Dynamic models of molecular networks and pathways enable in silico evaluations of the consistency of proposed interactions and the outcomes of perturbations as well as of hypotheses on system-level structure and function. We postulate a continuous model of the activation dynamics of the ethylene response factor 1 (ERF1) gene in response to ethylene signaling. This activation elicits the response of the plant defensin 1 (PDF1) gene, which also responds to jasmonic acid, and the inhibition of the putative auxin responsive factor 2 (ARF2) gene, that also responds to auxin. Our model allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated allows the effect of different ethylene concentrations in eliciting contrasting genetic and phenotypic responses to be evaluated and seems to consider key components of the ethylene pathway because the ERF1 dose-response curve that we predict has the same qualitative form as the phenotypic dose-response curves obtained experimentally. Therefore, our model suggests that the phenotypic dose-response curves obtained experimentally could be due, at least in part, to ERF1 changes to different ethylene concentrations. Stability analyses show that the model's results are robust to parameter estimates. Of interest is that our model predicts that the ethylene pathway may filter stochastic and rapid chaotic fluctuations in ethylene availability. This novel approach may be applied to any cellular signaling and response pathway in plants and animals.

Knowledge about the molecular basis of SARS-CoV-2 infection is incipient. However, recent experimental results about the virus interactome have shown that this single-positive stranded RNA virus produces a set of about 28 specific proteins grouped into 16 non-structural proteins (Nsp1 to Nsp16), four structural proteins (E, M, N, and S), and eight accessory proteins (orf3a, orf6, orf7a, orf7b, orf8, orf9b, orf9c, and orf10). In this brief communication, the network model of the interactome of these viral proteins with the host proteins is analyzed. The statistical analysis of this network shows that it has a modular scale-free topology in which the virus proteins orf8, M, and Nsp7 are the three nodes with the most connections (links). This result suggests the possibility that a simultaneous pharmacological attack on these hubs could assure the destruction of the network and the elimination of the virus.

In Arabidopsis thaliana, leaf and root epidermis hairs exhibit contrasting spatial arrangements even though the genetic networks regulating their respective cell-fate determination have very similar structures and components. We integrated available experimental data for leaf and root hair patterning in dynamic network models which may be reduced to activator-inhibitor models. This integration yielded expected results for these kinds of dynamic models, including striped and dotted cell patterns which are characteristic of root and leaf epidermis, respectively. However, these formal tools have led us to novel insights on current data and to put forward precise hypotheses which can be addressed experimentally. In particular, despite subtle differences in the root and leaf networks, these have equivalent dynamical behaviors. Our simulations also suggest that only when a biasing signal positively affects an activator in the network, the system recovers striped cellular patterns similar to those of root epidermis. We also postulate that cell shape may affect pattern stability in the root. Our results thus support the idea that in this and other cases, contrasting spatial cell patterns and other evolutionary morphogenetic novelties originate from conserved genetic network modules subject to divergent contextual traits.

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Background: We study root cells from the model plant Arabidopsis thaliana and the communication channel conformed by the ethylene signal transduction pathway. A basic equation taken from our previous work relates the probability of expression of the gene ERF1 to the concentration of ethylene.