KU Leuven, Leuven, Belgium.
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14
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Ajuwon V, Cruz BF, Carriço P, Kacelnik A, Monteiro T. GoFish: A low-cost, open-source platform for closed-loop behavioural experiments on fish. Behav Res Methods 2024; 56:318-329. [PMID: 36622558 PMCID: PMC10794453 DOI: 10.3758/s13428-022-02049-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2022] [Indexed: 01/10/2023]
Abstract
Fish are the most species-rich vertebrate group, displaying vast ecological, anatomical and behavioural diversity, and therefore are of major interest for the study of behaviour and its evolution. However, with respect to other vertebrates, fish are relatively underrepresented in psychological and cognitive research. A greater availability of easily accessible, flexible, open-source experimental platforms that facilitate the automation of task control and data acquisition may help to reduce this bias and improve the scalability and refinement of behavioural experiments in a range of different fish species. Here we present GoFish, a fully automated platform for behavioural experiments in aquatic species. GoFish includes real-time video tracking of subjects, presentation of stimuli in a computer screen, an automatic feeder device, and closed-loop control of task contingencies and data acquisition. The design and software components of the platform are freely available, while the hardware is open-source and relatively inexpensive. The control software, Bonsai, is designed to facilitate rapid development of task workflows and is supported by a growing community of users. As an illustration and test of its use, we present the results of two experiments on discrimination learning, reversal, and choice in goldfish (Carassius auratus). GoFish facilitates the automation of high-throughput protocols and the acquisition of rich behavioural data. Our platform has the potential to become a widely used tool that facilitates complex behavioural experiments in aquatic species.
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Affiliation(s)
- Victor Ajuwon
- Department of Biology, University of Oxford, Oxford, UK.
| | - Bruno F Cruz
- Champalimaud Neuroscience Programme, Champalimaud Foundation, Lisbon, Portugal
- NeuroGEARS Ltd., London, UK
| | - Paulo Carriço
- Champalimaud Research Scientific Hardware Platform, Champalimaud Foundation, Lisbon, Portugal
| | - Alex Kacelnik
- Department of Biology, University of Oxford, Oxford, UK
| | - Tiago Monteiro
- Department of Biology, University of Oxford, Oxford, UK.
- Domestication Lab, Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine Vienna, Vienna, Austria.
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15
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Randlett O. pi_tailtrack: A compact, inexpensive and open-source behaviour-tracking system for head-restrained zebrafish. J Exp Biol 2023; 226:jeb246335. [PMID: 37818550 DOI: 10.1242/jeb.246335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023]
Abstract
Quantifying animal behaviour during microscopy is crucial to associate optically recorded neural activity with behavioural outputs and states. Here, I describe an imaging and tracking system for head-restrained larval zebrafish compatible with functional microscopy. This system is based on the Raspberry Pi computer, Pi NoIR camera and open-source software for the real-time tail segmentation and skeletonization of the zebrafish tail at over 100 Hz. This allows for precise and long-term analyses of swimming behaviour, which can be related to functional signals recorded in individual neurons. This system offers a simple but performant solution for quantifying the behaviour of head-restrained larval zebrafish, which can be built for 340€.
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Affiliation(s)
- Owen Randlett
- Laboratoire MeLiS, Université Claude Bernard Lyon 1 - CNRS UMR5284 - Inserm U1314, Institut NeuroMyoGène, Faculté de Médecine et de Pharmacie, 8 Avenue Rockefeller, 69008 Lyon, France
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16
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Jones H, Willis JA, Firth LC, Giachello CNG, Gilestro GF. A reductionist paradigm for high-throughput behavioural fingerprinting in Drosophila melanogaster. eLife 2023; 12:RP86695. [PMID: 37938101 PMCID: PMC10631757 DOI: 10.7554/elife.86695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Abstract
Understanding how the brain encodes behaviour is the ultimate goal of neuroscience and the ability to objectively and reproducibly describe and quantify behaviour is a necessary milestone on this path. Recent technological progresses in machine learning and computational power have boosted the development and adoption of systems leveraging on high-resolution video recording to track an animal pose and describe behaviour in all four dimensions. However, the high temporal and spatial resolution that these systems offer must come as a compromise with their throughput and accessibility. Here, we describe coccinella, an open-source reductionist framework combining high-throughput analysis of behaviour using real-time tracking on a distributed mesh of microcomputers (ethoscopes) with resource-lean statistical learning (HCTSA/Catch22). Coccinella is a reductionist system, yet outperforms state-of-the-art alternatives when exploring the pharmacobehaviour in Drosophila melanogaster.
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Affiliation(s)
- Hannah Jones
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
| | - Jenny A Willis
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Lucy C Firth
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Carlo NG Giachello
- Syngenta, Jealott’s Hill International Research CentreBracknellUnited Kingdom
| | - Giorgio F Gilestro
- Department of Life Sciences, Imperial College LondonLondonUnited Kingdom
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17
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Banach-Latapy A, Rincheval V, Briand D, Guénal I, Spéder P. Differential adhesion during development establishes individual neural stem cell niches and shapes adult behaviour in Drosophila. PLoS Biol 2023; 21:e3002352. [PMID: 37943883 PMCID: PMC10635556 DOI: 10.1371/journal.pbio.3002352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/28/2023] [Indexed: 11/12/2023] Open
Abstract
Neural stem cells (NSCs) reside in a defined cellular microenvironment, the niche, which supports the generation and integration of newborn neurons. The mechanisms building a sophisticated niche structure around NSCs and their functional relevance for neurogenesis are yet to be understood. In the Drosophila larval brain, the cortex glia (CG) encase individual NSC lineages in membranous chambers, organising the stem cell population and newborn neurons into a stereotypic structure. We first found that CG wrap around lineage-related cells regardless of their identity, showing that lineage information builds CG architecture. We then discovered that a mechanism of temporally controlled differential adhesion using conserved complexes supports the individual encasing of NSC lineages. An intralineage adhesion through homophilic Neuroglian interactions provides strong binding between cells of a same lineage, while a weaker interaction through Neurexin-IV and Wrapper exists between NSC lineages and CG. Loss of Neuroglian results in NSC lineages clumped together and in an altered CG network, while loss of Neurexin-IV/Wrapper generates larger yet defined CG chamber grouping several lineages together. Axonal projections of newborn neurons are also altered in these conditions. Further, we link the loss of these 2 adhesion complexes specifically during development to locomotor hyperactivity in the resulting adults. Altogether, our findings identify a belt of adhesions building a neurogenic niche at the scale of individual stem cell and provide the proof of concept that niche properties during development shape adult behaviour.
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Affiliation(s)
- Agata Banach-Latapy
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
| | | | - David Briand
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
| | - Isabelle Guénal
- Université Paris-Saclay, UVSQ, LGBC, 78000, Versailles, France
| | - Pauline Spéder
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Structure and Signals in the Neurogenic Niche, Paris, France
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18
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Chowdhury B, Abhilash L, Ortega A, Liu S, Shafer O. Homeostatic control of deep sleep and molecular correlates of sleep pressure in Drosophila. eLife 2023; 12:e91355. [PMID: 37906092 PMCID: PMC10642965 DOI: 10.7554/elife.91355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/22/2023] [Indexed: 11/02/2023] Open
Abstract
Homeostatic control of sleep is typically addressed through mechanical stimulation-induced forced wakefulness and the measurement of subsequent increases in sleep. A major confound attends this approach: biological responses to deprivation may reflect a direct response to the mechanical insult rather than to the loss of sleep. Similar confounds accompany all forms of sleep deprivation and represent a major challenge to the field. Here, we describe a new paradigm for sleep deprivation in Drosophila that fully accounts for sleep-independent effects. Our results reveal that deep sleep states are the primary target of homeostatic control and establish the presence of multi-cycle sleep rebound following deprivation. Furthermore, we establish that specific deprivation of deep sleep states results in state-specific homeostatic rebound. Finally, by accounting for the molecular effects of mechanical stimulation during deprivation experiments, we show that serotonin levels track sleep pressure in the fly's central brain. Our results illustrate the critical need to control for sleep-independent effects of deprivation when examining the molecular correlates of sleep pressure and call for a critical reassessment of work that has not accounted for such non-specific effects.
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Affiliation(s)
- Budhaditya Chowdhury
- The Advanced Science Research Center, The City University of New York; The Graduate Center at the City University of New YorkNew YorkUnited States
| | - Lakshman Abhilash
- The Advanced Science Research Center, The City University of New York; The Graduate Center at the City University of New YorkNew YorkUnited States
| | - Antonio Ortega
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
| | - Sha Liu
- VIB-KU Leuven Center for Brain & Disease ResearchLeuvenBelgium
| | - Orie Shafer
- The Advanced Science Research Center, The City University of New York; The Graduate Center at the City University of New YorkNew YorkUnited States
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19
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Shekhar S, Wert KJ, Krämer H. Visual impairment cell non-autonomously dysregulates brain-wide proteostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563166. [PMID: 37961457 PMCID: PMC10634672 DOI: 10.1101/2023.10.19.563166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Loss of hearing or vision has been identified as a significant risk factor for dementia but underlying molecular mechanisms are unknown. In different Drosophila models of blindness, we observe non-autonomous induction of stress granules in the brain and their reversal upon restoration of vision. Stress granules include cytosolic condensates of p62, ATF4 and XRP1. This cytosolic restraint of the ATF4 and XRP1 transcription factors dampens expression of their downstream targets during cellular stress. Cytosolic condensates of p62 and ATF4 were also evident in the thalamus and hippocampus of mouse models of congenital or degenerative blindness. These data indicate conservation of the link between loss of sensory input and dysregulation of stress responses critical for protein quality control in the brain.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center; Dallas, TX
| | - Katherine J Wert
- Department of Ophthalmology, Department of Molecular Biology, UT Southwestern Medical Center; Dallas, TX
- O’Donnell Brain Institute, UT Southwestern Medical Center; Dallas, TX
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center; Dallas, TX
- O’Donnell Brain Institute, UT Southwestern Medical Center; Dallas, TX
- Department of Cell Biology, UT Southwestern Medical Center; Dallas, TX
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20
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Blackhurst L, Gilestro GF. Ethoscopy and ethoscope-lab: a framework for behavioural analysis to lower entrance barrier and aid reproducibility. BIOINFORMATICS ADVANCES 2023; 3:vbad132. [PMID: 37818176 PMCID: PMC10561991 DOI: 10.1093/bioadv/vbad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 07/28/2023] [Accepted: 09/18/2023] [Indexed: 10/12/2023]
Abstract
Summary High-throughput analysis of behaviour is a pivotal instrument in modern neuroscience, allowing researchers to combine modern genetics breakthrough to unbiased, objective, reproducible experimental approaches. To this extent, we recently created an open-source hardware platform (ethoscope; Geissmann Q, Garcia Rodriguez L, Beckwith EJ et al. Rethomics: an R framework to analyse high-throughput behavioural data. PLoS One 2019;14:e0209331) that allows for inexpensive, accessible, high-throughput analysis of behaviour in Drosophila or other animal models. Here we equip ethoscopes with a Python framework for data analysis, ethoscopy, designed to be a user-friendly yet powerful platform, meeting the requirements of researchers with limited coding expertise as well as experienced data scientists. Availability and implementation Ethoscopy is best consumed in a prebaked Jupyter-based docker container, ethoscope-lab, to improve accessibility and to encourage the use of notebooks as a natural platform to share post-publication data analysis. Ethoscopy is a Python package available on GitHub and PyPi. Ethoscope-lab is a docker container available on DockerHub. A landing page aggregating all the code and documentation is available at https://lab.gilest.ro/ethoscopy.
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Affiliation(s)
- Laurence Blackhurst
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Giorgio F Gilestro
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, United Kingdom
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21
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Yu J, Dancausse S, Paz M, Faderin T, Gaviria M, Shomar JW, Zucker D, Venkatachalam V, Klein M. Continuous, long-term crawling behavior characterized by a robotic transport system. eLife 2023; 12:e86585. [PMID: 37535068 PMCID: PMC10400072 DOI: 10.7554/elife.86585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 07/19/2023] [Indexed: 08/04/2023] Open
Abstract
Detailed descriptions of behavior provide critical insight into the structure and function of nervous systems. In Drosophila larvae and many other systems, short behavioral experiments have been successful in characterizing rapid responses to a range of stimuli at the population level. However, the lack of long-term continuous observation makes it difficult to dissect comprehensive behavioral dynamics of individual animals and how behavior (and therefore the nervous system) develops over time. To allow for long-term continuous observations in individual fly larvae, we have engineered a robotic instrument that automatically tracks and transports larvae throughout an arena. The flexibility and reliability of its design enables controlled stimulus delivery and continuous measurement over developmental time scales, yielding an unprecedented level of detailed locomotion data. We utilize the new system's capabilities to perform continuous observation of exploratory search behavior over a duration of 6 hr with and without a thermal gradient present, and in a single larva for over 30 hr. Long-term free-roaming behavior and analogous short-term experiments show similar dynamics that take place at the beginning of each experiment. Finally, characterization of larval thermotaxis in individuals reveals a bimodal distribution in navigation efficiency, identifying distinct phenotypes that are obfuscated when only analyzing population averages.
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Affiliation(s)
- James Yu
- Department of Physics, Northeastern UniversityBostonUnited States
| | - Stephanie Dancausse
- Department of Physics and Department of Biology, University of MiamiCoral GablesUnited States
| | - Maria Paz
- Department of Physics, Northeastern UniversityBostonUnited States
| | - Tolu Faderin
- Department of Physics, Northeastern UniversityBostonUnited States
| | - Melissa Gaviria
- Department of Physics and Department of Biology, University of MiamiCoral GablesUnited States
| | - Joseph W Shomar
- Department of Physics and Department of Biology, University of MiamiCoral GablesUnited States
| | | | | | - Mason Klein
- Department of Physics and Department of Biology, University of MiamiCoral GablesUnited States
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22
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Corley RB, Dawson W, Bishop TR. A simple method to account for thermal boundary layers during the estimation of CTmax in small ectotherms. J Therm Biol 2023; 116:103673. [PMID: 37527565 DOI: 10.1016/j.jtherbio.2023.103673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 08/03/2023]
Abstract
As temperatures rise, understanding how ectotherms will become impacted by thermal stress is of critical importance. In this context, many researchers quantify critical temperatures - these are the upper (CTmax) and lower (CTmin) thermal limits at which organisms can no longer function. Most studies estimate CTs using bath-based methods where organisms are submerged within a set thermal environment. Plate-based methods (i.e. hot plates), however, offer huge opportunity for automation and are readily available in many lab settings. Plates, however, generate a unidirectional thermal boundary layer above their surface which means that the temperatures experienced by organisms of different sizes is different. This boundary layer effect can bias estimates of critical temperatures. Here, we test the hypothesis that biases in critical temperature estimation on hot plates are driven by organism height. We also quantify the composition of the boundary layer in order to correct for these biases. We assayed four differently sized species of UK ants for their CTmax in dry baths (with no boundary layer) and on hot plates (with a boundary layer). We found that hot plates overestimated the CTmax values of the different ants, and that this overestimate was larger for taller species. By statistically modelling the thickness of the thermal boundary layer, and combining with estimates of species height, we were able to correct this overestimation and eliminate methodological differences. Our study provides two main findings. First, we provide evidence that organism height is positively related to the bias present in plate-based estimates of CTmax. Second, we show that a relatively simple statistical model can correct for this bias. By using simple corrections for boundary layer effects, as we have done here, researchers could open up a new possibility space in the design and implementation of thermal tolerance assays using plates rather than restrictive dry or water baths.
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Affiliation(s)
| | - Will Dawson
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Tom R Bishop
- School of Biosciences, Cardiff University, Cardiff, UK; Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa.
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23
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Shekhar S, Moehlman AT, Park B, Ewnetu M, Tracy C, Titos I, Pawłowski K, Tagliabracci VS, Krämer H. Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila. Nat Commun 2023; 14:2932. [PMID: 37217484 DOI: 10.1038/s41467-023-38485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 05/04/2023] [Indexed: 05/24/2023] Open
Abstract
In nervous systems, retrograde signals are key for organizing circuit activity and maintaining neuronal homeostasis. We identify the conserved Allnighter (Aln) pseudokinase as a cell non-autonomous regulator of proteostasis responses necessary for normal sleep and structural plasticity of Drosophila photoreceptors. In aln mutants exposed to extended ambient light, proteostasis is dysregulated and photoreceptors develop striking, but reversible, dysmorphology. The aln gene is widely expressed in different neurons, but not photoreceptors. However, secreted Aln protein is retrogradely endocytosed by photoreceptors. Inhibition of photoreceptor synaptic release reduces Aln levels in lamina neurons, consistent with secreted Aln acting in a feedback loop. In addition, aln mutants exhibit reduced night time sleep, providing a molecular link between dysregulated proteostasis and sleep, two characteristics of ageing and neurodegenerative diseases.
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Affiliation(s)
- Shashank Shekhar
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
| | - Andrew T Moehlman
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Brenden Park
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
| | - Michael Ewnetu
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Charles Tracy
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA
| | - Iris Titos
- Molecular Medicine Program, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Krzysztof Pawłowski
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences, Warsaw, 02-776, Poland
| | - Vincent S Tagliabracci
- Department of Molecular Biology UT Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Maryland, USA
| | - Helmut Krämer
- Department of Neuroscience, UT Southwestern Medical Center, Dallas, TX; O'Donnell Brain Institute, Dallas, USA.
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX, USA.
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24
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Cointe M, Burte V, Perez G, Mailleret L, Calcagno V. A double-spiral maze and hi-resolution tracking pipeline to study dispersal by groups of minute insects. Sci Rep 2023; 13:5200. [PMID: 36997620 PMCID: PMC10063622 DOI: 10.1038/s41598-023-31630-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Minute insects such as parasitic micro-wasps have high basic and applied importance for their widespread use as biocontrol agents. Their dispersal is a phenotype of particular interest. Classically, it is evaluated using field releases, but those are time consuming, costly, and their results highly variable, preventing high-throughput and repeatability. Alternatively, dispersal can be studied using small-scale assays, but those neglect important higher-scale processes. Consequently, proper evaluation of dispersal is often complicated or lacking in academic studies and biocontrol breeding programs. Here we introduce a new method, the double-spiral maze, that allows the study of spatial propagation of groups of micro-wasps at relevant scales (several hours and meters), retaining high throughput and experimental power. The method records the location of every individual at every time, enabling accurate estimates of diffusion coefficients or other dispersal metrics. We describe this affordable, scalable, and easy-to-implement method, and illustrate its application with a species of agricultural interest.
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Affiliation(s)
- M Cointe
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France.
| | - V Burte
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - G Perez
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
| | - L Mailleret
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
- Université Côte d'Azur, Inria, INRAE, CNRS, Sorbonne Université, Biocore, Sophia Antipolis, France
| | - V Calcagno
- Université Côte d'Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia Antipolis, France
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25
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Praschberger R, Kuenen S, Schoovaerts N, Kaempf N, Singh J, Janssens J, Swerts J, Nachman E, Calatayud C, Aerts S, Poovathingal S, Verstreken P. Neuronal identity defines α-synuclein and tau toxicity. Neuron 2023; 111:1577-1590.e11. [PMID: 36948206 DOI: 10.1016/j.neuron.2023.02.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
Pathogenic α-synuclein and tau are critical drivers of neurodegeneration, and their mutations cause neuronal loss in patients. Whether the underlying preferential neuronal vulnerability is a cell-type-intrinsic property or a consequence of increased expression levels remains elusive. Here, we explore cell-type-specific α-synuclein and tau expression in human brain datasets and use deep phenotyping as well as brain-wide single-cell RNA sequencing of >200 live neuron types in fruit flies to determine which cellular environments react most to α-synuclein or tau toxicity. We detect phenotypic and transcriptomic evidence of differential neuronal vulnerability independent of α-synuclein or tau expression levels. Comparing vulnerable with resilient neurons in Drosophila enabled us to predict numerous human neuron subtypes with increased intrinsic susceptibility to pathogenic α-synuclein or tau. By uncovering synapse- and Ca2+ homeostasis-related genes as tau toxicity modifiers, our work paves the way to leverage neuronal identity to uncover modifiers of neurodegeneration-associated toxic proteins.
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Affiliation(s)
- Roman Praschberger
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
| | - Sabine Kuenen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Nils Schoovaerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Natalie Kaempf
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Jeevanjot Singh
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Jasper Janssens
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Human Genetics, 3000 Leuven, Belgium
| | - Jef Swerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Eliana Nachman
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Carles Calatayud
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Human Genetics, 3000 Leuven, Belgium
| | | | - Patrik Verstreken
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven, Department of Neurosciences, Leuven Brain Institute, 3000 Leuven, Belgium.
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Marquand K, Roselli C, Cervantes-Sandoval I, Boto T. Sleep benefits different stages of memory in Drosophila. Front Physiol 2023; 14:1087025. [PMID: 36744027 PMCID: PMC9892949 DOI: 10.3389/fphys.2023.1087025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/20/2023] Open
Abstract
Understanding the physiological mechanisms that modulate memory acquisition and consolidation remains among the most ambitious questions in neuroscience. Massive efforts have been dedicated to deciphering how experience affects behavior, and how different physiological and sensory phenomena modulate memory. Our ability to encode, consolidate and retrieve memories depends on internal drives, and sleep stands out among the physiological processes that affect memory: one of the most relatable benefits of sleep is the aiding of memory that occurs in order to both prepare the brain to learn new information, and after a learning task, to consolidate those new memories. Drosophila lends itself to the study of the interactions between memory and sleep. The fruit fly provides incomparable genetic resources, a mapped connectome, and an existing framework of knowledge on the molecular, cellular, and circuit mechanisms of memory and sleep, making the fruit fly a remarkable model to decipher the sophisticated regulation of learning and memory by the quantity and quality of sleep. Research in Drosophila has stablished not only that sleep facilitates learning in wild-type and memory-impaired animals, but that sleep deprivation interferes with the acquisition of new memories. In addition, it is well-accepted that sleep is paramount in memory consolidation processes. Finally, studies in Drosophila have shown that that learning itself can promote sleep drive. Nevertheless, the molecular and network mechanisms underlying this intertwined relationship are still evasive. Recent remarkable work has shed light on the neural substrates that mediate sleep-dependent memory consolidation. In a similar way, the mechanistic insights of the neural switch control between sleep-dependent and sleep-independent consolidation strategies were recently described. This review will discuss the regulation of memory by sleep in Drosophila, focusing on the most recent advances in the field and pointing out questions awaiting to be investigated.
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Affiliation(s)
- Katie Marquand
- Department of Physiology, School of Medicine, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Camilla Roselli
- Trinity College Institute of Neuroscience, School of Genetics and Microbiology, Smurfit Institute of Genetics and School of Natural Sciences, Trinity College Dublin, Dublin, Ireland
| | - Isaac Cervantes-Sandoval
- Department of Biology, Georgetown University, Washington, DC, United States
- Interdisciplinary Program in Neuroscience, Georgetown University, Washington, DC, United States
| | - Tamara Boto
- Department of Physiology, School of Medicine, Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
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Masier S, Taudière A, Roy LJM, Carrasco D, Barnagaud JY, Planchon C, Soulié AS, Sleeckx N, Roy L. High-throughput behavioral phenotyping of tiny arthropods: Chemosensory traits in a mesostigmatic hematophagous mite. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:46-62. [PMID: 36052497 PMCID: PMC10087610 DOI: 10.1002/jez.2651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Pest management using attractive and/or repellent semiochemicals is a key alternative to synthetic insecticides. Its implementation requires a good understanding of the intra- and interspecific chemical interactions of arthropod pests, their interactions with their abiotic environment, as well as their evolutionary dynamics. Although mites include many pest species and biocontrol agents of economic importance in agriculture, their chemical ecology is largely understudied compared to insects. We developed a high-throughput ethomics system to analyze these small arthropods and conducted a study on Dermanyssus gallinae, a problematic poultry parasite in the egg industry. Our purpose was to elucidate the role played by host-derived odorants (synthetic kairomone) and conspecific odorants (mite body odors) in D. gallinae. After validating our nanocomputer controlled olfactometric system with volatile semiochemicals of known biological activity, we characterized response traits to kairomonal and/or pheromonal volatile blends in mites from different populations. We were able to accurately characterize the repulsion or attraction behaviors in >1000 individual specimens in a standardized way. Our results confirm the presence of a volatile aggregation pheromone emitted by D. gallinae and bring new elements to the effect of odor source presentation. Our results also confirm the attractive effect on Dermanyssus gallinae of a blend of volatile compounds contained in hen odor, while highlighting a repellent effect at high concentration. Significant interindividual and interpopulation variation was noted particularly in responses to synthetic kairomone. This information lays a valuable foundation for further exploring the emergence risk of resistance to semiochemicals.
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Affiliation(s)
- Stefano Masier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Adrien Taudière
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | | | - David Carrasco
- MiVEGEC, University of Montpellier, IRD, CNRS, Montpellier, France
| | - Jean-Yves Barnagaud
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Camille Planchon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Anne-Sophie Soulié
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | | | - Lise Roy
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
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Cabana-Domínguez J, Antón-Galindo E, Fernàndez-Castillo N, Singgih EL, O'Leary A, Norton WH, Strekalova T, Schenck A, Reif A, Lesch KP, Slattery D, Cormand B. The translational genetics of ADHD and related phenotypes in model organisms. Neurosci Biobehav Rev 2023; 144:104949. [PMID: 36368527 DOI: 10.1016/j.neubiorev.2022.104949] [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: 07/01/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Attention-deficit/hyperactivity disorder (ADHD) is a highly prevalent neurodevelopmental disorder resulting from the interaction between genetic and environmental risk factors. It is well known that ADHD co-occurs frequently with other psychiatric disorders due, in part, to shared genetics factors. Although many studies have contributed to delineate the genetic landscape of psychiatric disorders, their specific molecular underpinnings are still not fully understood. The use of animal models can help us to understand the role of specific genes and environmental stimuli-induced epigenetic modifications in the pathogenesis of ADHD and its comorbidities. The aim of this review is to provide an overview on the functional work performed in rodents, zebrafish and fruit fly and highlight the generated insights into the biology of ADHD, with a special focus on genetics and epigenetics. We also describe the behavioral tests that are available to study ADHD-relevant phenotypes and comorbid traits in these models. Furthermore, we have searched for new models to study ADHD and its comorbidities, which can be useful to test potential pharmacological treatments.
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Affiliation(s)
- Judit Cabana-Domínguez
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
| | - Ester Antón-Galindo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Noèlia Fernàndez-Castillo
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain
| | - Euginia L Singgih
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Aet O'Leary
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany; Division of Neuropsychopharmacology, Department of Psychology, University of Tartu, Tartu, Estonia
| | - William Hg Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Tatyana Strekalova
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - Annette Schenck
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Würzburg, Germany, and Department of Neuropsychology and Psychiatry, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, the Netherlands
| | - David Slattery
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital, Goethe University, Frankfurt, Germany
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Catalonia, Spain; Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues de Llobregat, Catalonia, Spain.
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A ShK-like Domain from Steinernema carpocapsae with Bioinsecticidal Potential. Toxins (Basel) 2022; 14:toxins14110754. [PMID: 36356004 PMCID: PMC9699480 DOI: 10.3390/toxins14110754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/27/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022] Open
Abstract
Entomopathogenic nematodes are used as biological control agents against a broad range of insect pests. We ascribed the pathogenicity of these organisms to the excretory/secretory products (ESP) released by the infective nematode. Our group characterized different virulence factors produced by Steinernema carpocapsae that underlie its success as an insect pathogen. A novel ShK-like peptide (ScK1) from this nematode that presents high sequence similarity with the ShK peptide from a sea anemone was successfully produced recombinantly in Escherichia coli. The secondary structure of ScK1 appeared redox-sensitive, exhibiting a far-UV circular dichroism spectrum consistent with an alpha-helical secondary structure. Thermal denaturation of the ScK1 allowed estimating the melting temperature to 59.2 ± 0.1 °C. The results from toxicity assays using Drosophila melanogaster as a model show that injection of this peptide can kill insects in a dose-dependent manner with an LD50 of 16.9 µM per adult within 24 h. Oral administration of the fusion protein significantly reduced the locomotor activity of insects after 48 h (p < 0.05, Tukey's test). These data show that this nematode expresses insecticidal peptides with potential as next-generation insecticides.
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Morris BI, Kittredge MJ, Casey B, Meng O, Chagas AM, Lamparter M, Thul T, Pask GM. PiSpy: An affordable, accessible, and flexible imaging platform for the automated observation of organismal biology and behavior. PLoS One 2022; 17:e0276652. [PMID: 36288371 PMCID: PMC9604989 DOI: 10.1371/journal.pone.0276652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
A great deal of understanding can be gleaned from direct observation of organismal growth, development, and behavior. However, direct observation can be time consuming and influence the organism through unintentional stimuli. Additionally, video capturing equipment can often be prohibitively expensive, difficult to modify to one's specific needs, and may come with unnecessary features. Here, we describe PiSpy, a low-cost, automated video acquisition platform that uses a Raspberry Pi computer and camera to record video or images at specified time intervals or when externally triggered. All settings and controls, such as programmable light cycling, are accessible to users with no programming experience through an easy-to-use graphical user interface. Importantly, the entire PiSpy system can be assembled for less than $100 using laser-cut and 3D-printed components. We demonstrate the broad applications and flexibility of PiSpy across a range of model and non-model organisms. Designs, instructions, and code can be accessed through an online repository, where a global community of PiSpy users can also contribute their own unique customizations and help grow the community of open-source research solutions.
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Affiliation(s)
- Benjamin I. Morris
- Program in Molecular Biology and Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- * E-mail: (BIM); (GMP)
| | - Marcy J. Kittredge
- Neuroscience Program, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Bea Casey
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Owen Meng
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - André Maia Chagas
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
- TReND in Africa, Brighton, United Kingdom
- Gathering for Open Science Hardware
| | - Matt Lamparter
- Department of Electrical and Computer Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Thomas Thul
- Department of Biomedical Engineering, Bucknell University, Lewisburg, Pennsylvania, United States of America
| | - Gregory M. Pask
- Program in Molecular Biology and Biochemistry, Middlebury College, Middlebury, Vermont, United States of America
- Department of Biology and Neuroscience Program, Middlebury College, Middlebury, Vermont, United States of America
- * E-mail: (BIM); (GMP)
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Shaible TM, Matzkin LM. Physiological and life history changes associated with seasonal adaptation in the cactophilic Drosophila mojavensis. Biol Open 2022; 11:bio059610. [PMID: 36285699 PMCID: PMC9637388 DOI: 10.1242/bio.059610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023] Open
Abstract
Many insects inhabiting temperate climates are faced with changing environmental conditions throughout the year. Depending on the species, these environmental fluctuations can be experienced within a single generation or across multiple generations. Strategies for dealing with these seasonal changes vary across populations. Drosophila mojavensis is a cactophilic Drosophila species endemic to the Sonoran Desert. The Sonoran Desert regularly reaches temperatures of 50°C in the summer months. As individuals of this population are rare to collect in the summer months, we simulated the cycling temperatures experienced by D. mojavensis in the Sonoran Desert from April to July (four generations) in a temperature- and light-controlled chamber, to understand the physiological and life history changes that allow this population to withstand these conditions. In contrast to our hypothesis of a summer aestivation, we found that D. mojavensis continue to reproduce during the summer months, albeit with lower viability, but the adult survivorship of the population is highly reduced during this period. As expected, stress resistance increased during the summer months in both the adult and the larval stages. This study examines several strategies for withstanding the Sonoran Desert summer conditions which may be informative in the study of other desert endemic species.
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Affiliation(s)
| | - Luciano M. Matzkin
- Department of Entomology, University of Arizona, Tucson, AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Dupray S, Blatrix R, Roy LJ, Soulié A, Dadu L, Degueldre D, Sleeckx N, Bicout DJ, Roy L. Population dynamics of a poultry hematophagous mite: characterization of the population growth and identification of factors of its slowdown using closed mesocosms. PEST MANAGEMENT SCIENCE 2022; 78:4151-4165. [PMID: 35674477 PMCID: PMC9546284 DOI: 10.1002/ps.7033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 05/30/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND A thorough knowledge of the population dynamics of pests and of the main factors affecting population growth is an important prerequisite for the development of effective control strategies. Failures of various treatments aimed at regulating populations of Dermanyssus gallinae are regularly reported in poultry farms and pullulations occur very quickly after first detection. To finely characterize population dynamics of D. gallinae, and to identify the factors modulating population growth, we conducted two successive multi-generation experiments using closed mesocosms equipped with or without automatic counters and housing a host full- or part-time (three nights per week). RESULTS Population growth was very rapid and the adult to juvenile ratio very different from the prediction by a mathematical model. A male-biased sex ratio was observed in some mesocosms from 21 days and in most mesocosms from 35 days of population growth originating from an inoculum of adult females. A dramatic slowdown in growth was measured in mesocosms equipped with trackers, where the mites' path to the host was constrained. The slowdown in population growth induced by the intermittent presence of the host compared to its full-time presence was much less marked. CONCLUSION These findings suggest avenues of research for new management methods. They question the relevance of a critical threshold based on traditional trap monitoring to manage D. gallinae. Our results highlight a unique characteristic of D. gallinae that makes it a recalcitrant case to threshold-based practices recommended for integrated pest management (IPM) against other arthropod pests. The dramatic effect of a physical constraint for the mite to access the host (unnatural constrained path) confirms an observation made in 1917 and is a reason to design perches that are less conducive to parasite traffic. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Sébastien Dupray
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Rumsais Blatrix
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | | | - Anne‐Sophie Soulié
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Liza Dadu
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - David Degueldre
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | | | - Dominique J Bicout
- Translational Innovation in Medicine and Complexity (TIMC, Grenoble Alpes University, VetAgro SupMarcy l'EtoileFrance
| | - Lise Roy
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3MontpellierFrance
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Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster. PLoS Pathog 2022; 18:e1010826. [PMID: 36129961 PMCID: PMC9529128 DOI: 10.1371/journal.ppat.1010826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/03/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022] Open
Abstract
Host behavioural changes are among the most apparent effects of infection. ‘Sickness behaviour’ can involve a variety of symptoms, including anorexia, depression, and changed activity levels. Here, using a real-time tracking and behavioural profiling platform, we show that in Drosophila melanogaster, several systemic bacterial infections cause significant increases in physical activity, and that the extent of this activity increase is a predictor of survival time in some lethal infections. Using multiple bacteria and D. melanogaster immune and activity mutants, we show that increased activity is driven by at least two different mechanisms. Increased activity after infection with Micrococcus luteus, a Gram-positive bacterium rapidly cleared by the immune response, strictly requires the Toll ligand spätzle. In contrast, increased activity after infection with Francisella novicida, a Gram-negative bacterium that cannot be cleared by the immune response, is entirely independent of both Toll and the parallel IMD pathway. The existence of multiple signalling mechanisms by which bacterial infections drive increases in physical activity implies that this effect may be an important aspect of the host response. Sickness behaviours are often observed during infection. Animals have been shown to change their feeding, mating, social and resting (sleeping) behaviours in response to infection. We show here that fruit-flies infected with bacteria respond by increasing their physical activity and decreasing the amount of time spent sleeping. This increase in activity is seen in some, but not all, bacterial infections, and appears to be driven by at least two different mechanisms: with some bacteria, activating the immune response is the only requirement to induce increased activity, while other bacteria induce increased activity independently of known immune detection pathways. The biological role of increased activity is unclear; flies in the wild may be driven to flee sites where infection risk or pathogen burden is high. Alternatively, increased activity could serve a less direct anti-microbial function. For example, active animals may be more likely to encounter potential mates or food resource.
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Oellermann M, Jolles JW, Ortiz D, Seabra R, Wenzel T, Wilson H, Tanner RL. Open Hardware in Science: The Benefits of Open Electronics. Integr Comp Biol 2022; 62:1061-1075. [PMID: 35595471 PMCID: PMC9617215 DOI: 10.1093/icb/icac043] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/30/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022] Open
Abstract
Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global “maker” community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.
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Affiliation(s)
- Michael Oellermann
- Technical University of Munich, TUM School of Life Sciences, Aquatic Systems Biology Unit, Mühlenweg 22, D-85354 Freising, Germany.,University of Tasmania, Institute for Marine and Antarctic Studies, Fisheries and Aquaculture Centre, Private Bag 49, Hobart, TAS 7001, Australia
| | - Jolle W Jolles
- Centre for Research on Ecology and Forestry Applications (CREAF), Campus UAB, Edifici C. 08193 Bellaterra Barcelona, Spain
| | - Diego Ortiz
- INTA, Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Manfredi, Ruta 9 Km 636, 5988, Manfredi, Córdoba, Argentina
| | - Rui Seabra
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Tobias Wenzel
- Pontificia Universidad Católica de Chile, Institute for Biological and Medical Engineering, Schools of Engineering (IIBM), Medicine and Biological Sciences, Santiago, Chile
| | - Hannah Wilson
- Utah State University, College of Science, Biology Department, 5305 Old Main Hill, Logan, UT, 84321, USA
| | - Richelle L Tanner
- Chapman University, Environmental Science and Policy Program, 1 University Drive, Orange, CA 92866, USA
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Garg V, André S, Giraldo D, Heyer L, Göpfert MC, Dosch R, Geurten BRH. A Markerless Pose Estimator Applicable to Limbless Animals. Front Behav Neurosci 2022; 16:819146. [PMID: 35418841 PMCID: PMC8997243 DOI: 10.3389/fnbeh.2022.819146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/09/2022] [Indexed: 11/25/2022] Open
Abstract
The analysis of kinematics, locomotion, and spatial tasks relies on the accurate detection of animal positions and pose. Pose and position can be assessed with video analysis programs, the “trackers.” Most available trackers represent animals as single points in space (no pose information available) or use markers to build a skeletal representation of pose. Markers are either physical objects attached to the body (white balls, stickers, or paint) or they are defined in silico using recognizable body structures (e.g., joints, limbs, color patterns). Physical markers often cannot be used if the animals are small, lack prominent body structures on which the markers can be placed, or live in environments such as aquatic ones that might detach the marker. Here, we introduce a marker-free pose-estimator (LACE Limbless Animal traCkEr) that builds the pose of the animal de novo from its contour. LACE detects the contour of the animal and derives the body mid-line, building a pseudo-skeleton by defining vertices and edges. By applying LACE to analyse the pose of larval Drosophila melanogaster and adult zebrafish, we illustrate that LACE allows to quantify, for example, genetic alterations of peristaltic movements and gender-specific locomotion patterns that are associated with different body shapes. As illustrated by these examples, LACE provides a versatile method for assessing position, pose and movement patterns, even in animals without limbs.
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Affiliation(s)
- Vranda Garg
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
| | - Selina André
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
| | - Diego Giraldo
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
| | - Luisa Heyer
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
| | - Martin C. Göpfert
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
| | - Roland Dosch
- Institute for Humangenetics, University Medical Center Göttingen, Georg-August-University Göttingen, Gottingen, Germany
| | - Bart R. H. Geurten
- Department of Cellular Neuroscience, Georg-August-University Göttingen, Gottingen, Germany
- *Correspondence: Bart R. H. Geurten
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Buchert SN, Murakami P, Kalavadia AH, Reyes MT, Sitaraman D. Sleep correlates with behavioral decision making critical for reproductive output in Drosophila melanogaster. Comp Biochem Physiol A Mol Integr Physiol 2022; 264:111114. [PMID: 34785379 PMCID: PMC9299756 DOI: 10.1016/j.cbpa.2021.111114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/30/2021] [Accepted: 11/03/2021] [Indexed: 02/03/2023]
Abstract
Balance between sleep, wakefulness and arousal is important for survival of organisms and species as a whole. While, the benefits of sleep both in terms of quantity and quality is widely recognized across species, sleep has a cost for organismal survival and reproduction. Here we focus on how sleep duration, sleep depth and sleep pressure affect the ability of animals to engage in courtship and egg-laying behaviors critical for reproductive success. Using isogenic lines from the Drosophila Genetic Reference Panel with variable sleep phenotypes we investigated the relationship between sleep and reproductive behaviors, courtship and oviposition. We found that three out of five lines with decreased sleep and increased arousal phenotypes, showed increased courtship and decreased latency to court as compared to normal and long sleeping lines. However, the male courtship phenotype is dependent on context and genotype as some but not all long sleeping-low courting lines elevate their courtship in the presence of short sleeping-high courting flies. We also find that unlike courtship, sleep phenotypes were less variable and minimally susceptible to social experience. In addition to male courtship, we also investigated egg-laying phenotype, a readout of female reproductive output and find oviposition to be less sensitive to sleep length and parameters that are indicative of switch between sleep and wake states. Taken together our extensive behavioral analysis here shows complex bidirectional interactions between genotype and environment and add to the growing evidence linking sleep duration and sleep-wake switch parameters to behavioral decision making critical to reproductive output.
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Affiliation(s)
- Steven N. Buchert
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Pomai Murakami
- Department of Psychological Sciences, College of Arts and Sciences, 5998 Alcala Park, University of San Diego, San Diego, CA 92110, United States of America
| | - Aashaka H. Kalavadia
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Martin T. Reyes
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America
| | - Divya Sitaraman
- Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America,Department of Psychological Sciences, College of Arts and Sciences, 5998 Alcala Park, University of San Diego, San Diego, CA 92110, United States of America,Corresponding author at: Department of Psychology, College of Science, 25800 Carlos Bee Blvd, California State University, Hayward, CA 94542, United States of America. (D. Sitaraman)
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37
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Mollá-Albaladejo R, Sánchez-Alcañiz JA. Behavior Individuality: A Focus on Drosophila melanogaster. Front Physiol 2021; 12:719038. [PMID: 34916952 PMCID: PMC8670942 DOI: 10.3389/fphys.2021.719038] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/11/2021] [Indexed: 12/02/2022] Open
Abstract
Among individuals, behavioral differences result from the well-known interplay of nature and nurture. Minute differences in the genetic code can lead to differential gene expression and function, dramatically affecting developmental processes and adult behavior. Environmental factors, epigenetic modifications, and gene expression and function are responsible for generating stochastic behaviors. In the last decade, the advent of high-throughput sequencing has facilitated studying the genetic basis of behavior and individuality. We can now study the genomes of multiple individuals and infer which genetic variations might be responsible for the observed behavior. In addition, the development of high-throughput behavioral paradigms, where multiple isogenic animals can be analyzed in various environmental conditions, has again facilitated the study of the influence of genetic and environmental variations in animal personality. Mainly, Drosophila melanogaster has been the focus of a great effort to understand how inter-individual behavioral differences emerge. The possibility of using large numbers of animals, isogenic populations, and the possibility of modifying neuronal function has made it an ideal model to search for the origins of individuality. In the present review, we will focus on the recent findings that try to shed light on the emergence of individuality with a particular interest in D. melanogaster.
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38
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Yildirim K, Winkler B, Pogodalla N, Mackensen S, Baldenius M, Garcia L, Naffin E, Rodrigues S, Klämbt C. Redundant functions of the SLC5A transporters Rumpel, Bumpel, and Kumpel in ensheathing glial cells. Biol Open 2021; 11:274028. [PMID: 34897385 PMCID: PMC8790523 DOI: 10.1242/bio.059128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022] Open
Abstract
Neuronal processing is energy demanding, and relies on sugar metabolism. To nurture the Drosophila nervous system, the blood-brain barrier forming glial cells take up trehalose from the hemolymph and then distribute the metabolic products further to all neurons. This function is provided by glucose and lactate transporters of the solute carrier (SLC) 5A family. Here we identified three SLC5A genes that are specifically expressed in overlapping sets of CNS glial cells, rumpel, bumpel and kumpel. We generated mutants in all genes and all mutants are viable and fertile, lacking discernible phenotypes. Loss of rumpel causes subtle locomotor phenotypes and flies display increased daytime sleep. In addition, in bumpel kumpel double mutants, and to an even greater extent in rumpel bumpel kumpel triple mutants, oogenesis is disrupted at the onset of the vitollegenic phase. This indicates a partially redundant functions between these genes. Rescue experiments exploring this effect indicate that oogenesis can be affected by CNS glial cells. Moreover, expression of heterologous mammalian SLC5A transporters, with known transport properties, suggest that Bumpel and/or Kumpel transport glucose or lactate. Overall, our results imply a redundancy in SLC5A nutrient sensing functions in Drosophila glial cells, affecting ovarian development and behavior.
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Affiliation(s)
- Kerem Yildirim
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany.,Centre for Organismal Studies (COS) Heidelberg, University of Heidelberg, Im Neuenheimer Feld 230, 9120 Heidelberg, Germany
| | - Bente Winkler
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Nicole Pogodalla
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Steffi Mackensen
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Marie Baldenius
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Luis Garcia
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Elke Naffin
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Silke Rodrigues
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
| | - Christian Klämbt
- Institute for Neuro- and Behavioral Biology, University of Münster, Badestr. 9, 48149 Münster, Germany
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39
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Flies sense the world while sleeping. Nature 2021; 598:423-424. [PMID: 34588643 DOI: 10.1038/d41586-021-02441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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40
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Sensory processing during sleep in Drosophila melanogaster. Nature 2021; 598:479-482. [PMID: 34588694 DOI: 10.1038/s41586-021-03954-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 08/25/2021] [Indexed: 12/28/2022]
Abstract
During sleep, most animal species enter a state of reduced consciousness characterized by a marked sensory disconnect. Yet some processing of the external world must remain intact, given that a sleeping animal can be awoken by intense stimuli (for example, a loud noise or a bright light) or by soft but qualitatively salient stimuli (for example, the sound of a baby cooing or hearing one's own name1-3). How does a sleeping brain retain the ability to process the quality of sensory information? Here we present a paradigm to study the functional underpinnings of sensory discrimination during sleep in Drosophila melanogaster. We show that sleeping vinegar flies, like humans, discern the quality of sensory stimuli and are more likely to wake up in response to salient stimuli. We also show that the salience of a stimulus during sleep can be modulated by internal states. We offer a prototypical blueprint detailing a circuit involved in this process and its modulation as evidence that the system can be used to explore the cellular underpinnings of how a sleeping brain experiences the world.
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41
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Jolles JW. Broad‐scale applications of the Raspberry Pi: A review and guide for biologists. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13652] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jolle W. Jolles
- Zukunftskolleg University of Konstanz Konstanz Germany
- Department of Collective Behaviour Max Planck Institute of Animal Behaviour Konstanz Germany
- Centre for Research on Ecology and Forestry Applications (CREAF) Barcelona Spain
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42
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Kostadinov B, Lee Pettibone H, Bell EV, Zhou X, Pranevicius A, Shafer OT, Fernandez MP. Open-source computational framework for studying Drosophila behavioral phase. STAR Protoc 2021; 2:100285. [PMID: 33532734 PMCID: PMC7829270 DOI: 10.1016/j.xpro.2020.100285] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
This protocol describes a standardized method for analyzing Drosophila behavioral rhythmicity under light dark cycles, temperature ramps, and free running conditions. The protocol constitutes a step-by-step guide from generation of appropriate Drosophila genetic crosses to behavioral experiments. We also provide an open-source computational framework using R for the analysis of the phase of behavior using circular statistics. An extended method for complete use is also provided. For complete details on the use and execution of this protocol, please refer to Fernandez et al. (2020). R framework for analysis of Drosophila behavioral phase and circular statistics analysis Visualization of activity, phase of behavior, and rose plots
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Affiliation(s)
- Boyan Kostadinov
- Mathematics Department, NYC College of Technology, City University of New York, Brooklyn, NY 11201, USA
| | - Hannah Lee Pettibone
- Advanced Science Research Center, The Graduate Center, City University of New York, New York, NY 10031, USA
| | - Evardra Valerie Bell
- Department of Neuroscience and Behavior, Barnard College of Columbia University, New York, NY 10027, USA
| | - Xiaona Zhou
- Mathematics Department, NYC College of Technology, City University of New York, Brooklyn, NY 11201, USA
| | - Ausra Pranevicius
- Department of Neuroscience and Behavior, Barnard College of Columbia University, New York, NY 10027, USA
| | - Orie Thomas Shafer
- Advanced Science Research Center, The Graduate Center, City University of New York, New York, NY 10031, USA
| | - Maria Paz Fernandez
- Department of Neuroscience and Behavior, Barnard College of Columbia University, New York, NY 10027, USA
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43
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Abstract
One in three epilepsy cases is drug resistant, and seizures often begin in infancy, when they are life-threatening and when therapeutic options are highly limited. An important tool for prioritizing and validating genes associated with epileptic conditions, which is suitable for large-scale screening, is disease modeling in Drosophila. Approximately two-thirds of disease genes are conserved in Drosophila, and gene-specific fly models exhibit behavioral changes that are related to symptoms of epilepsy. Models are based on behavior readouts, seizure-like attacks and paralysis following stimulation, and neuronal, cell-biological readouts that are in the majority based on changes in nerve cell activity or morphology. In this review, we focus on behavioral phenotypes. Importantly, Drosophila modeling is independent of, and complementary to, other approaches that are computational and based on systems analysis. The large number of known epilepsy-associated gene variants indicates a need for efficient research strategies. We will discuss the status quo of epilepsy disease modelling in Drosophila and describe promising steps towards the development of new drugs to reduce seizure rates and alleviate other epileptic symptoms.
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Affiliation(s)
- Paul Lasko
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Kevin Lüthy
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, Nijmegen, Netherlands
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44
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Spierer AN, Yoon D, Zhu CT, Rand DM. FreeClimber: automated quantification of climbing performance in Drosophila. J Exp Biol 2021; 224:jeb229377. [PMID: 33188065 PMCID: PMC7823161 DOI: 10.1242/jeb.229377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/05/2020] [Indexed: 12/26/2022]
Abstract
Negative geotaxis (climbing) performance is a useful metric for quantifying Drosophila health. Manual methods to quantify climbing performance are tedious and often biased, while many available computational methods have challenging hardware or software requirements. We present an alternative: FreeClimber. This open source, Python-based platform subtracts a video's static background to improve detection for flies moving across heterogeneous backgrounds. FreeClimber calculates a cohort's velocity as the slope of the most linear portion of a mean vertical position versus time curve. It can run from a graphical user interface for optimization or a command line interface for high-throughput and automated batch processing, improving accessibility for users with different expertise. FreeClimber outputs calculated slopes, spot locations for follow-up analyses (e.g. tracking), and several visualizations and plots. We demonstrate FreeClimber's utility in a longitudinal study for endurance exercise performance in Drosophila mitonuclear genotypes using six distinct mitochondrial haplotypes paired with a common D. melanogaster nuclear background.
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Affiliation(s)
- Adam N Spierer
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
| | - Denise Yoon
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chen-Tseh Zhu
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
- Global Plant Breeding, Bayer Crop Science, Chesterfield, MO 63017, USA
| | - David M Rand
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI 02912, USA
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45
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Abstract
Sleep is critical for diverse aspects of brain function in animals ranging from invertebrates to humans. Powerful genetic tools in the fruit fly Drosophila melanogaster have identified - at an unprecedented level of detail - genes and neural circuits that regulate sleep. This research has revealed that the functions and neural principles of sleep regulation are largely conserved from flies to mammals. Further, genetic approaches to studying sleep have uncovered mechanisms underlying the integration of sleep and many different biological processes, including circadian timekeeping, metabolism, social interactions, and aging. These findings show that in flies, as in mammals, sleep is not a single state, but instead consists of multiple physiological and behavioral states that change in response to the environment, and is shaped by life history. Here, we review advances in the study of sleep in Drosophila, discuss their implications for understanding the fundamental functions of sleep that are likely to be conserved among animal species, and identify important unanswered questions in the field.
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Affiliation(s)
- Orie T Shafer
- The Advanced Science Research Center, City University of New York, New York, NY 10031, USA.
| | - Alex C Keene
- Department of Biological Science, Florida Atlantic University, Jupiter, FL 33458, USA.
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46
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Jepson JEC. Sleep: Astrocytes Take Their Toll on Tired Flies. Curr Biol 2021; 31:R27-R30. [PMID: 33434483 DOI: 10.1016/j.cub.2020.10.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Calcium signalling in astrocytes modulates sleep, yet how astrocytes communicate with neural circuits that control sleep is unclear. A new study now uncovers a calcium-dependent relay between astrocytes and neurons that promotes sleep homeostasis in fruit flies.
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Affiliation(s)
- James E C Jepson
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, UK.
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47
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Melnattur K, Morgan E, Duong V, Kalra A, Shaw PJ. The Sleep Nullifying Apparatus: A Highly Efficient Method of Sleep Depriving Drosophila. J Vis Exp 2020. [PMID: 33369606 DOI: 10.3791/62105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Sleep homeostasis, the increase in sleep observed following sleep loss, is one of the defining criteria used to identify sleep throughout the animal kingdom. As a consequence, sleep deprivation and sleep restriction are powerful tools that are commonly used to provide insight into sleep function. Nonetheless, sleep deprivation experiments are inherently problematic in that the deprivation stimulus itself may be the cause of observed changes in physiology and behavior. Accordingly, successful sleep deprivation techniques should keep animals awake and, ideally, result in a robust sleep rebound without also inducing a large number of unintended consequences. Here, we describe a sleep deprivation technique for Drosophila melanogaster. The Sleep Nullifying Apparatus (SNAP) administers a stimulus every 10s to induce negative geotaxis. Although the stimulus is predictable, the SNAP effectively prevents >95% of nighttime sleep even in flies with high sleep drive. Importantly, the subsequent homeostatic response is very similar to that achieved using hand-deprivation. The timing and spacing of the stimuli can be modified to minimize sleep loss and thus examine non-specific effects of the stimulus on physiology and behavior. The SNAP can also be used for sleep restriction and to assess arousal thresholds. The SNAP is a powerful sleep disruption technique that can be used to better understand sleep function.
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Affiliation(s)
- Krishna Melnattur
- Department of Neuroscience, Washington University School of Medicine
| | - Ellen Morgan
- Department of Neuroscience, Washington University School of Medicine
| | - Vincent Duong
- Department of Neuroscience, Washington University School of Medicine
| | - Arjan Kalra
- Department of Neuroscience, Washington University School of Medicine
| | - Paul J Shaw
- Department of Neuroscience, Washington University School of Medicine;
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48
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Blum ID, Keleş MF, Baz ES, Han E, Park K, Luu S, Issa H, Brown M, Ho MCW, Tabuchi M, Liu S, Wu MN. Astroglial Calcium Signaling Encodes Sleep Need in Drosophila. Curr Biol 2020; 31:150-162.e7. [PMID: 33186550 DOI: 10.1016/j.cub.2020.10.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/17/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022]
Abstract
Sleep is under homeostatic control, whereby increasing wakefulness generates sleep need and triggers sleep drive. However, the molecular and cellular pathways by which sleep need is encoded are poorly understood. In addition, the mechanisms underlying both how and when sleep need is transformed to sleep drive are unknown. Here, using ex vivo and in vivo imaging, we show in Drosophila that astroglial Ca2+ signaling increases with sleep need. We demonstrate that this signaling is dependent on a specific L-type Ca2+ channel and is necessary for homeostatic sleep rebound. Thermogenetically increasing Ca2+ in astrocytes induces persistent sleep behavior, and we exploit this phenotype to conduct a genetic screen for genes required for the homeostatic regulation of sleep. From this large-scale screen, we identify TyrRII, a monoaminergic receptor required in astrocytes for sleep homeostasis. TyrRII levels rise following sleep deprivation in a Ca2+-dependent manner, promoting further increases in astrocytic Ca2+ and resulting in a positive-feedback loop. Moreover, our findings suggest that astrocytes then transmit this sleep need to a sleep drive circuit by upregulating and releasing the interleukin-1 analog Spätzle, which then acts on Toll receptors on R5 neurons. These findings define astroglial Ca2+ signaling mechanisms encoding sleep need and reveal dynamic properties of the sleep homeostatic control system.
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Affiliation(s)
- Ian D Blum
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mehmet F Keleş
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - El-Sayed Baz
- VIB Center for Brain and Disease Research and Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
| | - Emily Han
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Kristen Park
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Skylar Luu
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Habon Issa
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Matt Brown
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Margaret C W Ho
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Masashi Tabuchi
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Sha Liu
- VIB Center for Brain and Disease Research and Department of Neurosciences, KU Leuven, Leuven 3000, Belgium.
| | - Mark N Wu
- Department of Neurology, Johns Hopkins University, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, USA.
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49
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Tadres D, Louis M. PiVR: An affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior. PLoS Biol 2020; 18:e3000712. [PMID: 32663220 PMCID: PMC7360024 DOI: 10.1371/journal.pbio.3000712] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/09/2020] [Indexed: 12/19/2022] Open
Abstract
Tools enabling closed-loop experiments are crucial to delineate causal relationships between the activity of genetically labeled neurons and specific behaviors. We developed the Raspberry Pi Virtual Reality (PiVR) system to conduct closed-loop optogenetic stimulation of neural functions in unrestrained animals. PiVR is an experimental platform that operates at high temporal resolution (70 Hz) with low latencies (<30 milliseconds), while being affordable (
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Affiliation(s)
- David Tadres
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Matthieu Louis
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, California, United States of America
- Department of Physics, University of California, Santa Barbara, Santa Barbara, California, United States of America
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50
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Anton S, Gadenne C, Marion-Poll F. Frontiers in Invertebrate Physiology-An Update to the Grand Challenge. Front Physiol 2020; 11:186. [PMID: 32184737 PMCID: PMC7058698 DOI: 10.3389/fphys.2020.00186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/18/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Sylvia Anton
- UMR IGEPP INRA, Agrocampus Ouest, Université Rennes 1, Angers, France
| | | | - Frédéric Marion-Poll
- Evolution, Génomes, Comportement, Ecologie, CNRS, IRD, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.,AgroParisTech, Université Paris-Saclay, Paris, France
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