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Background: ​​The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or mycotoxin contamination in crops. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets for control strategies., Description: In response to these challenges, we developed the Fusarium Protein Toolkit (FPT), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum and F. verticillioides. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome based on 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework., Conclusion: FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium. FPT has the potential to deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets for control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats resulting from climate change. Thus, FPT has the potential to contribute to improving food security and safety worldwide., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Fresh produce is traditionally labeled with plastic price lookup (PLU) stickers that are attached to the produce surface using edible glue. However, both the stickers and glue are environmental contaminants, and the stickers can still easily detach from the produce surface during handling and disrupt traceability. An alternative method of labeling, the CO 2 laser-labeling technology (LLT), has been gaining attention in recent years. However, engraving Quick Response (QR) code using LLT is unique, and the performance of this technology varies from produce item to produce item, and information on its effects on postharvest quality, microbial safety, and economic feasibility has not been reported. The objectives of this study were to investigate the effect of laser-labeling technology on (1) postharvest quality, (2) microbial safety, and (3) economic analysis of this technology. Three horticultural crops, 'Red Delicious' apple (Malus pumila), green bell pepper (Capsicum annuum), and cucumber (Cucumis sativus) were procured from a local grocery store. Each produce was engraved with a Quick Response (QR) code or 6-digit alphanumerical (text) code using the commercially available Trotec Speedy 300 CO 2 laser engraver, followed by the application of edible wax. Fresh weight loss for laser-printed produce was higher compared to controls, but no difference in visual quality ratings was observed. The laser-labeled produce was assessed for microbial contamination by artificially inoculating rifampicin-resistant Escherichia coli (E. coli) log 10 6 CFU/mL to the labeled fruit. The results showed that the population of rifampicin-resistant E. coli was statistically higher in all three products labeled with text code compared to the nontreated controls. The QR-coded treatments were similar to the controls. The wax application did not affect the microbial attachment on the laser-labeled produce. The CO 2 laser labeling technology has the potential for industrial application., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Background: Environmental stress factors, such as biotic and abiotic stress, are becoming more common due to climate variability, significantly affecting global maize yield. Transcriptome profiling studies provide insights into the molecular mechanisms underlying stress response in maize, though the functions of many genes are still unknown. To enhance the functional annotation of maize-specific genes, MaizeGDB has outlined a data-driven approach with an emphasis on identifying genes and traits related to biotic and abiotic stress., Results: We mapped high-quality RNA-Seq expression reads from 24 different publicly available datasets (17 abiotic and seven biotic studies) generated from the B73 cultivar to the recent version of the reference genome B73 (B73v5) and deduced stress-related functional annotation of maize gene models. We conducted a robust meta-analysis of the transcriptome profiles from the datasets to identify maize loci responsive to stress, identifying 3,230 differentially expressed genes (DEGs): 2,555 DEGs regulated in response to abiotic stress, 408 DEGs regulated during biotic stress, and 267 common DEGs (co-DEGs) that overlap between abiotic and biotic stress. We discovered hub genes from network analyses, and among the hub genes of the co-DEGs we identified a putative NAC domain transcription factor superfamily protein (Zm00001eb369060) IDP275, which previously responded to herbivory and drought stress. IDP275 was up-regulated in our analysis in response to eight different abiotic and four different biotic stresses. A gene set enrichment and pathway analysis of hub genes of the co-DEGs revealed hormone-mediated signaling processes and phenylpropanoid biosynthesis pathways, respectively. Using phylostratigraphic analysis, we also demonstrated how abiotic and biotic stress genes differentially evolve to adapt to changing environments., Conclusions: These results will help facilitate the functional annotation of multiple stress response gene models and annotation in maize. Data can be accessed and downloaded at the Maize Genetics and Genomics Database (MaizeGDB)., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model., Competing Interests: Conflicts of interest: The authors declare no conflict of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2024.)

Summary: Understanding the effects of genetic variants is crucial for accurately predicting traits and functional outcomes. Recent approaches have utilized artificial intelligence and protein language models to score all possible missense variant effects at the proteome level for a single genome, but a reliable tool is needed to explore these effects at the pan-genome level. To address this gap, we introduce a new tool called PanEffect. We implemented PanEffect at MaizeGDB to enable a comprehensive examination of the potential effects of coding variants across 50 maize genomes. The tool allows users to visualize over 550 million possible amino acid substitutions in the B73 maize reference genome and to observe the effects of the 2.3 million natural variations in the maize pan-genome. Each variant effect score, calculated from the Evolutionary Scale Modeling (ESM) protein language model, shows the log-likelihood ratio difference between B73 and all variants in the pan-genome. These scores are shown using heatmaps spanning benign outcomes to potential functional consequences. In addition, PanEffect displays secondary structures and functional domains along with the variant effects, offering additional functional and structural context. Using PanEffect, researchers now have a platform to explore protein variants and identify genetic targets for crop enhancement., Availability and Implementation: The PanEffect code is freely available on GitHub (https://github.com/Maize-Genetics-and-Genomics-Database/PanEffect). A maize implementation of PanEffect and underlying datasets are available at MaizeGDB (https://www.maizegdb.org/effect/maize/)., (Published by Oxford University Press 2024.)

Ultraviolet-C (UV-C) light-assisted water treatment systems are an increasingly investigated alternative to chemical sanitizers for agricultural surface water decontamination. However, the relatively high concentration of particulate matter in surface water is a major challenge to expanding its application in the production of fresh produce. The objective of this project was to test the efficacy of two commercial UV-C devices to reduce the microbial risk of agricultural water in order to develop a web application to assist growers in decision-making related to the on-farm implementation of UV-C technologies for agricultural water treatment. An on-farm study using three agricultural water sources was performed to determine the microbial reduction efficacy of a low power, low flow (LP/LF; 1-9 gallons per minute (GPM), 1.34-gallon capacity) and a high powered, high flow (HP/HF; 1-110 GPM, 4.75-gallon capacity) device at flow rates of 6, 7, and 9 GPM. A threshold of 30% UVT for the HP/HF device was observed, wherein lower water transmissibility significantly impacted microbial inactivation. Although less effective at lower %UVT, the LP/LF device costs less to install, maintain, and operate. The observations were used to design an online tool for growers to calculate the predicted reduction of generic Escherichia coli using either device based on the %UVT of their water source. However, because this study utilized an exploratory and proof-of-concept approach, the experimental flow rates were limited to reflect the capacities of the smaller unit (9 GPM) for direct comparison to the larger unit. Thus, the preliminary model and tool are largely limited to the experimental conditions. Yet, these results of this study demonstrate the utility of UV-C light in reducing the microbial risk of agricultural water, and future studies using different UV-C devices and higher flow rates will expand the use of the decision-making tool., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Cover crops are plants seeded before or after cash crops to improve soil health, reduce weed pressure, and prevent erosion. Cover crops also produce various antimicrobial secondary metabolites (i.e., glucosinolates, quercetin), yet the role of cover crops in moderating the population of human pathogens in the soil has rarely been investigated. This study aims to determine the antimicrobial capacity of three cover crop species to reduce the population of generic Escherichia coli (E. coli) in contaminated agricultural soil. Four-week-old mustard greens (Brassicajuncea), sunn hemp (Crotalaria juncea), and buckwheat (Fagopyrum esculentum) were mixed into autoclaved soil and inoculated with rifampicin-resistant generic E. coli to achieve a starting concentration of 5 log CFU/g. The surviving microbial populations on days 0, 4, 10, 15, 20, 30, and 40 were enumerated. All three cover crops significantly reduced the population of generic E. coli compared to the control (p < 0.0001), particularly between days 10 and to 30. Buckwheat resulted in the highest reduction (3.92 log CFU/g). An inhibitory effect (p < 0.0001) on microbial growth was also observed in soils containing mustard greens and sunn hemp. This study provides evidence for the bacteriostatic and bactericidal effect of particular cover crops. More research regarding the secondary metabolites produced by certain cover crops and their potential as a bio mitigation strategy to improve on-farm produce safety is warranted., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Ultraviolet-C (UV-C) irradiation is a well-recognized technology for improving blueberry postharvest quality, and previous literature indicates that it has the potential for dual-use as an antimicrobial intervention for this industry. However, the practicality and feasibility of deploying this technology in fresh blueberry fruit are significantly hindered by the shadowing effect occurring at the blossom-end scar of the fruit. The purpose of this study was to determine if treating the blueberry fruit within a chamber fitted with UV-Light Emitting Diodes (LEDs) emitting a peak UV-C at 275 nm could minimize this shadowing and result in improved treatment efficacy. Ten blueberry fruits were dip-inoculated with E. coli at a concentration of 10 5  CFU/mL and irradiated within the system at doses of 0, 1.617, 3.234, 9.702, and 16.17 mJ/cm 2 (0, 30, 60, 180, and 300 s). Statistical analysis was performed to characterize the extent of microbial survival as well as the UV-C inactivation kinetics. A maximum of 0.91-0.95 log reduction was observed, which attenuated after 60 s of treatment. The microbial inactivation and survival were thus modeled using the Geeraerd-tail model in Microsoft Excel with the GInaFIt add-in (RMSE = 0.2862). Temperatures fluctuated between 23 ± 0.5°C and 39.5°C ± 0.5°C during treatment but did not statistically impact the treatment efficacy (P = 0.0823). The data indicate that the design of a UV-LED system may improve the antimicrobial efficacy of UV-C technology for the surface decontamination of irregularly shaped fruits, and that further optimization could facilitate its use in the industry., Competing Interests: Declaration of Competing Interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

With the plethora of commercially available UV-C devices exhibiting different intensity and lifespans, it is critical to consumer safety that companies verify and clearly communicate the efficacy of their devices as per the intended use. The purpose of this study was to define a low-cost protocol for investigating the antimicrobial efficacy of commercial UV devices for industry use. The tested devices included: a wall-mounted unit (Device A), a troffer unit (Device B), and an induction lamp unit (Device C). The devices were installed within an enclosed tower to prevent the transmission of UV-C radiation outside of the testing area. The procedure details determining the devices' antimicrobial efficacy using plastic coupons inoculated with Escherichia coli or Staphylococcus aureus. The protocol includes suggested time-distance treatments according to the potential application of each device type and reports the results as log CFU/mL reduction or percent reduction.