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Data and code from: Pyrrocidines A and B demonstrate synergistic inhibition of <i>Fusarium verticillioides</i> growth

Metadata Updated: June 5, 2025

This dataset contains all raw data and R statistical code needed to reproduce the model fitting, model predictions, and data/model visualizations from the article:Lofton, L.W., Read, Q.D., Hamilton, H.L., Glenn, A.E., Hawkins, J.A., Mitchell, T.R., & Gold, S.E. (2025). Pyrrocidines A and B demonstrate synergistic inhibition of Fusarium verticillioides growth. Front. Microbiol., vol. 15. https://doi.org/10.3389/fmicb.2024.1480920Fusarium verticillioides – a mycotoxigenic fungus and food safety threat – coinhabits maize kernels with Sarocladium zeae. This protective endophyte produces secondary metabolites of interest, pyrrocidines A and B, which inhibit the growth of F. verticillioides and specifically block fumonisin biosynthesis. Here, using pyrrocidine dose-response assays, we discovered a potent synergy between pyrrocidines A and B, where they functioned powerfully together to inhibit F. verticillioides growth. Further, results provided evidence that FvZBD1 confers partial tolerance to pyrrocidines, particularly pyrrocidine A, and that pyrrocidine functions through FvZBD1 to effectively eliminate fumonisin biosynthesis. Additionally, we showed that the FvABC3 (FVEG_11089) mutant, earlier described as hypersensitive to pyrrocidine, is particularly sensitive to pyrrocidine B. Thus, pyrrocidine A and B show different target specificity (FvZBD1 or FvABC3) and synergistic action.The primary data analysis is a Bayesian generalized additive mixed model (GAMM) fit to the optical density data recorded at regular intervals from F. verticillioides strains grown in Bioscreen microtiter plates under different conditions, in a full-factorial design crossing strain (wild-type and two mutant strains) with multiple levels of pyrrocidine A and B concentration. The RMarkdown notebook imports the data, makes plots of the raw observations, fits the model to the data, and uses the posterior samples from the model to make predictions. Predictions are shown in graphical and tabular form, and evidence for effects is assessed using credible intervals of predictions, and Bayesian maximum a posteriori p-values (pMAP). A secondary analysis is presented of a dose-response assay: this is a frequentist linear model fit to a log-transformed concentration as a function of pyrrocidine type and concentration, followed by post-hoc comparisons within each pyrrocidine type. Again, results are presented in graphical and tabular form.The following files are included:PyrrSynergy_MetaData.pdf: File with column metadata for the data objects listed belowbioscreen_data.csv: Primary results of Bioscreen assaybioscreen_data_wt1020.csv: Results of additional Bioscreen assay with concentration levels between 10 and 20AGlenn_Fvzbd1PyrrbFUM.xlsx: Results of dose-response assay 1 of 2LLofton_Fvzbd1PyrrFUM.xlsx: Results of dose-response assay 2 of 2pyrrocidine_bioscreen.html: HTML rendered output of R code notebook containing analysis and visualization of main dataset (Bioscreen assays)fumonisin_synthesis_analysis.html: HTML rendered output of R code notebook containing analysis and visualization of secondary dataset (dose-response assay)pyrrocidine_bioscreen.Rmd: RMarkdown notebook, main analysisfumonisin_synthesis_analysis.Rmd: RMarkdown notebook, secondary analysissplinefit_bioscreen_20240415.rds: Pre-fit model object, created by R package brms, so that notebook may be run to reproduce results without refitting model, which may take days to run

Access & Use Information

Public: This dataset is intended for public access and use. License: Creative Commons CCZero

Downloads & Resources

Dates

Metadata Created Date January 1, 2025
Metadata Updated Date June 5, 2025

Metadata Source

Harvested from USDA JSON

Additional Metadata

Resource Type Dataset
Metadata Created Date January 1, 2025
Metadata Updated Date June 5, 2025
Publisher Agricultural Research Service
Maintainer
Identifier 10.15482/USDA.ADC/26239976.v1
Data Last Modified 2025-05-06
Public Access Level public
Bureau Code 005:18
Metadata Context https://project-open-data.cio.gov/v1.1/schema/catalog.jsonld
Schema Version https://project-open-data.cio.gov/v1.1/schema
Catalog Describedby https://project-open-data.cio.gov/v1.1/schema/catalog.json
Harvest Object Id f5fb1dfc-4cfd-4425-aebd-c92410e21454
Harvest Source Id d3fafa34-0cb9-48f1-ab1d-5b5fdc783806
Harvest Source Title USDA JSON
License https://creativecommons.org/publicdomain/zero/1.0/
Program Code 005:040
Source Datajson Identifier True
Source Hash 500e1a350587e5d3cf448f78d4b82312615b3b3f6169a3c883599d10d2b86610
Source Schema Version 1.1
Temporal 2022-07-01/2023-04-30

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