title: Simple molecular networks that respond optimally to time-periodic stimulation.
abstract: BACKGROUND
  Bacteria or cells receive many signals from their environment and from other organisms. In order to process this large amount of information, Systems Biology shows that a central role is played by regulatory networks composed of genes and proteins. The objective of this paper is to present and to discuss simple regulatory network motifs having the property to maximize their responses under time-periodic stimulations. In elucidating the mechanisms underlying these responses through simple networks the goal is to pinpoint general principles which optimize the oscillatory responses of molecular networks.
  
  
  RESULTS
  We took a look at basic network motifs studied in the literature such as the Incoherent Feedforward Loop (IFFL) or the interlerlocked negative feedback loop. The former is also generalized to a diamond pattern, with network components being either purely genetic or combining genetic and signaling pathways. Using standard mathematics and numerical simulations, we explain the types of responses exhibited by the IFFL with respect to a train of periodic pulses. We show that this system has a non-vanishing response only if the inter-pulse interval is above a threshold. A slight generalisation of the IFFL (the diamond) is shown to work as an ideal pass-band filter. We next show a mechanism by which average of oscillatory response can be maximized by bursting temporal patterns. Finally we study the interlerlocked negative feedback loop, i.e. a 2-gene motif forming a loop where the nodes respectively activate and repress each other, and show situations where this system possesses a resonance under periodic stimulation.
  
  
  CONCLUSIONS
  We present several simple motif designs of molecular networks producing optimal output in response to periodic stimulations of the system. The identified mechanisms are simple and based on known network motifs in the literature, so that that they could be embodied in existing organisms, or easily implementable by means of synthetic biology. Moreover we show that these designs can be studied in different contexts of molecular biology, as for example in genetic networks or in signaling pathways.
authors.affiliation: Institut Non Linéaire de Nice, Université de Nice Sophia-Antipolis, CNRS, Valbonne, France. axel.cournac@inln.cnrs.fr
authors.forename: Axel
authors.initials: A
authors.lastname: Cournac
authors.forename: Jacques-Alexandre
authors.initials: JA
authors.lastname: Sepulchre
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D016014:Linear Models; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D017711:Nonlinear Dynamics; D015398:Signal Transduction; D049490:Systems Biology / Q000379:methods*; D013997:Time Factors