Publications
21 results found
Jones H, Willis J, Firth L, et al., 2023, A reductionist paradigm for high-throughput behavioural fingerprinting in Drosophila melanogaster, eLife, ISSN: 2050-084X
Blackhurst L, Gilestro G, 2023, Ethoscopy and ethoscope-lab: a framework for behavioural analysis to lower entrance barrier and aid reproducibility behavioural analysis to lower entrance barrier and aidreproducibility, Bioinformatics Advances, Vol: 3, ISSN: 2635-0041
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 et al., 2017)) 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. Ethoscopy is best consumed in a prebakedJupyter-based docker container, ethoscope-lab, to improve accessibility and to encourage the use of notebooks as anatural 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.
French A, Geissmann Q, Beckwith E, et al., 2021, Sensory processing during sleep in Drosophila melanogaster, Nature, Vol: 598, Pages: 479-482, ISSN: 0028-0836
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 name1,2,3). 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.
Gilestro GF, 2021, Sleep: Imaging the Fly Brain Reveals New Paradoxes, CURRENT BIOLOGY, Vol: 31, Pages: R140-R142, ISSN: 0960-9822
Geissmann Q, Beckwith E, Gilestro G, 2019, Most sleep does not serve a vital function: evidence from Drosophila melanogaster, Science Advances, Vol: 5, Pages: 1-10, ISSN: 2375-2548
Sleep appears to be a universally conserved phenomenon among the animal kingdom but whether this striking evolutionary conservation underlies a basic vital function is still an open question. Using a machine-learning based video-tracking technology, we conducted a detailed high-throughput analysis of sleep in the fruit fly Drosophila melanogaster,coupled with a life-long chronic and specific sleep restriction. Our results show that some wild-type flies are virtually sleepless in baseline conditions and that complete, forced sleep restriction is not necessarily a lethal treatment in wild-type Drosophila melanogaster. We also show that circadian drive, and not homeostatic regulation, is the main contributor to sleep pressure in flies. These results offer a new perspective on the biological role of sleep in Drosophilaand, potentially, in other species.
Geissmann Q, Garcia Rrodriguez L, Beckwith E, et al., 2019, Rethomics: an R framework to analyse high-throughput behavioural data, PLoS ONE, Vol: 14, ISSN: 1932-6203
The recent development of automatised methods to score various behaviours on a large number of animals provides biologists with an unprecedented set of tools to decipher these complex phenotypes. Analysing such data comes with several challenges that are largely shared across acquisition platform and paradigms. Here, we present rethomics, a set of R packages that unifies the analysis of behavioural datasets in an efficient and flexible manner. rethomics offers a computational solution to storing, manipulating and visualising large amounts of behavioural data. We propose it as a tool to bridge the gap between behavioural biology and data sciences, thus connecting computational and behavioural scientists. rethomics comes with a extensive documentation as well as a set of both practical and theoretical tutorials (available at https://rethomics.github.io).
Geissmann Q, Beckwith EJ, Gilestro GF, 2018, Most sleep does not serve a vital function. Evidence from <i>Drosophila melanogaster</i>
<jats:title>Abstract</jats:title><jats:p>Sleep appears to be a universally conserved phenomenon among the animal kingdom but whether this striking evolutionary conservation underlies a basic vital function is still an open question. Using novel technologies, we conducted an unprecedentedly detailed high-throughput analysis of sleep in the fruit fly <jats:italic>Drosophila melanogaster</jats:italic>, coupled with a life-long chronic and specific sleep restriction. Our results show that some wild-type flies are virtually sleepless in baseline conditions and that complete, forced sleep restriction is not necessarily a lethal treatment in wild-type <jats:italic>Drosophila melanogaster</jats:italic>. We also show that circadian drive, and not homeostatic regulation, is the main contributor to sleep pressure in flies. We propose a three-partite model framework of sleep function, according to which, total sleep accounts for three components: a vital component, a useful component, and an accessory component.</jats:p>
Geissmann Q, Rodriguez LG, Beckwith EJ, et al., 2018, Rethomics: an R framework to analyse high-throughput behavioural data
<jats:title>Abstract</jats:title><jats:p>The recent development of automatised methods to score various behaviours on a large number of animals provides biologists with an unprecedented set of tools to decipher these complex phenotypes. Analysing such data comes with several challenges that are largely shared across acquisition platform and paradigms. Here, we present <jats:monospace>rethomics</jats:monospace>, a set of <jats:monospace>R</jats:monospace> packages that unifies the analysis of behavioural datasets in an efficient and flexible manner. <jats:monospace>rethomics</jats:monospace> offers a computational solution to storing, manipulating and visualising large amounts of behavioural data. We propose it as a tool to bridge the gap between behavioural biology and data sciences, thus connecting computational and behavioural scientists. <jats:monospace>rethomics</jats:monospace> comes with a extensive documentation as well as a set of both practical and theoretical tutorials (available at <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="https://rethomics.github.io">https://rethomics.github.io</jats:ext-link>).</jats:p>
Geissmann Q, Garcia Rodriguez L, Beckwith EJ, et al., 2017, Ethoscopes: An open platform for high-throughput ethomics., PLoS Biology, Vol: 15, ISSN: 1544-9173
Here, we present the use of ethoscopes, which are machines for high-throughput analysis of behavior in Drosophila and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable. They perform, in real-time, tracking and profiling of behavior by using a supervised machine learning algorithm, are able to deliver behaviorally triggered stimuli to flies in a feedback-loop mode, and are highly customizable and open source. Ethoscopes can be built easily by using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at http://lab.gilest.ro/ethoscope.
Beckwith EJ, Geissmann Q, French AS, et al., 2017, Regulation of sleep homeostasis by sexual arousal, eLife, Vol: 6, Pages: 1-19, ISSN: 2050-084X
In all animals, sleep pressure is under continuous tight regulation. It is universally accepted that this regulation arises from a two-process model, integrating both a circadian and a homeostatic controller. Here we explore the role of environmental social signals as a third, parallel controller of sleep homeostasis and sleep pressure. We show that, in Drosophila melanogaster males, sleep pressure after sleep deprivation can be counteracted by raising their sexual arousal, either by engaging the flies with prolonged courtship activity or merely by exposing them to female pheromones.
Geissmann Q, Rodriguez LG, Beckwith EJ, et al., 2017, Ethoscopes: an open platform for high-throughput<i>ethomics</i>
<jats:title>Abstract</jats:title><jats:p>We present ethoscopes, machines for high-throughput analysis of behaviour in<jats:italic>Drosophila</jats:italic>and other animals. Ethoscopes provide a software and hardware solution that is reproducible and easily scalable; they perform, in real-time, tracking and profiling of behaviour using a supervised machine learning algorithm; they can deliver behaviourally-triggered stimuli to flies in a feedback-loop mode; and they are highly customisable and open source. Ethoscopes can be built easily using 3D printing technology and rely on Raspberry Pi microcomputers and Arduino boards to provide affordable and flexible hardware. All software and construction specifications are available at<jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://lab.gilest.ro/ethoscope">http://lab.gilest.ro/ethoscope</jats:ext-link>.</jats:p>
Gilestro GF, 2012, Video tracking and analysis of sleep in <i>Drosophila melanogaster</i>, NATURE PROTOCOLS, Vol: 7, Pages: 995-1007, ISSN: 1754-2189
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- Citations: 60
Gilestro GF, Cirelli C, 2009, pySolo: a complete suite for sleep analysis in <i>Drosophila</i>, BIOINFORMATICS, Vol: 25, Pages: 1466-1467, ISSN: 1367-4803
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- Citations: 112
Gilestro GF, Tononi G, Cirelli C, 2009, Widespread Changes in Synaptic Markers as a Function of Sleep and Wakefulness in <i>Drosophila</i>, SCIENCE, Vol: 324, Pages: 109-112, ISSN: 0036-8075
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- Citations: 240
Gilestro GF, 2008, Redundant Mechanisms for Regulation of Midline Crossing in <i>Drosophila</i>, PLOS ONE, Vol: 3, ISSN: 1932-6203
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- Citations: 26
Dickson BJ, Gilestro GF, 2006, Regulation of commissural axon pathfinding by slit and its robo receptors, ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, Vol: 22, Pages: 651-675, ISSN: 1081-0706
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- Citations: 268
Christensen C, Ambartsumian N, Gilestro G, et al., 2005, Proteolytic processing converts the repelling signal Sema3E into an inducer of invasive growth and lung metastasis, CANCER RESEARCH, Vol: 65, Pages: 6167-6177, ISSN: 0008-5472
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- Citations: 91
Artigiani S, Conrotto P, Fazzari P, et al., 2004, Plexin-B3 is a functional receptor for semaphorin 5A, EMBO REPORTS, Vol: 5, Pages: 710-714, ISSN: 1469-221X
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- Citations: 119
Giordano S, Corso S, Conrotto P, et al., 2002, The Semaphorin 4D receptor controls invasive growth by coupling with Met, NATURE CELL BIOLOGY, Vol: 4, Pages: 720-724, ISSN: 1465-7392
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- Citations: 349
Petrelli A, Gilestro GF, Lanzardo S, et al., 2002, The endophilin-CIN85-Cbl complex mediates ligand-dependent downregulation of c-Met, NATURE, Vol: 416, Pages: 187-190, ISSN: 0028-0836
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- Citations: 360
Gilestro GF, Cirelli C, pySolo
pySolo is a multiplatform software for analysis of sleep and locomotor activity in Drosophila melanogaster. pySolo provides a user-friendly graphic interface and it has been developed with the specific aim of being accessible, portable, fast and easily expandable through an intuitive plug-in structure. Support for development of additional plug-ins is provided through a community website. AVAILABILITY: Software and documentation are located at (http://www.pysolo.net). pySolo is a free software released under the GNU General Public License.
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