Characterization of noise in multistable genetic circuits reveals ways to modulate heterogeneity

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.

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Advancement of Emerging Tools in Synthetic Biology for the Designing and Characterization of Genetic Circuits

Systems and Synthetic Biology ◽

10.1007/978-94-017-9514-2_17 ◽

2014 ◽

pp. 327-339

Author(s):

Vijai Singh ◽

Indra Mani ◽

Dharmendra Kumar Chaudhary

Keyword(s):

Synthetic Biology ◽

Genetic Circuits

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Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits

ACS Synthetic Biology ◽

10.1021/acssynbio.0c00288 ◽

2020 ◽

Vol 9 (11) ◽

pp. 2917-2926

Author(s):

Mariana Gómez-Schiavon ◽

Galen Dods ◽

Hana El-Samad ◽

Andrew H. Ng

Keyword(s):

Genetic Circuits ◽

Modeling Accuracy

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Predicting Composition of Genetic Circuits with Resource Competition: Demand and Sensitivity

10.1101/2021.05.26.445862 ◽

2021 ◽

Author(s):

Cameron D McBride ◽

Domitilla Del Vecchio

Keyword(s):

Experimental Approach ◽

Resource Competition ◽

Genetic Circuits ◽

Shared Resources ◽

Resource Demand ◽

Sensor Module ◽

Resource Loading ◽

Genetic Module

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.

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Characterization of Diverse Homoserine Lactone Synthases in Escherichia coli

10.1101/279349 ◽

2018 ◽

Author(s):

René Daer ◽

Cassandra Barrett ◽

Ernesto Luna Melendez ◽

Jiaqi Wu ◽

Stefan Tekel ◽

...

Keyword(s):

Escherichia Coli ◽

Quorum Sensing ◽

Bacterial Species ◽

Homoserine Lactone ◽

Genetic Circuits ◽

Quantitative Evidence ◽

Bacterial Signaling ◽

Solid Agar ◽

Strong Stimulation

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.

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Morphological Characterization of Mycobacteriophage R1

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051281 ◽

1974 ◽

Vol 32 ◽

pp. 254-255

Author(s):

B. L. Soloff ◽

T. A. Rado

Keyword(s):

Carbon Source ◽

Stationary Phase ◽

Growth Phase ◽

Minimal Medium ◽

Morphological Characterization ◽

Logarithmic Growth Phase ◽

Complete Lysis ◽

Lysogenic Culture ◽

Logarithmic Growth

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.

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AEM analysis of crystallization in Ti-based amorphous alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100075142 ◽

1983 ◽

Vol 41 ◽

pp. 270-271

Author(s):

A.R. Pelton ◽

A.F. Marshall ◽

Y.S. Lee

Keyword(s):

Magnetic Properties ◽

Amorphous Alloys ◽

Amorphous Materials ◽

Isothermal Annealing ◽

Amorphous Matrix ◽

Nucleation And Growth ◽

Current Interest ◽

Amorphous Films ◽

Electrical And Magnetic Properties

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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Characterization of Coherent, Ordered Precipitates in Nickel-Base Alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071168 ◽

1973 ◽

Vol 31 ◽

pp. 144-145

Author(s):

B. H. Kear ◽

J. M. Oblak

Keyword(s):

Stable Phase ◽

Nickel Base Superalloy ◽

Alloy 718 ◽

Commercial Alloy ◽

Precipitate Morphology ◽

Continuous Precipitation ◽

Nickel Base ◽

Base Superalloy ◽

Strengthening Precipitate

A nickel-base superalloy is essentially a Ni/Cr solid solution hardened by additions of Al (Ti, Nb, etc.) to precipitate a coherent, ordered phase. In most commercial alloy systems, e.g. B-1900, IN-100 and Mar-M200, the stable precipitate is Ni3 (Al,Ti) γ′, with an LI2structure. In A lloy 901 the normal precipitate is metastable Nis Ti3 γ′ ; the stable phase is a hexagonal Do2 4 structure. In Alloy 718 the strengthening precipitate is metastable γ″, which has a body-centered tetragonal D022 structure.Precipitate MorphologyIn most systems the ordered γ′ phase forms by a continuous precipitation re-action, which gives rise to a uniform intragranular dispersion of precipitate particles. For zero γ/γ′ misfit, the γ′ precipitates assume a spheroidal.

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The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071107 ◽

1973 ◽

Vol 31 ◽

pp. 132-133 ◽

Cited By ~ 1

Author(s):

R. E. Herfert

Keyword(s):

Surface Characterization ◽

Analytical Techniques ◽

X Ray Diffraction ◽

Depth Of Penetration ◽

X Ray ◽

The Past ◽

Transmission Electron ◽

Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

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