De, P. S. | bioRxiv Science

bioRxiv2023

Sensitivity analysis identifies the factors driving the enzymatic saccharification of lignocellulose

Corn stover is the most abundant form of crop residue that can serve as a source of lignocellulosic biomass in biorefinery approaches, for instance for the production of bioethanol. In such biorefinery processes, the constituent polysaccharide biopolymers are typically broken down into simple monomeric sugars by enzymatic saccharification, for further downstream fermentation into bioethanol. However, the recalcitrance of this material to enzymatic saccharification invokes the need for innovative pre-treatment methods to increase sugar conversion yield. Here, we focus on experimental glucose conversion time-courses for corn stover lignocellulose that has been pre-treated with different acid-catalysed processes and intensities. We identify the key parameters that determine enzymatic saccharification dynamics by performing a Sobols sensitivity analysis on the comparison between the simulation results from our complex stochastic biophysical model, and the experimental data that we accurately reproduce. We find that the parameters relating to cellulose crystallinity and those associated with the cellobiohydrolase activity are predominantly driving the enzymatic saccharification dynamics. We confirm our computational results using mathematical calculations for a purely cellulosic substrate. On the one hand, having identified that only five parameters drastically influence the saccharification dynamics allows us to reduce the dimensionality of the parameter space (from nineteen to five parameters), which we expect will significantly speed up our fitting algorithm for comparison of experimental and simulated saccharification time-courses. On the other hand, these parameters directly highlight key targets for experimental endeavours in the optimisation of pre-treatment and saccharification conditions. Finally, this systematic and two-fold theoretical study, based on both mathematical and computational approaches, provides experimentalists with key insights that will support them in rationalising their complex experimental results. O_TEXTBOXSIGNIFICANCE The recalcitrance of lignocellulosic biomass to enzymatic saccharification processes necessitates innovative biorefinery pre-treatment processes with the goal of increasing glucose conversion yields. We implement a systematic Sobols sensitivity analysis on the comparison between the simulation results from our complex stochastic biophysical model, and experimental glucose conversion time-courses data for pre-treated corn stover lignocellulose that we accurately reproduce with our model. Our results, reinforced with analytical calculations, highlight the key parameters which govern the dynamics of enzymatic saccharification of lignocellulose. Thus, this study does not only drastically reduce the model parameter space from nineteen free parameters to only five key ones, but it also provides valuable insights that can guide future experiment design efforts, and the rationalisation of complex experimental datasets. C_TEXTBOX

biophysics↗

bioRxiv2021

Does cellular adaptation to force loading rate determine the biphasic vs monotonic response of actin retrograde flow with substrate rigidity?

The transmission of cytoskeletal forces to the extracellular matrix through focal adhesion complexes is essential for a multitude of biological processes such as cell migration, differentiation, tissue development, cancer progression, among others. During migration, focal adhesions arrest the actin retrograde flow towards the cell interior, allowing the cell front to move forward. Here, we address a puzzling observation of the existence of two distinct phenomena: a biphasic relationship of the retrograde flow and cell traction force with increasing substrate rigidity, with maximum traction force and minimum retrograde flow velocity being present at an optimal substrate stiffness; in contrast, a monotonic relationship between them where the retrograde flow decreases and traction force increases with substrate stiffness. We propose a theoretical model for cell-matrix adhesions at the leading edge of a migrating cell, incorporating a novel approach in force loading rate sensitive binding and reinforcement of focal adhesions assembly and the subsequent force-induced slowing down of actin flow. Our model unravels both biphasic and monotonic responses of the retrograde flow and cell traction force with increasing substrate rigidity, owing to the cells ability to sense and adapt to the fast-growing forces. Moreover, we also elucidate how the viscoelastic properties of the substrate regulate these nonlinear responses and alter cellular behaviours.

biophysics↗

bioRxiv2019

Stick-Slip Dynamics of Migrating Cells on Viscoelastic Substrates

Stick-slip motion, a common phenomenon observed during crawling of cells, is found to be strongly sensitive to the substrate stiffness. Stick-slip behaviours have previously been investigated typically using purely elastic substrates. For a more realistic understanding of this phenomenon, we propose a theoretical model to study the dynamics on a viscoelastic substrate. Our model based on a reaction-diffusion framework, incorporates known important interactions such as retrograde flow of actin, myosin contractility, force dependent assembly and disassembly of focal adhesions coupled with cell-substrate interaction. We show that consideration of a viscoelastic substrate not only captures the usually observed stick-slip jumps, but also predicts the existence of an optimal substrate viscosity corresponding to maximum traction force and minimum retrograde flow which was hitherto unexplored. Moreover, our theory predicts the time evolution of individual bond force that characterizes the stick-slip patterns on soft versus stiff substrates. Our analysis also elucidates how the duration of the stick-slip cycles are affected by various cellular parameters.

biophysics↗