Biological data and model Matlab scripts from Zolmon, Trummel, et al., (2006): Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhyhtms).
Beschreibung
# Biological and simulation data for Zolmon, Trummel, et al., 2026: Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhythms)
## File overview
This repository contains four files: One excel file with biological data and three Matlab files that contain the model code.
## Description Excel file with biological data
This excel file contains the data that is presented in Zolmon, Trummel, et al., 2026: Disrupting the cockroach circadian clock through RNAi-mediated knockdown of clock proteins (Journal of Biological Rhythms)
The data is organized in two sheets:
1. running wheel data,
2. qPCR data.
The sheet "running wheel data" contains 9 lines of metadata, an empty line, one line with column headers followed by the data. The first column is the day relative to dsRNA injection; the second column is the minute of that day, and subsequent columns contain wheel turns in 1 minute bins. Metadata contains (top to bottom): Unique animal identifier (animal ID); light condition as either constant darkness (DD) or constant light (LD); experiment category as either CYC only (CYC), CLK only (CLK), double knockdown (DKD), triple knockdown (TKD); knockdown treatment with the following targets GFP (as control), CLK, CYC, double knockdown (DKD: CLK + CYC), triple knockdown (TKD: PER, TIM1, CRY2) or WT (wild-type, no treatment); experimenter who performed the dsRNA injection and animal care in the running wheels; start date (DD.MM.YYYY) on which the running wheel assay was started; injection date (DD.MM.YYYY) on which dsRNA was injected; indication in which Figure the data from one particular animal was used as an illustrative example; indication as part of which Figure the data is displayed.
The sheet "qPCR data" contains 8 columns. The first column is the experiment ID; second column is the light condition in which the animals were kept, either constant darkness (DD), constant light (LL), or 12:12 hours light:dark (LD); third column is experiment category as either untreated wildtype randomly sampled from the breeding colony (WT), untreated wildtype with age-controlled sampling (WT_age_controlled), CLK knockdown (CLK_KD), CYC knockdown (CYC_KD); fourth column is knockdown treatment with the following targets: none (WT), GFP (as injection control), CLK, CYC, triple knockdown (TKD: PER, TIM1, CRY2); fifth column lists the day or zeitgeber time (ZT) or projected ZT of sacrifice for the qPCR; sixth column lists the target mRNA of the qPCR, seventh column lists the cycle threshold of the qPCR (red values were excluded from their triplets mean calculation); eighth column indicates in which figure the data point was used.
## Description Matlab files
This MATLAB code implements the discussed networks of the computational model to describe the cockroach circadian clock.
The code is divided into three different MATLAB scripts:
1. *clock\_network\_DD\_het.m*: This code simulates the cockroach clock, which is modeled by a heterarchical network. Effects of knockdown are investigated for constant darkness (DD).
2. *clock\_network\_DD\_hier.m*: The cockroach clock is modeled by a hierarchical network in constant darkness (DD).
3. *clock\_network\_LL\_het.m*: To examine the effects of knockdown in constant light (LL), the heterarchical network is adjusted according to LL conditions.
Each script can be run individually. The corresponding networks are represented by matrices using time-varying coupling gains. The parameters of the planar switching affine systems (PSAS), modeling the subsystems' dynamics, are given. The networked system can then be simulated. Finally, the simulation results of the computational model are visualized graphically.
For more details on modeling and discussion, see the corresponding paper.
### Software
* Version R2024b of MATLAB was used.
* Toolbox *Communications Toolbox* is requiered.
