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Register a new userDecomposing Noise in Biochemical Signalling Systems Highlights the Role of Protein Degradation
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The phenomena of stochasticity in biochemical processes have been intriguing life scientists for the past few decades. We now know that living cells take advantage of stochasticity in some cases and counteract stochastic effects in others. The source of intrinsic stochasticity in biomolecular systems are random timings of individual reactions, which cumulatively drive the variability in outputs of such systems. Despite the acknowledged relevance of stochasticity in the functioning of living cells no rigorous method have been proposed to precisely identify sources of variability. In this paper we propose a novel methodology that allows us to calculate contributions of individual reactions into the variability of a systems output. We demonstrate that some reactions have dramatically different effects on noise than others. Surprisingly, in the class of open conversion systems that serve as an approximate model of signal transduction, the degradation of an output contributes half of the total noise. We also demonstrate the importance of degradation in other relevant systems and propose a degradation feedback control mechanism that has the capability of an effective noise suppression. Application of our method to some well studied biochemical systems such as: gene expression, Michaelis-Menten enzyme kinetics, and the p53 system indicates that our methodology reveals an unprecedented insight into the origins of variability in biochemical systems. For many systems an analytical decomposition is not available; therefore the method has been implemented as a Matlab package and is available from the authors upon request.
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Stochasticity is an indispensable aspect of biochemical processes at the cellular level. Studies on how the noise enters and propagates in biochemical systems provided us with nontrivial insights into the origins of stochasticity, in total however they constitute a patchwork of different theoretical analyses. Here we present a flexible and generally applicable noise decomposition tool, that allows us to calculate contributions of individual reactions to the total variability of a systems output. With the package it is therefore possible to quantify how the noise enters and propagates in biochemical systems. We also demonstrate and exemplify using the JAK-STAT signalling pathway that it is possible to infer noise contributions resulting from individual reactions directly from experimental data. This is the first computational tool that allows to decompose noise into contributions resulting from individual reactions.
Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation techniques is now finding an important place in quantitative imaging of protein-protein interactions and intracellular physiology. We review here the recent developments in multiphoton FLIM methods and also present a description of a novel multiphoton FLIM system using a streak camera that was developed in our laboratory. We provide an example of a typical application of the system in which we measure the fluorescence resonance energy transfer between a donor/acceptor pair of fluorescent proteins within a cellular specimen.
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been extensive standardization efforts. For example, Tiwari et al. recently found that they could only repeat 50% of published simulation results in systems biology. Toward improving the reproducibility of computational systems research, we identified several resources that investigators can leverage to make their research more accessible, executable, and comprehensible by others. In particular, we identified several domain standards and curation services, as well as powerful approaches pioneered by the software engineering industry that we believe many investigators could adopt. Together, we believe these approaches could substantially enhance the reproducibility of systems biology research. In turn, we believe enhanced reproducibility would accelerate the development of more sophisticated models that could inform precision medicine and synthetic biology.
The ARF-AID (Auxin Response Factor-Auxin Inducible Degron) system is a re-engineered auxin-inducible protein degradation system. Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological system under study remains intact and functional until perturbation. This feature necessitates that the endogenous levels of the protein are maintained. However, endogenous tagging of genes with AID can result in chronic, auxin-independent proteasome-mediated degradation. The additional expression of the ARF-PB1 domain in the re-engineered ARF-AID system prevents chronic degradation of AID-tagged proteins while preserving rapid degradation of tagged proteins. Here we describe the protocol for engineering human cell lines to implement the ARF-AID system for specific and inducible protein degradation. These methods are adaptable and can be extended from cell lines to organisms.
The linear noise approximation is commonly used to obtain intrinsic noise statistics for biochemical networks. These estimates are accurate for networks with large numbers of molecules. However it is well known that many biochemical networks are characterized by at least one species with a small number of molecules. We here describe version 0.3 of the software intrinsic Noise Analyzer (iNA) which allows for accurate computation of noise statistics over wide ranges of molecule numbers. This is achieved by calculating the next order corrections to the linear noise approximations estimates of variance and covariance of concentration fluctuations. The efficiency of the methods is significantly improved by automated just-in-time compilation using the LLVM framework leading to a fluctuation analysis which typically outperforms that obtained by means of exact stochastic simulations. iNA is hence particularly well suited for the needs of the computational biology community.
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