Circadian oscillators in eukaryotes

Jolma, Ingunn W.; Lærum, Ole Didrik; Lillo, Cathrine; Ruoff, Peter

doi:10.1002/wsbm.81

Cited by 33 publications

(32 citation statements)

References 230 publications

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“…For example, Gin et al (2007) developed an ODE model to study the fluid secretion from adult parotid acinar cells. In addition, ODE modeling has been used extensively to study critical aspects of the cell cycle (Sveiczer et al, 2000;Tyson et al, 2001;Novak and Tyson, 2004) and the molecular interactions that cause circadian rhythms (Brown et al, 2000;Baker et al, 2011;Jolma et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network

Kim

Venkatesh

et al. 2013

Journal of Computational Biology

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In modern systems biology the modeling of longitudinal data, such as changes in mRNA concentrations, is often of interest. Fully parametric, ordinary differential equations (ODE)-based models are typically developed for the purpose, but their lack of fit in some examples indicates that more flexible Bayesian models may be beneficial, particularly when there are relatively few data points available. However, under such sparse data scenarios it is often difficult to identify the most suitable model. The process of falsifying inappropriate candidate models is called model discrimination. We propose here a formal method of discrimination between competing Bayesian mixture-type longitudinal models that is both sensitive and sufficiently flexible to account for the complex variability of the longitudinal molecular data. The ideas from the field of Bayesian analysis of computer model validation are applied, along with modern Markov Chain Monte Carlo (MCMC) algorithms, in order to derive an appropriate Bayes discriminant rule. We restrict attention to the two-model comparison problem and present the application of the proposed rule to the mRNA data in the de-differentiation network of three mRNA concentrations in mammalian salivary glands as well as to a large synthetic dataset derived from the model used in the recent DREAM6 competition.

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Section: Introductionmentioning

confidence: 99%

Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network

Kim

Venkatesh

et al. 2013

Journal of Computational Biology

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“…TC, as one of the defining features of circadian rhythms, refers to the relative insensitivity of the period length to ambient temperature over a range of physiologically relevant temperatures. The rate of a typical biochemical reaction doubles with an increase in temperature of 10°C (expressed as Q 10 =2), but the rate of the circadian clock is relatively constant (Q 10 ~ 1) (Jolma et al, 2010;McClung and Davis, 2010). The reactions induced by change in the ambient temperature are presumably constrained by the TC mechanism.…”

Section: Temperature Compensation (Tc)mentioning

confidence: 99%

“…The reactions induced by change in the ambient temperature are presumably constrained by the TC mechanism. Otherwise, the period of the clock would fluctuate greatly, depending on the ambient temperature (Jolma et al, 2010;McClung and Davis, 2010).…”

Section: Temperature Compensation (Tc)mentioning

confidence: 99%

“…To face such challenges actively, most organisms have evolved the capability to measure time. The circadian clock is the time measuring system that establishes an endogenous rhythm with a 24 hr period, called a circadian rhythm (Jolma et al, 2010;McClung, 2011). The rhythmic oscillation is persistent (self-sustaining), able to be synchronized to ambient environments (entrainable), and is stable in physiologically-ranged thermal environments (temperature compensated) (de Montaigu et al, 2010;McClung, 2011;McWatters and Devlin, 2011).…”

Section: The Plant Circadian Clockmentioning

confidence: 99%

“…Red solid arrow: activation; red dashed arrow: indirect activation; black perpendicular bars: repression. (TTFLs) (Baker et al, 2011;Jolma et al, 2010;McClung, 2011;McWatters and Devlin, 2011). Arabidopsis circadian oscillators, like those of many other eukaryotes, are based on multiple-interlocked TTFLs consisting of three main ones (Figure 1) (Harmer, 2009;Locke et al, 2006;McClung, 2011).…”

Section: The Clock Mechanismmentioning

confidence: 99%

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The Importance of the Plant Circadian Clock to Confer Heat Tolerance

Kim

Somers

Park

2014

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Through this system, most eukaryotic organisms appropriately respond to daily or seasonal environmental changes by regulating their physiology and development in a time-dependent manner, conferring the organism with an adaptive advantage. In plants, the endogenous timing system also controls many important physiological processes including flower opening, hormone synthesis, metabolic pathways and gene expression so that these sessile species may survive efficiently in changing environments. Temperature compensation (TC) is one of the defining features of the clock mechanism. Under this mechanism, the pace of the clock, or period, remains stable over a broad range of physiologically relevant temperatures, which is unlikely to happen in other biochemical reactions. Thus, this mechanism allows organisms to sustain their ordinary life in various thermal environments by providing an accurate measure of the passage of time, regardless of the ambient temperature. Considering the current global climate changes our planet is undergoing, understanding the fundamental mechanism underlying TC cannot be overemphasized. In this review, we discuss the molecular organization of the plant circadian clock and the concept of TC, as well as the significance of plant TC in conferring fitness under the current increasing thermal environments.

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Temporal Expression of the Clock Genes in the Water Flea Daphnia pulex (Crustacea: Cladocera)

et al. 2016

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The timekeeping mechanisms that operate at the core of circadian clocks (oscillators) are based on interacting molecular feedback loops consisting of clock and clock-associated genes. However, there is a lack of comprehensive studies on the expression of clock genes (particularly those forming its core) in single crustacean species at the mRNA and protein levels, and these studies could serve as a basis for constructing a model of the crustacean molecular oscillator. Studies on Daphnia pulex are well suited to fill this gap because this species is the only representative crustacean whose genome has been sequenced. We analyzed the abundance of 20 gene transcripts throughout the day in the whole bodies of D. pulex (single clone); we found that 15 of these genes were transcriptionally active, and most had daily expression level changes. According to the functional classification of their homologues in insects, these genes may represent elements of the Daphnia molecular oscillator core and its input and output pathways. Studies of PERIOD (PER) protein, one of the main clock components, revealed its rhythmic expression pattern in the epidermis, gut, and ovaries. Finally, the cycling levels of many of these clock components observed in animals reared in continuous light led to the conclusion that the Daphnia oscillator, even if it is structurally similar to the oscillators of other arthropods, can be considered a particularly important adaptive mechanism for living in environments with extreme photoperiods.

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Circadian oscillators in eukaryotes

Cited by 33 publications

References 230 publications

Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network

Model Discrimination in Dynamic Molecular Systems: Application to Parotid De-differentiation Network

The Importance of the Plant Circadian Clock to Confer Heat Tolerance

Temporal Expression of the Clock Genes in the Water Flea Daphnia pulex (Crustacea: Cladocera)

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