http://bnmc.caltech.edu/Forums/index.php @caltech.edu RDF feed http://bnmc.caltech.edu/Forums/index.php?t=rview&goto=272&th=266 Biological Network Modeling Center Seminar: "In vitro transcriptional<br /> circuits: design, dynamics, and robustness"<br /> <br /> Erik Winfree<br /> Associate Professor of Computer Science and Computation and Neural Systems<br /> Caltech<br /> <br /> Thursday, November 20, 2008<br /> 2:00PM - 3:00PM<br /> Beckman Institute Auditorium<br /> (refreshments at 1:45 in the lobby)<br /> <br /> Synthetic biochemical circuits both provide an opportunity to embed control<br /> logic within chemical systems for technological applications and provide a<br /> platform for probing our understanding of general principles for biochemical<br /> circuits. We have developed a general approach to the construction of in<br /> vitro biochemical circuits based on the transcription and degradation of RNA<br /> molecules.<br /> <br /> Consisting of just DNA templates and two enzymes, in principle arbitrary<br /> circuits can be systematically constructed, displaying a rich variety of<br /> dynamical and computational behavior. We have experimentally demonstrated<br /> individual transcriptional switches, a bistable network, and several<br /> oscillating circuits. In doing so, we have encountered a number of<br /> unexpected difficulties -- deviations from ideal circuit behavior -- that<br /> help frame the critical questions of how to model and design robust<br /> biochemical systems.<br /> <br /> <br /> <br /> _______________________________________________<br /> bnmc-announce mailing list<br /> <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a><br /> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a><br /> <br /> Linda Taddeo 2008-11-18T19:36:34-00:00 http://bnmc.caltech.edu/Forums/index.php?t=rview&goto=270&th=264 BNMC SEMINAR: COMPLEXITY AND CONTROL IN ANIMAL DEVELOPMENT<br /> <br /> Arthur D. Lander<br /> Professor, Department of Developmental and Cell Biology, Department of<br /> Biomedical Engineering Director, Center for Complex Biological Systems<br /> University of California, Irvine<br /> <br /> Thursday, November 06, 2008<br /> 2:00 PM to 3:00 PM<br /> Beckman Institute Auditorium<br /> (Refreshments at 1:45 PM)<br /> <br /> Explaining the development of multicellular animals--including processes<br /> such as growth, differentiation, patterning and regeneration--has long been<br /> a major goal of biology. Until recently, experimental work has focused<br /> almost entirely on the identification of mechanisms--cellular, molecular and<br /> genetic--that cause such processes to happen. Yet development is remarkable<br /> not only for the fact that it happens, but for the fact that it is extremely<br /> well controlled, precisely specifying pattern and size in the face of<br /> genetic, epigenetic and environmental variability and noise. My laboratory<br /> pursues the hypothesis that much of the (at times) perplexing complexity<br /> that has been observed in the signaling pathways underlying animal<br /> development evolved specifically for the purpose of control. To test this<br /> hypothesis, we use both modeling and experimentation to explore the<br /> potential benefits and drawbacks of complex developmental circuitry. My<br /> talk will focus on developmental events that are regulated by<br /> morphogens--diffusible molecules that coordinate the establishment of<br /> spatial pattern--and chalones--secreted feedback inhibitors of cell growth<br /> and lineage expansion. I will describe ways in which performance objectives<br /> such as parameter insensitivity, noise suppression, and desirable dynamics<br /> are served by some of the complex signaling networks within which such<br /> molecules are embedded.<br /> <br /> <br /> <br /> _______________________________________________<br /> bnmc-announce mailing list<br /> <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a><br /> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a><br /> <br /> Linda Taddeo 2008-10-31T00:17:32-00:00 http://bnmc.caltech.edu/Forums/index.php?t=rview&goto=269&th=263 BNMC SEMINAR - THE VISUAL ETHOLOGY OF FRUIT FLIES<br /> <br /> Michael Dickinson<br /> Esther M. and Abe M. Zarem Professor of Bioengineering, Caltech<br /> <br /> Thursday, October 30, 2008<br /> 2:00 PM to 3:00 PM<br /> Beckman Institute Auditorium<br /> (Refreshments: 1:45 PM)<br /> <br /> The fruit fly, Drosophila melanogaster, suffers a rather poor reputation as<br /> a pesky lab rat, better known for its rapid breeding chromosome number than<br /> for its behavioral repertoire. The research in my laboratory focuses on the<br /> sensory ethology of fruit flies, treating these tiny insects not simply as<br /> convenient laboratory models, but as real animals that have evolved a<br /> successful life history pattern. The goal of this work is to try to<br /> deconstruct the animal's behavior into a sequence of sensory-motor modules.<br /> Although these insects make use of many sensory modalities as they explore<br /> their environment, vision plays an essential role in nearly all aspects of<br /> their life history. My talk will focus on several visually-mediated<br /> components of behavior including take-off, navigation, predator avoidance,<br /> landing, and local exploration, as well as components of social behavior<br /> than ensue whenever two or more flies alight on the same piece of rotting<br /> fruit.<br /> <br /> _______________________________________________<br /> bnmc-announce mailing list<br /> <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a><br /> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a><br /> <br /> Linda Taddeo 2008-10-27T21:56:11-00:00 http://bnmc.caltech.edu/Forums/index.php?t=rview&goto=266&th=260 CACR Seminar<br /> 11:00AM<br /> Monday, Oct. 27<br /> Moore 080<br /> <br /> "Models of interactions of Ca(2+), CaM, and monomeric catalytic subunits of<br /> CaMKII: a piece of the post-synaptic signaling network puzzle"<br /> <br /> Dr. Shirley Pepke, Caltech Center for Advanced Computing Research<br /> <br /> Calcium (Ca) signal transduction is a fundamental driver of synaptic<br /> plasticity in neurons. The molecule Calmodulin (CaM) is an important second<br /> messenger in Ca signaling in the post-synaptic density, integrating Ca<br /> levels via four binding sites. CaM transmits Ca signal information<br /> downstream through selective binding to target enzymes such as<br /> calmodulin-activated kinase II (CaMKII). Prior models of Ca/CaM/CaMKII have<br /> focused on the role of the unique holoenzyme structure of CaMKII in<br /> generating sensitivity and selectivity in response to dynamic Ca input. I<br /> will present models of Ca/CaM/CaMKII binding and phosphorylation reactions<br /> (developed within the Kennedy lab) that incorporate detailed representations<br /> of Ca/CaM and Ca/CaM/CaMKII binding states and explore the resulting impact<br /> on phosphorylation rates of monomeric catalytic subunits of CaMKII. Ca/CaM<br /> state models are seen to be necessary to accurately predict CaMKII<br /> phosphorylation levels under the low Ca conditions that are typical in<br /> neurons. Additionally, specific kinetic rate ranges in the models are shown<br /> to confer frequency sensitivity independent of a CaMKII holoenzyme<br /> structure. Sensitivity analysis on the estimated model parameters confirm<br /> these findings across sampled ranges of all parameters and point to areas<br /> where further experiments are necessary to establish quantitative values.<br /> While the results presented will be for numerical integration of an ODE<br /> representation of the reaction network, the models are easily implemented<br /> within a stochastic simulation framework that allows analysis of the<br /> response to Ca inputs with low molecule numbers as well as gradients in both<br /> time and space. The models promise new insight into the relative roles of<br /> thermodynamics, kinetics, molecular structure, and spatial distributions of<br /> signaling proteins in determining the synaptic response to Ca influxes.<br /> <br /> <br /> <br /> _______________________________________________<br /> bnmc-announce mailing list<br /> <a href="mailto:bnmc-announce@caltech.edu" target="_blank">bnmc-announce@caltech.edu</a><br /> <a href="https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/bnmc-announce</a><br /> <br /> Linda Taddeo 2008-10-20T17:02:40-00:00 http://bnmc.caltech.edu/Forums/index.php?t=rview&goto=254&th=248 Dear colleagues,<br /> <br /> The editors of the Systems Biology Graphical Notation will run a tutorial <br /> on SBGN process diagram before the ICSB in Goteborg, Sweden.<br /> <br /> See:<br /> <a href="http://www.icsb-2008.org/downloads/tutorials/sbgn-tutorial.pdf" target="_blank">http://www.icsb-2008.org/downloads/tutorials/sbgn-tutorial.pdf</a><br /> <br /> The tutorial will take place on August 23, from 11:00 to 13:00.<br /> <br /> Registration is open until August 10 from the ICSB website.<br /> <br /> The aim of the tutorial is to provide participants with an understanding of <br /> what SBGN is, what problems it is designed to cover, and how SBGN <br /> constructs can be used to represent biological graphs such as signaling <br /> pathways, metabolic networks, or gene regulatory networks. To this end the <br /> tutorial will have the following structure:<br /> <br /> History of SBGN<br /> Rationale for a standardised graphical language, how SBGN started, what its <br /> goals are. Presentation of the three languages.<br /> <br /> SBGN-PD Level 1<br /> We will introduce the concepts behind the Process Diagram notation. The set <br /> of symbols will be presented, and we will teach the drawing rules (syntax <br /> and semantics). We will start of by describing how to draw a simple pathway <br /> diagram, and then move on to progressively more complex examples that <br /> illustrate some of the more complex rules of SBGN-PD.<br /> <br /> Futures plans<br /> We will outline the roadmap for future SBGN releases, in particular those <br /> for the Entity-Relationship and Activity Flow notations as well as SBGN <br /> Level 2.<br /> ____________________________________________________________<br /> To manage your sysbio list subscription, visit <br /> <a href="https://utils.its.caltech.edu/mailman/listinfo/sysbio" target="_blank">https://utils.its.caltech.edu/mailman/listinfo/sysbio</a><br /> <br /> For a web interface to the sysbio mailing list, visit<br /> <a href="http://bnmc.caltech.edu/Forums/" target="_blank">http://bnmc.caltech.edu/Forums/</a><br /> <br /> For questions or feedback about the sysbio list,<br /> contact <a href="mailto:bnmc-help@caltech.edu" target="_blank">bnmc-help@caltech.edu</a><br /> Nicolas Le Novere 2008-07-31T09:00:11-00:00