196,734 research outputs found
PID Control of Biochemical Reaction Networks
Principles of feedback control have been shown to naturally arise in
biological systems and successfully applied to build synthetic circuits. In
this work we consider Biochemical Reaction Networks (CRNs) as a paradigm for
modelling biochemical systems and provide the first implementation of a
derivative component in CRNs. That is, given an input signal represented by the
concentration level of some species, we build a CRN that produces as output the
concentration of two species whose difference is the derivative of the input
signal. By relying on this component, we present a CRN implementation of a
feedback control loop with Proportional-Integral-Derivative (PID) controller
and apply the resulting control architecture to regulate the protein expression
in a microRNA regulated gene expression model.Comment: 8 Pages, 4 figures, Submitted to CDC 201
When kinases meet mathematics: the systems biology of MAPK signalling
The mitogen activated protein kinase/extracellular signal regulated kinase pathway regulates fundamental cellular function such as cell proliferation, survival, differentiation and motility, raising the question how these diverse functions are specified and coordinated. They are encoded through the activation kinetics of the pathway, a multitude of feedback loops, scaffold proteins, subcellular compartmentalisation, and crosstalk with other pathways. These regulatory motifs alone or in combination can generate a multitude of complex behaviour. Systems biology tries to decode this complexity through mathematical modelling and prediction in order to gain a deeper insight into the inner works of signalling networks
The Computer System Architecture of our first real-time real-world experiment of adaptive traffic signals with "connected" vehicles
Abstract Connected vehicles can transmit real-time information to traffic control management systems. Despite the recent technical advances of telecommunication networks and mobile computing there have been no real-time adaptive traffic signal control experiments with connected vehicles. Most of the research in this field has been carried out only with simulations. In this work we present the computer system that was adopted to regulate traffic signals in real-time with "smartphone-connected" vehicles as the only source of information. We introduce the description of the computer system architecture that was deployed in an experiment of a Floating Car Data (FCD)-based adaptive traffic signal in which a traffic signal has been regulated in real-time with 100% "smartphone-connected" vehicles. The description of the system based on commonly-used technologies could help others to develop and deploy new traffic signal management systems in new "connected" intersections
Toward a systems-level view of dynamic phosphorylation networks
To better understand how cells sense and respond to their environment, it is important to understand the organization and regulation of the phosphorylation networks that underlie most cellular signal transduction pathways. These networks, which are composed of protein kinases, protein phosphatases and their respective cellular targets, are highly dynamic. Importantly, to achieve signaling specificity, phosphorylation networks must be regulated at several levels, including at the level of protein expression, substrate recognition, and spatiotemporal modulation of enzymatic activity. Here, we briefly summarize some of the traditional methods used to study the phosphorylation status of cellular proteins before focusing our attention on several recent technological advances, such as protein microarrays, quantitative mass spectrometry, and genetically-targetable fluorescent biosensors, that are offering new insights into the organization and regulation of cellular phosphorylation networks. Together, these approaches promise to lead to a systems-level view of dynamic phosphorylation networks
Examining effects of the DNA regulator Lrp on quorum sensing gene expression in Pseudomonas aeruginosa
Pseudomonas aeruginosa is an opportunistic human pathogen that has the capacity to express multiple virulence factors that are regulated through an extensive quorum sensing network. Three major quorum sensing systems have been identified in Pseudomonas species: the acyl homoserine lactones of las and rhl, and the Pseudomonas Quinolone Signal (PQS). We seek to investigate the involvement of a global regulator, Lrp with the expression of these three networks. Specifically, we will compare expression levels of las, rhl, and pqs in wild type P. aeruginosa (MPAO1) with an lrp transposon insertion mutant using quantitative PCR. Through this comparative qPCR analysis, we hope to support the identification of novel roles of the Lrp DNA regulator involvement in cross-talk with the quorum sensing pathways that has not been previously recognized. Due to the virulence of Pseudomonas aeruginosa, if Lrp can be identified as a factor in the regulation of the quorum sensing networks, it could potentially be used as a therapeutic target in the disruption of the production of many virulence factors such biofilms, siderophores, toxins and motility which are all regulated by the quorum sensing networks
A Systemic Receptor Network Triggered by Human cytomegalovirus Entry
Virus entry is a multistep process that triggers a variety of cellular
pathways interconnecting into a complex network, yet the molecular complexity
of this network remains largely unsolved. Here, by employing systems biology
approach, we reveal a systemic virus-entry network initiated by human
cytomegalovirus (HCMV), a widespread opportunistic pathogen. This network
contains all known interactions and functional modules (i.e. groups of
proteins) coordinately responding to HCMV entry. The number of both genes and
functional modules activated in this network dramatically declines shortly,
within 25 min post-infection. While modules annotated as receptor system, ion
transport, and immune response are continuously activated during the entire
process of HCMV entry, those for cell adhesion and skeletal movement are
specifically activated during viral early attachment, and those for immune
response during virus entry. HCMV entry requires a complex receptor network
involving different cellular components, comprising not only cell surface
receptors, but also pathway components in signal transduction, skeletal
development, immune response, endocytosis, ion transport, macromolecule
metabolism and chromatin remodeling. Interestingly, genes that function in
chromatin remodeling are the most abundant in this receptor system, suggesting
that global modulation of transcriptions is one of the most important events in
HCMV entry. Results of in silico knock out further reveal that this entire
receptor network is primarily controlled by multiple elements, such as EGFR
(Epidermal Growth Factor) and SLC10A1 (sodium/bile acid cotransporter family,
member 1). Thus, our results demonstrate that a complex systemic network, in
which components coordinating efficiently in time and space contributes to
virus entry.Comment: 26 page
A quantitative comparison of sRNA-based and protein-based gene regulation
Small, non-coding RNAs (sRNAs) play important roles as genetic regulators in
prokaryotes. sRNAs act post-transcriptionally via complementary pairing with
target mRNAs to regulate protein expression. We use a quantitative approach to
compare and contrast sRNAs with conventional transcription factors (TFs) to
better understand the advantages of each form of regulation. In particular, we
calculate the steady-state behavior, noise properties, frequency-dependent gain
(amplification), and dynamical response to large input signals of both forms of
regulation. While the mean steady-state behavior of sRNA-regulated proteins
exhibits a distinctive tunable threshold-linear behavior, our analysis shows
that transcriptional bursting leads to significantly higher intrinsic noise in
sRNA-based regulation than in TF-based regulation in a large range of
expression levels and limits the ability of sRNAs to perform quantitative
signaling. Nonetheless, we find that sRNAs are better than TFs at filtering
noise in input signals. Additionally, we find that sRNAs allow cells to respond
rapidly to large changes in input signals. These features suggest a niche for
sRNAs in allowing cells to transition quickly yet reliably between distinct
states. This functional niche is consistent with the widespread appearance of
sRNAs in stress-response and quasi-developmental networks in prokaryotes.Comment: 26 pages, 8 figures; accepted for publication in Molecular Systems
Biolog
Intelligent control of agricultural irrigation system based on wireless sensor and actuator networks
Optimizing water usage is the primary objective of intelligent and eco-friendly agricultural irrigation systems. In irrigation systems, the flow and pressure of water is usually regulated by controlling the position of the valve. The proportioning electronic actuator accepts a signal from the control system and moves the valve to allow the valve to partially open or close. Varying speed of pump motor can also control the usage of water. The integration of wireless sensor and actuator networks (WSANs) into irrigation management promises to overcome the excessive watering problem while providing additional functionality. This paper presents a case study on the use of WSAN for irrigation activities and investigates the application of fuzzy logic based valve aperture control. The results show that the proposed strategy can be effective in water flow control
Hybrid Millimeter-Wave Systems: A Novel Paradigm for HetNets
Heterogeneous Networks (HetNets) are known to enhance the bandwidth
efficiency and throughput of wireless networks by more effectively utilizing
the network resources. However, the higher density of users and access points
in HetNets introduces significant inter-user interference that needs to be
mitigated through complex and sophisticated interference cancellation schemes.
Moreover, due to significant channel attenuation and presence of hardware
impairments, e.g., phase noise and amplifier nonlinearities, the vast bandwidth
in the millimeter-wave band has not been fully utilized to date. In order to
enable the development of multi-Gigabit per second wireless networks, we
introduce a novel millimeter-wave HetNet paradigm, termed hybrid HetNet, which
exploits the vast bandwidth and propagation characteristics in the 60 GHz and
70-80 GHz bands to reduce the impact of interference in HetNets. Simulation
results are presented to illustrate the performance advantage of hybrid HetNets
with respect to traditional networks. Next, two specific transceiver structures
that enable hand-offs from the 60 GHz band, i.e., the V-band to the 70-80 GHz
band, i.e., the E-band, and vice versa are proposed. Finally, the practical and
regulatory challenges for establishing a hybrid HetNet are outlined.Comment: 12 pages, 5 Figures, IEEE Communication Magazine. In pres
Noise Management by Molecular Networks
Fluctuations in the copy number of key regulatory macromolecules (“noise”) may cause physiological heterogeneity in populations of (isogenic) cells. The kinetics of processes and their wiring in molecular networks can modulate this molecular noise. Here we present a theoretical framework to study the principles of noise management by the molecular networks in living cells. The theory makes use of the natural, hierarchical organization of those networks and makes their noise management more understandable in terms of network structure. Principles governing noise management by ultrasensitive systems, signaling cascades, gene networks and feedback circuitry are discovered using this approach. For a few frequently occurring network motifs we show how they manage noise. We derive simple and intuitive equations for noise in molecule copy numbers as a determinant of physiological heterogeneity. We show how noise levels and signal sensitivity can be set independently in molecular networks, but often changes in signal sensitivity affect noise propagation. Using theory and simulations, we show that negative feedback can both enhance and reduce noise. We identify a trade-off; noise reduction in one molecular intermediate by negative feedback is at the expense of increased noise in the levels of other molecules along the feedback loop. The reactants of the processes that are strongly (cooperatively) regulated, so as to allow for negative feedback with a high strength, will display enhanced noise
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