A Tug-of-War Mechanism for Pattern Formation in a Genetic Network

Synthesizing spatial patterns with genetic networks is an ongoing challenge in synthetic biology. A successful demonstration of pattern formation would imply a better understanding of systems in the natural world and advance applications in synthetic biology. In developmental systems, transient patterning may suffice in order to imprint instructions for long-term development. In this paper we show that transient but persistent patterns can emerge from a realizable synthetic gene network based on a toggle switch. We show that a bistable system incorporating diffusible molecules can generate patterns that resemble Turing patterns but are distinctly different in the underlying mechanism: diffusion of mutually inhibiting molecules creates a prolonged "tug-of-war" between patches of cells at opposing bistable states. The patterns are transient but longer wavelength patterns persist for extended periods of time. Analysis of a representative small scale model implies the eigenvalues of the persistent modes are just above the threshold of stability. The results are verified through simulation of biologically relevant models

TRİFLURALİN'İN TOPRAKTA NİTRİFİKASYON VE KATALAZ AKTİVİTESİNE ETKİLERİ

Çıkış öncesi herbisit olarak kullanı lan Trifluralin' in toprakta nitrifıkasyon ve toprak katalaz aktivitesi üzerine etkileri ince tekstürlü toprak örne ğinde üç farkl ı dozda 0.0, 200 ve 400 ml. aktif madde. da- I olacak şekilde % 48'lik treflanden 0.0, 0.4 ve 0.8 mg aktif madde. kg - I trifluralin uygulanarak; üç farkl ı nem düzeyinde tarla kapasitesinin % 75, % 100 ve % 150 , 27 °C de ve 18 gün süreyle inkübe edilerek ara ştınlmıştır. Uygulanan trifluralin dozlan zaman ve nem düzeylerine ba ğlı olarak katalaz aktivitesi de ğişimini önemli düzeyde P< 0.01 etkilemiştir. Nitrifıkasyon olayı ise nem düzeylerine bağlı olarak zaman içinde P< 0.01 düzeyinde önemli bir art ış göstermiştir

Sign patterns for chemical reaction networks

Most differential equations found in chemical reaction networks (CRNs) have the form $dx/dt=f(x)= Sv(x)$, where $x$ lies in the nonnegative orthant, where $S$ is a real matrix (the stoichiometric matrix) and $v$ is a column vector consisting of real-valued functions having a special relationship to $S$. Our main interest will be in the Jacobian matrix, $f'(x)$, of $f(x)$, in particular in whether or not each entry $f'(x)_{ij}$ has the same sign for all $x$ in the orthant, i.e., the Jacobian respects a sign pattern. In other words species $x_j$ always acts on species $x_i$ in an inhibitory way or its action is always excitatory. In Helton, Klep, Gomez we gave necessary and sufficient conditions on the species-reaction graph naturally associated to $S$ which guarantee that the Jacobian of the associated CRN has a sign pattern. In this paper, given $S$ we give a construction which adds certain rows and columns to $S$, thereby producing a stoichiometric matrix $\widehat S$ corresponding to a new CRN with some added species and reactions. The Jacobian for this CRN based on $\hat S$ has a sign pattern. The equilibria for the $S$ and the $\hat S$ based CRN are in exact one to one correspondence with each equilibrium $e$ for the original CRN gotten from an equilibrium $\hat e$ for the new CRN by removing its added species. In our construction of a new CRN we are allowed to choose rate constants for the added reactions and if we choose them large enough the equilibrium $\hat e$ is locally asymptotically stable if and only if the equilibrium $e$ is locally asymptotically stable. Further properties of the construction are shown, such as those pertaining to conserved quantities and to how the deficiencies of the two CRNs compare.Comment: 23 page

Guaranteed optimal reachability control of reaction-diffusion equations using one-sided Lipschitz constants and model reduction

We show that, for any spatially discretized system of reaction-diffusion, the approximate solution given by the explicit Euler time-discretization scheme converges to the exact time-continuous solution, provided that diffusion coefficient be sufficiently large. By "sufficiently large", we mean that the diffusion coefficient value makes the one-sided Lipschitz constant of the reaction-diffusion system negative. We apply this result to solve a finite horizon control problem for a 1D reaction-diffusion example. We also explain how to perform model reduction in order to improve the efficiency of the method

A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser

Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the “activator-inhibitor” models of Meinhardt and Gierer. Systems based on this model are notoriously difficult to engineer. We present the first demonstration that Turing pattern formation can arise in a new family of oscillator-driven gene network topologies, specifically when a second feedback loop is introduced which quenches oscillations and incorporates a diffusible molecule. We provide an analysis of the system that predicts the range of kinetic parameters over which patterning should emerge and demonstrate the system's viability using stochastic simulations of a field of cells using realistic parameters. The primary goal of this paper is to provide a circuit architecture which can be implemented with relative ease by practitioners and which could serve as a model system for pattern generation in synthetic multicellular systems. Given the wide range of oscillatory circuits in natural systems, our system supports the tantalizing possibility that Turing pattern formation in natural multicellular systems can arise from oscillator-driven mechanisms