Abstract：
:As engineering foundations such as standards and abstraction begin to mature within synthetic biology, it is vital that genetic design automation (GDA) tools be developed to enable synthetic biologists to automatically select standardized DNA components from a library to meet the behavioral specification for a genetic circuit. To this end, we have developed a genetic technology mapping algorithm that builds on the directed acyclic graph (DAG) based mapping techniques originally used to select parts for digital electronic circuit designs and implemented it in our GDA tool, iBioSim. It is among the first genetic technology mapping algorithms to adapt techniques from electronic circuit design, in particular the use of a cost function to guide the search for an optimal solution, and perhaps that which makes the greatest use of standards for describing genetic function and structure to represent design specifications and component libraries. This paper demonstrates the use of our algorithm to map the specifications for three different genetic circuits against four randomly generated libraries of increasing size to evaluate its performance against both exhaustive search and greedy variants for finding optimal and near-optimal solutions.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Roehner N,Myers CJdoi
10.1021/sb400135tsubject
Has Abstractpub_date
2014-08-15 00:00:00pages
543-55issue
8issn
2161-5063journal_volume
3pub_type
杂志文章abstract：:Scarless genetic manipulation of genomes is an essential tool for biological research. The restriction-modification (R-M) system is a defense system in bacteria that protects against invading genomes on the basis of its ability to distinguish foreign DNA from self DNA. Here, we designed an R-M system-mediated genome e...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.7b00254
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abstract：:The methods to execute biological experiments are evolving. Affordable fluid handling robots and on-demand biology enterprises are making automating entire experiments a reality. Automation offers the benefit of high-throughput experimentation, rapid prototyping, and improved reproducibility of results. However, learn...
journal_title：ACS synthetic biology
pub_type： 杂志文章
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journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.6b00025
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journal_title：ACS synthetic biology
pub_type： 杂志文章
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更新日期：2014-11-21 00:00:00
abstract：:To program cells in a dynamic manner, synthetic biologists require precise control over the threshold levels and timing of gene expression. However, in practice, modulating gene expression is widely carried out using prototypical ligand-inducible promoters, which have limited tunability and spatiotemporal resolution. ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
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abstract：:The cell contents are encapsulated within a compartment, the volume of which is a fundamental physical parameter that may affect intracompartmental reactions. However, there have been few studies to elucidate whether and how volume changes alone can affect the reaction kinetics. It is difficult to address these questi...
journal_title：ACS synthetic biology
pub_type： 杂志文章
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更新日期：2012-09-21 00:00:00
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journal_title：ACS synthetic biology
pub_type： 杂志文章
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journal_title：ACS synthetic biology
pub_type： 杂志文章
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更新日期：2015-10-16 00:00:00
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journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.5b00048
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
pub_type： 杂志文章
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更新日期：2015-10-16 00:00:00
abstract：:As fast terminators of G-protein coupled receptor (GPCR) signaling, regulators of G-protein signaling (RGS) serve critical roles in fine-tuning second messenger levels and, consequently, cellular responses to external stimuli. Here, we report the creation of an optogenetic RGS2 (opto-RGS2) that suppresses agonist-evok...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.8b00065
更新日期：2018-06-15 00:00:00
abstract：:The deeply red-colored natural compound prodigiosin is a representative of the prodiginine alkaloid family, which possesses bioactivities as antimicrobial, antitumor, and antimalarial agents. Various bacteria including the opportunistic human pathogen Serratia marcescens and different members of the Streptomycetaceae ...
journal_title：ACS synthetic biology
pub_type： 杂志文章
doi：10.1021/acssynbio.7b00099
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journal_title：ACS synthetic biology
pub_type： 杂志文章
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abstract：:Cell-free protein synthesis (CFPS) is a widely used research tool in systems and synthetic biology. However, if CFPS is to become a mainstream technology for applications such as point of care manufacturing, we must understand the performance limits and costs of these systems. Toward this question, we used sequence sp...
journal_title：ACS synthetic biology
pub_type： 杂志文章
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
pub_type： 信件
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更新日期：2018-03-16 00:00:00
abstract：:Phenazine-1-carboxamide (PCN) produced by multifarious Pseudomonas strains represents a promising candidate as a new metabolite pesticide due to its broad-spectrum antifungal activity and capacity to induce systemic resistance in plants. The rice rhizosphere Pseudomonas strain PA1201 contains two reiterated gene clust...
journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
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journal_title：ACS synthetic biology
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