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PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity and Sleep under Entrainment

View ORCID ProfileJ.L. Persons, View ORCID ProfileL. Abhilash, View ORCID ProfileA.J. Lopatkin, A. Roelofs, E.V. Bell, View ORCID ProfileM.P. Fernandez, View ORCID ProfileO.T. Shafer
doi: https://doi.org/10.1101/2021.12.14.472617
J.L. Persons
1Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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L. Abhilash
2Advanced Science Research Center at The Graduate Center of The City University of New York, New York, NY
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A.J. Lopatkin
3Department of Biology, Barnard College. New York, NY 10027
4Data Science Institute, Columbia University. New York, NY 10027
5Department of Ecology, Evolution, and Environmental Biology, Columbia University. New York, NY 10027
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A. Roelofs
6Technology Services, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI 48109
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E.V. Bell
7Department of Neuroscience and Behavior, Barnard College. New York, NY 10027
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M.P. Fernandez
7Department of Neuroscience and Behavior, Barnard College. New York, NY 10027
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  • For correspondence: oshafer@gc.cuny.edu mfernand@barnard.edu
O.T. Shafer
2Advanced Science Research Center at The Graduate Center of The City University of New York, New York, NY
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  • For correspondence: oshafer@gc.cuny.edu mfernand@barnard.edu
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Abstract

The problem of entrainment is central to circadian biology. In this regard, Drosophila has been an important model system. Owing to the simplicity of its nervous system and the availability of powerful genetic tools, the system has shed significant light on the molecular and neural underpinnings of entrainment. However, much remains to be learned regarding the molecular and physiological mechanisms underlying this important phenomenon. Under cyclic light/dark conditions, Drosophila melanogaster displays crepuscular patterns of locomotor activity with one peak anticipating dawn and the other anticipating dusk. These peaks are characterized through an estimation of their phase relative to the environmental light cycle and the extent of their anticipation of light transitions. In Drosophila chronobiology, estimations of phases are often subjective, and anticipation indices vary significantly between studies. Though there is increasing interest in building flexible analysis software tools in the field, none incorporates objective measures of Drosophila activity peaks in combination with the analysis of fly activity/sleep in the same program. To this end, we have developed PHASE, a MATLAB-based program that is simple and easy to use and (i) supports the visualization and analysis of activity and sleep under entrainment, (ii) allows analysis of both activity and sleep parameters within user-defined windows within a diurnal cycle, (iii) uses a smoothing filter for the objective identification of peaks of activity (and therefore can be used to quantitatively characterize them), and (iv) offers a series of analyses for the assessment of behavioral anticipation of environmental transitions.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/ajlopatkin/PHASE/tree/master/Installer%20Downloads

  • https://github.com/ajlopatkin/PHASE

  • https://www.trikinetics.com

  • https://github.com/ajlopatkin/PHASE/tree/master/Example%20datasets

  • https://www.mathworks.com/help/signal/ug/prominence.html

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 16, 2021.
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PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity and Sleep under Entrainment
J.L. Persons, L. Abhilash, A.J. Lopatkin, A. Roelofs, E.V. Bell, M.P. Fernandez, O.T. Shafer
bioRxiv 2021.12.14.472617; doi: https://doi.org/10.1101/2021.12.14.472617
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PHASE: A MATLAB Based Program for the Analysis of Drosophila Phase, Activity and Sleep under Entrainment
J.L. Persons, L. Abhilash, A.J. Lopatkin, A. Roelofs, E.V. Bell, M.P. Fernandez, O.T. Shafer
bioRxiv 2021.12.14.472617; doi: https://doi.org/10.1101/2021.12.14.472617

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