4,029 research outputs found
Collective oscillation period of inter-coupled biological negative cyclic feedback oscillators
A number of biological rhythms originate from networks comprised of multiple
cellular oscillators. But analytical results are still lacking on the
collective oscillation period of inter-coupled gene regulatory oscillators,
which, as has been reported, may be different from that of an autonomous
oscillator. Based on cyclic feedback oscillators, we analyze the collective
oscillation pattern of coupled cellular oscillators. First we give a condition
under which the oscillator network exhibits oscillatory and synchronized
behavior. Then we estimate the collective oscillation period based on a novel
multivariable harmonic balance technique. Analytical results are derived in
terms of biochemical parameters, thus giving insight into the basic mechanism
of biological oscillation and providing guidance in synthetic biology design.Comment: arXiv admin note: substantial text overlap with arXiv:1203.125
Oscillation patterns in negative feedback loops
Organisms are equipped with regulatory systems that display a variety of
dynamical behaviours ranging from simple stable steady states, to switching and
multistability, to oscillations. Earlier work has shown that oscillations in
protein concentrations or gene expression levels are related to the presence of
at least one negative feedback loop in the regulatory network. Here we study
the dynamics of a very general class of negative feedback loops. Our main
result is that in these systems the sequence of maxima and minima of the
concentrations is uniquely determined by the topology of the loop and the
activating/repressing nature of the interaction between pairs of variables.
This allows us to devise an algorithm to reconstruct the topology of
oscillating negative feedback loops from their time series; this method applies
even when some variables are missing from the data set, or if the time series
shows transients, like damped oscillations. We illustrate the relevance and the
limits of validity of our method with three examples: p53-Mdm2 oscillations,
circadian gene expression in cyanobacteria, and cyclic binding of cofactors at
the estrogen-sensitive pS2 promoter.Comment: 10 pages, 8 figure
Oscillations and temporal signalling in cells
The development of new techniques to quantitatively measure gene expression
in cells has shed light on a number of systems that display oscillations in
protein concentration. Here we review the different mechanisms which can
produce oscillations in gene expression or protein concentration, using a
framework of simple mathematical models. We focus on three eukaryotic genetic
regulatory networks which show "ultradian" oscillations, with time period of
the order of hours, and involve, respectively, proteins important for
development (Hes1), apoptosis (p53) and immune response (NFkB). We argue that
underlying all three is a common design consisting of a negative feedback loop
with time delay which is responsible for the oscillatory behaviour
Rapid cell-free forward engineering of novel genetic ring oscillators
While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free systems are appealing alternative environments, but it remains questionable whether biological networks behave similarly in cell-free systems and in cells. We characterized in a cell-free system the 'repressilator,' a three-node synthetic oscillator. We then engineered novel three, four, and five-gene ring architectures, from characterization of circuit components to rapid analysis of complete networks. When implemented in cells, our novel 3-node networks produced population-wide oscillations and 95% of 5-node oscillator cells oscillated for up to 72 hours. Oscillation periods in cells matched the cell-free system results for all networks tested. An alternate forward engineering paradigm using cell-free systems can thus accurately capture cellular behavior
Evolutionarily stable and fragile modules of yeast biochemical network
Gene and protein interaction networks have evolved to precisely
specify cell fates and functions. Here, we analyse
whether the architecture of these networks affects evolvability.
We find evidence to suggest that in yeast these networks are
mainly acyclic, and that evolutionary changes in these parts do
not affect their global dynamic properties. In contrast, feedback
loops strongly influence dynamic behaviour and are often
evolutionarily conserved. Feedback loops are often found to
reside in a clustered manner by means of coupling and nesting
with each other in the molecular interaction network of yeast.
In these clusters some feedback mechanisms are biologically
vital for the operation of the module and some provide auxiliary
functional assistance. We find that the biologically vital
feedback mechanisms are highly conserved in both transcription
regulation and protein interaction network of yeast. In
particular, long feedback loops and oscillating modules in protein
interaction networks are found to be biologically vital and
hence highly conserved. These data suggest that biochemical
networks evolve differentially depending on their structure
with acyclic parts being permissive to evolution while cyclic
parts tend to be conserved
Mathematical models for somite formation
Somitogenesis is the process of division of the anterior–posterior vertebrate embryonic axis into similar morphological units known as somites. These segments generate the prepattern which guides formation of the vertebrae, ribs and other associated features of the body trunk. In this work, we review and discuss a series of mathematical models which account for different stages of somite formation. We begin by presenting current experimental information and mechanisms explaining somite formation, highlighting features which will be included in the models. For each model we outline the mathematical basis, show results of numerical simulations, discuss their successes and shortcomings and avenues for future exploration. We conclude with a brief discussion of the state of modeling in the field and current challenges which need to be overcome in order to further our understanding in this area
Mathematical models for somite formation
Somitogenesis is the process of division of the anterior–posterior vertebrate embryonic axis into similar morphological units known as somites. These segments generate the prepattern which guides formation of the vertebrae, ribs and other associated features of the body trunk. In this work, we review and discuss a series of mathematical models which account for different stages of somite formation. We begin by presenting current experimental information and mechanisms explaining somite formation, highlighting features which will be included in the models. For each model we outline the mathematical basis, show results of numerical simulations, discuss their successes and shortcomings and avenues for future exploration. We conclude with a brief discussion of the state of modeling in the field and current challenges which need to be overcome in order to further our understanding in this area
Reliability of Transcriptional Cycles and the Yeast Cell-Cycle Oscillator
A recently published transcriptional oscillator associated with the yeast cell cycle provides clues and raises questions about the mechanisms underlying autonomous cyclic processes in cells. Unlike other biological and synthetic oscillatory networks in the literature, this one does not seem to rely on a constitutive signal or positive auto-regulation, but rather to operate through stable transmission of a pulse on a slow positive feedback loop that determines its period. We construct a continuous-time Boolean model of this network, which permits the modeling of noise through small fluctuations in the timing of events, and show that it can sustain stable oscillations. Analysis of simpler network models shows how a few building blocks can be arranged to provide stability against fluctuations. Our findings suggest that the transcriptional oscillator in yeast belongs to a new class of biological oscillators
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