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Because of the pervasiveness, persistence, and toxicity of per- and polyfluoroalkyl substances (PFAS), there is growing concern over PFAS contamination, exposures, and health effects. The diversity of potential PFAS is astounding, with nearly 10,000 PFAS catalogued in databases to date (and growing). The ability to detect the thousands of known PFAS, and discover previously uncatalogued PFAS, is necessary to understand the scope of PFAS contamination and to identify appropriate remediation and regulatory solutions. Current non-targeted methods for PFAS analysis require manual curation and are time-consuming, prone to error, and not comprehensive. FluoroMatch Flow 2.0 is the first software to cover all steps of data processing for PFAS discovery in liquid chromatography–high-resolution tandem mass spectrometry samples. These steps include feature detection, feature blank filtering, exact mass matching to catalogued PFAS, mass defect filtering, homologous series detection, retention time pattern analysis, class-based MS/MS screening, fragment screening, and predicted MS/MS from SMILES structures. In addition, a comprehensive confidence level criterion is implemented to help users understand annotation certainty and integrate various layers of evidence to reduce overreporting. Applying the software to aqueous film forming foam analysis, we discovered over one thousand likely PFAS including previously unreported species. Furthermore, we were able to filter out 96% of features which were likely not PFAS. FluoroMatch Flow 2 increased coverage of likely PFAS by over tenfold compared to the previous release. This software will enable researchers to better characterize PFAS in the environment and in biological systems.

To decipher the molecular bases governing seed germination, this study presents the pivotal role of the cap-binding complex (CBC), comprising CBP20 and CBP80, in modulating the inhibitory effects of abscisic acid (ABA) in barley. Using both single and double barley mutants in genes encoding the CBC, we revealed that the double mutant hvcbp20.ab/hvcbp80.b displays ABA insensitivity, in stark contrast to the hypersensitivity observed in single mutants during germination. Our comprehensive transcriptome and metabolome analysis not only identified significant alterations in gene expression and splicing patterns but also underscored the regulatory nexus among CBC, ABA, and brassinosteroid (BR) signaling pathways.

Background/Objectives: Spray drying is a technique widely employed in the food and nutraceutical industries to convert liquid extracts into stable powders, preserving their functional properties. Ginger (Zingiber officinale) is rich in bioactive compounds such as gingerols, shogaols, and zingerone, which contribute to its health benefits. This study aimed to investigate the impact of spray drying on the chemical profile of ginger, particularly focusing on the transformation of gingerols into shogaols and related compounds. Methods: Fresh ginger juice was spray-dried using various carrier agents, including Clear Gum (CO03), pea protein, and inulin. Mass spectra of the resulting powders were acquired using High-Resolution Flow Infusion Electrospray Ionisation Mass Spectrometry (HR-FIE-MS) to obtain fingerprint data. Key bioactive compounds were tentatively identified to Level 2, and their relative intensities were assessed to evaluate the effects of different carriers on the chemical composition of the ginger powders. Results: Spray drying with the commercial carrier CO03 resulted in an increase in shogaol analogues ([10]-, [8]-, and cis-[8]-shogaol), gingerenone B, and oxidation products such as 6-hydroxyshogaol, 6-dehydroshogaol, and zingerone. In contrast, natural carriers like pea protein and inulin led to lower relative intensities of these bioactives, suggesting limited capacity for promoting thermal transformations. Spray drying without a carrier produced a shogaol-dominant profile but resulted in powders with poor handling properties, such as stickiness and agglomeration. Antioxidant and total polyphenol assays showed that spray drying reduced antioxidant capacity, while total polyphenol content was more preserved; natural carriers such as inulin better maintained bioactivity compared to modified starch or pea protein. Conclusions: Among the five formulations evaluated—ginger juice with no carrier, with CO03 (two dilutions), pea protein, or inulin—CO03-based samples showed the greatest chemical transformation, while inulin and pea protein better preserved antioxidant capacity but induced fewer metabolite changes. Thus, choice of carrier in the spray-drying process influences the chemical profile and functional characteristics of resultant ginger powders. While CO03 effectively enhances the formation of bioactive shogaols and related compounds, its ultra-processed nature may not align with clean-label product trends. Natural carriers, although more label-friendly, may not create the desired chemical transformations. Therefore, optimising carrier selection is important to balance bioactivity, product stability, and consumer acceptability in the development of ginger-based functional products.

Background Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. To address this, we analyzed transcriptomic and metabolomic changes in ABA-treated germinating barley ( Hordeum vulgare ) embryos. To map ABA-responsive gene expression across embryonic tissues, we employed the Visium Spatial Transcriptomics (10× Genomics). This approach, which remains technically challenging to be applied in plant tissues, enabled the precise localization of gene expression across six embryo regions, offering insights into tissue-specific expression patterns that cannot be resolved by traditional RNA-seq. Results Transcriptomic analysis indicated that ABA acts primarily as a germination repressor. Gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses linked ABA-inhibited genes to energy metabolism, lignin biosynthesis, cell wall organization, and photosynthesis, while induced genes were associated with environmental adaptation and phytohormone signaling. Differentially expressed genes (DEGs) correlated with metabolites involved in phytohormone pathways, including gibberellins, jasmonates, brassinosteroids, salicylic acid, auxins, and ABA metabolism. Comparisons with developing seed transcriptomes suggested an ABA-associated gene expression signature in embryos. Spatial transcriptomics technique made possible the precise identification of ABA-induced transcriptional changes within distinct embryonic tissues. Conclusions Integrating transcriptomics, metabolomics and spatial transcriptomics defined the molecular signature of ABA-induced modulation of phytohormonal crosstalk, energy metabolism, and tissue-specific gene activity in germinating seeds. The successful use of spatial transcriptomics adds a novel layer of resolution for understanding tissue-specific ABA responses during barley seed germination. These findings offer new insights into the ABA role in seed germination and potential strategies for enhancing crop resilience.

Background Fagopyrum tataricum (Tartary buckwheat) is known for its high phenolic content, particularly rutin. High concentrations of these compounds secreted in the tissue culture medium can lead to its darkening and the eventual death of explants in in vitro cultures. This study aims to enhance the morphogenesis of F. tataricum callus cultures by utilising phenylalanine ammonia-lyase (PAL) inhibitors and polyvinylpyrrolidone (PVP) to mitigate oxidative browning and improve tissue viability. Results We analysed the response of protoplasts isolated from morphogenic callus to media supplemented with varying concentrations of PAL inhibitors (AIP, AOPP, OBHA) and PVP. The flow cytometry results revealed that 10 µM AIP and 1% PVP yielded exclusively diploid plants, whereas higher concentrations (100 µM AIP and 3% PVP) failed to regenerate plants. Moreover, AOPP and OBHA addition resulted in the regeneration of tetraploid plants. Further analysis of proembryogenic cell complexes (PECCs) isolated from Tartary buckwheat morphogenic calli responses to AIP and PVP indicated that 100 µM AIP was most effective for plant regeneration. Metabolomic analysis showed that AIP treatments reduced phenolic compounds, notably rutin, and increased the GSH/GSSG ratio, indicating reduced oxidative stress. Gene expression analysis highlighted elevated expression of somatic embryogenesis-related genes ( LEC2 , BBM ) and WUSCHEL in AIP-treated callus. Conclusions This study demonstrates that AIP enhances the regeneration potential of F. tataricum callus cultures, offering valuable insights for optimising tissue culture techniques for industrial crops. Additionally, we have detailed the metabolomic changes in calli treated with PVP and AIP, highlighting their impact on metabolism. Graphical Abstract

The lack of robust measures of dietary exposure hinders a quantitative understanding of causal relationships between diet and health. Non-targeted metabolite fingerprinting was used to explore the relationships between citrus exposure in free-living human subjects, estimated by a FFQ, and the chemical content of urine. Volunteers (study 1, n 12; study 2, n 11) were classified into high-, medium- and low-frequency citrus consumption groups. Overnight and spot fasting urine samples were obtained after exposure to a standardised citrus-free evening meal. The urine samples were analysed by flow injection electrospray-ionisation MS followed by supervised multivariate data classification analysis to discover discriminatory features associated with the level of citrus exposure. Good separation of high and low citrus consumption classes was achieved. Deeper exploration of high-ranked explanatory mass signals revealed several correlated signals derived from proline betaine. Targeted analysis of the relative levels of proline betaine in both fasting and overnight urine samples demonstrated good correlation with FFQ exposure data. Acute exposure of volunteers to orange juice resulted in the appearance of proline betaine and several biotransformed products in postprandial urine samples. Biomarker validation showed sensitivities of 80·8–92·2 % and specificities of 74·2–94·1 % (false discovery rate-adjusted P values < 0·05) for elevated proline betaine in participants who reported high citrus consumption. Proline betaine biotransformation products displayed weaker quantitative relationships with habitual citrus exposure. Targeted screening for the presence of biotransformation products of hesperidin and narirutin, known to be abundant in oranges, revealed that they were relatively poor indicators of citrus exposure.

Traditional Chinese medicine (TCM) has been used to treat infectious diseases and could offer potential drug leads. This study evaluates the in vitro antimicrobial activities from commercially sourced Dryopteris crassirhizoma Nakai (Polypodiaceae) whose authenticity was confirmed by DNA barcoding based on the ribulose bisphosphate carboxylase ( rbcL ) gene. Powdered rhizomes were sequentially extracted using n- hexane, dichloromethane, ethyl acetate, and methanol at ambient temperature. The dried extracts at different concentrations were tested for antimicrobial activities against Escherichia coli , Pseudomonas aeruginosa , Staphylococcus aureus , methicillin-resistant Staphylococcus aureus (MRSA), and Mycobacterium smegmatis . D. crassirhizoma extracts exhibited significant antimicrobial activities only against MRSA (minimum inhibitory concentration: 3.125 μg/ml n- hexane extract). Activity-led fractionations of D. crassirhizoma and characterization by ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) targeted a fraction (A3), with two anti-MRSA phloroglucinol derivatives, flavaspidic acid AB and norflavaspidic acid AB—being greatly enriched in the latter. The impact of A3 on MRSA cells was examined using untargeted metabolomic analysis and compared to that of other established antibiotics (all treatments normalized to MIC 50 at 6 h). This suggested that norflavaspidic acid AB had distinctive effects, one of which involved targeting bioenergetic transformation, metabolism, and particularly acetyl-CoA, on MRSA cells. No cytotoxicity was observed for the norflavaspidic acid AB-enriched fraction against murine HepG2 cells. This study requires further experimental validation but can have indicated a naturally available compound that could help counter the threat of clinically relevant strains with antibiotic resistance.

There was a provenance issue with the seed varieties in the original publication [...]

[This corrects the article DOI: 10.3389/fphar.2022.961087.].