Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F47813059%3A19240%2F17%3AA0000085" target="_blank" >RIV/47813059:19240/17:A0000085 - isvavai.cz</a>

Výsledek na webu

<a href="https://link.springer.com/article/10.1007%2Fs11047-016-9595-9" target="_blank" >https://link.springer.com/article/10.1007%2Fs11047-016-9595-9</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1007/s11047-016-9595-9" target="_blank" >10.1007/s11047-016-9595-9</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments

Popis výsledku v původním jazyce

Recent links between computer science and synthetic biology allow for construction of many kinds of algorithmic processes within cells, obtained either by a direct engineered design or by an evolutionary search. In the latter case, horizontal gene transfer and especially transfer of plasmids by conjugation is generally respected as a crucial source of genetic diversity in bacteria. While some previous studies focused on mutations as the crucial principle to obtain diversity for engineered evolution, here we consider conjugation itself as a tool to generate diversity from a pre-determined library of biocircuits basic components. The recent development of CRISPR-Cas9 and its programmable DNA cutting ability makes it a powerful selection tool able to remove nonfunctional biocircuits from a cell population. In this paper, we describe a framework for controlled bacterial evolution of biocircuits based on conjugation and on CRISPR-Cas9, resulting in a direct biological implementation of an evolutionary algorithm. In silico experiments provide data to estimate the computational/search capability of plasmid-based engineered evolution.

Název v anglickém jazyce

Directed evolution of biocircuits using conjugative plasmids and CRISPR-Cas9: design and in silico experiments

Popis výsledku anglicky

Recent links between computer science and synthetic biology allow for construction of many kinds of algorithmic processes within cells, obtained either by a direct engineered design or by an evolutionary search. In the latter case, horizontal gene transfer and especially transfer of plasmids by conjugation is generally respected as a crucial source of genetic diversity in bacteria. While some previous studies focused on mutations as the crucial principle to obtain diversity for engineered evolution, here we consider conjugation itself as a tool to generate diversity from a pre-determined library of biocircuits basic components. The recent development of CRISPR-Cas9 and its programmable DNA cutting ability makes it a powerful selection tool able to remove nonfunctional biocircuits from a cell population. In this paper, we describe a framework for controlled bacterial evolution of biocircuits based on conjugation and on CRISPR-Cas9, resulting in a direct biological implementation of an evolutionary algorithm. In silico experiments provide data to estimate the computational/search capability of plasmid-based engineered evolution.

Druh

J_SC - Článek v periodiku v databázi SCOPUS

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/LQ1602" target="_blank" >LQ1602: IT4Innovations excellence in science</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2017

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Natural Computing

ISSN

1567-7818

e-ISSN

—

Svazek periodika

16

Číslo periodika v rámci svazku

3

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

9

Strana od-do

497-505

Kód UT WoS článku

000407824400010

EID výsledku v databázi Scopus

2-s2.0-85006414967