Foundations for the design and implementation of synthetic genetic circuits : Abstract : Nature Reviews Genetics. Efficient and sequence-independent ... [Proc Natl Acad Sci U S A. 2012. Foundations for the design and implementation of synthetic genetic circuits : Abstract : Nature Reviews Genetics. Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012. Natural strategies for the spatial optimizatio... [Nat Chem Biol. 2012. Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012. Rapid and orthogonal logic gating with a gibbe... [Nat Chem Biol. 2012. A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids.
We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Reprogramming the Genetic Code. Synthetic Biology: Mapping the Scientific Landscape. Results The Rise of Synthetic Biology As of January 2012 a total of 1,255 publications were listed in Web of Science for synthetic biology and synthetic genomics in the period to the end of December 2011 (Figure 1).
Synthetic Genetic Polymers Capable of Heredity and Evolution. Genetic information storage and processing rely on just two polymers, DNA and RNA, yet whether their role reflects evolutionary history or fundamental functional constraints is currently unknown.
With the use of polymerase evolution and design, we show that genetic information can be stored in and recovered from six alternative genetic polymers based on simple nucleic acid architectures not found in nature [xeno-nucleic acids (XNAs)]. We also select XNA aptamers, which bind their targets with high affinity and specificity, demonstrating that beyond heredity, specific XNAs have the capacity for Darwinian evolution and folding into defined structures. Thus, heredity and evolution, two hallmarks of life, are not limited to DNA and RNA but are likely to be emergent properties of polymers capable of information storage. Synthetic Genetic Polymers Capable of Heredity and Evolution. Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit.
Abstract Gene expression actualizes the organismal phenotypes encoded within the genome in an environment-dependent manner.
Among all encoded phenotypes, cell population growth rate (fitness) is perhaps the most important, since it determines how well-adapted a genotype is in various environments. Traditional biological measurement techniques have revealed the connection between the environment and fitness based on the gene expression mean. Yet, recently it became clear that cells with identical genomes exposed to the same environment can differ dramatically from the population average in their gene expression and division rate (individual fitness).
Trends in Biotechnology - Distributed computation: the new wave of synthetic biology devices. Distributed computation: the new wave of synthetic biology devices Volume 30, Issue 6 , Pages 342-349, Publication Date 18 April 2012 Copyright © 2012 Elsevier Ltd All rights reserved. DOI: 10.1016/j.tibtech.2012.03.006 Javier Macía. Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012. A Biobrick Library for Cloning Custom Eukaryotic Plasmids. Researchers often require customised variations of plasmids that are not commercially available.
Here we demonstrate the applicability and versatility of standard synthetic biological parts (biobricks) to build custom plasmids. For this purpose we have built a collection of 52 parts that include multiple cloning sites (MCS) and common protein tags, protein reporters and selection markers, amongst others. Importantly, most of the parts are designed in a format to allow fusions that maintain the reading frame. MIT-CSAIL-TR-2012-008. Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency. Abstract Cellular efficiency in protein translation is an important fitness determinant in rapidly growing organisms.
It is widely believed that synonymous codons are translated with unequal speeds and that translational efficiency is maximized by the exclusive use of rapidly translated codons. Here we estimate the in vivo translational speeds of all sense codons from the budding yeast Saccharomyces cerevisiae. Surprisingly, preferentially used codons are not translated faster than unpreferred ones. We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency under tRNA shortage. Current Opinion in Biotechnology - A retrosynthetic biology approach to therapeutics: from conception to delivery. Volume 23, Issue 6, December 2012, Pages 948–956 Phosphorus biotechnology • Pharmaceutical biotechnology Edited By Andrew N Shilton, Lars M Blank, Francis E Nano and José F Rodríguez De novo biosynthetic pathways are designed, assembled and optimized to produce high-value compounds such as drugs and chemical building blocks from renewable resources.
Engineering Molecular Circuits Usin... [Annu Rev Chem Biomol Eng. 2012. Integrated Electromicrobial Conversion of CO2 to Higher Alcohols. 1203808109.full. Rationally designed families of orthogonal RNA... [Nat Chem Biol. 2012. A Sensitive Switch for Visualizing Natural Gene Silencing in Single Cells - ACS Synthetic Biology. † School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona 85287, United States ‡ Laboratory of Cellular and Molecular Engineering, University of Bologna, I-47521 Cesena, Italy § Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
Signaling-mediated bacterial persister formation. [Nat Chem Biol. 2012. Signaling-mediated bacterial persister formation. [Nat Chem Biol. 2012. Generation of a Synthetic Memory Trace. The Imaginary Mind of a Mouse. Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology. Yeast is an ideal organism for the development and application of synthetic biology, yet there remain relatively few well-characterised biological parts suitable for precise engineering of this chassis.
In order to address this current need, we present here a strategy that takes a single biological part, a promoter, and re-engineers it to produce a fine-graded output range promoter library and new regulated promoters desirable for orthogonal synthetic biology applications. A highly constitutive Saccharomyces cerevisiae promoter, PFY1p, was identified by bioinformatic approaches, characterised in vivo and diversified at its core sequence to create a 36-member promoter library.
1108.3752. Phase transitions in the assembly of multivalent sign... [Nature. 2012. A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads. We describe an autonomous DNA nanorobot capable of transporting molecular payloads to cells, sensing cell surface inputs for conditional, triggered activation, and reconfiguring its structure for payload delivery.
The device can be loaded with a variety of materials in a highly organized fashion and is controlled by an aptamer-encoded logic gate, enabling it to respond to a wide array of cues. We implemented several different logical AND gates and demonstrate their efficacy in selective regulation of nanorobot function. As a proof of principle, nanorobots loaded with combinations of antibody fragments were used in two different types of cell-signaling stimulation in tissue culture. Our prototype could inspire new designs with different selectivities and biologically active payloads for cell-targeting tasks.
An Engineered Microbial Platform for Direct Biofuel Production from Brown Macroalgae. Synthetic biology: Simplifying design. [Nat Rev Genet. 2012. A sensing array of radically coupled genetic 'biopixels' [Nature. 2011. Synthetic quorum-sensing circuit to control consortial biofilm formation and dispersal in a microfluidic device : Nature Communications. Microfluidic biofilm engineering circuit The microfluidic biofilm engineering (μBE) signalling circuit was constructed in E. coli using two engineered biofilm-dispersing proteins, Hha13D6 (ref. 15) and BdcAE50Q16, along with the P. aeruginosa LasI/LasR QS system (Fig. 1a) for use in the novel microfluidic device (Fig. 1b).
E. coli hha31 was used as the host as deletion of hha increases biofilm formation14 and provides a background in which there is no wild-type Hha. Lactococcal promoter CP2532 was used as the strong constitutive promoter for two of the three proteins on each plasmid. Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression. Emerging biomedical applications of synthetic biology : Abstract : Nature Reviews Genetics. In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology. We show that difficulties in regulating cellular behavior with synthetic biological circuits may be circumvented using in silico feedback control. By tracking a circuit's output in Saccharomyces cerevisiae in real time, we precisely control its behavior using an in silico feedback algorithm to compute regulatory inputs implemented through a genetically encoded light-responsive module.
Moving control functions outside the cell should enable more sophisticated manipulation of cellular processes whenever real-time measurements of cellular variables are possible. View full text Figures. From DNA to Targeted Therapeutics: Bringing Synthetic Biology to the Clinic. Science Translational Medicinestm.sciencemag.org Sci Transl Med 26 October 2011: Vol. 3, Issue 106, p. 106ps42 Sci. Transl. Med. DOI: 10.1126/scitranslmed.3002944 Perspective Bioengineering. Bayesian design of synthetic biological systems. Author Affiliations Edited by Peter J. Bickel, University of California, Berkeley, CA, and approved July 27, 2011 (received for review December 1, 2010) Abstract Here we introduce a new design framework for synthetic biology that exploits the advantages of Bayesian model selection. We will argue that the difference between inference and design is that in the former we try to reconstruct the system that has given rise to the data that we observe, whereas in the latter, we seek to construct the system that produces the data that we would like to observe, i.e., the desired behavior.
Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology : Nature Communications. Arming yeast for synthetic biology : Nature Biotechnology. Sequential Establishment of Stripe Patterns in an Expanding Cell Population. 110118_imaginenano. NanoBioMed2011_Douglas_Shawn_shawn.douglas.
Yeast thrives with partially synthetic genome. Entrainment of a Population of Synthetic Genetic Oscillators. Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells. Chemical and Genetic Engineering of Selective Ion Channel–Ligand Interactions. A Grand Challenge in Biology. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In. Science Magazine: Sign In.
The Allure of Synthetic Biology. Expanding the Genetic Code of Escherichia coli with Phosphoserine. Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks. Bringing It Together with RNA. Organization of Intracellular Reactions with Rationally Designed RNA Assemblies. Methods in Enzymology : Multiplexed Genome Engineering and Genotyping Methods : : Applications for Synthetic Biology and Metabolic Engineering. Chip chips away at the cost of a genome. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement. Microfluidic technologies for synthetic biology. [Int J Mol Sci. 2011] - PubMed result.
GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. SCRM paper - revision draft 13 - Powered by Google Docs. Organization of Intracellular Reactions with Rationally Designed RNA Assemblies. Synthetic Physiology. A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice. Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades. Synthetic Biology. Amit_2010. Boston University: Applied BioDynamics Laboratory. Engineering microbial biofuel tolerance. Tunable_signal. Informing Biological Design by Integration of Systems and Synthetic Biology.
In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology. In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology. In silico feedback for in vivo regulation of a gene expression circuit : Nature Biotechnology.