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1. Not all gut cellular circadian oscillators are food entrainable

   https://doi.org/10.1073/pnas.2601012123  

   Magaña, Isabel; Taufique, S_K Tahajjul; Shan, Yongli; Shen, Melody; Ehichioya, David E; Takahashi, Joseph S; Yamazaki, Shin; Obata, Yuuki (June 2026, Proceedings of the National Academy of Sciences)

   Circadian rhythms are ubiquitous, and most of the organs in the body contain circadian oscillators. The intestine comprises diverse cell types with distinct developmental origins and physiological functions. However, which intestinal cells contain cell-autonomous circadian oscillators and how circadian oscillators in distinct intestinal cell types synchronize with one another and with environmental daily cycles remain poorly understood. To address these questions, we generated a Cre-dependent PER2::LUCIFERASE reporter knock-in mouse that enables ex vivo measurement of circadian oscillations in defined cell populations. Ex vivo gut explants from mice expressing the reporter in one of five major cell types of the muscularis externa—enteric neurons (ENs), enteric glial cells (EGCs), interstitial cells of Cajal (ICCs), smooth muscle cells (SMCs), and muscularis macrophages (MMs)—exhibited robust, self-sustained circadian bioluminescence rhythms, demonstrating that each of these cell types harbors a cell-autonomous circadian oscillator. Importantly, circadian oscillators in ENs, EGCs, SMCs, and MMs entrained to feeding-fasting cycles, whereas circadian oscillators in ICCs remained resistant to food entrainment. These findings reveal that distinct intestinal cell types possess unique entrainment properties, and feeding during inactive time induces heterogeneous phase shifts across gut circadian oscillators, leading to temporal circadian misalignment within the intestine. As circadian disruptions, such as those associated with shift work, contribute to intestinal disorders, including inflammatory bowel disease and disorders of the gut–brain interaction, studying how intercellular circadian desynchrony influences intestinal homeostasis should provide chronobiology-based therapeutic strategies to combat these diseases. 

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2. Bode meets Kuramoto: Synchronized Clusters in Oscillatory Networks

   Favaretto, C; Bassett, Danielle S; Cenedese, A; Pasqualetti, F (January 2017, American Control Conference)

   In this paper we study cluster synchronization in a network of Kuramoto oscillators, where groups of oscillators evolve cohesively and at different frequencies from the neigh- boring oscillators. Synchronization is critical in a variety of systems, where it enables complex functionalities and behaviors. Synchronization over networks depends on the oscillators’ dynamics, the interaction topology, and coupling strengths, and the relationship between these different factors can be quite intricate. In this work we formally show that three network properties enable the emergence of cluster synchronization. Specifically, weak inter-cluster connections, strong intra-cluster connections, and sufficiently diverse natural frequencies among oscillators belonging to different groups. Our approach relies on system-theoretic tools, and is validated with numerical studies. 

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3. Core clock protein subcellular dynamics coordinate local and global circadian control in syncytia

   https://doi.org/10.1083/jcb.202509044  

   Wang, Ziyan; Bartholomai, Bradley M; Wang, Bin; Ritz, David; Schultz, Daniel; Loros, Jennifer J; Dunlap, Jay C (June 2026, Journal of Cell Biology)

   Circadian rhythms are pervasive among eukaryotes, and the underlying clocks share a common regulatory architecture—a negative feedback loop. A wealth of genetic and biochemical data underpin current perceptions of circadian oscillators but aspects of their cell biology remain cryptic, especially in syncytial systems like Neurospora crassa. We employed novel microfluidic systems and a light-blind mutant that retains circadian function to simultaneously track multiple clock components in vivo across circadian cycles in Neurospora. Despite heterogeneity of clock gene (frq) expression, we find robust, synchronous cycles in FRQ nuclear localization among all nuclei and document free diffusion of multiple clock components among nuclei. Within nuclei, clock components form small, highly dynamic nuclear bodies that persist throughout the cycle and exhibit time-dependent changes in composition, including transient colocalization between the positive and negative components for circadian regulatory functions. This rich context of in vivo spatiotemporal information illustrates how dynamic subnuclear organization and internuclear exchange of clock proteins ensure synchronous regulation of cellular activities across a macroscopic, multinucleated syncytium. 

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4. Conserved eukaryotic factors XCT and COP1 work together to control circadian clock function and reproductive timing in plants

   https://doi.org/10.1038/s44323-025-00057-x  

   Kumimoto, Roderick W; Marshall, Carine M; Zhang, Hongtao; Harmer, Stacey L (December 2026, npj Biological Timing and Sleep)

   Abstract Circadian rhythms align biological processes with environmental cycles to enhance fitness. Eukaryotic circadian oscillators rely on transcriptional–translational feedback loops, although specific oscillator components vary among lineages. The plant oscillator consists of a uniquely complex network of transcriptional regulators. These clock genes regulate each other’s expression and influence key developmental processes such as the transition from vegetative to reproductive growth. Here, we investigate the function of XAP5 CIRCADIAN TIMEKEEPER (XCT), a protein conserved across eukaryotes and previously implicated in RNA processing and circadian regulation inArabidopsis thaliana. We show that XCT genetically and physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase also conserved across eukaryotes. Both XCT and COP1 regulate the abundance and activity of the oscillator component EARLY FLOWERING3 (ELF3) to modulate circadian function and flowering time. These findings demonstrate how broadly conserved factors collaborate with plant-specific regulators to maintain circadian integrity and coordinate developmental timing. 

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5. Emergent hypernetworks in weakly coupled oscillators

   https://doi.org/10.1038/s41467-022-32282-4  

   Nijholt, Eddie; Ocampo-Espindola, Jorge Luis; Eroglu, Deniz; Kiss, István Z.; Pereira, Tiago (December 2022, Nature Communications)

   Abstract Networks of weakly coupled oscillators had a profound impact on our understanding of complex systems. Studies on model reconstruction from data have shown prevalent contributions from hypernetworks with triplet and higher interactions among oscillators, in spite that such models were originally defined as oscillator networks with pairwise interactions. Here, we show that hypernetworks can spontaneously emerge even in the presence of pairwise albeit nonlinear coupling given certain triplet frequency resonance conditions. The results are demonstrated in experiments with electrochemical oscillators and in simulations with integrate-and-fire neurons. By developing a comprehensive theory, we uncover the mechanism for emergent hypernetworks by identifying appearing and forbidden frequency resonant conditions. Furthermore, it is shown that microscopic linear (difference) coupling among units results in coupled mean fields, which have sufficient nonlinearity to facilitate hypernetworks. Our findings shed light on the apparent abundance of hypernetworks and provide a constructive way to predict and engineer their emergence. 

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