Direct reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) can be achieved by overexpression of Oct4, Sox2, Klf4 and c-Myc transcription factors, but only a minority of donor somatic cells can be reprogrammed to pluripotency. Here we demonstrate that reprogramming is a continuous stochastic process where almost all donor cells eventually give rise to iPSCs upon continued growth and transcription factor expression. Additional inhibition the p53/p21 pathway or overexpression of Lin28 increased the cell division rate and resulted in an accelerated kinetics of iPSC formation that was directly proportional to the increase in cell proliferation. In contrast, Nanog overexpression accelerated reprogramming in a predominantly cell division rate independent manner. Quantitative analyses define distinct cell division rate dependent and independent modes for accelerating the stochastic course of reprogramming, and suggest that the number of cell divisions is a key parameter driving epigenetic reprogramming to pluripotency.

Although major progress has been made in uncovering the machinery underlying individual biological clocks, much less is known about how multiple clocks coordinate their oscillations. We present a general framework that describes coupled cyclic processes in single cells and apply this to the interaction between the circadian and cell-division cycles in the cyanobacterium Synechococcus elongatus. We simultaneously track cell-division events and circadian phases of individual cells and use this information to determine when cell-cycle progression is slowed down as a function of circadian and cell-cycle phases. We infer that cell-cycle progression in cyanobacteria slows down during a specific circadian interval, but is uniform across cell-cycle phase. Our framework is applicable to the quantification of the coupling between any biological oscillators in other organisms.

Coping with variations in network dosage is crucial for maintaining optimal function in gene networks. Here we explore how network architecture facilitates network-level dosage compensation. Using the yeast galactose network as a model, we combinatorially deleted one of the two copies of its four regulatory genes and found that network activity was robust to the change in network dosage. A mathematical analysis revealed that a 2-component genetic circuit with elements of opposite regulatory sign (activator and inhibitor) constitutes a minimal requirement for network-dosage invariance. Specific interaction topologies and a 1-to−1 interaction stoichiometry between the activating and inhibiting agents were additional essential elements facilitating dosage invariance. This mechanism of network-dosage invariance could represent a general design for gene network architecture in cells.

Puffs are localized Ca(2+) signals that arise in oocytes in response to inositol 1,4,5-trisphosphate (IP(3)). They are analogous to the sparks of myocytes and are believed to be the result of the liberation of Ca(2+) from the endoplasmic reticulum through the coordinated opening of IP(3) receptor/channels clustered at a functional release site. In this article, we analyze sequences of puffs that occur at the same site to help elucidate the mechanisms underlying puff dynamics. In particular, we show a dependence of the interpuff time on the amplitude of the preceding puff, and of the amplitude of the following puff on the preceding interval. These relationships can be accounted for by an inhibitory role of the Ca(2+) that is liberated during puffs. We construct a stochastic model for a cluster of IP(3) receptor/channels that quantitatively replicates the observed behavior, and we determine that the characteristic time for a channel to escape from the inhibitory state is of the order of seconds.