Screening of Genetic Switches Based on the Twister Ribozyme Motif

2016 ◽  
pp. 225-239 ◽  
Author(s):  
Michele Felletti ◽  
Benedikt Klauser ◽  
Jörg S. Hartig
Keyword(s):  
Genetic Switches

scholarly journals Rapid and Liquid-Based Selection of Genetic Switches Using Nucleoside Kinase Fused with Aminoglycoside Phosphotransferase

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0120243 ◽  
Author(s):  
Masahiro Tominaga ◽  
Kohei Ike ◽  
Shigeko Kawai-Noma ◽  
Kyoichi Saito ◽  
Daisuke Umeno
Keyword(s):  
Aminoglycoside Phosphotransferase ◽  
Genetic Switches ◽  
Selection Of

scholarly journals Reconstructing an epigenetic landscape using a genetic ‘pulling’ approach

2019 ◽  
Author(s):  
Michael Assaf ◽  
Shay Be’er ◽  
Elijah Roberts
Keyword(s):  
Simulated Data ◽  
Stable Gene ◽  
Epigenetic Landscape ◽  
Developmental Pathway ◽  
Developmental Networks ◽  
Genetic Switches ◽  
Fundamental Quantity ◽  
Developmental Dynamics ◽  
Stable Gene Expression ◽  
General Method

Cells use genetic switches to shift between alternate stable gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Conceptually, these stable phenotypes can be considered as attractive states on an epigenetic landscape with phenotypic changes being transitions between states. Measuring these transitions is challenging because they are both very rare in the absence of appropriate signals and very fast. As such, it has proven difficult to experimentally map the epigenetic landscapes that are widely believed to underly developmental networks. Here, we introduce a new nonequilibrium perturbation method to help reconstruct a regulatory network’s epigenetic landscape. We derive the mathematical theory needed and then use the method on simulated data to reconstruct the landscapes. Our results show that with a relatively small number of perturbation experiments it is possible to recover an accurate representation of the true epigenetic landscape. We propose that our theory provides a general method by which epigenetic landscapes can be studied. Finally, our theory suggests that the total perturbation impulse required to induce a switch between metastable states is a fundamental quantity in developmental dynamics.

scholarly journals Noise Treatment in Models of Genetic Switches

2015 ◽  
Vol 108 (2) ◽  
pp. 313a-314a
Author(s):  
Mahua Roy ◽  
Elizabeth L. Read
Keyword(s):  
Genetic Switches

scholarly journals Design of orthogonal genetic switches based on a crosstalk map of σs, anti‐σs, and promoters

2013 ◽  
Vol 9 (1) ◽  
pp. 702 ◽  
Author(s):  
Virgil A Rhodius ◽  
Thomas H Segall‐Shapiro ◽  
Brian D Sharon ◽  
Amar Ghodasara ◽  
Ekaterina Orlova ◽  
...  
Keyword(s):  
Genetic Switches

scholarly journals Genetic switches designed for eukaryotic cells and controlled by serine integrases

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Mayna S. Gomide ◽  
Thais T. Sales ◽  
Luciana R. C. Barros ◽  
Cintia G. Limia ◽  
Marco A. de Oliveira ◽  
...  
Keyword(s):  
Eukaryotic Cells ◽  
Genetic Switches

Spatial Fluctuations and the Flipping of the Genetic Switch in a Cellular System

2000 ◽  
Vol 651 ◽  
Author(s):  
Ralf Metzler
Keyword(s):  
Cellular System ◽  
Genetic Switch ◽  
Cellular Processes ◽  
Genetic Switches ◽  
Spatial Fluctuations ◽  
Messenger Molecules

Abstract– It has been realised that noise plays an important rôle in cellular processes where fluctuation induced number fluctuations of certain messenger molecules become non–negligible, due to the small total number of these molecules within one cell. In the following, it is argued that spatial fluctuations of such molecules and their impact on genetic switches should be considered as well.

scholarly journals Modular and Versatile Trans‐Encoded Genetic Switches

2020 ◽  
Vol 132 (46) ◽  
pp. 20508-20512
Author(s):  
Avishek Paul ◽  
Eliza M. Warszawik ◽  
Mark Loznik ◽  
Arnold J. Boersma ◽  
Andreas Herrmann
Keyword(s):  
Genetic Switches

scholarly journals Design of Ligand-Controlled Genetic Switches Based on RNA Interference

2018 ◽  
pp. 169-179
Author(s):  
Shunnichi Kashida ◽  
Hirohide Saito
Keyword(s):  
Rna Interference ◽  
Genetic Switches

Maximum Caliber Can Characterize Genetic Switches with Multiple Hidden Species

2018 ◽  
Vol 122 (21) ◽  
pp. 5666-5677 ◽  
Author(s):  
Taylor Firman ◽  
Stephen Wedekind ◽  
T. J. McMorrow ◽  
Kingshuk Ghosh
Keyword(s):  
Genetic Switches

scholarly journals Control of ϕC31 integrase-mediated site-specific recombination by protein trans-splicing

2019 ◽  
Vol 47 (21) ◽  
pp. 11452-11460 ◽  
Author(s):  
Femi J Olorunniji ◽  
Makeba Lawson-Williams ◽  
Arlene L McPherson ◽  
Jane E Paget ◽  
W Marshall Stark ◽  
...  
Keyword(s):  
Genome Engineering ◽  
Genetic Circuits ◽  
Reporter System ◽  
Site Specific ◽  
Site Specific Recombination ◽  
Recombination System ◽  
Split Intein ◽  
Genetic Switches ◽  
Trans Splicing

Abstract Serine integrases are emerging as core tools in synthetic biology and have applications in biotechnology and genome engineering. We have designed a split-intein serine integrase-based system with potential for regulation of site-specific recombination events at the protein level in vivo. The ϕC31 integrase was split into two extein domains, and intein sequences (Npu DnaEN and Ssp DnaEC) were attached to the two termini to be fused. Expression of these two components followed by post-translational protein trans-splicing in Escherichia coli generated a fully functional ϕC31 integrase. We showed that protein splicing is necessary for recombination activity; deletion of intein domains or mutation of key intein residues inactivated recombination. We used an invertible promoter reporter system to demonstrate a potential application of the split intein-regulated site-specific recombination system in building reversible genetic switches. We used the same split inteins to control the reconstitution of a split Integrase-Recombination Directionality Factor fusion (Integrase-RDF) that efficiently catalysed the reverse attR x attL recombination. This demonstrates the potential for split-intein regulation of the forward and reverse reactions using the integrase and the integrase-RDF fusion, respectively. The split-intein integrase is a potentially versatile, regulatable component for building synthetic genetic circuits and devices.

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