Toward endosymbiosis modeling using reaction networks

Reaction Network Modeling of Complex Ecological Interactions: Endosymbiosis and Multilevel Regulation

“…Next, we explain how to represent the regulation mechanisms occurring between these two levels. is model extends previous work [49].…”

“…Reaction network-like models of biological interactions have only recently been investigated [28,48,49], but seem to provide the necessary versatility to incorporate multilevel regulatory mechanisms in a sensible way. However, this approach is in its infancy and requires extensions.…”

“…In our model, which complements a reaction network model of endosymbiosis between corals and dinoflagellates of the genus Symbiodinium [49], we incorporate biochemical species (R H , R C , R C , Cal, and x), thermodynamic species (E), cellular species (H, S, and HS), and a regulatory factor (F inh ). In addition, we incorporated a bilevel regulatory mechanism for the proliferation of the endosymbiotic cell HS which is fostered by the increase of its energy (occurring at the nutrient traffic level) but also regulated by the release of F inh when the byproduct x of the energy production surpasses a threshold (occurring at the cellular proliferation level).…”

Special issue “International Symposium on Molecular Logic and Computational Synthetic Biology: MLCSB18”

“…This special issue includes seven peer-reviewed articles about synthetic biology, whose aim is to develop formal models for biological-like phenomena, specially in the context of molecular logic (Djordević and Silva 2019;Nemati and Torres 2020;Santiago et al 2020;Braccini et al 2020;Moreira et al 2020;Tavares et al 2021;Veloz and Flores 2021). Molecular logic focuses on understanding logical and operational aspects on molecules and their interactions, providing a fruitful conceptual crossover between chemistry and computation with unsuspected applications.…”

“…The aim of MLSCB18 was harnessing logical and algebraic methods for modeling and verifying systems on the interaction of Nature and Computation, around two main themes, which can also serve to split the list of articles published in this special issue: The development of biological computation models and devices (Djordević and Silva 2019;Braccini et al 2020;Tavares et al 2021;Veloz and Flores 2021), and the application of new computing paradigms to the design of biological systems (Nemati and Torres 2020;Santiago et al 2020;Moreira et al 2020).…”