Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session Y1: Engineering Biomolecules and Circuits by Rational Design and Genetic Selection |
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Sponsoring Units: DCMP DBP Chair: Andrea Liu, University of Pennsylvania Room: Baltimore Convention Center Ballroom IV |
Friday, March 17, 2006 8:00AM - 8:36AM |
Y1.00001: Molecular Evolution of Gene Expression in E. coli Invited Speaker: Understanding the evolution of gene regulation is an outstanding challenge to systems biology. Here we use molecular methods to study in detail the evolution of promoter sequences needed to express gene(s) essential to the growth of E. coli cells. We quantitatively characterize changes in the genotype and phenotype of the evolving population, and study how different challenges imposed by the environment affect the dynamics and the final outcome of the evolutionary process. [Preview Abstract] |
Friday, March 17, 2006 8:36AM - 9:12AM |
Y1.00002: Tinkering with Genetic Networks In Vivo Invited Speaker: Synthetic genetic networks have recently emerged as an alternative experimental framework for studying cellular networks. Biological systems have evolved through a process of blind molecular tinkering. I will present an experimental genetic system which mimics this tinkering process. This system is composed of a few well characterized genetic elements: the promoters and genes of lambda cI, LacR and TetR. Using a combinatorial synthesis method we create libraries of simple genetic networks with various connectivities that function as logical gates. We observe how new computational functions arise through one-step changes in network connectivity. The connectivity-function map is found to be many-to-many even for these small networks. [Preview Abstract] |
Friday, March 17, 2006 9:12AM - 9:48AM |
Y1.00003: Directed Evolution of Bacterial Chemoreceptors Invited Speaker: The methyl-accepting chemotaxis proteins are a family of receptors in bacteria that mediate chemotaxis to diverse signals. We have developed a simple method for selecting bacteria that swim towards target attractants, which makes it possible to isolate novel chemoreceptors. The procedure is based on establishing a diffusive gradient in semi-soft agar and does not require that the attractant be metabolized or degraded. We have applied this method to evolve the \textit{E. coli} aspartate receptor, Tar, to mediate chemotaxis to new attractants. We found that Tar is quite plastic and can be readily mutated to respond to diverse compounds. The overall change in specificity depended on the target attractant. In some cases the mutated receptors still showed significant sensitivity to aspartate, indicating that the receptors had a broadened specificity relative to wild-type Tar. In other cases, however, the Tar variants showed a dramatic decrease in their response to aspartate. This occurred in the absence of any counter-selection steps. For many of the receptors, the maximal sensitivity that was obtained could not be attributed solely to substitutions within the ligand binding pocket. The receptors that we have isolated, together with additional variants that may be obtained with our technique, provide new tools for exploring the molecular mechanisms of signal transduction by chemoreceptors. Our selection method will also be useful for constructing new receptors for the development of biosensors and for engineering bacteria for applications in biotechnology. [Preview Abstract] |
Friday, March 17, 2006 9:48AM - 10:24AM |
Y1.00004: Building a cellular oscillator from metabolic and cell signaling components Invited Speaker: One of the key features of cellular oscillators is their interaction with metabolism and cellular physiology. To understand such interaction and to uncover operating principles behind these networks, we designed a synthetic gene-metabolic oscillator that links metabolism with gene regulation. The conceptual design was inspired by physical and mathematical insight, but constrained by biological and chemical realities. Biological implementation was built on detailed understanding of the physiology of the organism of interest. Non-linear dynamic analysis was used to guide the search of experimental conditions and evaluate different design. Interestingly, most of the predictions were experimentally verified, suggesting that the underlying mechanisms were properly captured by the conceptual and mathematical models. [Preview Abstract] |
Friday, March 17, 2006 10:24AM - 11:00AM |
Y1.00005: An artificial cell based on gene expression in vesicle Invited Speaker: A new experimental approach is presented to build an artificial cell using the translation machinery of a cell-free expression system as the hardware and a DNA synthetic program as the software. Cytoplasmic extracts, encapsulated in phospholipid vesicles, are used to assemble custom-made genetic circuits to develop the functions of a minimal cell. The objective is to understand how a DNA algorithm can be designed to build an operating system that has some of the properties of life. We show how a long-lived bioreactor is built to carry out in vitro transcription and translation in cell-sized vesicles. To develop the synthetic membrane into an active interface, a few amphipathic peptides and an insertion mechanism of integral membrane proteins have been tested. With vesicles composed of different phospholipids, the fusion protein alpha-hemolysin-eGFP can be expressed to reveal patterns on the membrane. Finally, specific degradation mechanisms are introduced to create a sink for the synthesized messengers and proteins. Perspectives and limitations of this approach will be discussed. [Preview Abstract] |
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