A Computational Method to Quantify Fly Circadian Activity

Summary

A method to quantify the main temporal features seen in fly circadian locomotor rhythms is presented. The quantification is achieved by fitting fly activity with a multi-parametric model waveform. The model parameters describe the shape and size of the morning and evening peaks of daily activity.

Abstract

In most animals and plants, circadian clocks orchestrate behavioral and molecular processes and synchronize them to the daily light-dark cycle. Fundamental mechanisms that underlie this temporal control are widely studied using the fruit fly Drosophila melanogaster as a model organism. In flies, the clock is typically studied by analyzing multiday locomotor recording. Such a recording shows a complex bimodal pattern with two peaks of activity: a morning peak that happens around dawn, and an evening peak that happens around dusk. These two peaks together form a waveform that is very different from sinusoidal oscillations observed in clock genes, suggesting that mechanisms in addition to the clock have profound effects in producing the observed patterns in behavioral data. Here we provide instructions on using a recently developed computational method that mathematically describes temporal patterns in fly activity. The method fits activity data with a model waveform that consists of four exponential terms and nine independent parameters that fully describe the shape and size of the morning and evening peaks of activity. The extracted parameters can help elucidate the kinetic mechanisms of substrates that underlie the commonly observed bimodal activity patterns in fly locomotor rhythms.

Introduction

The circadian clock is an endogenous biochemical oscillator with a period of approximately 24 hours and is almost ubiquitous in animals and plants^1,2. The clock helps synchronize an organism's internal processes and behavior to the external light dark cycle. The genetic structure of the circadian clock has been widely studied since the 1960s using the fruit fly, D. melanogaster. In this insect, the core of the circadian clock consists of four proteins: PERIOD, TIMELESS, CLOCK, and CYCLE. These core components together with other molecules form a feedback loop that produces nearly sinusoidal oscill....

Protocol

1. Measuring Fly Locomotion Using Drosophila Activity Monitor (DAM)

NOTE: For more details see reference⁵.

1. Prepare individual fly tubes with food on one end and cotton on the other. The end with food should be sealed to prevent the food from drying out.
   1. Put 5-6 g of fly food in a 50 mL beaker. Cut the food into small pieces so that it is easier to melt it.
   2. Connect 32 individual glass tubes with a rubber band.
   3. Melt the food in the beaker by heating it in a microwave oven for 10-15 s. Stop the microwave every 5 s and carefully shake the beaker to ensure equal melting of foo....

Results

The method presented here allows quantification of the main features in fly locomotion pattern. The quantification is achieved by fitting the activity data with a model that consists of four exponential terms:

Discussion

This work presents instructions for using a computational tool that provides a quantitative description of fly locomotion pattern. The tool fits locomotion data with a mathematical model consisting of four exponential terms that together describe the shape and size of the M and E peaks. The final values for the model parameters are obtained from fitting the power spectra of the data, where the use of the raw data can avoid artefactual effects that data binning or filtering can impose on parameter values. The model parame.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Drosophila Activity Monitor	TriKinetics	DAM2, DAM5	Measures fly locootion using single infrared beam
MatLab	Mathworks		Computing environment and programming language, MatLab should include Optimization and Symbolic Math toolboxes
Drosophila melanogaster		per[S], per[L], iso31(wild type)	Our analysis can be performed with fly mutants of any circadian period