Literature DB >> 34099656

Towards an engineering theory of evolution.

Simeon D Castle1, Claire S Grierson1,2, Thomas E Gorochowski3,4.   

Abstract

Biological technologies are fundamentally unlike any other because biology evolves. Bioengineering therefore requires novel design methodologies with evolution at their core. Knowledge about evolution is currently applied to the design of biosystems ad hoc. Unless we have an engineering theory of evolution, we will neither be able to meet evolution's potential as an engineering tool, nor understand or limit its unintended consequences for our biological designs. Here, we propose the evotype as a helpful concept for engineering the evolutionary potential of biosystems, or other self-adaptive technologies, potentially beyond the realm of biology.

Entities:  

Year:  2021        PMID: 34099656     DOI: 10.1038/s41467-021-23573-3

Source DB:  PubMed          Journal:  Nat Commun        ISSN: 2041-1723            Impact factor:   14.919


  98 in total

1.  Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity.

Authors:  E T Boder; K S Midelfort; K D Wittrup
Journal:  Proc Natl Acad Sci U S A       Date:  2000-09-26       Impact factor: 11.205

2.  Memory and Combinatorial Logic Based on DNA Inversions: Dynamics and Evolutionary Stability.

Authors:  Jesus Fernandez-Rodriguez; Lei Yang; Thomas E Gorochowski; D Benjamin Gordon; Christopher A Voigt
Journal:  ACS Synth Biol       Date:  2015-11-24       Impact factor: 5.110

3.  Directed evolution of a thermostable esterase.

Authors:  L Giver; A Gershenson; P O Freskgard; F H Arnold
Journal:  Proc Natl Acad Sci U S A       Date:  1998-10-27       Impact factor: 11.205

Review 4.  Engineering reduced evolutionary potential for synthetic biology.

Authors:  Brian A Renda; Michael J Hammerling; Jeffrey E Barrick
Journal:  Mol Biosyst       Date:  2014-02-21

5.  Directed evolution of protein switches and their application to the creation of ligand-binding proteins.

Authors:  Gurkan Guntas; Thomas J Mansell; Jin Ryoun Kim; Marc Ostermeier
Journal:  Proc Natl Acad Sci U S A       Date:  2005-08-01       Impact factor: 11.205

6.  Programming cells by multiplex genome engineering and accelerated evolution.

Authors:  Harris H Wang; Farren J Isaacs; Peter A Carr; Zachary Z Sun; George Xu; Craig R Forest; George M Church
Journal:  Nature       Date:  2009-07-26       Impact factor: 49.962

7.  A system for the continuous directed evolution of biomolecules.

Authors:  Kevin M Esvelt; Jacob C Carlson; David R Liu
Journal:  Nature       Date:  2011-04-10       Impact factor: 49.962

8.  Engineering and ethical perspectives in synthetic biology. Rigorous, robust and predictable designs, public engagement and a modern ethical framework are vital to the continued success of synthetic biology.

Authors:  James Anderson; Natalja Strelkowa; Guy-Bart Stan; Thomas Douglas; Julian Savulescu; Mauricio Barahona; Antonis Papachristodoulou
Journal:  EMBO Rep       Date:  2012-06-29       Impact factor: 8.807

9.  Synthetic biology: new engineering rules for an emerging discipline.

Authors:  Ernesto Andrianantoandro; Subhayu Basu; David K Karig; Ron Weiss
Journal:  Mol Syst Biol       Date:  2006-05-16       Impact factor: 11.429

10.  Predicting how evolution will beat us.

Authors:  Tom Ellis
Journal:  Microb Biotechnol       Date:  2018-11-20       Impact factor: 5.813

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  7 in total

1.  Design and Analysis of Massively Parallel Reporter Assays Using FORECAST.

Authors:  Pierre-Aurelien Gilliot; Thomas E Gorochowski
Journal:  Methods Mol Biol       Date:  2023

2.  paraSBOLv: a foundation for standard-compliant genetic design visualization tools.

Authors:  Charlie J Clark; James Scott-Brown; Thomas E Gorochowski
Journal:  Synth Biol (Oxf)       Date:  2021-08-30

3.  Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning.

Authors:  Rachapun Rotrattanadumrong; Yohei Yokobayashi
Journal:  Nat Commun       Date:  2022-08-17       Impact factor: 17.694

4.  The context matrix: Navigating biological complexity for advanced biodesign.

Authors:  Camillo Moschner; Charlie Wedd; Somenath Bakshi
Journal:  Front Bioeng Biotechnol       Date:  2022-08-23

5.  Synthetic evolution of herbicide resistance using a T7 RNAP-based random DNA base editor.

Authors:  Haroon Butt; Jose Luis Moreno Ramirez; Magdy Mahfouz
Journal:  Life Sci Alliance       Date:  2022-09-28

6.  Massively parallel characterization of engineered transcript isoforms using direct RNA sequencing.

Authors:  Matthew J Tarnowski; Thomas E Gorochowski
Journal:  Nat Commun       Date:  2022-01-21       Impact factor: 14.919

7.  Forecasting of phenotypic and genetic outcomes of experimental evolution in Pseudomonas protegens.

Authors:  Jennifer T Pentz; Peter A Lind
Journal:  PLoS Genet       Date:  2021-08-05       Impact factor: 5.917

  7 in total

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