Framework estimation of stochastic gene activation using transcription average level

Gene activation is usually a non-Markovian process that has been modeled as various frameworks that consist of multiple rate-limiting steps. Understanding the exact activation framework for a gene of interest is a central problem for single-cell studies. In this paper, we focus on the dynamical data of the average transcription level M(t), which is typically neglected when deciphering gene activation. Firstly, the smooth trend lines of M(t) data present rich, visually dynamic features. Secondly, tractable analysis of M(t) allows the establishment of bijections between M(t) dynamics and system parameter regions. Because of these two clear advantages, we can rule out frameworks that fail to capture M(t) features and we can further test potential competent frameworks by fitting M(t) data. We implemented this procedure to determine an exact activation framework for a large number of mouse fibroblast genes under tumor necrosis factor induction; the cross-talk between the signaling and basal pathways is crucial to trigger the first peak of M(t), while the following damped gentle M(t) oscillation is regulated by the multi-step basal pathway. Moreover, the fitted parameters for the mouse genes tested revealed two distinct regulation scenarios for transcription dynamics. Taken together, we were able to develop an efficient procedure for using traditional M(t) data to estimate the gene activation frameworks and system parameters. This procedure, together with sophisticated single-cell transcription data, may facilitate a more accurate understanding of stochastic gene activation.

Optimal Tumor Necrosis Factor Induction by Plasmodium falciparum Requires the Highly Localized Release of Parasite Products

ABSTRACT Overproduction of tumor necrosis factor (TNF) has been linked with the pathogenesis of Plasmodium falciparum malaria. Here, we examined why the high levels of TNF-inducing activity associated with P. falciparum-parasitized erythrocytes (PE) appear to be lost after cell lysis. Static coculture of PE and peripheral blood mononuclear cells (PBMC), with or without separation by porous membranes, demonstrated that rupture of live PE in the presence of responder cells was required for optimal TNF induction. Although the insoluble fraction of lysed PE was found to partially inhibit TNF responses, supernatants prepared from large numbers of lysed PE still contained only low levels of TNF-inducing activity, which showed no evidence of instability. A dramatic reduction in TNF levels resulted when noncytoadherent PE lines were maintained under low-cell-proximity conditions by suspension coculture. This reduction was much less marked with PE capable of adhering to PBMC, despite the fact that cytoadherent and noncytoadherent parasite lines induced comparable levels of TNF in high-cell-proximity, static coculture. These results suggest that rupture of PE in a highly localized setting, facilitated by either static coculture or the more biologically relevant phenomenon of cytoadherence to PBMC, can result in considerable enhancement of the P. falciparum-induced TNF response.

Akt-Dependent Phosphorylation Specifically Regulates Cot Induction of NF-κB-Dependent Transcription

ABSTRACT The Akt (or protein kinase B) and Cot (or Tpl-2) serine/threonine kinases are associated with cellular transformation. These kinases have also been implicated in the induction of NF-κB-dependent transcription. As a member of the mitogen-activated protein kinase kinase kinase (MAP3K) family, Cot can also activate MAP kinase signaling pathways that target AP-1 and NFAT family transcription factors. Here we show that Akt and Cot physically associate and functionally cooperate. Akt appears to function upstream of Cot, as Akt can enhance Cot induction of NF-κB-dependent transcription, and dominant-negative Cot blocks the activation of this element by Akt. Furthermore, deletion analysis shows that binding to Akt is critical for Cot function. The regulation of NF-κB-dependent transcription by Cot requires Akt-dependent phosphorylation of serine 400 (S400), near the carboxy terminus of Cot. However, phosphorylation at this site is not required for Cot kinase activity or AP-1 induction, suggesting it specifically regulates Cot effector function at the level of the NF-κB pathway. Mutation of S400 in Cot does indeed abolish its ability to activate IκB-kinase (IKK) complexes, but paradoxically it allows for increased Cot association with the IKK complex. This mutated form of Cot also acts as a dominant negative for T-cell antigen receptor/CD28- or Akt/phorbol myristate acetate-induced NF-κB induction, while having relatively little effect on tumor necrosis factor induction of NF-κB. These findings suggest that the activation of different signaling pathways by MAP3Ks may be regulated separately and may provide evidence for how such discrimination by one member of this kinase family occurs.