life inspired

"[We] discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics." Full article @ Reports on Progress in PhysicsEmail alert RSS feed

Labels: design principles, gene circuits, synthetic biology

"Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics1. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits2, 3, 4, 5, 6, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. [...] Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output." Full article @ Nature

Labels: gene circuits, synthetic biology

"To take control of biological systems, Tabor et al. argue, we need the ability to predict the behavior of complex genetic programs, which are analogous in some ways to electronic circuits that allow logical operations in computers. One strategy to obtain such an understanding is to build such circuits and to observe and to model mathematically their behavior. Tabor et al. used a combination of simple genetic circuits in combination to build a program that allowed a layer of bacteria on a Petri dish to function as an "edge detector" sensitive to areas of transition between high and low illumination (light-dark)." Editor's choice at Science Signaling.

Article:
J. J. Tabor, H. M. Salis, Z. B. Simpson, A. A. Chevalier, A. Levskaya, E. M. Marcotte, C. A. Voight, A. D. Ellington. A synthetic genetic edge detection program. Cell 137, 1272–1281 (2009).

Labels: bacteria, gene circuits

"Orthogonal, parallel and independent, systems are one key foundation for synthetic biology. The synthesis of orthogonal systems that are uncoupled from evolutionary constraints, and selectively abstracted from cellular regulation, is an emerging approach to making biology more amenable to engineering. Here, we combine orthogonal transcription by T7 RNA polymerase and translation by orthogonal ribosomes (O-ribosomes), creating an orthogonal gene expression pathway in Escherichia coli. We design and implement compact, orthogonal gene expression networks. In particular we focus on creating transcription–translation feed-forward loops (FFLs). The transcription–translation FFLs reported cannot be created by using the cells' gene expression machinery and introduce information-processing delays on the order of hours into gene expression. We refactor the rRNA operon, uncoupling the synthesis of the orthogonal 16S rRNA for the O-ribosome from the synthesis and processing of the rest of the rRNA operon, thereby defining a minimal module that can be added to the cell for O-ribosome production. The minimal O-ribosome permits the rational alteration of the delay in an orthogonal gene expression FFL. Overall this work demonstrates that system-level dynamic properties are amenable to rational manipulation and design in orthogonal systems. In the future this system may be further evolved and tuned to provide a spectrum of tailored dynamics in gene expression and investigate the effects of delays in cellular decision-making processes." Full paper: Synthesis of orthogonal transcription-translation networks — PNAS

Labels: engineering, gene circuits, systems biology

"How's this for creativity? Take Escherichia coli bacteria. Transform them into light-sensitive organisms by fusing a photoreceptor from the cyanobacterium Synechocystis to a protein in the E. coli membrane. Make a film (in both senses) of such bacteria and use them to record an image with a resolution of 100 megapixels per square inch". For more details see the Special Issue on Synthetic Biology @ Nature

Labels: artificial gene regulation, gene circuits, synthetic bioology, synthetic life