753 research outputs found
Crosstalk and the Dynamical Modularity of Feed-Forward Loops in Transcriptional Regulatory Networks
Network motifs, such as the feed-forward loop (FFL), introduce a range of complex behaviors to transcriptional regulatory networks, yet such properties are typically determined from their isolated study. We characterize the effects of crosstalk on FFL dynamics by modeling the cross regulation between two different FFLs and evaluate the extent to which these patterns occur in vivo. Analytical modeling suggests that crosstalk should overwhelmingly affect individual protein-expression dynamics. Counter to this expectation we find that entire FFLs are more likely than expected to resist the effects of crosstalk (approximate to 20% for one crosstalk interaction) and remain dynamically modular. The likelihood that cross-linked FFLs are dynamically correlated increases monotonically with additional crosstalk, but is independent of the specific regulation type or connectivity of the interactions. Just one additional regulatory interaction is sufficient to drive the FFL dynamics to a statistically different state. Despite the potential for modularity between sparsely connected network motifs, Escherichia coli (E. coli) appears to favor crosstalk wherein at least one of the cross-linked FFLs remains modular. A gene ontology analysis reveals that stress response processes are significantly overrepresented in the cross-linked motifs found within E. coli. Although the daunting complexity of biological networks affects the dynamical properties of individual network motifs, some resist and remain modular, seemingly insulated from extrinsic perturbations-an intriguing possibility for nature to consistently and reliably provide certain network functionalities wherever the need arise
Elucidation of molecular kinetic schemes from macroscopic traces using system identification
Overall cellular responses to biologically-relevant stimuli are mediated by networks of simpler lower-level processes. Although information about some of these processes can now be obtained by visualizing and recording events at the molecular level, this is still possible only in especially favorable cases. Therefore the development of methods to extract the dynamics and relationships between the different lower-level (microscopic) processes from the overall (macroscopic) response remains a crucial challenge in the understanding of many aspects of physiology. Here we have devised a hybrid computational-analytical method to accomplish this task, the SYStems-based MOLecular kinetic scheme Extractor (SYSMOLE). SYSMOLE utilizes system-identification input-output analysis to obtain a transfer function between the stimulus and the overall cellular response in the Laplace-transformed domain. It then derives a Markov-chain state molecular kinetic scheme uniquely associated with the transfer function by means of a classification procedure and an analytical step that imposes general biological constraints. We first tested SYSMOLE with synthetic data and evaluated its performance in terms of its rate of convergence to the correct molecular kinetic scheme and its robustness to noise. We then examined its performance on real experimental traces by analyzing macroscopic calcium-current traces elicited by membrane depolarization. SYSMOLE derived the correct, previously known molecular kinetic scheme describing the activation and inactivation of the underlying calcium channels and correctly identified the accepted mechanism of action of nifedipine, a calcium-channel blocker clinically used in patients with cardiovascular disease. Finally, we applied SYSMOLE to study the pharmacology of a new class of glutamate antipsychotic drugs and their crosstalk mechanism through a heteromeric complex of G protein-coupled receptors. Our results indicate that our methodology can be successfully applied to accurately derive molecular kinetic schemes from experimental macroscopic traces, and we anticipate that it may be useful in the study of a wide variety of biological systems
Modelling and analysis of biochemical signalling pathway cross-talk
Signalling pathways are abstractions that help life scientists structure the coordination of cellular activity. Cross-talk between pathways accounts for many of the complex behaviours exhibited by signalling pathways and is often critical in producing the correct signal-response relationship. Formal models of signalling pathways and cross-talk in particular can aid understanding and drive experimentation. We define an approach to modelling based on the concept that a pathway is the (synchronising) parallel composition of instances of generic modules (with internal and external labels). Pathways are then composed by (synchronising) parallel composition and renaming; different types of cross-talk result from different combinations of synchronisation and renaming. We define a number of generic modules in PRISM and five types of cross-talk: signal flow, substrate availability, receptor function, gene expression and intracellular communication. We show that Continuous Stochastic Logic properties can both detect and distinguish the types of cross-talk. The approach is illustrated with small examples and an analysis of the cross-talk between the TGF-b/BMP, WNT and MAPK pathways
Secrecy Sum-Rates for Multi-User MIMO Regularized Channel Inversion Precoding
In this paper, we propose a linear precoder for the downlink of a multi-user
MIMO system with multiple users that potentially act as eavesdroppers. The
proposed precoder is based on regularized channel inversion (RCI) with a
regularization parameter and power allocation vector chosen in such a
way that the achievable secrecy sum-rate is maximized. We consider the
worst-case scenario for the multi-user MIMO system, where the transmitter
assumes users cooperate to eavesdrop on other users. We derive the achievable
secrecy sum-rate and obtain the closed-form expression for the optimal
regularization parameter of the precoder using
large-system analysis. We show that the RCI precoder with
outperforms several other linear precoding schemes, and
it achieves a secrecy sum-rate that has same scaling factor as the sum-rate
achieved by the optimum RCI precoder without secrecy requirements. We propose a
power allocation algorithm to maximize the secrecy sum-rate for fixed .
We then extend our algorithm to maximize the secrecy sum-rate by jointly
optimizing and the power allocation vector. The jointly optimized
precoder outperforms RCI with and equal power allocation
by up to 20 percent at practical values of the signal-to-noise ratio and for 4
users and 4 transmit antennas.Comment: IEEE Transactions on Communications, accepted for publicatio
Modular modelling of signalling pathways and their crosstalk
Signalling pathways are well-known abstractions that explain the mechanisms whereby cells respond to signals. Collections of pathways form networks, and interactions between pathways in a network, known as cross-talk, enables further complex signalling behaviours. While there are several formal modelling approaches for signalling pathways, none make cross-talk explicit; the aim of this paper is to define and categorise cross-talk in a rigorous way. We define a modular approach to pathway and network modelling, based on the module construct in the PRISM modelling language, and a set of generic signalling modules. Five different types of cross-talk are defined according to various biologically meaningful combinations of variable sharing, synchronisation labels and reaction renaming. The approach is illustrated with a case-study analysis of cross-talk between the TGF-β, WNT and MAPK pathways
Diffusive MIMO Molecular Communications: Channel Estimation, Equalization and Detection
In diffusion-based communication, as for molecular systems, the achievable
data rate is low due to the stochastic nature of diffusion which exhibits a
severe inter-symbol-interference (ISI). Multiple-Input Multiple-Output (MIMO)
multiplexing improves the data rate at the expense of an inter-link
interference (ILI). This paper investigates training-based channel estimation
schemes for diffusive MIMO (D-MIMO) systems and corresponding equalization
methods. Maximum likelihood and least-squares estimators of mean channel are
derived, and the training sequence is designed to minimize the mean square
error (MSE). Numerical validations in terms of MSE are compared with Cramer-Rao
bound derived herein. Equalization is based on decision feedback equalizer
(DFE) structure as this is effective in mitigating diffusive ISI/ILI.
Zero-forcing, minimum MSE and least-squares criteria have been paired to DFE,
and their performances are evaluated in terms of bit error probability. Since
D-MIMO systems are severely affected by the ILI because of short transmitters
inter-distance, D-MIMO time interleaving is exploited as countermeasure to
mitigate the ILI with remarkable performance improvements. The feasibility of a
block-type communication including training and data equalization is explored
for D-MIMO, and system-level performances are numerically derived.Comment: Accepted paper at IEEE transaction on Communicatio
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