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Biology subjects

Fontana, W.

Publications and source records attributed to Fontana, W..

2 recordsLinked to original sources

PyKappa: Rule-based modeling in Python

Rule-based languages have proven effective for modeling systems of interacting structured entities as typically encountered in chemistry and molecular biology. We present PyKappa, a rule-based modeling package written in Python whose interpreted nature enables interactive simulation and analysis, including by agentic AI. The package seeks to broaden the base of developers by utilizing a widely known programming language and serves as an easy-to-deploy teaching tool. Using PyKappa, we conduct a case study of phase separation.

systems biology↗

Age-dependence and aging-dependence: The case of neuronal loss and lifespan in a C. elegans model of Parkinson’s disease

It is often assumed, but not established, that the major neurodegenerative diseases, such as Parkinsons disease, are not just age-dependent (their incidence changes with time) but actually aging-dependent (their incidence is coupled to the process that determines lifespan). To determine a dependence on the aging process requires the joint probability distribution of disease onset and lifespan. For human Parkinsons disease, such a joint distribution is not available because the disease cuts lifespan short. To acquire a joint distribution, we resorted to an established C. elegans model of Parkinsons disease in which the loss of dopaminergic neurons is not fatal. We find that lifespan is not correlated with the loss of neurons and that a lifespan-extending intervention into insulin/IGF1 signaling accelerates neuronal loss, while leaving death and neuronal loss times uncorrelated. This suggests that distinct and compartmentalized instances of the same genetically encoded insulin/IGF1 signaling machinery act independently to control neurodegeneration and lifespan in C. elegans. Although the human context might well be different, our study calls attention to maintaining a rigorous distinction between age-dependence and aging-dependence.

developmental biology↗