AHCODA-DB


3 days Spontaneous behavior (Kinematics)

LSID: http://syli.cz/urn:lsid:public.sylics.com:automatedtest:EG87-4286-2B5A

Materials and Methods
Mice were singly housed on sawdust in standard Makrolon type II cages enriched with cardboard nesting material for at least one week prior to experiments, with water and food ad libitum (7:00/19:00 lights on/off; providing an abrupt phase transition).

Activity in the home cage was automatically recorded by video tracking in specially designed cages (PhenoTyper model 3000, Noldus Information Technology, www.noldus.com/phenotyper). Each cage contains a top unit with built-in hardware for video-tracking, that is, an infrared-sensitive video camera. The latter provide constant and even illumination of the cage. An infrared filter placed in front of the camera prevents interference with room illumination. This method allows continuous behavioural recordings in both dark and light periods. EthoVision was used as video tracking and trial control software. PhenoTyper cages were connected in a specially designed computer network. The cages (L =30 × W =30 × H =35 cm) were made of transparent Perspex walls with an opaque Perspex floor covered with bedding based on cellulose. A feeding station and a water bottle were attached on to two adjacent walls outside of the cage. A shelter (height: 10 cm, diameter: 9 cm; non-transparent material) was fixed in one of the corners. The X-Y coordinates of the centre of gravity of mice were acquired and smoothed using EthoVision software and processed to generate behavioural parameters using AHCODA analysis software (Synaptologics BV, Amsterdam, The Netherlands, http://www.sylics.com/bioinformatics/ahcodatm-data-analysis/).

Associated Mammalian Phenotype Ontologies (MGI)
- MP:0001392 abnormal locomotor behaviour

Spontaneous behavior
With respect to spontaneous behaviors in the first three days in the PhenoTyper, 6 groups of behavioral parameters are defined as described below. The first two groups describe specific behavioral elements related to kinematics of mice (description of movement characteristics, group1) and sheltering behavior (group 2). These behavioral parameters were analyzed with respect to temporal aspects, in particular over 4 different time scales, i.e., habituation effects across multiple days (group 3), effects of DarkLight phase across 24h (group 4), differences in the pattern of behavior in the few hours before and after phase shifts (group5), and differences in activity bout properties on the sub-minute time scale (group 6).

Group 1: kinematics
Movement segments:
Mice make short movements, such as turning or rearing against the wall, as well as long movements when mice travel from one location in the cage to the next. These two types of movement, i.e. short and long, can be distinguished by plotting the frequency distribution of all move segment distances over three days in the cage, yielded a bimodal distribution. For instance, see the "histogram of movement distance" at the bottom of this page for C57BL/6J mice:
http://mousedata.sylics.com/?page=strainhtp&loaded=true&s=11&htpid=53&e=9&batch=1&t=&texp=&list=batches&tdose=
An animal-centered threshold that was defined by the intersection of the two Gaussian distance curves obtained after Gaussian mixture model fitting of data of each individual mouse.
Arrest segments:
Most arrest durations are relatively short, and occur in between move segments when mice reorient themselves. In addition, mice infrequently made long arrests when they were consuming food or water, or when they were resting outside their shelter. An animal-centered threshold was set distinguishing the 90% shortest arrests (short) from the 10% longest arrests (long), separating brief from long arrests. For instance, see the "histogram of arrest durations" at the bottom of this page for C57BL/6J mice:
http://mousedata.sylics.com/?page=strainhtp&loaded=true&s=11&htpid=55&e=9&batch=1&t=&texp=&list=batches&tdose=



Parameter information
Parameter nameUnitsExplanation
Long movement fraction of total movementfractionThe fraction of movement segments with distance larger than long movement threshold
*Long movement max. velocitycm/sAverage velocity of the 95th percentile fastest long movement segments
*Long arrest thresholdlog2(s)Cut-off value to separate short and long arrests
Short arrest duration - darksCummulative duration of short arrests during the dark phase
Mean short arrest duration - darksMean duration per short arrest during the dark phase
Short arrest number - darkfrequencyCummulative number of short arrests during the dark phase
Long arrest duration - darksCummulative duration of long arrests during the dark phase
Mean long arrest duration - darksMean duration per long arrest during the dark phase
Long arrest number - darkfrequencyCummulative number of long arrests during the dark phase
Long movement distance - darkcmCummulative long movement distance during the dark phase
Mean long movement distance - darkcmMean distance per long movement during the dark phase
Long movement number - darkfrequencyCummulative long movement number during the dark phase
Short movement distance - darkcmCummulative short movement distance during the dark phase
Mean short movement distance - darkcmMean distance per short movement during the dark phase
Short movement number - darkfrequencyCummulative short movement number during the dark phase
Short arrest duration - lightsCummulative duration of short arrests during the light phase
Mean short arrest duration - lightsMean duration per short arrest during the light phase
Short arrest number - lightfrequencyCummulative number of short arrests during the light phase
Long arrest duration - lightsCummulative duration of long arrests during the light phase
*Mean long arrest duration - lightsMean duration per long arrest during the light phase
Long arrest number - lightfrequencyCummulative number of long arrests during the light phase
Long movement distance - lightcmCummulative long movement distance during the light phase
Mean long movement distance - lightcmMean distance per long movement during the light phase
Long movement number - lightfrequencyCummulative long movement number during the light phase
Short movement distance - lightcmCummulative short movement distance during the light phase
Mean short movement distance - lightcmMean distance per short movement during the light phase
Short movement number - lightfrequencyCummulative short movement number during the light phase
*Long movement thresholdlog2(cm)Cut-off value to separate short and long movements