Starts 24 Nov 2022 11:00
Ends 24 Nov 2022 12:00
Central European Time
QLS Seminar: Stochasticity in cellular processes
ICTP
Central Area, 2nd floor, old SISSA building
Via Beirut, 2
All cellular processes are characterized by stochasticity (or noise) and the kind of noise involved has profound effects on their dynamics. In this talk, I will discuss the effects of noise on two specific biological processes viz. (i) mRNA translation process and (ii) virus-immune response pathway.
In the first problem we model extrinsic noise in mRNA translation, and find, among other effects, the residence time distribution broadens significantly when the noise influences the entry rate (initiation rate of ribosome on the mRNA) in comparison to the exit rate of ribosomes. The ribosome residence time distribution obtained due to the presence of extrinsic noise in the translation initiation rate is also similar to that obtained for the natural codon specific variation of initiation rates [1].
In the second problem, I will discuss our model of the interaction between T cells (immune cells) and viruses. We introduced fractional Gaussian noise in order to account for variability in the dynamics of the entities and obtain an analytical expression for the joint probability density function of these variables and the average viral load in the early and late stages of infection [2]. In further extensions, we developed and studied a more complex model through simulations [3]. Upon comparing the theoretically predicted average virus levels to those of COVID-19 patients, we hypothesize that the long-lived dynamics that are characteristic of such viral infections are due to the long range correlations in the temporal fluctuations of the virions.
The effects of noise on these specific cellular processes illustrate the importance of studying variability in these systems.
References:
[1] Extrinsic noise effects on ribosomal traffic during the translation process. Rati Sharma*. J. Stat. Mech: Theory Exp. 053504 (2022).
[2] A near analytic solution of a stochastic immune response model considering variability in virus and T cell dynamics. Abhilasha Batra and Rati Sharma*. J. Chem. Phys. 154, 195104 (2021).
[3] Persistent correlation in cellular noise determines longevity of viral infections. Abhilasha Batra, Shoubhik Chandan Banerjee and Rati Sharma*. J. Phys. Chem. Lett. 13, 7252 (2022).
In the first problem we model extrinsic noise in mRNA translation, and find, among other effects, the residence time distribution broadens significantly when the noise influences the entry rate (initiation rate of ribosome on the mRNA) in comparison to the exit rate of ribosomes. The ribosome residence time distribution obtained due to the presence of extrinsic noise in the translation initiation rate is also similar to that obtained for the natural codon specific variation of initiation rates [1].
In the second problem, I will discuss our model of the interaction between T cells (immune cells) and viruses. We introduced fractional Gaussian noise in order to account for variability in the dynamics of the entities and obtain an analytical expression for the joint probability density function of these variables and the average viral load in the early and late stages of infection [2]. In further extensions, we developed and studied a more complex model through simulations [3]. Upon comparing the theoretically predicted average virus levels to those of COVID-19 patients, we hypothesize that the long-lived dynamics that are characteristic of such viral infections are due to the long range correlations in the temporal fluctuations of the virions.
The effects of noise on these specific cellular processes illustrate the importance of studying variability in these systems.
References:
[1] Extrinsic noise effects on ribosomal traffic during the translation process. Rati Sharma*. J. Stat. Mech: Theory Exp. 053504 (2022).
[2] A near analytic solution of a stochastic immune response model considering variability in virus and T cell dynamics. Abhilasha Batra and Rati Sharma*. J. Chem. Phys. 154, 195104 (2021).
[3] Persistent correlation in cellular noise determines longevity of viral infections. Abhilasha Batra, Shoubhik Chandan Banerjee and Rati Sharma*. J. Phys. Chem. Lett. 13, 7252 (2022).