A Boolean Model of Microvascular Rarefaction to Predict Treatment Outcomes in Renal Disease

Cell-based regenerative medicine for renovascular disease

Renal artery stenosis (RAS) elicits the development of hypertension and post-stenotic kidney damage, which may become irresponsive to restoration of arterial patency. Rather than mere losses of blood flow or oxygen supply, irreversible intrarenal microvascular rarefaction, tubular injury, and interstitial fibrosis are now attributed to intrinsic pathways activated within the kidney, focusing attention on the kidney parenchyma as a therapeutic target. Several regenerative approaches involving the delivery of reparative cells or products have achieved kidney repair in experimental models of RAS and the delivery of mesenchymal stem/stromal cells (MSCs) has already been translated to human subjects with RAS with promising results. The ongoing development of innovative approaches in kidney disease awaits application, validation, and acceptance as routine clinical treatment to avert kidney damage in RAS.

A practical guide to mechanistic systems modeling in biology using a logic-based approach

Mechanistic computational models enable the study of regulatory mechanisms implicated in various biological processes. These models provide a means to analyze the dynamics of the systems they describe, and to study and interrogate their properties, and provide insights about the emerging behavior of the system in the presence of single or combined perturbations. Aimed at those who are new to computational modeling, we present here a practical hands-on protocol breaking down the process of mechanistic modeling of biological systems in a succession of precise steps. The protocol provides a framework that includes defining the model scope, choosing validation criteria, selecting the appropriate modeling approach, constructing a model and simulating the model. To ensure broad accessibility of the protocol, we use a logical modeling framework, which presents a lower mathematical barrier of entry, and two easy-to-use and popular modeling software tools: Cell Collective and GINsim. The complete modeling workflow is applied to a well-studied and familiar biological process-the lac operon regulatory system. The protocol can be completed by users with little to no prior computational modeling experience approximately within 3 h.