Cargando…
PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies
[Image: see text] We present here a newly developed workflow—which we have called PASIV—designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
|
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8938949/ https://www.ncbi.nlm.nih.gov/pubmed/35261238 http://dx.doi.org/10.1021/acssynbio.1c00562 |
_version_ | 1784672654423228416 |
---|---|
author | Casas, Alexis Bultelle, Matthieu Motraghi, Charles Kitney, Richard |
author_facet | Casas, Alexis Bultelle, Matthieu Motraghi, Charles Kitney, Richard |
author_sort | Casas, Alexis |
collection | PubMed |
description | [Image: see text] We present here a newly developed workflow—which we have called PASIV—designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (caused by either the metabolite or an intermediary), making it unreliable or impossible to proceed to the screening phase? PASIV—standing for pooled approach, screening, identification, and visualization—was designed so the (viable) region of interest can be made to appear through an interplay between biology and software. This was achieved by combining multiplex construction in a pooled approach (one-pot reaction) with a viability assay and with a range of bioinformatics tools (including a novel construct matching tool). PASIV was tested on the exemplar of the lycopene pathway—under stressful constitutive expression—yielding a region of interest with comparatively stronger producers. |
format | Online Article Text |
id | pubmed-8938949 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-89389492022-03-29 PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies Casas, Alexis Bultelle, Matthieu Motraghi, Charles Kitney, Richard ACS Synth Biol [Image: see text] We present here a newly developed workflow—which we have called PASIV—designed to provide a solution to a practical problem with design of experiments (DoE) methodology: i.e., what can be done if the scoping phase of the DoE cycle is severely hampered by burden and toxicity issues (caused by either the metabolite or an intermediary), making it unreliable or impossible to proceed to the screening phase? PASIV—standing for pooled approach, screening, identification, and visualization—was designed so the (viable) region of interest can be made to appear through an interplay between biology and software. This was achieved by combining multiplex construction in a pooled approach (one-pot reaction) with a viability assay and with a range of bioinformatics tools (including a novel construct matching tool). PASIV was tested on the exemplar of the lycopene pathway—under stressful constitutive expression—yielding a region of interest with comparatively stronger producers. American Chemical Society 2022-03-09 2022-03-18 /pmc/articles/PMC8938949/ /pubmed/35261238 http://dx.doi.org/10.1021/acssynbio.1c00562 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Casas, Alexis Bultelle, Matthieu Motraghi, Charles Kitney, Richard PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title | PASIV: A Pooled Approach-Based Workflow to Overcome
Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title_full | PASIV: A Pooled Approach-Based Workflow to Overcome
Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title_fullStr | PASIV: A Pooled Approach-Based Workflow to Overcome
Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title_full_unstemmed | PASIV: A Pooled Approach-Based Workflow to Overcome
Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title_short | PASIV: A Pooled Approach-Based Workflow to Overcome
Toxicity-Induced Design of Experiments Failures and Inefficiencies |
title_sort | pasiv: a pooled approach-based workflow to overcome
toxicity-induced design of experiments failures and inefficiencies |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8938949/ https://www.ncbi.nlm.nih.gov/pubmed/35261238 http://dx.doi.org/10.1021/acssynbio.1c00562 |
work_keys_str_mv | AT casasalexis pasivapooledapproachbasedworkflowtoovercometoxicityinduceddesignofexperimentsfailuresandinefficiencies AT bultellematthieu pasivapooledapproachbasedworkflowtoovercometoxicityinduceddesignofexperimentsfailuresandinefficiencies AT motraghicharles pasivapooledapproachbasedworkflowtoovercometoxicityinduceddesignofexperimentsfailuresandinefficiencies AT kitneyrichard pasivapooledapproachbasedworkflowtoovercometoxicityinduceddesignofexperimentsfailuresandinefficiencies |