Functional Characterization of Insulation Effect for Synthetic Gene Circuits in Mammalian Cells

2018 ◽  
Vol 7 (2) ◽  
pp. 412-418 ◽  
Author(s):  
Weixi Liao ◽  
Bing Liu ◽  
Chih-Chun Chang ◽  
Ling-Jun Lin ◽  
Che Lin ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Functional Characterization ◽  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits ◽  
Insulation Effect

scholarly journals Synthetic Gene Circuits for Antimicrobial Resistance and Cancer Research

2021 ◽  
Author(s):  
Kevin S. Farquhar ◽  
Michael Tyler Guinn ◽  
Gábor Balázsi ◽  
Daniel A. Charlebois
Keyword(s):  
Mammalian Cells ◽  
Rational Design ◽  
Study Drug ◽  
Quantitative Model ◽  
Synthetic Gene ◽  
Modeling Tools ◽  
Gene Circuits ◽  
Novel Treatments ◽  
Synthetic Gene Circuits ◽  
Temporal Dimensions

Mathematical models and synthetic gene circuits are powerful tools to develop novel treatments for patients with drug-resistant infections and cancers. Mathematical modeling guides the rational design of synthetic gene circuits. These systems are then assembled into unified constructs from existing and/or modified genetic components from a range of organisms. In this chapter, we describe modeling tools for the design and characterization of chemical- and light-inducible synthetic gene circuits in different organisms and highlight how synthetic gene circuits are advancing biomedical research. Specifically, we demonstrate how these quantitative model systems are being used to study drug resistance in microbes and to probe the spatial–temporal dimensions of cancer in mammalian cells.

scholarly journals Scalable dynamic characterization of synthetic gene circuits

2019 ◽  
Author(s):  
Neil Dalchau ◽  
Paul K. Grant ◽  
Prashant Vaidyanathan ◽  
Carlo Spaccasassi ◽  
Colin Gravill ◽  
...  
Keyword(s):  
Dynamic Behavior ◽  
Time Window ◽  
Population Level ◽  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits ◽  
Microtiter Plates ◽  
Correct Function ◽  
Complex Circuits

AbstractThe dynamic behavior of synthetic gene circuits plays a key role in ensuring their correct function. Although there has been substantial work on modeling dynamic behavior after circuit construction, the forward engineering of dynamic behavior remains a major challenge. Previous engineering methods have focused on quantifying average behaviors of circuits over an extended time window, however this provides a static characterization of behavior that is a poor predictor of dynamics. Here we present a method for characterizing the dynamic behavior of synthetic gene circuits, using parameter inference of dynamical system models applied to time-series measurements of cell cultures growing in microtiter plates. We demonstrate that the behaviors of simple devices can be characterized dynamically and used to predict the behaviors of more complex circuits. Specifically, we compose 23 biological parts into 9 devices and use them to design 9 synthetic gene circuits in E. coli that provide core functionality for engineering cell behavior at the population level, including relays, receivers and a degrader. We embody our method in a software package and corresponding programming language. Our method supports the notion of an inference graph for iterative inference of models as new circuits are constructed, without the need to infer all models from scratch, and lays the foundation for characterizing large libraries of synthetic gene circuits in a scalable manner.

scholarly journals Structural and Functional Characterization of SARS-CoV-2 RBD Domains Produced in Mammalian Cells

2021 ◽  
Author(s):  
Christoph Gstöttner ◽  
Tao Zhang ◽  
Anja Resemann ◽  
Sophia Ruben ◽  
Stuart Pengelley ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Functional Characterization

Synthetic Gene Circuits: Design, Implement, and Apply

2021 ◽  
pp. 1-18
Author(s):  
Andrew Lezia ◽  
Arianna Miano ◽  
Jeff Hasty
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

Synthetic Gene Circuits

2014 ◽  
pp. 1-56 ◽  
Author(s):  
Barbara Jusiak ◽  
Ramiz Daniel ◽  
Fahim Farzadfard ◽  
Lior Nissim ◽  
Oliver Purcell ◽  
...  
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits

Identification and functional characterization of a novel human protein highly related to the yeast dynamin-like GTPase Vps1p

1998 ◽  
Vol 111 (10) ◽  
pp. 1341-1349 ◽  
Author(s):  
M. Imoto ◽  
I. Tachibana ◽  
R. Urrutia
Keyword(s):  
Endoplasmic Reticulum ◽  
Cho Cells ◽  
Mammalian Cells ◽  
Functional Characterization ◽  
Luciferase Reporter ◽  
Pleckstrin Homology ◽  
Rich Region ◽  
Gtpase Domain ◽  
Proline Rich Region

Dynamin proteins containing a GTPase domain, a pleckstrin homology motif and a proline-rich tail participate in receptor-mediated endocytosis in organisms ranging from insects to vertebrates. In addition, dynamin-related GTPases, such as the yeast Golgi protein Vps1p, which lack both the pleckstrin homology motif and the proline-rich region, participate in vesicular transport within the secretory pathway in lower eukaryotes. However, no data is available on the existence of Vps1p-like proteins in mammalian cells. In this study, we report the identification and characterization of a novel gene encoding a human dynamin-related protein, DRP1, displaying high similarity to the Golgi dynamin-like protein Vps1p from yeast and to a Caenorhabditis elegans protein deposited in the databank. These proteins are highly conserved in their N-terminal tripartite GTPase domain but lack the pleckstrin homology motif and proline-rich region. Northern blot analysis reveals that the DRP1 mRNA is detected at high levels in human muscle, heart, kidney and brain. Immunolocalization studies in Chinese hamster ovary (CHO) cells using an epitope-tagged form of DRP1 and confocal microscopy show that this protein is concentrated in a perinuclear region that labels with the endoplasmic reticulum marker DiOC6(3) and the Golgi marker C5-DMB-Cer. In addition, the localization of DRP1 is highly similar to the localization of the endoplasmic reticulum and cis-Golgi GTPase Rab1A, but not to the staining for the trans-Golgi GTPase Rab6. Furthermore, overexpression of a cDNA encoding a GTP binding site mutant of DRP1 (DRP1(K38E)) in CHO cells decreases the amount of a secreted luciferase reporter protein, whereas the overexpression of wild-type DRP1 increases the secretion of this marker. Together, these results constitute the first structural and functional characterization of a mammalian protein similar to the yeast dynamin-related GTPase Vps1p and indicate that the participation of these proteins in secretion has been conserved throughout evolution.

scholarly journals Two cellular resource‐based models linking growth and parts characteristics aids the study and optimisation of synthetic gene circuits

2017 ◽  
Vol 1 (1) ◽  
pp. 30-39 ◽  
Author(s):  
Huijuan Wang ◽  
Maurice H.T. Ling ◽  
Tze Kwang Chua ◽  
Chueh Loo Poh
Keyword(s):  
Synthetic Gene ◽  
Gene Circuits ◽  
Synthetic Gene Circuits
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