Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits

2020 ◽  
Vol 9 (11) ◽  
pp. 2917-2926
Author(s):  
Mariana Gómez-Schiavon ◽  
Galen Dods ◽  
Hana El-Samad ◽  
Andrew H. Ng
Author(s):  
Pascal A. Pieters ◽  
Bryan L. Nathalia ◽  
Ardjan J. van der Linden ◽  
Peng Yin ◽  
Jongmin Kim ◽  
...  

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0194779 ◽  
Author(s):  
Sayuri Katharina Hortsch ◽  
Andreas Kremling
Keyword(s):  

2016 ◽  
Vol 44 (3) ◽  
pp. 681-683 ◽  
Author(s):  
James R. Johnson ◽  
Rosalinda D'Amore ◽  
Simon C. Thain ◽  
Thomas Craig ◽  
Hannah V. McCue ◽  
...  

GeneMill officially launched on 4th February 2016 and is an open access academic facility located at The University of Liverpool that has been established for the high-throughput construction and testing of synthetic DNA constructs. GeneMill provides end-to-end design, construction and phenotypic characterization of small to large gene constructs or genetic circuits/pathways for academic and industrial applications. Thus, GeneMill is equipping the scientific community with easy access to the validated tools required to explore the possibilities of Synthetic Biology.


2021 ◽  
Author(s):  
Cameron D McBride ◽  
Domitilla Del Vecchio

The design of genetic circuits typically relies on characterization of constituent modules in isolation to predict the behavior of modules' composition. However, it has been shown that the behavior of a genetic module changes when other modules are in the cell due to competition for shared resources. In order to engineer multi-module circuits that behave as intended, it is thus necessary to predict changes in the behavior of a genetic module when other modules load cellular resources. Here, we introduce two characteristics of circuit modules: the demand for cellular resources and the sensitivity to resource loading. When both are known for every genetic module in a circuit, they can be used to predict any module's behavior upon addition of any other module to the cell. We develop an experimental approach to measure both characteristics for any circuit module using a resource sensor module. Using the measured resource demand and sensitivity for each module in a library, the outputs of the modules can be accurately predicted when they are inserted in the cell in arbitrary combinations. These resource competition characteristics may be used to inform the design of genetic circuits that perform as predicted despite resource competition.


2018 ◽  
Author(s):  
René Daer ◽  
Cassandra Barrett ◽  
Ernesto Luna Melendez ◽  
Jiaqi Wu ◽  
Stefan Tekel ◽  
...  

AbstractQuorum sensing networks have been identified in over one hundred bacterial species to date. A subset of these networks regulate group behaviors, such as bioluminescence, virulence, and biofilm formation, by sending and receiving small molecules called homoserine lactones (HSLs). Bioengineers have incorporated quorum sensing pathways into genetic circuits to connect logical operations. However, the development of higher-order genetic circuitry is inhibited by crosstalk, in which one quorum sensing network responds to HSLs produced by a different network. Here, we report the construction and characterization of a library of ten synthases including some that are expected to produce HSLs that are incompatible with the Lux pathway, and therefore show no crosstalk. We demonstrated their function in a common lab chassis, Escherichia coli BL21, and in two contexts, liquid and solid agar cultures, using decoupled Sender and Receiver pathways. We observed weak or strong stimulation of a Lux Receiver by longer-chain or shorter-chain HSL-generating Senders, respectively. We also considered the under-investigated risk of unintentional release of incompletely deactivated HSLs in biological waste. We found that HSL-enriched media treated with bleach is still bioactive, while autoclaving deactivates LuxR induction. This work represents the most extensive comparison of quorum sensing synthases to date and greatly expands the bacterial signaling toolkit while recommending practices for disposal based on empirical, quantitative evidence.


2008 ◽  
Vol 381-382 ◽  
pp. 317-320
Author(s):  
G.X. Jia ◽  
Xing Hua Qu ◽  
H. Gong ◽  
S.H. Ye

This paper describes a method to characterizing the digital camera. The nonlinear relationship between the RGB signals generated by a digital camera and original image CIEXYZ values was obtained using the polynomial regression procedures. The reasonable structures of the polynomial were found for two digital cameras. The better number of polynomial terms was 19, yielding a modeling accuracy typically averaging 2.1~2.2 E ∆ units and maximally 9.5~10.9 E ∆ units. The experiments results showed that the polynomial regression could be used to characterize commonly digital camera.


Author(s):  
B. L. Soloff ◽  
T. A. Rado

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.


Author(s):  
A.R. Pelton ◽  
A.F. Marshall ◽  
Y.S. Lee

Amorphous materials are of current interest due to their desirable mechanical, electrical and magnetic properties. Furthermore, crystallizing amorphous alloys provides an avenue for discerning sequential and competitive phases thus allowing access to otherwise inaccessible crystalline structures. Previous studies have shown the benefits of using AEM to determine crystal structures and compositions of partially crystallized alloys. The present paper will discuss the AEM characterization of crystallized Cu-Ti and Ni-Ti amorphous films.Cu60Ti40: The amorphous alloy Cu60Ti40, when continuously heated, forms a simple intermediate, macrocrystalline phase which then transforms to the ordered, equilibrium Cu3Ti2 phase. However, contrary to what one would expect from kinetic considerations, isothermal annealing below the isochronal crystallization temperature results in direct nucleation and growth of Cu3Ti2 from the amorphous matrix.


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