Editing Escherichia coli (section)

== Uses in biological computing ==
Since 1961, scientists proposed the idea of genetic circuits used for computational tasks.  Collaboration between biologists and computing scientists has allowed designing digital logic gates on the metabolism of ''E. coli''. As [[Lac operon]] is a two-stage process, genetic regulation in the bacteria is used to realize computing functions. The process is controlled at the transcription stage of DNA into messenger RNA.<ref name="as">{{cite web |vauthors = Hayes B |title=Computing Comes to Life |url=https://www.americanscientist.org/article/computing-comes-to-life |website=American Scientist |access-date=28 November 2021 |date=6 February 2017}}</ref>

Studies are being performed attempting to program ''E. coli'' to solve complicated mathematics problems, such as the [[Hamiltonian path problem]].<ref>{{cite journal | vauthors = Baumgardner J, Acker K, Adefuye O, Crowley ST, Deloache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Poet JL, Eckdahl TT | display-authors = 6 | title = Solving a Hamiltonian Path Problem with a bacterial computer | journal = Journal of Biological Engineering | volume = 3 | pages = 11 | date = July 2009 | pmid = 19630940 | pmc = 2723075 | doi = 10.1186/1754-1611-3-11 | doi-access = free }}</ref>

A computer to control protein production of ''E. coli'' within [[yeast cell]]s has been developed.<ref>{{cite journal | vauthors = Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J | display-authors = 6 | title = In silico feedback for in vivo regulation of a gene expression circuit | journal = Nature Biotechnology | volume = 29 | issue = 12 | pages = 1114–1116 | date = November 2011 | pmid = 22057053 | doi = 10.1038/nbt.2018 | pmc = 4565053 }}</ref> A method has also been developed to use bacteria to behave as an [[Liquid-crystal display|LCD screen]].<ref>{{cite web | vauthors = Sawyer E |title=Computer Controlled Yeast and an E. coli LCD Screen {{!}} Bio 2.0 {{!}} Learn Science at Scitable |url=https://www.nature.com/scitable/blog/bio2.0/computer_controlled_yeast_and_an/ |website=www.nature.com |access-date=28 November 2021 }}</ref><ref>{{cite journal | vauthors = Prindle A, Samayoa P, Razinkov I, Danino T, Tsimring LS, Hasty J | title = A sensing array of radically coupled genetic 'biopixels' | journal = Nature | volume = 481 | issue = 7379 | pages = 39–44 | date = December 2011 | pmid = 22178928 | doi = 10.1038/nature10722 | pmc = 3259005 }}</ref>

In July 2017, separate experiments with ''E. coli'' published on Nature showed the potential of using living cells for computing tasks and storing information.<ref>{{cite web | vauthors = Waltz E |title=Biocomputer and Memory Built Inside Living Bacteria |url=https://spectrum.ieee.org/biocomputer-and-memory-built-inside-living-bacteria |website=IEEE Spectrum |access-date=28 November 2021 |date=23 August 2017}}</ref> A team formed with collaborators of the [[The Biodesign Institute|Biodesign Institute]] at [[Arizona State University]] and Harvard's [[Wyss Institute for Biologically Inspired Engineering]] developed a biological computer inside ''E. coli'' that responded to a dozen inputs. The team called the computer "ribocomputer", as it was composed of [[RNA|ribonucleic acid]].<ref>{{cite web | vauthors = Waltz E |title=Complex Biological Computer Commands Living Cells |url=https://spectrum.ieee.org/biological-computer-commands-living-cells-to-light-up |website=IEEE Spectrum |access-date=28 November 2021 |date=26 July 2017}}</ref><ref>{{cite journal | vauthors = Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P | title = Complex cellular logic computation using ribocomputing devices | journal = Nature | volume = 548 | issue = 7665 | pages = 117–121 | date = August 2017 | pmid = 28746304 | doi = 10.1038/nature23271 | pmc = 6078203 | bibcode = 2017Natur.548..117G | access-date =  }}</ref> Meanwhile, Harvard researchers probed that is possible to store information in bacteria after successfully archiving images and movies in the DNA of living ''E. coli'' cells.<ref>{{cite web | vauthors = Waltz E |title=Scientists Store Video Data in the DNA of Living Organisms |url=https://spectrum.ieee.org/scientists-store-video-data-in-the-dna-of-living-organisms |website=IEEE Spectrum |access-date=28 November 2021 |date=12 July 2017}}</ref><ref>{{cite journal | vauthors = Shipman SL, Nivala J, Macklis JD, Church GM | title = CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria | journal = Nature | volume = 547 | issue = 7663 | pages = 345–349 | date = July 2017 | pmid = 28700573 | doi = 10.1038/nature23017 | pmc = 5842791 | bibcode = 2017Natur.547..345S | access-date =  }}</ref>  In 2021, a team led by biophysicist Sangram Bagh realized a study with ''E. coli'' to solve [[Maze|2 × 2 maze problems]] to probe the principle for [[distributed computing]] among cells.<ref>{{cite journal | vauthors = Sarkar K, Chakraborty S, Bonnerjee D, Bagh S | title = Distributed Computing with Engineered Bacteria and Its Application in Solving Chemically Generated 2 × 2 Maze Problems | journal = ACS Synthetic Biology | volume = 10 | issue = 10 | pages = 2456–2464 | date = October 2021 | pmid = 34543017 | doi = 10.1021/acssynbio.1c00279 | s2cid = 237583555 | access-date =  }}</ref><ref>{{cite web | vauthors = Roberts S |title=An ''E. coli'' biocomputer solves a maze by sharing the work |url=https://www.technologyreview.com/2021/11/09/1039107/e-coli-maze-solving-biocomputer/ |website=MIT Technology Review |access-date=27 November 2021|date=9 November 2021}}</ref>