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Experimentally driven verification of synthetic biological circuits

B. Yordanov, E. Appleton, R. Ganguly, E. A. Gol, S. B. Carr, S. Bhatia, T. Haddock, C. Belta, D. Densmore
2012 2012 Design, Automation & Test in Europe Conference & Exhibition (DATE)  
We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits.  ...  We describe experimental procedures to acquire characterization data for the assigned parts and construct mathematical models capturing all possible behaviors of the generated GRN.  ...  This material is based upon work supported by the Office of Naval Research under Grant No. N00014-11-1-0725.  ... 
doi:10.1109/date.2012.6176468 dblp:conf/date/YordanovAGGCBHBD12 fatcat:fo4yakstijh47n3x6hyuc735dy

Systems biology: new institute and applications

Jieming Chen
2011 The Yale Journal of Biology and Medicine  
This article includes a brief overview of the different topics presented at the symposium, followed by a discussion of the advantages and challenges of practical application of systems biology.  ...  The symposium served to provide Yale's scientific community with a glimpse into the wide range of research at the forefront of this interdisciplinary field.  ...  Different constraints are applied until components achieving the desired effects are found by in silico analyses, followed by experimental verification.  ... 
pmid:21451788 pmcid:PMC3064249 fatcat:6lqu7fudw5aevgpzewhwslnx6e

Recent development on synthetic biological devices treating bladder cancer

Zhicong Chen, Anbang He, Yuchen Liu, Weiren Huang, Zhiming Cai
2016 Synthetic and Systems Biotechnology  
We claimed that the Chinese synthetic biologists are promoting the basic research productions of tumor synthetic biology into the clinic.  ...  Thanks to the tremendous advances in genomics and the chemical synthesis of DNA in the past decade, scientists are now able to engineer genetic devices and circuits for cancer research and intervention  ...  Even though synthetic circuit therapy is making its way to treat a number of human cancers since the recent years of basic experimental research, the safe and effective use of gene delivery system remains  ... 
doi:10.1016/j.synbio.2016.08.001 pmid:29062946 pmcid:PMC5625735 fatcat:aeukmlukffboljc7ooteuexc6y

The role of predictive modelling in rationally re-engineering biological systems

Tie Koide, Wyming Lee Pang, Nitin S. Baliga
2009 Nature Reviews Microbiology  
However, large-scale re-engineering of a biological circuit will require systems-level optimization that will come from a deep understanding of operational relationships among all the constituent parts  ...  The integrated framework necessary for conducting such complex bioengineering requires the convergence of systems and synthetic biology.  ...  Acknowledgments This work was supported by grants from the National Institutes of Health (NIH; P50GM076547 and 1R01GM077398-01A2), Department of Environment (DoE; DE-FG02-07ER64327 and DE-FG02-07ER64327  ... 
doi:10.1038/nrmicro2107 pmid:19252506 pmcid:PMC2734281 fatcat:bqo77xkgujhcdk4msqnubsvcie

Sensitivity of Biological Models to Errors in Parameter Estimates

Robert S. Erb, George S. Michaels
1998 Biocomputing '99  
Turing's paper proposing a mathematical basis for pattern formation in developing organisms many mathematical approaches have been proposed to model biological phenomenon.  ...  The level of data now available demands the development of well-characterized and tested computational tools.  ...  The R is the rate of synthesis of the Figure 2 : Synthetic, three-gene circuit that demonstrates several biologically relevant relationships -periodicity, promoter / suppressor, and lead / lag phasing  ... 
doi:10.1142/9789814447300_0006 fatcat:zmanghwzibguzlokuyvmscdt3y

Noise-Aided Logic in an Electronic Analog of Synthetic Genetic Networks

Edward H. Hellen, Syamal K. Dana, Jürgen Kurths, Elizabeth Kehler, Sudeshna Sinha, Derek Abbott
2013 PLoS ONE  
We report the experimental verification of noise-enhanced logic behaviour in an electronic analog of a synthetic genetic network, composed of two repressors and two constitutive promoters.  ...  We observe good agreement between circuit measurements and numerical prediction, with the circuit allowing for robust logic operations in an optimal window of noise.  ...  analog circuit provides valuable verification.  ... 
doi:10.1371/journal.pone.0076032 pmid:24124531 pmcid:PMC3790844 fatcat:o7y73limojdc3fx6soocgdlc2m

Integrative metabolic engineering

George H McArthur IV, Pooja P Nanjannavar, Emily H Miller, Stephen S Fong
2015 AIMS Bioengineering  
Recent advances in experimental and computational synthetic biology are extremely useful for achieving metabolic engineering objectives.  ...  The integration of synthetic biology and metabolic engineering within an iterative design-build-test framework will improve the practice of metabolic engineering by relying more on efficient design strategies  ...  Fisher and other members of the Fong Lab for helpful discussions and for comments on the manuscript.  ... 
doi:10.3934/bioeng.2015.3.93 fatcat:2s26fw57nzauphsmyz2iledite

Composable Modular Models for Synthetic Biology

Goksel Misirli, Jennifer Hallinan, Anil Wipat
2014 ACM Journal on Emerging Technologies in Computing Systems  
The synthetic biology design process typically involves the composition of genetic circuits from individual parts.  ...  The synthetic biology design process typically involves the composition of genetic circuits from individual parts.  ...  This approach is clearly applicable to the design of synthetic genetic circuits.  ... 
doi:10.1145/2631921 fatcat:zz3khigjhneotnu3f2sxu73dlq

Synthetic Morphology: A Vision of Engineering Biological Form

Gabriele Gramelsberger
2020 Journal of the History of Biology  
The paper investigates the development of synthetic morphology and its relation to synthetic biology as well as its epistemic gains.  ...  In 2008 "synthetic morphology" was proposed as a prospective approach to engineering self-constructing anatomies by Jamie A. Davies of the University of Edinburgh.  ...  To view a copy of this licence, visit http://creat iveco mmons .org/licen ses/by/4.0/.  ... 
doi:10.1007/s10739-020-09601-w pmid:32358710 fatcat:jrymkkcszvfjzmc7wlwjaldhuy

Design Automation for Synthetic Biological Systems

Douglas Densmore, Soha Hassoun
2012 IEEE Design & Test of Computers  
Editors' notes: Through principled engineering methods, synthetic biology aims to build specialized biological components that can be modularly composed to create complex systems.  ...  This article outlines bio-design automation using two complementary design approaches, bottom-up modular construction from biological primitives and pathway-based approaches.  ...  This article highlighted the state of BDA tools and design flows for designing synthetic biological circuits and pathways, and outlined computational challenges that span specifying desired biological  ... 
doi:10.1109/mdt.2012.2193370 fatcat:zxaiso254bf63cxkskgdbatuti

Synthetic Morphology : a Vision of Engineering Biological Form

Gabriele Gramelsberger
2020 Journal of the History of Biology  
The paper investigates the development of synthetic morphology and its relation to synthetic biology as well as its epistemic gains.  ...  In 2008 "synthetic morphology" was proposed as a prospective approach to engineering self-constructing anatomies by Jamie A. Davies of the University of Edinburgh.  ...  Using CRISPR/Cas to engineer larger genetic circuits by linking the outputs of genetic circuits opens up new possibilities for synthetic biology.  ... 
doi:10.18154/rwth-2020-05352 fatcat:3pmh4b7xgva3nn2s4hpzbd5wle

Theoretical Design of Paradoxical Signaling-Based Synthetic Population Control Circuit in E. coli [article]

Michaëlle N Mayalu, Richard M Murray
2020 bioRxiv   pre-print
Here, we explore stability and robustness of a conceptualized synthetic circuit.  ...  Furthermore, we asses possible design principles that could exist among a subset of paradoxical circuit implementations.  ...  Green for help with conceptualizing circuit components within design and elucidating mechanisms. The authors acknowledge funding support from the Burroughs Wellcome Fund. The efforts  ... 
doi:10.1101/2020.01.27.921734 fatcat:nfhe3dj4yjh7hihpw6rn65r3ji

Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology [article]

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
2020 arXiv   pre-print
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models  ...  Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology.  ...  funded by the Engineering and Physical Sciences Research Council (EPSRC) within the remits of the Big Ideas initiative.  ... 
arXiv:2006.02720v1 fatcat:zyv26a5mhvfxnfm2wsmcyjn5km

Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit

Qiang Tang, Chunbo Lou, Shuang-Jiang Liu
2017 Journal of Biological Engineering  
As a proof of concept, we validated the EXIT circuit in Escherichia coli by harnessing homing endonuclease I-SceI and its cleavage site.  ...  Results: To bridge this gap, we designed a novel EXIT circuit with the homing endonuclease, which can be exploited for rapid and efficient elimination of various plasmids with diverse replication origins  ...  Availability of data and materials The data supporting the conclusions of this article is included within the article and its Additional file 1.  ... 
doi:10.1186/s13036-017-0072-5 pmid:28878819 pmcid:PMC5582390 fatcat:ljcokjtlgrhhzhxqzb5xhgdwji

Transcription Factor Target Gene Network governs the Logical Abstraction Analysis of the Synthetic Circuit in Leishmaniasis

Milsee Mol, Dipali Kosey, Ramanamurthy Boppana, Shailza Singh
2018 Scientific Reports  
A chimeric protein kinase C (PKC) is incorporated in the synthetic circuit, under the transcriptional regulation of Lac repressor and IPTG, as an inducer.  ...  Network analysis showed that NFkB links the signaling and gene network, used as a point of intervention through a synthetic circuit embedded within the negative autoregulatory feedback loop.  ...  In vitro verification of the working of the synthetic circuit. The designed synthetic construct with a negative autoregulatory loop, was synthesized by GeneArt, Invitrogen ® .  ... 
doi:10.1038/s41598-018-21840-w pmid:29472639 pmcid:PMC5823942 fatcat:jhjugaazlrdfbpksr756xvmmxm
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