Understanding systems-level properties: timely stories from the study of clocks

JB Hogenesch, HR Ueda - Nature Reviews Genetics, 2011 - nature.com
After several decades dominated by reductionist approaches in biology, researchers are
returning to the study of complex biology with a litany of new and old techniques—this …

Biological timing and the clock metaphor: oscillatory and hourglass mechanisms

L Rensing, U Meyer-Grahle, P Ruoff - Chronobiology international, 2001 - Taylor & Francis
Living organisms have developed a multitude of timing mechanisms—“biological clocks.”
Their mechanisms are based on either oscillations (oscillatory clocks) or unidirectional …

CKIε/δ-dependent phosphorylation is a temperature-insensitive, period-determining process in the mammalian circadian clock

Y Isojima, M Nakajima, H Ukai… - Proceedings of the …, 2009 - National Acad Sciences
A striking feature of the circadian clock is its flexible yet robust response to various
environmental conditions. To analyze the biochemical processes underlying this flexible-yet …

Temperature and nitrogen effects on regulators and products of the flavonoid pathway: experimental and kinetic model studies

KM Olsen, R Slimestad, US Lea, C Brede… - Plant, Cell & …, 2009 - Wiley Online Library
The flavonoid pathway is known to be up‐regulated by different environmental stress factors.
Down‐regulation of the pathway is much less studied and is emphasized in the present …

A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM

JJ Tyson, CI Hong, CD Thron, B Novak - Biophysical journal, 1999 - cell.com
Many organisms display rhythms of physiology and behavior that are entrained to the 24-h
cycle of light and darkness prevailing on Earth. Under constant conditions of illumination …

Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock

KD Edwards, JR Lynn, P Gyula, F Nagy, AJ Millar - Genetics, 2005 - academic.oup.com
Temperature compensation is a defining feature of circadian oscillators, yet no components
contributing to the phenomenon have been identified in plants. We tested 27 accessions of …

Mutation of a PER2 phosphodegron perturbs the circadian phosphoswitch

S Masuda, R Narasimamurthy… - Proceedings of the …, 2020 - National Acad Sciences
Casein kinase 1 (CK1) plays a central role in regulating the period of the circadian clock. In
mammals, PER2 protein abundance is regulated by CK1-mediated phosphorylation and …

The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock

P Ruoff, JJ Loros, JC Dunlap - Proceedings of the National …, 2005 - National Acad Sciences
Temperature compensation is an important property of all biological clocks. In Neurospora
crassa, negative-feedback regulation on the frequency (frq) gene's transcription by the FRQ …

Biological switches and clocks

JJ Tyson, R Albert, A Goldbeter… - Journal of The …, 2008 - royalsocietypublishing.org
To introduce this special issue on biological switches and clocks, we review the historical
development of mathematical models of bistability and oscillations in chemical reaction …

The Goodwin oscillator: on the importance of degradation reactions in the circadian clock

P Ruoff, M Vinsjevik, C Monnerjahn… - Journal of biological …, 1999 - journals.sagepub.com
This article focuses on the Goodwin oscillator and related minimal models, which describe
negative feedback schemes that are of relevance for the circadian rhythms in Neurospora …