Combining theoretical and experimental approaches to understand the circadian clock

This review is intended as a summary of our work carried out as part of the German Research Association (DFG) Center Program on Circadian Rhythms. Over the last six years, our approach to understanding circadian systems combined theoretical and experimental tools, and Gonyaulax and Neurospora have proven ideal for these efforts. Both of these model organisms demonstrate that even simple circadian systems can have multiple light input pathways and more than one rhythm generator. They have both been used to elaborate basic circadian features in conjunction with formal models. The models introduce the “zeitnehmer,” i.e., a clock-regulated input pathway, to the conceptual framework of circadian systems, and proposes networks of individual feedbacks as the basis for circadian rhythmicity.     

Addition of a non-photic component to a light-based mathematical model of the human circadian pacemaker

Mathematical models have become vital to the study of many biological processes in humans due to the complexity of the physiological mechanisms underlying these processes and systems. While our current mathematical representation of the human circadian pacemaker has proven useful in many experimental situations, it uses as input only a direct effect of light on the circadian pacemaker. Although light (a photic stimulus) has been shown to be the primary synchronizer of the circadian pacemaker across a number of species, studies in both animals and humans have confirmed the existence of non-photic effects that also contribute to phase shifting and entrainment. We modified our light-based circadian mathematical model to reflect evidence from these studies that the sleep-wake cycle and/or associated behaviors have a non-photic effect on the circadian pacemaker. In our representation, the sleep-wake cycle and its associated behaviors provides a non-photic drive on the circadian pacemaker that acts both independently and concomitantly with light stimuli. Further experiments are required to validate fully our model and to understand the exact effect of the sleep-wake cycle as a non-photic stimulus for the human circadian pacemaker.     

Photobiology of the Gonyaulax circadian system. II. Allopurinol inhibits blue-light effects

Light is the main environmental signal (zeitgeber) for practically all circadian systems, but little is known about the transduction mechanisms by which light signals reach the circadian oscillator. To identify components involved in the circadian light transduction pathway in the unicellular alga Gonyaulax polyedra Stein, we assayed inhibitors of pigment synthesis and of flavo-enzymes for their effects on circadian properties such as phase and period. We found that allopurinol, an inhibitor of xanthine oxidoreductase, specifically inhibits the period and phase effects mediated by the blue-light-sensitive input pathway, while the other light input of the Gonyaulax circadian system, that is sensitive to both red and blue light, appears to be unaffected. Received: 27 November 1996 / Accepted: 30 January 1997     

Cellular Mechanisms of Entrainment

This review summarizes our current understanding of the signal transduction cascade by which light causes phase shifts of the circadian oscillators found in the eye of Bulla and Aplysia. The isolated retina of these marine mollusks contains a circadian oscillator, a photoreceptor, and a light transduction pathway sufficient for entrainment. This preparation offers unique advantages for the cellular analysis of entrainment and the generation of circadian oscillations. There is evidence that similar cellular mechanisms may underlie mammalian and molluskan circadian oscillations. Thus, the models developed to explain entrainment in the molluskan retina are likely to have utility in exploring the mammalian supra-chiasmatic nucleus.     

The circadian program of algae

The endogenous circadian program enables organisms to cope with the temporal ecology of their environment. It is driven by a molecular pacemaker, which is found in animals as well as plants at the level of the single cell. Unicellular organisms are, therefore, ideal model systems for the study of circadian systems because rhythms can be investigated in single cells at the molecular, physiological, behavioral and environmental level. In this review, we discuss the possible driving forces for the evolution of circadian rhythmicity in unicellular marine organisms. The current knowledge about the cellular and molecular mechanisms involved in the different components of the circadian system (input, oscillator and output) are described primarily with reference to the marine dinoflagellate,Gonyaulax polyedra. Light is the most important and best described environmental signal synchronizing the endogenous rhythms to the 24-hour solar day. However, little is known about the nature of circadian light receptors, which appear to be distinct from those that control behavioral light responses such as phototaxis. It has recently been shown inGonyaulaxthat nutrients, namely nitrate, can act as a non-photic zeitgeber for the circadian system. In this alga, bioluminescence is under circadian control, and the molecular mechanisms of this circadian output have been investigated in detail. The circadian program turns out to be more complex than simply consisting of an input pathway, a pacemaker and the driven rhythms. Different rhythms appear to be controlled by separate pacemakers, even in single cells, and both circadian inputs and outputs contain feedback loops. The functional advantages of this complexity are discussed. Finally, we outline the differences between the circadian program under laboratory and natural conditions.     

Circadian Input Kinases and Their Homologs in Cyanobacteria: Evolutionary Constraints Versus Architectural Diversification

The circadian input kinase A (cikA) gene encodes a protein relaying environmental signal to the central circadian oscillator in cyanobacteria. The CikA protein has a variable architecture and usually consists of four tandemly arrayed domains: GAF, histidine kinase (HisKA), histidine kinase-like ATPase (HATPase_c), and a pseudo-receiver (REC). Among them, HisKA and HATPase_c are the least polymorphic, and REC is not present in heterocystic filamentous cyanobacteria. CikA contains several conserved motifs that are likely important for circadian function. There are at least three types of circadian systems, each of which possesses a different set of circadian genes. The originally described circadian system (kaiABC system) possesses both cikA and kaiA, while the others lack either only cikA (kaiABC ^Δ) or both (kaiBC). The results we obtained allowed us to approximate the time of the cikA origin to be about 2600–2200 MYA and the time of its loss in the species with the kaiABC ^Δ or kaiBC system between 1100 and 600 MYA. Circadian specialization of CikA, as opposed to its non-circadian homologs, is a result of several factors, including the unique conserved domain architecture and high evolutionary constraints of some domains and regions, which were previously identified as critical for the circadian function of the gene.     

Circadian clock rhythms in different adipose tissue model systems

ABSTRACT

Circadian clock-controlled 24-h oscillations in adipose tissues play an important role in the regulation of energy homeostasis, thus representing a potential drug target for prevention and therapy of metabolic diseases. For pharmacological screens, scalable adipose model systems are needed that largely recapitulate clock properties observed in vivo. In this study, we compared molecular circadian clock regulation in different ex vivo and in vitro models derived from murine adipose tissues. Explant cultures from three different adipose depots of PER2::LUC circadian reporter mice revealed stable and comparable rhythms of luminescence ex vivo. Likewise, primary pre- and mature adipocytes from these mice displayed stable luminescence rhythms, but with strong damping in mature adipocytes. Stable circadian periods were also observed using Bmal1-luc and Per2-luc reporters after lentiviral transduction of wild-type pre-adipocytes. SV40 immortalized adipocytes of murine brown, subcutaneous and epididymal adipose tissue origin showed rhythmic mRNA expression of the core clock genes Bmal1, Per2, Dbp and REV-erbα in pre- and mature adipocytes, with a maturation-associated increase in overall mRNA levels and amplitudes. A comparison of clock gene mRNA rhythm phases revealed specific changes between in vivo and ex vivo conditions. In summary, our data indicate that adipose culture systems to a large extent mimic in vivo tissue clock regulation. Thus, both explant and cell systems may be useful tools for large-scale screens for adipose clock regulating factors.     

Photobiology of the Gonyaulax circadian system. I. Different phase response curves for red and blue light

Phase responses to red and blue light pulses were measured at different times during the circadian cycle (phase response curves, PRC) in the marine unicellular dinoflagellate Gonyaulaxpolyedra Stein. Pulses were given during a 24-h period of darkness; thereafter, cultures were released into constant dim red light for the assessment of phase and period. The results confirmed earlier findings that the Gonyaulax circadian system receives light signals via two distinct input pathways. During the subjective day and for the first 3 h of the subjective night, red and blue light pulses led to identical phase responses. For the rest of the circadian cycle, however, phase responses to pulses of either red or blue light differed drastically both in their amplitude and direction (advances or delays). Thus, the Gonyaulax light PRC is generated by two distinct light responses. One of these represents responses via a light input that is responsive both to red and blue light mainly producing small delays. The other represents responses of a primarily blue-sensitive input system leading to large advances restricted to the subjective night. Via feed-back, the blue-sensitive light input appears to be under the control of the circadian system. Received: 27 November 1996/Accepted: 30 January 1997     

Serotonergic innervation of the hypothalamic suprachiasmatic nucleus and photic regulation of circadian rhythms

Converging lines of evidence have firmly established that the hypothalamic suprachiasmatic nucleus (SCN) is a light-entrainable circadian oscillator in mammals, critically important for the expression of behavioral and physiological circadian rhythms. Photic information essential for the daily phase resetting of the SCN circadian clock is conveyed directly to the SCN from retinal ganglion cells via the retinohypothalamic tract. The SCN also receives a dense serotonergic innervation arising from the mesencephalic raphe. The terminal fields of retinal and serotonergic afferents within the SCN are co-extensive, and serotonergic agonists can modify the response of the SCN circadian oscillator to light. However, the functional organization and subcellular localization of 5HT receptor subtypes in the SCN are just beginning to be clarified. This information is necessary to understand the role 5HT afferents play in modulating photic input to the SCN. In this paper, we review evidence suggesting that the serotonergic modulation of retinohypothalamic neurotransmission may be achieved via at least two different cellular mechanisms: 1) a postsynaptic mechanism mediated via 5HT_1A or 5ht₇ receptors located on SCN neurons; and 2) a presynaptic mechanism mediated via 5HT_1B receptors located on retinal axon terminals in the SCN. Activation of either of these 5HT receptor mechanisms in the SCN by specific 5HT agonists inhibits the effects of light on circadian function. We hypothesize that 5HT modulation of photic input to the SCN may serve to set the gain of the SCN circadian system to light.     

The circadian conidiation rhythm inNeurospora crassa

The filamentous fungusNeurospora crassais one of the best organisms for analysing the molecular basis of the circadian rhythm observed in asexual spore formation, conidiation. Many clock mutants in which the circadian conidiation rhythm has different characteristics compared to those in the wild-type strain have been isolated since the early 1970s. With the cloning of one of these clock genes,frq, the molecular basis of the circadian clock inNeurosporahas become gradually clearer. Physiological and pharmacological studies have also contributed to our understanding of the physiological basis of the circadian clock inNeurospora. These studies strongly indicate that the circadian clock is based on or is closely related to a network of metabolic processes for cellular activities. Based on these studies, it may be possible to isolate new types of clock mutants which should contribute to a better understanding of the molecular basis of the circadian clock inNeurospora.     

Importance of feature selection in decision-tree and artificial-neural-network ecological applications. Alburnus alburnus alborella: A practical example

Recent advances in computing technology have increased interest in applying data mining to ecology. Machine learning is one of the methods used in most of these data mining applications. As is well known, approximately 80% of the resources in most data mining applications are devoted to cleaning and preprocessing the data. However, there are few studies on preprocessing the ecological data used as the input in these data mining systems. In this study, we use four different feature selection methods (χ², Information Gain, Gain Ratio, and Symmetrical Uncertainty) and evaluate their effectiveness in preprocessing the input data to be used for inducing artificial neural networks (ANNs) and decision trees (DTs). The presence/absence of fish is the data item used to illustrate our models. Feature selection is fundamental in order to increase the performances of the models obtained. Accuracy of classification improves when a small set of optimally selected features is used. DTs and ANNs are very useful tools when applied to modeling presence/absence of Alburnus alburnus alborella. ANNs generally performed better than DT models.     

Robustness of Circadian Timing Systems Evolves in the Fruit Fly Drosophila melanogaster as a Correlated Response to Selection for Adult Emergence in a Narrow Window of Time

Robustness is a fundamental property of biological timing systems that is likely to ensure their efficient functioning under a wide range of environmental conditions. Here we report the findings of our study aimed at examining robustness of circadian clocks in fruit fly Drosophila melanogaster populations selected to emerge as adults within a narrow window of time. Previously, we have reported that such flies display enhanced synchrony, accuracy, and precision in their adult emergence and activity/rest rhythms. Since it is expected that accurate and precise circadian clocks may confer enhanced stability in circadian time-keeping, we decided to examine robustness in circadian rhythms of flies from the selected populations by subjecting them to a variety of environmental conditions comprising of a range of photoperiods, light intensities, ambient temperatures, and constant darkness. The results revealed that adult emergence and activity/rest rhythms of flies from the selected stocks were more robust than controls, as they displayed enhanced stability under a wide variety of environmental conditions. These results suggest that selection for adult emergence within a narrow window of time results in the evolution of robustness in circadian timing systems of the fruit fly D. melanogaster. (Author correspondence: vsharma@jncasr.ac.in or vksharmas@gmail.com)     

The Drosophila melanogaster circadian pacemaker circuit

As an experimental model system, the fruit fly Drosophila melanogaster has been seminal in shaping our understanding of the circadian clockwork. The wealth of genetic tools at our disposal over the past four decades has enabled discovery of the genetic and molecular bases of circadian rhythmicity. More recently, detailed investigation leading to the anatomical, neuro-chemical and electrophysiological characterization of the various neuronal subgroups that comprise the circadian machinery has revealed pathways through which these neurons come together to act as a neuronal circuit. Thus the D. melanogaster circadian pacemaker circuit presents a relatively simple and attractive model for the study of neuronal circuits and their functions.     

Interaction of MAGED1 with nuclear receptors affects circadian clock function

The circadian clock has a central role in physiological adaption and anticipation of day/night changes. In a genetic screen for novel regulators of circadian rhythms, we found that mice lacking MAGED1 (Melanoma Antigen Family D1) exhibit a shortened period and altered rest–activity bouts. These circadian phenotypes are proposed to be caused by a direct effect on the core molecular clock network that reduces the robustness of the circadian clock. We provide in vitro and in vivo evidence indicating that MAGED1 binds to RORα to bring about positive and negative effects on core clock genes of Bmal1, Rev‐erbα and E4bp4 expression through the Rev‐Erbα/ROR responsive elements (RORE). Maged1 is a non‐rhythmic gene that, by binding RORα in non‐circadian way, enhances rhythmic input and buffers the circadian system from irrelevant, perturbing stimuli or noise. We have thus identified and defined a novel circadian regulator, Maged1, which is indispensable for the robustness of the circadian clock to better serve the organism.     

Astronomical cycles

Abstract

Talorchestia quoyana, a sand beach amphipod, shows a rhythm of locomotor activity controlled by a circadian clock and an inhibitory circatidal clock. This article reports on an investigation of the entrainment of the circadian dock to skeleton photoperiods. Four important mathematical models for circadian rhythms are examined with respect to the results of the entrainment experiments and to predictions from the phase response curve for Talorchestia. Significant differences between the models are described, and properties of circadian rhythms not accounted for by present models are outlined.     

Egg-laying rhythm in <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

Extensive research has been carried out to understand how circadian clocks regulate various physiological processes in organisms. The discovery of clock genes and the molecular clockwork has helped researchers to understand the possible role of these genes in regulating various metabolic processes. In Drosophila melanogaster, many studies have shown that the basic architecture of circadian clocks is multi-oscillatory. In nature, different neuronal subgroups in the brain of D. melanogaster have been demonstrated to control different circadian behavioural rhythms or different aspects of the same circadian rhythm. Among the circadian phenomena that have been studied so far in Drosophila, the egg-laying rhythm is unique, and relatively less explored. Unlike most other circadian rhythms, the egg-laying rhythm is rhythmic under constant light conditions, and the endogenous or free-running period of the rhythm is greater than those of most other rhythms. Although the clock genes and neurons required for the persistence of adult emergence and activity/rest rhythms have been studied extensively, those underlying the circadian egg-laying rhythm still remain largely unknown. In this review, we discuss our current understanding of the circadian egg-laying rhythm in D. melanogaster, and the possible molecular and physiological mechanisms that control the rhythmic output of the egg-laying process.