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PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.

ABSTRACT: 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.

SUBMITTER: Casas A

PROVIDER: S-EPMC8938949 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature

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PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.

Casas Alexis A Bultelle Matthieu M Motraghi Charles C Kitney Richard R

ACS synthetic biology 20220309 3

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 ...[more]

PMID: 35261238

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Project description:Realization of graphene-based sensors and electronic devices remains challenging, in part due to integration challenges with current fabrication and manufacturing processes. Thus, scalable methods for in situ fabrication of high-quality graphene-like materials are essential. Low-cost CO2 laser engravers can be used for site-selective conversion of polyimide under ambient conditions to create 3-D, rotationally disordered, few-layer, porous, graphene-like electrodes. However, the influences of non-linear parameter terms and interactions between key parameters on the graphitization process present challenges for rapid, resource-efficient optimization. An iterative optimization strategy was developed to identify promising regions in parameter space for two key parameters, laser power and scan speed, with the goal of optimizing electrode performance while maximizing scan speed and hence fabrication throughput. The strategy employed iterations of Design of Experiments Response Surface (DoE-RS) methods combined with choices of readily measurable parameters to minimize measurement resources and time. The initial DoE-RS experiment set employed visual response parameters, while subsequent iterations used sheet resistance as the optimization parameter. The final model clearly demonstrates that laser graphitization through raster scanning is a highly non-linear process requiring polynomial terms in scan speed and laser power up to fifth order. Two regions of interest in parameter space were identified using this strategy: Region 1 represents the global minimum for sheet resistance for this laser (∼16 Ω/sq), found at a low scan speed (70 mm/s) and a low average power (2.1 W) . Region 2 is a local minimum for sheet resistance (36 Ω/sq), found at higher values for scan speed (340 mm/s) and average power (3.4 W), allowing ∼5-fold reduction in write time. Importantly, these minima do not correspond to constant ratios of average laser power to scan speed. This highlights the benefits of DoE-RS methods in rapid identification of optimum parameter combinations that would be difficult to discover using traditional one-factor-at-a-time optimization. Verification data from Raman spectroscopy showed sharp 2D peaks with mean full-width-at-half-maximum intensity values <80 cm-1 for both regions, consistent with high-quality 3D graphene-like carbon. Graphene-based electrodes fabricated using the parameters from the respective regions yielded similar performance when employed as capacitive humidity sensors with hygroscopic dielectric layers. Devices fabricated using Region 1 parameters (16 Ω/sq) yielded capacitance responses of 0.78 ± 0.04 pF at 0% relative humidity (RH), increasing to 31 ± 7 pF at 85.1% RH. Region 2 devices (36 Ω/sq) showed comparable responses (0.88 ± 0.04 pF at 0% RH, 28 ± 5 pF at 85.1% RH).

Dataset Information

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.

Publications

PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies.

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