Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery

On time-discretized versions of the stochastic SIS epidemic model: a comparative analysis

In this paper, the interest is in the use of time-discretized models as approximations to the continuous-time birth-death (BD) process [Formula: see text] describing the number I(t) of infective hosts at time t in the stochastic [Formula: see text] (SIS) epidemic model under the assumption of an additional source of infection from the environment. We illustrate some simple techniques for analyzing discrete-time versions of the continuous-time BD process [Formula: see text], and we show the similarities and differences between the discrete-time BD process [Formula: see text] of Allen and Burgin (Math Biosci 163:1-33, 2000), which is inspired from the infinitesimal transition probabilities of [Formula: see text], and an alternative discrete-time Markov chain [Formula: see text], which is defined in terms of the number [Formula: see text] of infective hosts at a sequence [Formula: see text] of inspection times. Processes [Formula: see text] and [Formula: see text] can be thought of as a uniformized version and the discrete skeleton of process [Formula: see text], respectively, and are commonly used to derive, in the more general setting of Markov chains, theorems about a continuous-time Markov chain by applying known theorems for discrete-time Markov chains. We shall demonstrate here that the continuous-time BD process [Formula: see text] and its discrete-time counterparts [Formula: see text] and [Formula: see text] behave asymptotically the same in the limit of large time index, while the processes [Formula: see text] and [Formula: see text] differ from the continuous-time BD process [Formula: see text] in terms of the random length of an outbreak, or when considering their dynamics during a predetermined time interval [Formula: see text]. To compare the dynamics of process [Formula: see text] with those of the discrete-time processes [Formula: see text] and [Formula: see text] during [Formula: see text], we consider extreme values (i.e., maximum and minimum number of infectives simultaneously observed during [Formula: see text]) in these three processes. Finally, we illustrate our analytical results by means of a number of numerical examples, where we use the Hellinger distance between two probability distributions to quantify the similarity between the resulting extreme value distributions of either [Formula: see text] and [Formula: see text], or [Formula: see text] and [Formula: see text].

Fate of a Naive T Cell: A Stochastic Journey

The homeostasis of T cell populations depends on migration, division and death of individual cells (1). T cells migrate between spatial compartments (spleen, lymph nodes, lung, liver, etc.), where they may divide or differentiate, and eventually die (2). The kinetics of recirculation influences the speed at which local infections are detected and controlled (3). New experimental techniques have been developed to measure the lifespan of cells, and their migration dynamics; for example, fluorescence-activated cell sorting (4), in vitro time-lapse microscopy (5), or in vivo stable isotope labeling (e.g., deuterium) (6). When combined with mathematical and computational models, they allow estimation of rates of migration, division, differentiation and death (6, 7). In this work, we develop a stochastic model of a single cell migrating between spatial compartments, dividing and eventually dying. We calculate the number of division events during a T cell's journey, its lifespan, the probability of dying in each compartment and the number of progeny cells. A fast-migration approximation allows us to compute these quantities when migration rates are larger than division and death rates. Making use of published rates: (i) we analyse how perturbations in a given spatial compartment impact the dynamics of a T cell, (ii) we study the accuracy of the fast-migration approximation, and (iii) we quantify the role played by direct migration (not via the blood) between some compartments.

Quantifying the phosphorylation timescales of receptor-ligand complexes: a Markovian matrix-analytic approach

Cells interact with the extracellular environment by means of receptor molecules on their surface. Receptors can bind different ligands, leading to the formation of receptor-ligand complexes. For a subset of receptors, called receptor tyrosine kinases, binding to ligand enables sequential phosphorylation of intra-cellular residues, which initiates a signalling cascade that regulates cellular function and fate. Most mathematical modelling approaches employed to analyse receptor signalling are deterministic, especially when studying scenarios of high ligand concentration or large receptor numbers. There exist, however, biological scenarios where low copy numbers of ligands and/or receptors need to be considered, or where signalling by a few bound receptor-ligand complexes is enough to initiate a cellular response. Under these conditions stochastic approaches are appropriate, and in fact, different attempts have been made in the literature to measure the timescales of receptor signalling initiation in receptor-ligand systems. However, these approaches have made use of numerical simulations or approximations, such as moment-closure techniques. In this paper, we study, from an analytical perspective, the stochastic times to reach a given signalling threshold for two receptor-ligand models. We identify this time as an extinction time for a conveniently defined auxiliary absorbing continuous time Markov process, since receptor-ligand association/dissociation events can be analysed in terms of quasi-birth-and-death processes. We implement algorithmic techniques to compute the different order moments of this time, as well as the steady-state probability distribution of the system. A novel feature of the approach introduced here is that it allows one to quantify the role played by each kinetic rate in the timescales of signal initiation, and in the steady-state probability distribution of the system. Finally, we illustrate our approach by carrying out numerical studies for the vascular endothelial growth factor and one of its receptors, the vascular endothelial growth factor receptor of human endothelial cells.