A synthetic multicellular system for programmed pattern formation

Pattern formation is a hallmark of coordinated cell behaviour in both single and multicellular organisms. It typically involves cell–cell communication and intracellular signal processing. Here we show a synthetic multicellular system in which genetically engineered ‘receiver’ cells are programmed to form ring-like patterns of differentiation based on chemical gradients of an acyl-homoserine lactone (AHL) signal that is synthesized by ‘sender’ cells. In receiver cells, ‘band-detect’ gene networks respond to user-defined ranges of AHL concentrations. By fusing different fluorescent proteins as outputs of network variants, an initially undifferentiated ‘lawn’ of receivers is engineered to form a bullseye pattern around a sender colony. Other patterns, such as ellipses and clovers, are achieved by placing senders in different configurations. Experimental and theoretical analyses reveal which kinetic parameters most significantly affect ring development over time. Construction and study of such synthetic multicellular systems can improve our quantitative understanding of naturally occurring developmental processes and may foster applications in tissue engineering, biomaterial fabrication and biosensing

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

Engineered biosynthetic pathways have the potential to produce high-value molecules from inexpensive feedstocks, but a key limitation is engineering enzymes with high activity and specificity for new reactions. Here, we developed a method for combining structure-based computational protein design with library-based enzyme screening, in which inter-residue correlations favored by the design are encoded into a defined-sequence library. We validated this approach by engineering a glucose 6-oxidase enzyme for use in a proposed pathway to convert D-glucose into D-glucaric acid. The most active variant, identified after only one round of diversification and screening of only 10,000 wells, is approximately 400-fold more active on glucose than is the wild-type enzyme. We anticipate that this strategy will be broadly applicable to the discovery of new enzymes for engineered biological pathways.United States. Office of Naval Research. Young Investigator Program (Grant N000140510656)National Science Foundation (U.S.) (Synthetic Biology Engineering Research Center. Grant EEC-0540879)MIT Faculty Start-up FundCodon Devices, Inc

Synthetic biology: new engineering rules for an emerging discipline

Synthetic biologists engineer complex artificial biological systems to investigate natural biological phenomena and for a variety of applications. We outline the basic features of synthetic biology as a new engineering discipline, covering examples from the latest literature and reflecting on the features that make it unique among all other existing engineering fields. We discuss methods for designing and constructing engineered cells with novel functions in a framework of an abstract hierarchy of biological devices, modules, cells, and multicellular systems. The classical engineering strategies of standardization, decoupling, and abstraction will have to be extended to take into account the inherent characteristics of biological devices and modules. To achieve predictability and reliability, strategies for engineering biology must include the notion of cellular context in the functional definition of devices and modules, use rational redesign and directed evolution for system optimization, and focus on accomplishing tasks using cell populations rather than individual cells. The discussion brings to light issues at the heart of designing complex living systems and provides a trajectory for future development

Theory for Hydration Forces in Thin Films of Aqueous Electrolytes

A theory is presented to quantify the electrostatic forces in thin aqueous electrolyte films between two charge regulating surfaces. The Poisson-Boltzmann equation (PBE) is modified to include the effects of dielectric saturation of the double layer and the corresponding change in hydration free energy of ions. The results obtained agree remarkably well with the experimental data of Pashley (1981) and Israelachvili et. al. (1978) at low electrolyte concentration and pH. At higher concentration and pH, the model provides qualitative agreement with experimental observations. Finite ion sizes needs to be incorporated into the PBE to obtain quantitative agreement with experimental data in the high ion concentration range. The reduction in dielectric constant with increasing electric field increases the hydration energy of the ions in the double layer, giving rise to a repulsive hydration force. It is concluded that dielectric saturation of the double layer near a charged interface plays an important role in the electrostatic interactions in thin electrolyte films.Petroleum and Geosystems Engineerin

Engineering signal processing in cells: Towards molecular concentration band detection

Abstract. We seek to couple protein-ligand interactions with synthetic gene networks in order to equip cells with the ability to process internal and environmental information in novel ways. In this paper, we propose and analyze a new genetic signal processing circuit that can be configured to detect various chemical concentration ranges of ligand molecules. These molecules freely diffuse from the environment into the cell. The circuit detects acyl-homoserine lactone ligand molecules, determines if the molecular concentration falls within two prespecified thresholds, and reports the outcome with a fluorescent protein. In the analysis of the circuit and the description of preliminary experimental results, we demonstrate how to adjust the concentration band thresholds by altering the kinetic properties of specific genetic elements, such as ribosome binding site efficiencies or dna-binding protein affinities to their operators. Key words: cellular computation, cell-cell communications, genetic signal processing, synthetic gene networks 1

The Pro-Trade Bias of Offshoring

Technological advance and improvements in communication technologies have facilitated the offshoring of jobs worldwide, where a typical scene following the supply chain involves developing countries importing finished products from developed countries that contain developing country labor content. We demonstrate that this pattern of offshoring can harbor a pro-trade bias, but only among countries upstream along the global supply chain. This upstream-downstream asymmetry has important implications on countries’ (i) incentive to violate trade agreements, and (ii) ability to leverage the dispute settlement procedures to punish violators. We then show that a well-enforced set of labor standards in developing countries, such as a binding minimum wage, resolves this conundrum by reviving the ability of the developing countries to use countervailing tariffs to punish trade agreement violators