NDLI: Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations

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Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations

Content Provider	ACM Digital Library
Author	De los Santos, Hannah Hurley, Jennifer M. Collins, Emily J. Bennett, Kristin P.
Abstract	Circadian rhythms are endogenous cycles of approximately 24 hours reinforced by external cues such as light. These cycles are typically modeled as harmonic oscillators with fixed amplitude peaks. Using experimental data measuring global gene transcription in Neurospora crassa over 48 hours in the dark (i.e. with external queues removed), we demonstrate that many circadian genes frequently exhibit either damped harmonic oscillations, in which the peak amplitudes decrease each day, or driven harmonic oscillations, in which the peak amplitudes increase each day. By fitting extended harmonic oscillator models which include a damping ratio coefficient, we detected additional circadian genes that were not identified by the current standard tools that use fixed amplitude waves as reference, e.g. JTK_CYCLE. Functional Catalogue analysis confirms that our identified damped or driven genes exhibit distinct biological functions. The application of extended damped/driven harmonic oscillator models thus can elucidate, not only previously unidentified circadian genes, but also characterize gene subsets with expression patterns of biological relevance. Thus, expanded harmonic oscillators provide a powerful new tool for circadian system biology.
Starting Page	455
Ending Page	463
Page Count	9
File Format	PDF
ISBN	9781450347228
DOI	10.1145/3107411.3107420
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2017-08-20
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Damped harmonic oscillator Circadian rhythm Driven harmonic oscillator Gene transcription Harmonic oscillator
Content Type	Text
Resource Type	Article

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