Open AccessDissertation
An E. coli cell-free transcription- translation system: modeling gene expression and characterizing CRISPR elements and gene circuits
Ryan Marshall
- 01 Sep 2019
2
TL;DR: This dissertation aims to provide a history of particle magnetism in the Large Hadron Collider and some of the techniques used to characterize the fluid mechanics of magnetism.
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Abstract: University of Minnesota Ph.D. dissertation. September 2019. Major: Physics. Advisor: Vincent Noireaux. 1 computer file (PDF); xi, 125 pages.
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Citations
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References
Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
Sergey Shmakov,Omar O. Abudayyeh,Kira S. Makarova,Yuri I. Wolf,Jonathan S. Gootenberg,Ekaterina Semenova,Leonid Minakhin,Julia Joung,Silvana Konermann,Konstantin Severinov,Konstantin Severinov,Konstantin Severinov,Feng Zhang,Eugene V. Koonin +13 more
- 01 Oct 2015
TL;DR: Comparison analysis indicates that Class 2 CRISPR-Cas systems evolved on multiple occasions through recombination of Class 1 adaptation modules with effector proteins acquired from distinct mobile elements.
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CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3
Edze R. Westra,Paul B. G. van Erp,Tim Künne,Shi Pey Wong,Raymond H.J. Staals,Christel L.C. Seegers,Sander Bollen,Matthijs M. Jore,Ekaterina Semenova,Konstantin Severinov,Konstantin Severinov,Willem M. de Vos,Willem M. de Vos,Remus T. Dame,Renko de Vries,Stan J. J. Brouns,John van der Oost +16 more
TL;DR: It is shown that Cascade efficiently locates target sequences in negatively supercoiled DNA, but only if these are flanked by a protospacer-adjacent motif (PAM), which exclusively involves the crRNA-complementary DNA strand.
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Inhibition of CRISPR-Cas9 with Bacteriophage Proteins
Benjamin J. Rauch,Melanie R. Silvis,Judd F. Hultquist,Judd F. Hultquist,Christopher S. Waters,Michael J. McGregor,Michael J. McGregor,Nevan J. Krogan,Nevan J. Krogan,Joseph Bondy-Denomy +9 more
TL;DR: Four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages present tools that can be used to regulate the genome engineering activities of CRISpr-Cas 9.
499
Engineering dynamic pathway regulation using stress-response promoters
Robert H. Dahl,Fuzhong Zhang,Jorge Alonso-Gutierrez,Jorge Alonso-Gutierrez,Edward E. K. Baidoo,Edward E. K. Baidoo,Tanveer S. Batth,Tanveer S. Batth,Alyssa M. Redding-Johanson,Alyssa M. Redding-Johanson,Christopher J. Petzold,Christopher J. Petzold,Aindrila Mukhopadhyay,Aindrila Mukhopadhyay,Taek Soon Lee,Taek Soon Lee,Paul D. Adams,Paul D. Adams,Paul D. Adams,Jay D. Keasling +19 more
TL;DR: This paper applied whole-genome transcript arrays to identify promoters that respond to the accumulation of toxic intermediates, and then used these promoters to control accumulation of the intermediate and improve the final titers of a desired product.
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Mimicking the Escherichia coli cytoplasmic environment activates long‐lived and efficient cell‐free protein synthesis
TL;DR: By more closely replicating the physiological conditions of the cytoplasm of Escherichia coli, the Cytomim system provides a stable energy supply for protein expression without phosphate accumulation, pH change, exogenous enzyme addition, or the need for expensive high‐energy phosphate compounds.
455