Suppressing effect of Ca^{2+} blips on puff amplitudes by inhibiting channels to prevent recovery

Biphasic amplitude oscillator characterized by distinct dynamics of trough and crest

Biphasic amplitude dynamics (BAD) of oscillation have been observed in many biological systems. However, the specific topology structure and regulatory mechanisms underlying these biphasic amplitude dynamics remain elusive. Here, we searched all possible two-node circuit topologies and identified the core oscillator that enables robust oscillation. This core oscillator consists of a negative feedback loop between two nodes and a self-positive feedback loop of the input node, which result in the fast and slow dynamics of the two nodes, thereby achieving relaxation oscillation. Landscape theory was employed to study the stochastic dynamics and global stability of the system, allowing us to quantitatively describe the diverse positions and sizes of the Mexican hat. With increasing input strength, the size of the Mexican hat exhibits a gradual increase followed by a subsequent decrease. The self-activation of input node and the negative feedback on input node, which dominate the fast dynamics of the input node, were observed to regulate BAD in a bell-shaped manner. Both deterministic and statistical analysis results reveal that BAD is characterized by the linear and nonlinear dependence of the oscillation trough and crest on the input strength. In addition, combining with computational and theoretical analysis, we addressed that the linear response of trough to input is predominantly governed by the negative feedback, while the nonlinear response of crest is jointly regulated by the negative feedback loop and the self-positive feedback loop within the oscillator. Overall, this study provides a natural and physical basis for comprehending the occurrence of BAD in oscillatory systems, yielding guidance for the design of BAD in synthetic biology applications.

Mapping Interpuff Interval Distribution to the Properties of Inositol Trisphosphate Receptors

Tightly clustered inositol trisphosphate receptors (IP₃Rs) control localized Ca²⁺ liberation from the endoplasmic reticulum to generate repetitive Ca²⁺ puffs. Distributions of the interpuff interval (IPI), i.e., the waiting time between successive puffs, are found to be well characterized by a probability density function involving only two parameters, λ and ξ, which represent the basal rate of puff generation and the recovery rate from refractoriness, respectively. However, how the two parameters depend on the kinetic parameters of single IP₃Rs in a cluster is still unclear. In this article, using a stochastic puff model and a single-channel data-based IP₃R model, we establish the dependencies of λ and ξ on two important IP₃R model parameters, IP₃ concentration ([IP₃]) and the recovery rate from Ca²⁺ inhibition (r_low). By varying [IP₃] and r_low in physiologically plausible ranges, we find that the ξ-λ plane is comprised of only two disjoint regions, a biologically impermissible region and a region where each parameter set (ξ, λ) can be caused by using two different combinations of [IP₃] and r_low. The two combinations utilize very different mechanisms to maintain the same IPI distribution, and the mechanistic difference provides a way of identifying IP₃R kinetic parameters by observing properties of the IPI.