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Publications of Eduardo D. Sontag jointly with E.V. Nikolaev
Articles in journal or book chapters
  1. E.V. Nikolaev, A. Zloza, and E.D. Sontag. Immunobiochemical reconstruction of influenza lung infection - melanoma skin cancer interactions. Frontiers in Immunology, 10:Article 4, 2019. [PDF] Keyword(s): cancer, tumors, infections, immunology, checkpoint inhibition, systems biology.
    Abstract:
    Recent experimental results from the Zloza lab combined a mouse model of influenza A virus (IAV) infection (A/H1N1/PR8) and a highly aggressive model of infection-unrelated cancer, B16-F10 skin melanoma. This paper showed that acute influenza infection of the lung promotes distal melanoma growth in the dermis of the flank and leads to decreased host survival. Here, we proceed to ground the experimental observations in a mechanistic immunobiochemical model that incorporates the T cell receptor signaling pathway, various transcription factors, and a gene regulatory network (GRN). A core component of our model is a biochemical motif, which we call a Triple Incoherent Feed-Forward Loop (TIFFL), and which reflects known interactions between IRF4, Blimp-1, and Bcl-6. The different activity levels of the TIFFL components, as a function of the cognate antigen levels and the given inflammation context, manifest themselves in phenotypically distinct outcomes. Specifically, both the TIFFL reconstruction and quantitative estimates obtained from the model allowed us to formulate a hypothesis that it is the loss of the fundamental TIFFL-induced adaptation of the expression of PD-1 receptors on anti-melanoma CD8+ T cells that constitutes the essence of the previously unrecognized immunologic factor that promotes the experimentally observed distal tumor growth in the presence of acute non-ocogenic infection. We therefore hope that this work can further highlight the importance of adaptive mechanisms by which immune functions contribute to the balance between self and non-self immune tolerance, adaptive resistance, and the strength of TCR-induced activation, thus contributing to the understanding of a broader complexity of fundamental interactions between pathogens and tumors.


  2. E.V. Nikolaev, S.J. Rahi, and E.D. Sontag. Chaos in simple periodically-forced biological models. Biophysical Journal, 114:1232-1240, 2018. [PDF] Keyword(s): chaos, entrainment, systems biology, periodic inputs, subharmonic responses, biochemical systems, forced oscillations.
    Abstract:
    What complicated dynamics can arise in the simplest biochemical systems, in response to a periodic input? This paper discusses two models that commonly appear as components of larger sensing and signal transduction pathways in systems biology: a simple two-species negative feedback loop, and a prototype nonlinear integral feedback. These systems have globally attracting steady states when unforced, yet, when subject to a periodic excitation, subharmonic responses and strange attractors can arise via period-doubling cascades. These behaviors are similar to those exhibited by classical forced nonlinear oscillators such as those described by van der Pol or Duffing equations. The lack of entrainment to external oscillations, in even the simplest biochemical networks, represents a level of additional complexity in molecular biology.


  3. E.V. Nikolaev and E.D. Sontag. Quorum-sensing synchronization of synthetic toggle switches: A design based on monotone dynamical systems theory. PLoS Computational Biology, 12:e1004881, 2016. [PDF] Keyword(s): quorum sensing, toggle switches, monotone systems.
    Abstract:
    Synthetic constructs in biotechnology, bio-computing, and proposed gene therapy interventions are often based on plasmids or transfected circuits which implement some form of on-off (toggle or flip-flop) switch. For example, the expression of a protein used for therapeutic purposes might be triggered by the recognition of a specific combination of inducers (e.g., antigens), and memory of this event should be maintained across a cell population until a specific stimulus commands a coordinated shut-off. The robustness of such a design is hampered by molecular (intrinsic) or environmental (extrinsic) noise, which may lead to spontaneous changes of state in a subset of the population and is reflected in the bimodality of protein expression, as measured for example using flow cytometry. In this context, a majority-vote correction circuit, which brings deviant cells back into the required state, is highly desirable. To address this concrete challenge, we have developed a new theoretical design for quorum-sensing (QS) synthetic toggles. QS provides a way for cells to broadcast their states to the population as a whole so as to facilitate consensus. Our design is endowed with strong theoretical guarantees, based on monotone dynamical systems theory, of global stability and no oscillations, and which leads to robust consensus states.


  4. M. Skataric, E.V. Nikolaev, and E.D. Sontag. A fundamental limitation to fold-change detection by biological systems with multiple time scales. IET Systems Biology, 9:1-15, 2015. [PDF] Keyword(s): singular perturbations, scale invariance, systems biology, transient behavior, symmetries, fcd, fold-change detection, incoherent feedforward loop, feedforward, IFFL.
    Abstract:
    The phenomenon of fold-change detection, or scale invariance, is exhibited by a variety of sensory systems, in both bacterial and eukaryotic signaling pathways. It has been often remarked in the systems biology literature that certain systems whose output variables respond at a faster time scale than internal components give rise to an approximate scale-invariant behavior, allowing approximate fold-change detection in stimuli. This paper establishes a fundamental limitation of such a mechanism, showing that there is a minimal fold-change detection error that cannot be overcome, no matter how large the separation of time scales is. To illustrate this theoretically predicted limitation, we discuss two common biomolecular network motifs, an incoherent feedforward loop and a feedback system, as well as a published model of the chemotaxis signaling pathway of Dictyostelium discoideum.


Conference articles
  1. M. Skataric, E.V. Nikolaev, and E.D. Sontag. Scale-invariance in singularly perturbed systems. In Proc. IEEE Conf. Decision and Control, Los Angeles, Dec. 2014, pages 3035-3040, 2014. [PDF] Keyword(s): singular perturbations, scale invariance, systems biology, transient behavior, symmetries, fcd, fold-change detection, incoherent feedforward loop, feedforward, IFFL.
    Abstract:
    This conference paper (a) summarizes material from "A fundamental limitation to fold-change detection by biological systems with multiple time scales" (IET Systems Biology 2014) and presents additional remarks regarding (b) expansion techniques to compute FCD error and (c) stochastic adaptation and FCD



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Last modified: Mon Mar 18 12:24:41 2019
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