arXiv subjects

Ryan LeFebre

Publications and source records attributed to Ryan LeFebre.

3 recordsLinked to original sources

arXiv2026

Restoring information in aged gene regulatory networks by single knock-ins

A hallmark of aging is loss of information in gene regulatory networks. These networks are tightly connected, raising the question of whether information could be restored by perturbing single genes. We develop a simple theoretical framework for information transmission in gene regulatory networks that describes the information gained or lost when a gene is "knocked in" (exogenously expressed). Applying the framework to gene expression data from muscle cells in young and old mice, we find that single knock-ins can restore network information by up to 10%. Our work advances the study of information flow in networks and identifies potential gene targets for rejuvenation.

q-bio.MN↗

arXiv2023

Role of signal degradation in directional chemosensing

Directional chemosensing is ubiquitous in cell biology, but some cells such as mating yeast paradoxically degrade the signal they aim to detect. While the data processing inequality suggests that such signal modification cannot increase the sensory information, we show using a reaction-diffusion model and an exactly solvable discrete-state reduction that it can. We identify a non-Markovian step in the information chain allowing the system to evade the data processing inequality, reflecting the nonlocal nature of diffusion. Our results apply to any sensory system in which degradation couples to diffusion. Experimental data suggest that mating yeast operate in the beneficial regime where degradation improves sensing.

physics.bio-ph↗

arXiv2022

Temporal signals drive the emergence of multicellular information networks

Coordinated responses to environmental stimuli are critical for multicellular organisms. To overcome the obstacles of cell-to-cell heterogeneity and noisy signaling dynamics within individual cells, cells must effectively exchange information with peers. However, the dynamics and mechanisms of collective information transfer driven by external signals is poorly understood. Here we investigate the calcium dynamics of neuronal cells that form confluent monolayers and respond to cyclic ATP stimuli in microfluidic devices. Using Granger inference to reconstruct the underlying causal relations between the cells, we find that the cells self-organize into spatially decentralized and temporally stationary networks to support information transfer via gap junction channels. The connectivity of the causal networks depend on the temporal profile of the external stimuli, where short periods, or long periods with small duty fractions, lead to reduced connectivity and fractured network topology. We build a theoretical model based on communicating excitable units that reproduces our observations. The model further predicts that connectivity of the causal network is maximal at an optimal communication strength, which is confirmed by the experiments. Together, our results show that information transfer between neuronal cells is externally regulated by the temporal profile of the stimuli, and internally regulated by cell-cell communication.

physics.bio-ph↗