life inspired

"For the first time, synthetic biologists have created a genetic device that mimics one of the widgets on which all of modern electronics is based, the three-terminal transistor. Like standard electronic transistors, the new biological transistor is expected to work in many different biological circuit designs. Together with other advances in crafting genetic circuitry, that should make it easier for scientists to program cells to do everything from monitor pollutants and the progression of disease to turning on the output of medicines and biofuels." Full news article @ ScienceNOW

Labels: circuits, computation, computational biology, systems biology

"Combining transcriptomic and signaling data, we develop an evolutionary computational procedure that allows obtaining alternative genomic transcriptional regulatory network (GTRN) that still maintains its adaptability to dynamic environments. We apply our methodology to an E. coli GTRN and show that it could be rewired to simpler transcriptional regulatory structures." Full paper @
PNAA

Labels: evolutionary algorithms, gene regulation, synthetic biology, systems biology

"Engineered biological systems that integrate multi-input sensing, sophisticated information processing, and precisely regulated actuation in living cells could be useful in a variety of applications." Full article @ Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells. Science 2 September 2011: Vol. 333 no. 6047 pp. 1307-1311

Labels: synthetic biology, systems biology

"Synthetic biology goes beyond classic genetic engineering as it attempts to engineer living systems to perform new functions not found in nature. Ten years ago this week, Nature published a pair of seminal papers that stimulated 'systems biology' thinking in the field. This web focus gathers these two papers together with papers more recently published by Nature in the same spirit."

Labels: synthetic biology, systems biology

"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

Four computational modeling strategies and the data that build them. Full story @ The Scientist

Labels: systems biology

"Some peculiar microorganisms are showing systems biology can color in what's missing from models of biochemical and cellular networks." Full article @ The Scientist

Labels: complex systems, systems biology