Emergent robust oscillatory dynamics in the interlocked feedback-feedforward loops.

Decision letter: NF-κB oscillations translate into functionally related patterns of gene expression

Circadian (∼24 h) timekeeping is essential for the lives of many organisms. To understand the biochemical mechanisms of this timekeeping, we have developed a detailed mathematical model of the mammalian circadian clock. Our model can accurately predict diverse experimental data including the phenotypes of mutations or knockdown of clock genes as well as the time courses and relative expression of clock transcripts and proteins. Using this model, we show how a universal motif of circadian timekeeping, where repressors tightly bind activators rather than directly binding to DNA, can generate oscillations when activators and repressors are in stoichiometric balance. Furthermore, we find that an additional slow negative feedback loop preserves this stoichiometric balance and maintains timekeeping with a fixed period. The role of this mechanism in generating robust rhythms is validated by analysis of a simple and general model and a previous model of the Drosophila circadian clock. We propose a double-negative feedback loop design for biological clocks whose period needs to be tightly regulated even with large changes in gene dosage.

Proteins in the Neurospora Circadian Clockworks

Temperature compensation and robustness to biological noise are two key characteristics of the circadian clock. These features allow the circadian pacemaker to maintain a steady oscillation in a wide range of environmental conditions. The presence of a time-delayed negative feedback loop in the regulatory network generates autonomous circadian oscillations in eukaryotic systems. In comparison, the circadian clock of cyanobacteria is controlled by a strong positive feedback loop. Positive feedback loops with substrate depletion can also generate oscillations, inspiring other circadian clock models. What makes a circadian oscillatory network robust to extrinsic noise is unclear. We investigated four basic circadian oscillators with negative, positive, and combinations of positive and negative feedback loops to explore network features necessary for circadian clock resilience. We discovered that the negative feedback loop system performs the best in compensating temperature changes. We also show that a positive feedback loop can reduce extrinsic noise in periods of circadian oscillators, while intrinsic noise is reduced by negative feedback loops.

A tale of two rhythms: Locked clocks and chaos in biology.

The Circadian Timekeeping System of Drosophila

Circadian molecular clock disruption in chronic pulmonary diseases.

Molecular timekeeping in Neurospora crassa is robust even under severe limitation of carbon sources and the efficient adaptation to changing nutrient availability is dependent on the positive component of the circadian clock.

Molecular timekeeping in Neurospora crassa is robust even under severe limitation of carbon sources and the efficient adaptation to changing nutrient availability is dependent on the positive component of the circadian clock.

Molecular timekeeping in Neurospora crassa is robust even under severe limitation of carbon sources and the efficient adaptation to changing nutrient availability is dependent on the positive component of the circadian clock.

A physiological mathematical model of chronic myeloid leukemia, validated by experiments in transgenic mice and clinical data, identifies mechanisms underlying the response to tyrosine kinase inhibitor therapy, predicts biomarkers of primary resistance, and suggests new strategies to improve treatment outcomes.

Author response: Predictive nonlinear modeling of malignant myelopoiesis and tyrosine kinase inhibitor therapy

Circadian Clocks: Running on Redox

Many cellular and physiological processes have been shown to display a rhythm of about 24 hours. This so-called circadian rhythm is based on a system of interlocked negative and positive molecular feedback loops. Here we extend a previous model of the circadian oscillator by including REV-ERBalpha as an additional component. This new model will allow us to investigate the function of an additional negative feedback loop via REV-ERBalpha. We obtain circadian oscillations with the correct period and phase relations between clock components. Parameter variations that correspond to clock-gene mutations reproduce experimental results: With parameter variations mimicking the Bmal1(-/-) and the Per2(Brdm1) mutation the oscillations cease to exist. In contrast, the system shows sustained oscillations if we use a parameter set that reflects the Rev-erbalpha mutation. The model also accounts for the differential effect of the Cry1(-/-) and Cry2(-/-) mutations on the circadian period. The simulations of the extended model indicate that the original model is robust with respect to the incorporation of the additional component. Depending on the kinetics of the Per2/Cry transcriptional activation by BMAL1, an increasing BMAL1 expression leads to either an increase or decrease of the clock period. This indicates that overexpression experiments could help to characterize the impact of BMAL1 on Per2/Cry transcription.

Every fall, Northeastern America monarch butterflies ( Danaus plexippus ) undergo an extraordinary migration to their overwintering site in Central Mexico. During their long migration, monarch migrants use sun compass to navigate. To maintain a southward flying direction, monarch migrants compensate for the continuously changing position of the sun by providing timing information to the compass using their circadian clock. Animal circadian clocks depend primarily on a negative transcriptional feedback loop to track time. I started my work to re-construct the monarch butterfly circadian clock negative feedback loop in cell culture, focusing on homologs of Drosophila clock genes. It turned out that in addition to a Drosophila -like cryptochrome (cry1) gene, a second mammalian-like cry2 gene exists in monarch butterflies and many other insects, except in Drosophila . The two CRYs showed distinct functions in our initial assays in cultured Drosophila Schneider 2 (S2) cells. CRY2 functions as a potent transcriptional repressor, while CRY1 is light sensitive but shows no obvious transcriptional activity. The existence of two cry genes in insects changed the Drosophila -centric view of insect circadian clock. During the course of my study, our lab obtained a monarch cell line called DpN1 cells. These cells possess a light-driven clock and contributed tremendously to the research on monarch circadian clock. Using this cell line, I provided strong evidence supporting monarch CRY2’s role as a major circadian clock repressor and identified a protein-protein protective interaction cascade underlying the CRY1-mediated resetting of the molecular oscillator in DpN1 cells. I continued my work trying to understand how insect CRY2 inhibits transcription. I provided evidence suggesting the involvement of monarch PER in promoting CRY2 nuclear entry in both S2 cells and DpN1 cells. Finally, I mapped CRY2’s transcriptional inhibitory activity onto its N-terminal domain. Collectively, my research helped to change our view of insect clocks from a Drosophila -centric standpoint to a much more diverse picture. My studies also advanced the understanding of monarch circadian clock mechanism, and provides a foundation for further studies.