TLRs Go Linear – On the Ubiquitin Edge

Toll-like receptors (TLRs) are crucial in protecting the host from pathogens. However, their exact role in disease remains incompletely understood. TLR signaling is tightly controlled because too little or too much TLR activation can result in immunodeficiency or autoinflammation, respectively. There is increasing evidence that linear ubiquitination, mediated by the linear ubiquitin chain assembly complex (LUBAC), plays a pivotal role in the regulation of TLR signaling. Recent advances have identified an intricate interaction between LUBAC and TLRs, with immunological consequences for infection and the development of autoinflammation in the host. We propose that defective linear ubiquitination contributes to TLR-mediated disease pathogenesis and that perturbed TLR signaling contributes to the phenotype observed in inherited LUBAC deficiency in humans and mice

Holding RIPK1 on the Ubiquitin Leash in TNFR1 Signaling

The kinase RIPK1 is an essential signaling node in various innate immune signaling pathways being most extensively studied in the TNFR1 signaling pathway. TNF signaling can result in different biological outcomes including gene activation and cell death induction in the form of apoptosis or necroptosis. RIPK1 is believed to be crucial for regulating the balance between these opposing outcomes. It is therefore not surprising that RIPK1 is highly regulated, most notably by phosphorylation, ubiquitination, and their respective reversals. In this review, we discuss the biological functions of RIPK1 within the context of TNFR1 signaling. Finally, we discuss recent advances in the knowledge on three ubiquitin E3 ligases that exert regulatory functions on RIPK1 signaling: cIAP1, cIAP2, and LUBAC

Telling time with an intrinsically noisy clock

Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: the finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we provide a method for solving for the complete probabilistic description of intrinsically noisy oscillatory driving. We derive and numerically verify a number of simple scaling laws. Unlike in the case of measuring a static quantity, response to an oscillatory driving can exhibit a resonant frequency which maximizes information transmission. Further, we show that the optimal regulatory design is dependent on the biophysical constraints (i.e., the allowed copy number and response time). The resulting phase diagram illustrates under what conditions threshold regulation outperforms linear regulation.Comment: 10 pages, 5 figure

Electron transport through multilevel quantum dot

Quantum transport properties through some multilevel quantum dots sandwiched between two metallic contacts are investigated by the use of Green's function technique. Here we do parametric calculations, based on the tight-binding model, to study the transport properties through such bridge systems. The electron transport properties are significantly influenced by (a) number of quantized energy levels in the dots, (b) dot-to-electrode coupling strength, (c) location of the equilibrium Fermi energy $E_F$ and (d) surface disorder. In the limit of weak-coupling, the conductance ($g$) shows sharp resonant peaks associated with the quantized energy levels in the dots, while, they get substantial broadening in the strong-coupling limit. The behavior of the electron transfer through these systems becomes much more clearly visible from our study of current-voltage ($I$-$V$) characteristics. In this context we also describe the noise power of current fluctuations ($S$) and determine the Fano factor ($F$) which provides an important information about the electron correlation among the charge carriers. Finally, we explore a novel transport phenomenon by studying the surface disorder effect in which the current amplitude increases with the increase of the surface disorder strength in the strong disorder regime, while, the amplitude decreases in the limit of weak disorder. Such an anomalous behavior is completely opposite to that of bulk disordered system where the current amplitude always decreases with the disorder strength. It is also observed that the current amplitude strongly depends on the system size which reveals the finite quantum size effect.Comment: 12 pages, 7 figure

Spectral solutions to stochastic models of gene expression with bursts and regulation

Signal-processing molecules inside cells are often present at low copy number, which necessitates probabilistic models to account for intrinsic noise. Probability distributions have traditionally been found using simulation-based approaches which then require estimating the distributions from many samples. Here we present in detail an alternative method for directly calculating a probability distribution by expanding in the natural eigenfunctions of the governing equation, which is linear. We apply the resulting spectral method to three general models of stochastic gene expression: a single gene with multiple expression states (often used as a model of bursting in the limit of two states), a gene regulatory cascade, and a combined model of bursting and regulation. In all cases we find either analytic results or numerical prescriptions that greatly outperform simulations in efficiency and accuracy. In the last case, we show that bimodal response in the limit of slow switching is not only possible but optimal in terms of information transmission

NEMO regulates a cell death switch in TNF signaling by inhibiting recruitment of RIPK3 to the cell death-inducing complex II

Incontinentia Pigmenti (IP) is a rare X-linked disease characterized by early male lethality and multiple abnormalities in heterozygous females. IP is caused by NF-κB essential modulator (NEMO) mutations. The current mechanistic model suggests that NEMO functions as a crucial component mediating the recruitment of the IκB-kinase (IKK) complex to tumor necrosis factor receptor 1 (TNF-R1), thus allowing activation of the pro-survival NF-κB response. However, recent studies have suggested that gene activation and cell death inhibition are two independent activities of NEMO. Here we describe that cells expressing the IP-associated NEMO-A323P mutant had completely abrogated TNF-induced NF-κB activation, but retained partial antiapoptotic activity and exhibited high sensitivity to death by necroptosis. We found that robust caspase activation in NEMO-deficient cells is concomitant with RIPK3 recruitment to the apoptosis-mediating complex. In contrast, cells expressing the ubiquitin-binding mutant NEMO-A323P did not recruit RIPK3 to complex II, an event that prevented caspase activation. Hence NEMO, independently from NF-κB activation, represents per se a key component in the structural and functional dynamics of the different TNF-R1-induced complexes. Alteration of this process may result in differing cellular outcomes and, consequently, also pathological effects in IP patients with different NEMO mutations

Time-dependent information transmission in a model regulatory circuit

Many biological regulatory systems respond with a physiological delay when processing signals. A simple model of regulation which respects these features shows how the ability of a delayed output to transmit information is limited: at short times by the time scale of the dynamic input, at long times by that of the dynamic output. We find that topologies of maximally informative networks correspond to commonly occurring biological circuits linked to stress response and that circuits functioning out of steady state may exploit absorbing states to transmit information optimally

Reconstructing nonlinear plasma wakefields using a generalized temporally encoded spectral shifting analysis

We generalize the temporally encoded spectral shifting (TESS) analysis for measuring plasma wakefields using spectral interferometry to dissimilar probe pulses of arbitrary spectral profile and to measuring nonlinear wakefields. We demonstrate that the Gaussian approximation used up until now results in a substantial miscalculation of the wakefield amplitude, by a factor of up to two. A method to accurately measure higher amplitude quasilinear and nonlinear wakefields is suggested, using an extension to the TESS procedure, and we place some limits on its accuracy in these regimes. These extensions and improvements to the analysis demonstrate its potential for rapid and accurate on-shot diagnosis of plasma wakefields, even at low plasma densities