Rhythmic locomotor activity is a commonly used readout of general circadian function in animals. For instance, measuring the activity of rodents in their home cages can provide information about ...circadian phase and period in response to genetic, pharmacological, and environmental manipulations. Herein, the use of infrared light sensors to measure circadian locomotor activity is described. Furthermore, we provide information about data handling, analysis and software use as well as points to consider when performing the experiment.
While the rapid development of personal computers and high-throughput recording systems for circadian rhythms allow chronobiologists to produce huge amounts of data, the software to analyze them ...often lags behind. Here, we announce newly developed chronobiology software that is easy to use, compatible with many different systems, and freely available. Our system can perform the most frequently used analyses: actogram drawing, periodogram analysis, and waveform analysis. The software is distributed as a pure Java plug-in for ImageJ and so works on the 3 main operating systems: Linux, Macintosh, and Windows. We believe that this free software raises the speed of data analyses and makes studying chronobiology accessible to newcomers.
Research on circadian rhythms often requires researchers to estimate period, robustness/power, and phase of the rhythm. These are important to estimate, owing to the fact that they act as readouts of ...different features of the underlying clock. The commonly used tools, to this end, suffer from being very expensive, having very limited interactivity, being very cumbersome to use, or a combination of these. As a step toward remedying the inaccessibility to users who may not be able to afford them and to ease the analysis of biological time-series data, we have written RhythmicAlly, an open-source program using R and Shiny that has the following advantages: (1) it is free, (2) it allows subjective marking of phases on actograms, (3) it provides high interactivity with graphs, (4) it allows visualization and storing of data for a batch of individuals simultaneously, and (5) it does what other free programs do but with fewer mouse clicks, thereby being more efficient and user-friendly. Moreover, our program can be used for a wide range of ultradian, circadian, and infradian rhythms from a variety of organisms, some examples of which are described here. The first version of RhythmicAlly is available on Github, and we aim to maintain the program with subsequent versions having updated methods of visualizing and analyzing time-series data.
Fetal motility is a widely accepted indicator of the well-being of a fetus. In previous research, it has be shown that fetal motion (FM) is coherent with fetal heart rate accelerations and an ...indicator for active/rest cycles of the fetus. The most common approach for FM and fetal heart rate (FHR) assessment is by Doppler ultrasound (DUS). While DUS is the most common approach for studying the mechanical activities of the heart, noninvasive fetal electrocardiogram (ECG) and magnetocardiogram (MCG) recording and processing techniques have been considered as a possible competitor (or complement) for the DUS. In this study, a fully automatic and robust framework is proposed for the extraction, ranking and alignment of fetal QRS-complexes from noninvasive fetal ECG/MCG. Using notions from subspace tracking, two measures, namely the actogram and rotatogram, are defined for fetal motion tracking. The method is applied to four fetal ECG/MCG databases, including twin MCG recordings. By defining a novel measure of causality, it is shown that there is significant coherency and causal relationship between the actogram/rotatogram and FHR accelerations/decelerations. Using this measure, it is shown that in many cases, the actogram and rotatogram precede the FHR variations, which supports the idea of motion-induced FHR accelerations/decelerations for these cases and raises attention for the non-motion-induced FHR variations, which can be associated to the fetal central nervous system developments. The results of this study can lead to novel perspectives of the fetal sympathetic and parasympathetic brain systems and future requirements of fetal cardiac monitoring.
The Hierarchical Factor Segmentation (HFS) method is a non-parametric statistical method for detection of the phase of a biological rhythm shown in an actogram. The detection accuracy of this method ...was measured on actograms showing only circadian rhythms with a constant ratio of signal to noise (S/N). In the present study, we generated 84 types of artificial actograms including circadian or circatidal rhythms by using three parameters: α/ρ, S/N and period length τ, and evaluated the effectiveness of our devised adaptation of the HFS method, the cycle-by-cycle adaptation. The results showed the effectiveness of the cycle-by-cycle adaptation was high even though S/N or τ was fluctuating through a whole actogram. These suggested that the cycle-by-cycle adaptation could be effectively applied to various kinds of rhythmic activity data. The C++ source code of the cycle-by-cycle adaptation is available on the website at https://github.com/KazukiSakura/cHFS.git .
Circadian clocks are internal timekeepers present in almost all organisms. Driven by a genetic network of highly conserved structure, they generate self-sustained oscillations that entrain to ...periodic external signals such as the 24 h light–dark cycle. Vertebrates possess multiple, functionally overlapping homologues of the core clock genes. Furthermore, vertebrate clocks entrain to a range of periods three times as narrow as that of other organisms. We asked whether genetic redundancies play a role in governing entrainment properties and analysed locomotor activity rhythms of genetically modified mice lacking one set of clock homologues. Exposing them to non-24 h light–dark cycles, we found that the mutant mice have a wider entrainment range than the wild types. Spectral analysis furthermore revealed nonlinear phenomena of periodically forced self-sustained oscillators for which the entrainment range relates inversely to oscillator amplitude. Using the forced oscillator model to explain the observed differences in entrainment range between mutant and wild-type mice, we sought to quantify the overall oscillator amplitude of their clocks from the activity rhythms and found that mutant mice have weaker circadian clocks than wild types. Our results suggest that genetic redundancy strengthens the circadian clock leading to a narrow entrainment range in vertebrates.
Actograms are well-established methods used for visualizing periodic activity of animals in chronobiological research. They help in the understanding of the overall characteristics of rhythms and are ...instrumental in defining the direction of subsequent detailed analysis. Although there exists specialized software for creating actograms, new users such as students and researchers from other fields often find it inconvenient to use. In this study, we demonstrate a fast and easy method to create actograms using Microsoft Excel. As operations in Excel are simple and user-friendly, it takes only a few minutes to create an actogram. Using this method, it is possible to obtain a visual understanding of the characteristics of rhythms not only from typical activity data, but also from any kind of time-series data such as body temperature, blood sugar level, gene expressions, sleep electroencephalogram, heartbeat, and so on. The actogram thus created can also be converted to the "heatogram" shown by color temperature. As opposed to conventional chronograms, this new type of chronogram facilitates easy understanding of rhythmic features in a more intuitive manner. This method is therefore convenient and beneficial for a broad range of researchers including students as it aids in the better understanding of periodic phenomena from a large amount of time-series data.
Humans come in different chronotypes: The phase of their sleep-wake cycle with respect to the phase of the external, sidereal cycle of night and day differs. Colloquially, the early chronotypes are ...addressed as "larks," the late ones as "owls." The human chronotype can be quantified in hours and minutes of local time by determining the median of the sleep phase. Demographically, early and late human chronotypes differ with respect to the stability of their rhythms and the prevalence of several widespread diseases and risk factors, such as depression, nicotine abuse, and others. Inbred mice are widely used in chronobiological research as model organisms, but up to now there was no way to chronotype them. We have developed a method to chronotype mice in hours and fractions of hours by measuring the median of activity (MoA) and have shown that different mouse strains have significantly different MoAs and, thus, chronotypes. We have further developed methods to estimate the stability of the behavioral rhythms and found that "late" mice have relatively instable rhythms. Our methods permit the use of inbred mice for investigations into the molecular and genetic background of the chronotype and the prevalence of risks and diseases that are associated with it.
A method was developed for the noninvasive mapping of the primary motor cortex in humans. Magnetic responses evoked by repeated voluntary movements of the right index finger were studied in 18 ...healthy right-handed subjects. Finger movement periods were assessed using accelerometer signals. Continuous evoked brain magnetic activity recorded in the subjects throughout the experimental sessions was assembled into a single sequence which was then fragmented into independent components by independent components analysis and ranked in terms of the quantity of mutual information with the modified accelerometer signal. Averaging of the independent components demonstrating strongest links with finger movements was performed relative to the moment at which the movement started. Modeling of the distribution of the cerebral sources of the two independent components with the largest amounts of mutual information showed that their sources were located in the contralateral motor areas of the cortex, corresponding to anatomical markers of the hand representation area in the primary motor and primary somatosensory cortex. This method provided the fundamental ability to localize the M1 zone at the group level in healthy subjects.
Our recent studies demonstrate that the murine homolog of the human tumor suppressor promyelocytic leukemia (PML) regulates circadian behavior of mice. To further gather insight into PML's ...contribution to circadian behavior, we generated two strains of mice deficient in one of the two period (Per) genes and the PML gene, with Per1-/-/Pml-/- and Per2-/-/Pml-/- genotypes.
Here we report the circadian behavior of these mice based on wheel-running behavioral analysis. In a free-running environment, the Per1-/-/Pml-/- mice maintained circadian rhythm but displayed a significantly shorter period of 22.2 h. In addition, these mice displayed significantly enhanced phase response to a light pulse given at zeitgeber time (ZT) 14 and 22. The Per2-/-/Pml-/- mice lose persistent rhythm when in a free-running environment, as also the case for Per2-/- mice. A transient post-light pulse rhythm seen in the arrhythmic Per2-/- mice was less apparent in Per2-/-/Pml-/- mice. Both the Per1-/-/Pml-/- and Per2-/-/Pml-/- mice displayed a more advanced phase angle of entrainment activity during light-dark cycles than the single gene deficient mice.
Beyond merely regulating PER1 and PER2, the current behavioral studies suggest PML has additional roles in mouse circadian behavior.
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