We defined α as the duration of nocturnal activity between activity onset and offset. Activity onset was defined as the first bout of activity that remained above the daily mean for ≥ 30 min, and activity offset was the last bout of activity above the daily mean before activity fell below the mean for ≥ 30 min. An activity profile was created for individual days and activity onsets and offsets were determined manually for each day (ClockLab, Actimetrics, Evanston, IL); α was quantified for days on which hamsters were tested for SA behavior. To determine the length of time animals needed to reentrain to the LD cycle, animals had to exhibit clear reentrainment based on visual inspection of the actograms. The exact days on which activity onsets and offsets reentrained were determined by fitting a line over the last 10 days of entrained activity onsets and offsets on the actograms. That line was then extended upward across all previous days in the actograms (ClockLab, Actimetrics, Evanston, IL). The first day of reentrainment for activity onsets and offsets was defined as the first onset and offset to occur after the extended line. A similar procedure was also used for animals housed in constant darkness (DD) in experiment 1, but in those animals, we were limited to fitting a line over 5 days because DD tends to alter circadian period after that time.
Clocklab
Manufactured by Actimetrics
Sourced in United States
ClockLab is a data acquisition system designed for recording and analyzing circadian rhythms and other periodic phenomena. It provides a platform for synchronizing and monitoring multiple experimental setups simultaneously. The system includes hardware components and software for data collection, processing, and visualization.
Automatically generated - may contain errors
Lab products found in correlation
Matlab, by MathWorks (9 mentions)
Drosophila activity monitoring system, by Trikinetics (5 mentions)
Daylight deluxe fluorescent lamps, by Philips (4 mentions)
Optical beam motion detection, by Starr Life Sciences (4 mentions)
Clocklab analysis software, by Actimetrics (3 mentions)
Minimitter vitalview 5, by Actimetrics (3 mentions)
Drosophila activity monitor system, by Trikinetics (3 mentions)
Sas 9, by SAS Institute (3 mentions)
Agarose, by Thermo Fisher Scientific (2 mentions)
Sucrose, by Merck Group (2 mentions)
Activity monitors, by Trikinetics (2 mentions)
Lumicycle luminometer, by Actimetrics (2 mentions)
Vitalview, by Philips (2 mentions)
Mini mitter, by Philips (2 mentions)
Actiwatch sleep analysis software, by CamNtech (2 mentions)
Dam system, by Trikinetics (2 mentions)
C57bl 6 mice, by Charles River Laboratories (2 mentions)
Sigmaplot 11, by Grafiti LLC (1 mentions)
Drosophila activity monitors dam2, by Trikinetics (1 mentions)
Sam chloride dihydrochloride, by Merck Group (1 mentions)
181 protocols using clocklab
1
Circadian Entrainment and Activity Patterns
2
Characterizing Circadian Wheel Running Activity
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All cages were equipped with either traditional stainless steel 6 in. diameter running wheels or 6.10 in. running wheel discs. Traditional running wheel data was collected as revolutions per minute with ClockLab (Actimetrics, Wilmette, IL) and running disc data was collected with Med Associates (St. Albans, VT); data was qualified and quantified using ClockLab. Experiments in regular LD cycles were performed using the running wheels and the skeleton photoperiod data in the supplementary data file used the running discs. Due to differences in data collection between wheels, comparisons between studies using different wheels were not made. The use of two different wheel systems was necessary in order to complete the studies in a timely manner. Activity profiles were calculated as an average activity per animal and per genotype as follows: baseline, averaged 4 day baseline and restricted feeding averaged over days three through eight. Activity profiles were created using total revolutions per hour as a percentage of total 24 h baseline activity. Food anticipatory activity (FAA) was defined as activity measured during the 3 h (ZT 3-6) prior to food presentation. This 3 h period was chosen based on a review of the FAA literature and to provide for a consistent measurement interval.
3
Circadian Rhythm Monitoring in Mice
4
Locomotor Activity in Pregnant Females
5
Irregular Light Cycle Effects on Circadian Rhythms
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Single-housed mice were exposed to regular light-dark cycles (T24, 12-hour light:12-hour dark) for 1 week to acclimate. Afterward, animals were housed either under the T24 cycle or irregular light cycles (T7 cycle) for 2 weeks. The ultradian T7 cycle consists of 3.5 hours of light followed by 3.5 hours of dark; light intensity is ~500 lux (provided by KOR 3500 K fluorescent bulbs), measured using a light meter (ExTech Lux Light Meter, 401025). Throughout the experiment, the general activity of mice was monitored using infrared motion detectors (IR) from Mini Mitter (Respironics) mounted to the top of the cages. Data were collected in 5-min bins using VitalView software (Mini Mitter, OR). The total activity and period lengths were calculated using ClockLab (Actimetrics, IL). Circadian period length was determined by fitting a regression line to the onsets of activity over a 10-day period using ClockLab (Actimetrics IL). Last, CT was calculated on the basis of individual animal locomotor activity, with CT12 defined as the onset of activity.
6
Circadian Rhythm Phase Shift Assay
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All free-running periods were calculated with ClockLab (Actimetrics) using the onsets of activity on days 10–17 of constant darkness similar to [3] (link). Phase shifts were calculated similar to [3] (link) and described as follows: an onset for the day after the light pulse was predicted based on the onsets of the previous 7 days. Phase shifts were then determined based on the difference between the predicted onset and the shifted onset on the day after the light pulse. For all animals, the free-running period in constant light was measured with ClockLab (Actimetrics) using the onsets of activity on days 3–10 of constant light. Some animals (2 WT, 1 Gna15 KO, 2 Gnaq; Gna11 DKOs, 1 Gna11; Gna14 DKO, and 1 MKO) reduced their activity so much that an accurate period could not be measured and they were thus excluded.
7
Circadian Rhythm Shift in Mice
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C57Bl6/J male mice (n = 10–20, 80 days or older) were maintained as singly housed in shoe-box cages equipped with running wheels in light tight chambers on a 12:12 L:D cycle (100 lux from white LED lamps). On stable entrainment (typically achieved within 1 week under a stable light dark cycle), at ZT6 (Zeitgeber Time 6, which is six hours after the onset of light), the animals received an intraperitoneal injection (10 ml/kg) of drug constituted as above. The L:D cycle was immediately advanced by 6 h, simulating landing in a time zone 6 h ahead. Onset of activity on each day was used to measure phase relative to the L:D cycle, data analysed on Clocklab (Actimetrics, Wilmette, IL), and animals were allowed up to 2 weeks to entrain to the new LD cycle. On achieving stable entrainment, the animals underwent the same procedure with the specific dose/treatment rotated between the subjects. Up to 4 rotations were undertaken on any one animal, after which the animal was sacrificed. N = 10–20 for each condition.
8
Wheel-Running Activity Analysis Protocol
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Analysis of locomotor activity parameters was done by monitoring wheel-running activity, as described in Jud et al. (2005) (link), and calculated using the ClockLab software (Actimetrics). Briefly, for the analysis of free-running rhythms, animals were entrained to LD 12:12 and subsequently released into constant darkness (DD). Internal period length (τ) was determined from a regression line drawn through the activity onsets of ten days of stable rhythmicity under constant conditions. Total and daytime activity, as well as activity distribution profiles, was calculated using the respective inbuilt functions of the ClockLab software (Acquisition Version 3.208, Analysis version 6.0.36). Numbers of animals used in the behavioral studies are indicated in the corresponding figure legends.
9
Circadian Rhythm Monitoring in Mice
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Mice were housed individually with a 4.5-inch running wheel and ad libitum food and water. Wheel running was monitored using Vitalview (Mini Mitter). Photoentrainment was assayed in a 12 hr:12 hr light:dark cycle (LD). Free-running circadian rhythms were assessed in constant darkness (DD) and constant light (LL). Light intensity in LD and LL was ~600 lux, provided by Philips Daylight deluxe fluorescent lamps. Clocklab (Actimetrics) was used to generate actograms and measure circadian periods. A 3 hr light pulse from ZT 14–17 was used to measure acute activity suppression (masking) by light. Wheel revolutions were quantified during the pulse and normalized to the previous day where mice were undisturbed in the dark. A 1-week 3.5 hr:3.5 hr light:dark ultradian light cycle was also used to measure masking. Wheel revolutions were quantified to determine total activity during light and dark phases. Data were analyzed by Student's t test.
10
Circadian Rhythm Analysis of Fly Locomotor Activity
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Raw data obtained from the DAM system were scanned and binned into activity counts of 15 min interval using DAM Filescan. Data was analyzed using the CLOCKLAB software (Actimetrics, Wilmette, IL) or RhythmicAlly (Abhilash and Sheeba, 2019 (link)). Values of period and power of rhythm were calculated for a period of 7–8 days using the Chi-square periodogram with a cut-off of p = 0.05. The period and power values of all the flies for a particular experimental genotype were compared against the parental controls using one-way ANOVA with genotype as the fixed factor followed by post-hoc analysis using Tukey’s Honest Significant Difference (HSD) test. The details on the statistical comparisons and the no. of flies used in a given experiment are indicated in the respective figure legends section. Representative actograms were generated using ActogramJ plugin of ImageJ (Schmid et al., 2011 (link)).
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