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Akademický článek

Analysis of localized cAMP perturbations within a tissue reveal the effects of a local, dynamic gap junction state on ERK signaling.

Autor: João Pedro Fonseca, Elham Aslankoohi, Andrew H Ng, Michael Chevalier

Publikováno v: PLoS Computational Biology, Vol 18, Iss 3, p e1009873 (2022)

Beyond natural stimuli such as growth factors and stresses, the ability to experimentally modulate at will the levels or activity of specific intracellular signaling molecule(s) in specified cells within a tissue can be a powerful tool for uncovering

Externí odkaz: https://doaj.org/article/872bc8e78aee4415afd556e61d596db2

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Akademický článek

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

Autor: Kale Kundert, James E. Lucas, Kyle E. Watters, Christof Fellmann, Andrew H. Ng, Benjamin M. Heineike, Christina M. Fitzsimmons, Benjamin L. Oakes, Jiuxin Qu, Neha Prasad, Oren S. Rosenberg, David F. Savage, Hana El-Samad, Jennifer A. Doudna, Tanja Kortemme

Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)

Control of CRISPR-Cas9 activity allows for fine-tuning of editing and gene expression. Here the authors use gRNAs modified with RNA aptamers to enable small molecule control in bacterial systems.

Externí odkaz: https://doaj.org/article/75a198d8f2ba47a985055e98863b4ffd

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Competitive Displacement of De Novo Designed HeteroDimers Can Reversibly Control Protein–Protein Interactions and Implement Feedback in Synthetic Circuits

Autor: Taylor H. Nguyen, Galen Dods, Mariana Gómez-Schiavon, Muziyue Wu, Zibo Chen, Ryan Kibler, David Baker, Hana El-Samad, Andrew H. Ng

Publikováno v: GEN Biotechnology. 1:91-100

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::358fdf6384761e87561add2ed8a69de6
https://doi.org/10.1089/genbio.2021.0011

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Modular and tunable biological feedback control using a de novo protein switch

Autor: Lucas M. Waldburger, David Baker, Taylor H. Nguyen, Mariana Gómez-Schiavon, Andrew H. Ng, Galen Dods, John E. Dueber, Hana El-Samad, Jennifer A. Samson, Scott E. Boyken, Robert A. Langan

Publikováno v: Nature. 572:265-269

De novo-designed proteins1-3 hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins4-7. One such designer protein-degronLOCKR, which is based on 'latching orthogonal cage-ke

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::57819c46fcc2efb94d08a23ddf558fa2
https://doi.org/10.1038/s41586-019-1425-7

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De Novo Design of Bioactive Protein Switches

Autor: Galen Dods, Zibo Chen, Andrew H. Ng, Marc J. Lajoie, Jennifer A. Samson, David Baker, Taylor H. Nguyen, Alexandra Westbrook, John E. Dueber, Walter R. P. Novak, Robert A. Langan, Vikram Khipple Mulligan, Stephanie Berger, Hana El-Samad, Scott E. Boyken

Publikováno v: Nature
Nature, vol 572, iss 7768

Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switch

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6c1838660a70806a925f9aba15ef1595
http://europepmc.org/articles/PMC6733528

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Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

Autor: Benjamin L. Oakes, Tanja Kortemme, Christof Fellmann, James E. Lucas, Kyle E. Watters, Jennifer A. Doudna, Hana El-Samad, Benjamin M. Heineike, Christina M. Fitzsimmons, Andrew H. Ng, David F. Savage, Oren S. Rosenberg, Neha K. Prasad, Kale Kundert, Jiuxin Qu

Publikováno v: Nature Communications, Vol 10, Iss 1, Pp 1-11 (2019)
Kundert, Kale; Lucas, James E; Watters, Kyle E; Fellmann, Christof; Ng, Andrew H; Heineike, Benjamin M; et al.(2019). Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.. Nature communications, 10(1), 2127. doi: 10.1038/s41467-019-09985-2. UC Berkeley: Retrieved from: http://www.escholarship.org/uc/item/3t52t2n5
Nature communications, vol 10, iss 1
Nature Communications

The CRISPR-Cas9 system provides the ability to edit, repress, activate, or mark any gene (or DNA element) by pairing of a programmable single guide RNA (sgRNA) with a complementary sequence on the DNA target. Here we present a new method for small-mo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9c3291d81b3c5a60343dbc25a91d356
https://doaj.org/article/75a198d8f2ba47a985055e98863b4ffd

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Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits

Autor: Galen Dods, Hana El-Samad, Mariana Gómez-Schiavon, Andrew H. Ng

Publikováno v: ACS synthetic biology. 9(11)

Mathematical models can aid the design of genetic circuits, but may yield inaccurate results if individual parts are not modeled at the appropriate resolution. To illustrate the importance of this concept, we study transcriptional cascades consisting

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d197c4e81f96469e914b98b08033e69
https://pubmed.ncbi.nlm.nih.gov/33166452

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