Showing papers by "Andrey V. Kuznetsov published in 2023"

Computational investigation of the effect of reduced dynein velocity and reduced cargo diffusivity on slow axonal transport

Abstract: Contributions of three components of slow axonal transport (SAT) were studied using a computational model: the anterograde motor (kinesin)-driven component, the retrograde motor (dynein)-driven component, and the diffusion-driven component. The contribution of these three components of SAT was investigated in three different segments of the axon: the proximal portion, the central portion, and the distal portion of the axon. MAP1B protein was used as a model system to study SAT because there are published experimental data reporting MAP1B distribution along the axon length and average velocity of MAP1B transport in the axon. This allows the optimization approach to be used to find values of model kinetic constants that give the best fit with published experimental data. The effects of decreasing the value of cargo diffusivity on the diffusion-driven component of SAT and decreasing the value of dynein velocity on the retrograde motor-driven component of SAT were investigated. We found that for the case when protein diffusivity and dynein velocity are very small, it is possible to obtain an analytical solution to model equations. We found that, in this case, the protein concentration in the axon is uniform. This shows that anterograde motor-driven transport alone cannot simulate a variation of cargo concentration in the axon. Most proteins are non-uniformly distributed in axons. They may exhibit, for example, an increased concentration closer to the synapse. The need to reproduce a non-uniform distribution of protein concentration may explain why SAT is bidirectional (in addition to an anterograde component, it also contains a retrograde component).

Why slow axonal transport is bidirectional – can axonal transport of tau protein rely only on motor-driven anterograde transport?

Abstract: Slow axonal transport (SAT) moves multiple proteins from the soma, where they are synthesized, to the axon terminal. Due to the great lengths of axons, SAT almost exclusively relies on active transport, which is driven by molecular motors. The puzzling feature of slow axonal transport is its bidirectionality. Although the net direction of SAT is anterograde, from the soma to the terminal, experiments show that it also contains the retrograde component. One of the proteins transported by SAT is microtubule-associated protein tau. To better understand why the retrograde component in tau transport is needed, we used the perturbation technique. We analyzed the simplification of the full tau SAT model for the case when retrograde motor-driven transport and diffusion-driven transport of tau are negligible, and tau is driven only by anterograde (kinesin) motors. The solution of the simplified equations shows that the tau concentration along the axon length stays almost uniform (decreases very slightly), which is inconsistent with the tau concentration at the outlet boundary (at the axon tip). Thus kinesin-driven transport alone is not enough to explain the experimentally observed distribution of tau, and the retrograde motor-driven component in SAT is needed.

Dynein dysfunction prevents maintenance of high concentrations of slow axonal transport cargos at the axon terminal: a computational study

Abstract: Here we report computational studies of bidirectional transport in an axon, specifically focusing on predictions when the retrograde motor becomes dysfunctional. We are motivated by reports that mutations in dynein-encoding genes can cause diseases associated with peripheral motor and sensory neurons, such as type 2O Charcot-Marie-Tooth disease. We use two different models to simulate bidirectional transport in an axon: an anterograde-retrograde model, which neglects passive transport by diffusion in the cytosol, and a full slow transport model, which includes passive transport by diffusion in the cytosol. As dynein is a retrograde motor, dysfunction should not directly influence anterograde transport. However, our modeling results unexpectedly predict that slow axonal transport fails to transport cargos against their concentration gradient without dynein. The reason is the lack of a physical mechanism for the reverse information flow from the axon terminal, which is required so that the cargo concentration at the terminal could influence the cargo concentration distribution in the axon. Mathematically speaking, to achieve a prescribed concentration at the terminal, equations governing cargo transport must allow for the imposition of a boundary condition postulating the cargo concentration at the terminal. Perturbation analysis for the case when the retrograde motor velocity becomes close to zero predicts uniform cargo distributions along the axon. The obtained results explain why slow axonal transport must be bidirectional to allow for the maintenance of concentration gradients along the axon length. Our result is limited to small cargo diffusivity, which is a reasonable assumption for many slow axonal transport cargos (such as cytosolic and cytoskeletal proteins, neurofilaments, actin, and microtubules) which are transported as large multiprotein complexes or polymers.

Heat and mass transfer in free surface flows with solidification

Abstract: The objective of this paper is to discuss the theory of free surface flows with solidification. This type of open-channel flows is relevant to a number of important manufacturing processes, such as the horizontal continuous casting of carbon steel. Since carbon steel is a binary alloy, in formulating a mathematical model in addition to accounting for fluid flow and heat transfer, it is also necessary to account for the solute transport and for the two-phase region (the mushy zone) effects. Difficulties of the theory are discussed.

Flow and heat transfer in an almost circular microtube with rough walls

Abstract: Steady laminar flow of an incompressible fluid through a tube of almost circular cross-section is examined analytically, first for the case of a tube whose wall is wavy in the azimuthal direction, and then for one wavy in the axial direction. For the first case, a complete solution of the flow and forced convection heat transfer (for constant flux at the boundary) is possible for a wall of arbitrary cross-section. It is shown that, for a fixed axial pressure gradient, any departure from circularity leads to a reduction in volume flux and a reduction in heat transfer. For the second case no simple analytic solution is possible, but estimates of the increase in resistance due to a departure from circularity have been made.

Absorption rate governs cell transduction in dry macroporous scaffolds.

Abstract: Developing the next generation of cellular therapies will depend on fast, versatile, and efficient cellular reprogramming. Novel biomaterials will play a central role in this process by providing scaffolding and bioactive signals that shape cell fate and function. Previously, our lab reported that dry macroporous alginate scaffolds mediate retroviral transduction of primary T cells with efficiencies that rival the gold-standard clinical spinoculation procedures, which involve centrifugation on Retronectin-coated plates. This scaffold transduction required the scaffolds to be both macroporous and dry. Transduction by dry, macroporous scaffolds, termed "Drydux transduction," provides a fast and inexpensive method for transducing cells for cellular therapy, including for the production of CAR T cells. In this study, we investigate the mechanism of action by which Drydux transduction works through exploring the impact of pore size, stiffness, viral concentration, and absorption speed on transduction efficiency. We report that Drydux scaffolds with macropores ranging from 50-230 μm and with Young's moduli ranging from 25-620 kPa all effectively transduce primary T cells, suggesting that these parameters are not central to the mechanism of action, but also demonstrating that Drydux scaffolds can be tuned without losing functionality. Increasing viral concentrations led to significantly higher transduction efficiencies, demonstrating that increased cell-virus interaction is necessary for optimal transduction. Finally, we discovered that the rate with which the cell-virus solution is absorbed into the scaffold is closely correlated to viral transduction efficiency, with faster absorption producing significantly higher transduction. A computational model of liquid flow through porous media validates this finding by showing that increased fluid flow substantially increases collisions between virus particles and cells in a porous scaffold. Taken together, we conclude that the rate of liquid flow through the scaffolds, rather than pore size or stiffness, serves as a central regulator for efficient Drydux transduction.