In JoVE (1)
Other Publications (7)
- Nature Genetics
- Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
- IEEE Transactions on Bio-medical Engineering
- Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
- Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
- Proceedings of the National Academy of Sciences of the United States of America
- PLoS Computational Biology
Articles by Richard M. Murray in JoVE
Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology Zachary Z. Sun*1, Clarmyra A. Hayes*2, Jonghyeon Shin3, Filippo Caschera4, Richard M. Murray2, Vincent Noireaux4 1Department of Biology, California Institute of Technology, 2Department of Bioengineering, California Institute of Technology, 3Synthetic Biology Center, Department of Bioengineering, Massachusetts Institute of Technology, 4School of Physics and Astronomy, University of Minnesota This five-day protocol outlines all steps, equipment, and supplemental software necessary for creating and running an efficient endogenous Escherichia coli based TX-TL cell-free expression system from scratch. With reagents, the protocol takes 8 hours or less to setup a reaction, collect, and process data.
Other articles by Richard M. Murray on PubMed
Regulatory Activity Revealed by Dynamic Correlations in Gene Expression Noise Nature Genetics. Dec, 2008 | Pubmed ID: 19029898 Gene regulatory interactions are context dependent, active in some cellular states but not in others. Stochastic fluctuations, or 'noise', in gene expression propagate through active, but not inactive, regulatory links. Thus, correlations in gene expression noise could provide a noninvasive means to probe the activity states of regulatory links. However, global, 'extrinsic', noise sources generate correlations even without direct regulatory links. Here we show that single-cell time-lapse microscopy, by revealing time lags due to regulation, can discriminate between active regulatory connections and extrinsic noise. We demonstrate this principle mathematically, using stochastic modeling, and experimentally, using simple synthetic gene circuits. We then use this approach to analyze dynamic noise correlations in the galactose metabolism genes of Escherichia coli. We find that the CRPGalS-GalE feed-forward loop is inactive in standard conditions but can become active in a GalR mutant. These results show how noise can help analyze the context dependence of regulatory interactions in endogenous gene circuits.
Dynamics and Stability of a Class of Low Reynolds Number Swimmers Near a Wall Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. Apr, 2009 | Pubmed ID: 19518287 We study the dynamic stability of low Reynolds number swimming near a plane wall from a control-theoretic viewpoint. We consider a special class of swimmers having a constant shape, focus on steady motion parallel to the wall, and derive conditions under which it is passively stable without sensing or feedback. We study the geometric structure of the swimming equation and highlight the relation between stability and reversing symmetry of the dynamical system. Finally, our numerical simulations reveal the existence of stable periodic motion. The results have implications for design of miniature robotic swimmers, as well as for explaining the attraction of micro-organisms to surfaces.
Flight Dynamics and Control of Evasive Maneuvers: the Fruit Fly's Takeoff IEEE Transactions on Bio-medical Engineering. Sep, 2009 | Pubmed ID: 19643699 We have approached the problem of reverse-engineering the flight control mechanism of the fruit fly by studying the dynamics of the responses to a visual stimulus during takeoff. Building upon a prior framework [G. Card and M. Dickinson, J. Exp. Biol., vol. 211, pp. 341-353, 2008], we seek to understand the strategies employed by the animal to stabilize attitude and orientation during these evasive, highly dynamical maneuvers. As a first step, we consider the dynamics from a gray-box perspective: examining lumped forces produced by the insect's legs and wings. The reconstruction of the flight initiation dynamics, based on the unconstrained motion formulation for a rigid body, allows us to assess the fly's responses to a variety of initial conditions induced by its jump. Such assessment permits refinement by using a visual tracking algorithm to extract the kinematic envelope of the wings [E. I. Fontaine, F. Zabala, M. Dickinson, and J. Burdick, "Wing and body motion during flight initiation in Drosophila revealed by automated visual tracking," submitted for publication] in order to estimate lift and drag forces [F. Zabala, M. Dickinson, and R. Murray, "Control and stability of insect flight during highly dynamical maneuvers," submitted for publication], and recording actual leg-joint kinematics and using them to estimate jump forces [F. Zabala, "A bio-inspired model for directionality control of flight initiation," to be published.]. In this paper, we present the details of our approach in a comprehensive manner, including the salient results.
Controlling Biological Networks by Time-delayed Signals Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences. Jan, 2010 | Pubmed ID: 20008410 This paper describes the use of time-delayed feedback to regulate the behaviour of biological networks. The general ideas on specific transcriptional regulatory and neural networks are demonstrated. It is shown that robust yet tunable controllers can be constructed that provide the biological systems with model-engineered inputs. The results indicate that time delay modulation may serve as an efficient biocompatible control tool.
Autonomous Driving in Urban Environments: Approaches, Lessons and Challenges Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences. Oct, 2010 | Pubmed ID: 20819826 The development of autonomous vehicles for urban driving has seen rapid progress in the past 30 years. This paper provides a summary of the current state of the art in autonomous driving in urban environments, based primarily on the experiences of the authors in the 2007 DARPA Urban Challenge (DUC). The paper briefly summarizes the approaches that different teams used in the DUC, with the goal of describing some of the challenges that the teams faced in driving in urban environments. The paper also highlights the long-term research challenges that must be overcome in order to enable autonomous driving and points to opportunities for new technologies to be applied in improving vehicle safety, exploiting intelligent road infrastructure and enabling robotic vehicles operating in human environments.
Synergistic Dual Positive Feedback Loops Established by Molecular Sequestration Generate Robust Bimodal Response Proceedings of the National Academy of Sciences of the United States of America. Nov, 2012 | Pubmed ID: 23150580 Feedback loops are ubiquitous features of biological networks and can produce significant phenotypic heterogeneity, including a bimodal distribution of gene expression across an isogenic cell population. In this work, a combination of experiments and computational modeling was used to explore the roles of multiple feedback loops in the bimodal, switch-like response of the Saccharomyces cerevisiae galactose regulatory network. Here, we show that bistability underlies the observed bimodality, as opposed to stochastic effects, and that two unique positive feedback loops established by Gal1p and Gal3p, which both regulate network activity by molecular sequestration of Gal80p, induce this bimodality. Indeed, systematically scanning through different single and multiple feedback loop knockouts, we demonstrate that there is always a concentration regime that preserves the system's bimodality, except for the double deletion of GAL1 and the GAL3 feedback loop, which exhibits a graded response for all conditions tested. The constitutive production rates of Gal1p and Gal3p operate as bifurcation parameters because variations in these rates can also abolish the system's bimodal response. Our model indicates that this second loss of bistability ensues from the inactivation of the remaining feedback loop by the overexpressed regulatory component. More broadly, we show that the sequestration binding affinity is a critical parameter that can tune the range of conditions for bistability in a circuit with positive feedback established by molecular sequestration. In this system, two positive feedback loops can significantly enhance the region of bistability and the dynamic response time.
Discriminating External and Internal Causes for Heading Changes in Freely Flying Drosophila PLoS Computational Biology. 2013 | Pubmed ID: 23468601 As animals move through the world in search of resources, they change course in reaction to both external sensory cues and internally-generated programs. Elucidating the functional logic of complex search algorithms is challenging because the observable actions of the animal cannot be unambiguously assigned to externally- or internally-triggered events. We present a technique that addresses this challenge by assessing quantitatively the contribution of external stimuli and internal processes. We apply this technique to the analysis of rapid turns ("saccades") of freely flying Drosophila melanogaster. We show that a single scalar feature computed from the visual stimulus experienced by the animal is sufficient to explain a majority (93%) of the turning decisions. We automatically estimate this scalar value from the observable trajectory, without any assumption regarding the sensory processing. A posteriori, we show that the estimated feature field is consistent with previous results measured in other experimental conditions. The remaining turning decisions, not explained by this feature of the visual input, may be attributed to a combination of deterministic processes based on unobservable internal states and purely stochastic behavior. We cannot distinguish these contributions using external observations alone, but we are able to provide a quantitative bound of their relative importance with respect to stimulus-triggered decisions. Our results suggest that comparatively few saccades in free-flying conditions are a result of an intrinsic spontaneous process, contrary to previous suggestions. We discuss how this technique could be generalized for use in other systems and employed as a tool for classifying effects into sensory, decision, and motor categories when used to analyze data from genetic behavioral screens.