bims-ciryme 2025-08-10 papers

Nat Commun. 2025 Aug 05. 16(1): 7223

Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock.

Connor Reynolds, Joshua Colmer, Hannah Rees, Ehsan Khajouei, Rachel Rusholme-Pilcher, Hiroshi Kudoh, Antony N Dodd, Anthony Hall.

The circadian clock of plants contributes to their survival and fitness. However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. Generating these datasets is labour-intensive, costly and, in most cases, performed under tightly controlled laboratory conditions. To overcome these barriers, we have developed ChronoGauge: an ensemble model that can reliably estimate the endogenous circadian time of Arabidopsis plants using the expression of a handful of time-indicating genes within a single time-pointed transcriptomic sample. ChronoGauge can predict a plant's circadian time with high accuracy across unseen Arabidopsis bulk RNA-seq and microarray samples, and can be further applied to make non-random predictions across samples in non-model species, including field samples. Finally, we demonstrate how ChronoGauge can be applied to generate hypotheses regarding the response of the circadian transcriptome to specific genotypes or environmental conditions.

DOI: https://doi.org/10.1038/s41467-025-62196-w

Sci Rep. 2025 Aug 02. 15(1): 28279

The cycle gene is essential for both daily responses and seasonal reproduction in the Northern house mosquito, Culex pipiens.

Matthew Wolkoff, Mizuki Yoshida, Taylor Lowmiller, Cheolho Sim, Megan E Meuti.

The insect circadian clock synchronizes daily activities, such as feeding, eclosion, and mating to diurnal light:dark cycles, while the photoperiodic clock synchronizes development and reproduction to the appropriate season. Despite mounting evidence that the circadian and photoperiodic timekeeping systems are linked, it is unclear whether the circadian clock as a whole or individual genes within the circadian clock are responsible for measuring daylength, releasing hormones and/or inducing diapause phenotypes. To interrogate the role of a core circadian transcription factor, cycle, in mediating both seasonal and daily behaviors we used CRISPR/Cas-9 genome editing to introduce a deletion mutation into cycle in the Northern house mosquito, Culex pipiens. Females homozygous for this deletion exhibited high rates of reproductive arrest characteristic of an overwintering diapause even when reared in summer-like conditions, while a minority remained reproductive even when reared in winter-like conditions. Nearly all (79%) homozygotes lacked robust behavioral rhythms in constant darkness, while 52% of heterozygotes carrying one wild-type copy of the cycle gene lacked robust rhythmicity in constant darkness. Heterozygotes and homozygotes were more active in constant darkness than WT mosquitoes, but this difference was abolished under light:dark conditions. Lastly, the daily transcription profiles of various circadian genes, especially timeless and vrille, were disrupted in homozygous females even when they were reared under long and short days with light:dark cycles. These results demonstrate that cycle is essential for coordinating both daily activity and transcript abundance and seasonal diapause in Cx. pipiens.

Keywords: Bmal ; Period ; Timeless ; Circadian biology; Diapause; Juvenile hormone signaling

DOI: https://doi.org/10.1038/s41598-025-06637-y

Commun Biol. 2025 Aug 07. 8(1): 1178

The cost of re-synchronization in a leaf-cutter ant colony.

Mila Maria Pamplona-Barbosa, Marcelo Arruda Fiuza de Toledo, Gisele Akemi Oda, André Frazão Helene.

Biological rhythms are essential components of organisms' physiology and behavior. In social insects, biological rhythms can be studied at varying levels of a colony, revealing interesting aspects about how rhythms arise from the individual and collective levels. Here, by developing a video-tracking software based on machine learning techniques, we investigated the emergent collective rhythms of a leaf-cutter ant colony under laboratory conditions. The colony displayed rhythmic, daily foraging activity, with most of its foraging occurring during the dark phase of the day. The same pattern is found in the leaf-cutting activity. After being exposed to a 6-hour phase shift of the light-dark cycle, the daily rhythm of colony activity resynchronized with the new cycle phase after a few transient days. During these transient days, an increase in its daily leaf intake was measured. Under synchronized conditions, the ratio between foraging and leaf intake of the colony was higher during the light phase and decreased in the transient days after the phase shift, revealing that temporal synchronization plays an important role in the organization of the colony. Our findings illustrate the dynamic aspects of temporal synchronization in complex eusocial systems, pointing to these systems as exciting new models for comparative research.

DOI: https://doi.org/10.1038/s42003-025-08117-5

Neuron. 2025 Aug 04. pii: S0896-6273(25)00517-3. [Epub ahead of print]

Reconstructed cell-type-specific rhythms in human brain link Alzheimer's pathology, circadian stress, and ribosomal disruption.

Henry C Hollis, Ashish Sharma, Patrick W Sheehan, Leonard B Maggi, Jason D Weber, Jan A Hammarlund, David A Bennett, Vilas Menon, Erik S Musiek, Ron C Anafi.

Alzheimer's disease (AD) disrupts behavioral circadian rhythms, but its effects on molecular rhythms in the human brain are poorly understood. Using single-nucleus RNA sequencing (snRNA-seq) from post-mortem cortical samples, we informatically estimated the relative circadian phases of 409 persons with and without AD dementia, reconstructing circadian expression profiles across cell types. Although core clock rhythms were preserved in AD, many cell-type-specific circadian outputs were disrupted. Rhythms in ribosomal biogenesis and oxidative phosphorylation were dampened across cell types. Similar losses in ribosomal gene expression rhythms were observed in amyloid precursor protein/presenilin 1 (APP/PS1) mice, which showed further reductions in ribosomal protein expression and polysome-mediated translation after circadian desynchrony. Exploratory computational modeling reveals that altered translation may contribute to the increased circadian variability seen in AD patients. These findings reveal altered cell-type-specific circadian output rhythms in the brains of AD-affected patients and highlight disrupted ribosomal rhythms as a feature of AD.

Keywords: Alzheimer’s disease; astrocyte; circadian; glia; machine learning; microglia; neuron; ribosome; sleep; transcriptome

DOI: https://doi.org/10.1016/j.neuron.2025.07.010