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Journal of Agricultural and Food Chemistry

American Chemical Society (ACS)

Preprints posted in the last 90 days, ranked by how well they match Journal of Agricultural and Food Chemistry's content profile, based on 14 papers previously published here. The average preprint has a 0.04% match score for this journal, so anything above that is already an above-average fit.

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Process optimization and antidepression multi-target mechanisms of Total Flavonoids from Hemerocallis citrina Baroni: An integrated approach combining DES-UAE, network pharmacology, and experimental validation

Zhang, G.; Gao, L.; Ji, H.; Zhang, T.; Zhang, Y.

2026-03-02 pharmacology and toxicology 10.64898/2026.02.27.708446 medRxiv
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ObjectiveThis study aimed to establish a green and efficient ultrasonic-assisted deep eutectic solvent (DES) extraction method for total flavonoids from Hemerocallis citrina Baroni (TFHC) and to elucidate its multi-target antidepressant mechanism using an integrated strategy of network pharmacology, molecular docking, and in vitro validation. MethodsAn ultrasonic-assisted DES extraction using choline chloride-ethylene glycol was optimized via response surface methodology. The TFHC extract was profiled by UPLC-ESI-MS/MS. A network pharmacology approach was employed to predict core targets and pathways of TFHC constituents against depression, with key interactions validated by molecular docking. The neuroprotective effects of TFHC were evaluated in vitro using a corticosterone (CORT)-induced injury model in PC-12 cells, assessing cell viability (MTT assay) and levels of 5-HT, BDNF, TNF-, and CORT (ELISA). ResultsThe optimized DES extraction yielded 16.63 {+/-} 0.13 mg/g of TFHC. UPLC-ESI-MS/MS identified fourteen flavonoids, with quercetin, kaempferol, and rutin being most abundant. Network pharmacology revealed six core targets (AKT1, TNF, IL6, IL1{beta}, TP53, PTGS2) and implicated pathways including PI3K-AKT and TNF. Molecular docking confirmed strong binding affinities ([≤] -4.25 kcal/mol) between major flavonoids and core targets. In vitro, TFHC significantly alleviated CORT-induced cytotoxicity, restored 5-HT and BDNF levels, and suppressed TNF- and CORT elevation, with effects comparable or superior to fluoxetine. ConclusionsTFHC exerts antidepressant-like effects through a multi-target mechanism involving neuroinflammation suppression, neurotrophic support, and HPA axis modulation. The green DES extraction combined with mechanistic insights positions TFHC as a promising candidate for phytotherapeutic antidepressant development.

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Isolation and characterization of novel banana rhizosphere bacteria for the control of Fusarium oxysporum f. sp. cubense TR4

Cohen, D.-d.; Doron-Faigenboim, A.; Cohen, J.; Maymon, M.; Freeman, S.; Carmeli, S.; Minz, D.

2026-01-29 microbiology 10.64898/2026.01.29.702532 medRxiv
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Fusarium wilt of banana, caused by Fusarium oxysporum f. sp. cubense race TR4 (Foc), is one of the most destructive diseases threatening global banana production, particularly the Cavendish cultivar. Conventional control strategies, including chemical treatments and quarantine, remain largely ineffective and unsustainable, underscoring the urgent need for alternative approaches. Biological control using rhizosphere-associated microorganisms offers a promising and environmentally friendly strategy. In this study, we isolated 436 bacterial strains from the rhizosphere of healthy banana plants and screened them for antifungal activity against Foc. Out of the screened isolates, 93 exhibited significant in-vitro inhibitions, and 64 of these were subsequently evaluated in greenhouse assays. We found that 22 strains reduced Fusarium wilt severity by 45-85% compared to untreated controls. Among them, two isolates, DDC20 and DDC_NEW2, consistently demonstrated strong biocontrol activity. In addition, cell-free culture media (CFCM) and crude extracts inhibited spore germination in fluorescence-based assays, indicating the involvement of secreted antifungal metabolites. Microscopy and confocal observations of GFP-tagged Foc revealed hyphal abnormalities in the presence of bacterial treatments, including swelling, irregular branching, and distortion, accompanied by excessive sporulation characterized by abundant microconidia, macroconidia, and chlamydospores. Whole-genome sequencing and comparative analyses placed both isolates within the genus Bacillus. Genome mining using antiSMASH identified multiple biosynthetic gene clusters encoding known antifungal compounds such as surfactin, fengycin, bacillibactin, and difficidin, as well as putative novel clusters. LC-MS confirmed the presence of surfactin and fengycin in bacterial extracts, supporting the genomic predictions. Collectively, these findings highlight the potential of DDC20 and DDC_NEW2 (related to Bacillus spp.) from the banana rhizosphere as effective biocontrol agents against Foc TR4. This integrated approach, combining phenotypic assays, microscopy, and genome mining, provides a strong foundation for the development of sustainable strategies to manage Fusarium wilt in banana cultivation.

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An omega glutathione S-transferase in Apis mellifera contributes to chemical adaptation through pesticide sequestration and antioxidant defense

Koirala BK, S.; Moural, T. W.; Bhattarai, G.; Phan, N. T.; Rajottea, E. G.; Biddinger, D. J.; Zhu, F.

2026-03-05 biochemistry 10.64898/2026.03.03.709375 medRxiv
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The European honey bee (Apis mellifera L.) is a key agricultural pollinator frequently exposed to pesticide residues, yet the molecular basis of its chemical adaptation, particularly glutathione S-transferases (GSTs) involved in xenobiotic detoxification, remain incompletely understood. In this study, AmGSTO1 was structurally and functionally characterized to evaluate its role in agrochemical interaction and protection against oxidative stress. The crystal structure of AmGSTO1 in complex with glutathione revealed its 3D architecture and key active-site residues were identified by structural analysis and site-directed mutagenesis. Fluorescence binding assays demonstrated measurable affinity for multiple agrochemicals, including TCP, fenoprop, 2,4-D, tetramethrin, nicotine, and 3-phenoxybenzaldehyde. However, HPLC analysis showed no detectable substrate depletion, suggesting ligand binding to AmGSTO1 without catalytic turnover. AmGSTO1 exhibited antioxidant activity toward cumene hydroperoxide, hydrogen peroxide, and paraquat, as well as dehydroascorbate reductase activity. These findings indicate that AmGSTO1 may contribute to agrochemical tolerance through ligand sequestration and redox protection mechanisms.

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Identification and Functional Characterization of Isoflavone Synthase Gene Family in Pea (Pisum sativum): The Entry Point to Pisatin Biosynthesis

Tahir, M. S.; Kuflu, K.; Islam, N. S.; Mcdowell, T.; Dhaubhadel, S.

2026-01-22 biochemistry 10.64898/2025.12.22.696109 medRxiv
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Isoflavone synthase (IFS), a cytochrome P450 monooxygenase of the CYP93C subfamily, catalyzes the conversion of flavanones into isoflavones, the first committed step in the biosynthesis of isoflavonoid phytoalexins. In pea (Pisum sativum L.), the phytoalexin pisatin plays a pivotal role in defense against pathogens. However, the molecular basis underlying IFS function in pea remains poorly understood. In this study, we performed a comprehensive genome-wide identification and characterization of IFS genes in pea. Three IFS candidates, PsIFS7A, PsIFS7B, and PsIFS7C, were identified that reside on chromosome 7, each harboring all conserved cytochrome P450 signature motifs. PsIFS genes exhibited predominant expression in root tissue, with transcript levels induced rapidly upon Aphanomyces euteiches infection. Enzymatic assays confirmed their catalytic activity in converting the flavanones naringenin and liquiritigenin into the isoflavones genistein and daidzein, respectively, both in vitro and in planta systems. Furthermore, all three PsIFS genes were found in close proximity to quantitative trait loci (QTL) associated with Aphanomyces root rot resistance. Together, these findings provide novel insights into the IFS gene family in pea and lay a foundation for metabolic engineering or molecular breeding strategies to enhance disease resistance through targeted modulation of pisatin biosynthesis.

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Functional Network Analysis of Fungal Pathogen Colletotrichum sublineola Effectors in Sorghum Anthracnose

Lerma-Ortiz, C.; Edirisinghe, J. N.; Nandi, P.; Magill, C. W.; Ramos-Melendez, D.; Liu, Q.; Henry, C. S.

2026-03-10 pathology 10.64898/2026.03.07.710159 medRxiv
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Colletotrichum sublineola (Cs) is a hemibiotrophic fungal pathogen that causes anthracnose in Sorghum bicolor, leading to significant yield losses. To enable infection, Cs secretes effectors - proteins, small RNAs, and metabolites - that damage the plant cell wall or enter the plant cell to suppress immune responses and manipulate host metabolism. Effectors can detoxify host antimicrobials, alter nutrient processing, and evade host immunity. Paradoxically, some effectors can also trigger pattern-triggered immunity (PTI), especially in biotrophic and necrotrophic fungi. More than half of fungal protein effectors lack conserved domains and functional network annotations. In this study, we identified prospective Cs effectors, separating those with non-conserved domains and classifying those with conserved domains by protein families. Comparative genomics is employed to predict effector functions and analyze their roles. Using their predicted locations and domains, we mapped the effectors into functional subsystems related to PTI. These include interactions in the apoplast, oxidative stress response, protein modification and degradation systems, and Cysteine-rich Fungus-specific Epidermal Growth Factor-like Module (CFEM) domain proteins involved in immune regulation. Our functional network analysis advances the understanding of Cs pathogenicity and offers insights into effector infection mechanisms.

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Natural variation in the atypical resistance gene Pita2 confers broad-spectrum neck blast resistance in rice

Navea, I. P.; Monsur, M. A.; Telebanco-Yanoria, M. J.; De La Rosa, D. G.; Hechanova, S. L.; Tuano, A. P.; Cumagun, C. J.; Choi, I.-R.; Kadaru, S.; Kim, S.-R.; Zhou, B.; Schepler-Luu, V.

2026-02-02 pathology 10.64898/2026.01.31.702980 medRxiv
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Neck blast (NB), caused by Magnaporthe oryzae, damages rice panicles and reduces yield. Knowledge of NB resistance remains limited due to the lack of reliable resistance evaluation methods. Here, we applied a newly established neck injection method and performed a GWAS on 335 diverse accessions from the 3K Rice Genomes Project to identify loci associated with NB resistance. We detected a significant association on chromosome 12, explaining 15-18% of the symptom variations caused by a highly virulent Philippine blast isolate (M64-1-3-9-1). Linkage disequilibrium analysis refined this region to a 42.3-kb interval containing Pita2, a known leaf blast resistance gene. We found that two Pita2 allelic variants, Pita2a and Pita2c, both harboring the variant A/G (Lys879) in the last exon (Chr12:10,833,400), are associated with NB resistance. IR64 and a CO39 near-isogenic line (NIL) IRBLta2-Pi[CO] harboring Pita2a were resistant, whereas CRISPR-Cas9 knock-out of Pita2a in IR64 caused susceptibility to M64-1-3-9-1 and IK81-25. These results indicate that Pita2a is required for NB resistance. Furthermore, the CO39 NIL, IRBLta2-Pi[CO], and Lijiangxintuanheigu monogenic line (IRBLta2-Pi) harboring the Pita2a allele exhibited broad-spectrum resistance to 75% and 80% of Philippine differential blast isolates, respectively. The superior haplotype of Pita2 contains two major SNPs (A/G and A/C at Chr12:10,833,400 and Chr12:10,845,095) occurs in 83% of IRRI elite breeding lines and can be used to select NB-resistant genotypes with an accuracy of 86%. Our findings identify Pita2a as a major gene for NB resistance and provide a valuable genetic resource for developing blast-resistant rice. PLAIN LANGUAGE SUMMARYRice blast, caused by the fungus Magnaporthe oryzae, is a major threat to global rice production. Neck blast (NB) is the most severe type of blast, however, the genetic basis of NB resistance remains poorly understood. In this study, we analyzed 335 rice accessions to identify genes underlying the resistance against a Philippine blast isolate. We found that allelic variants Pita2a and Pita2c are strongly-associated with NB resistance. Knock-out of Pita2a allele made resistant rice plants susceptible while introgression into susceptible rice lines enhanced resistance to multiple blast isolates, confirming its role in NB resistance. Importantly, the superior alleles of Pita2 are already present in 83% of elite breeding lines and can be used to select NB-resistant genotypes with an accuracy of 86%. Our findings clarify the genetic control of NB resistance and offer new tools for protecting rice yields in blast-endemic regions.

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A comparison of commercially available Saccharomyces mead yeasts.

Nemeth, B.; Kallai, Z.; Toxeitova, A.; Horvath, G.; Antunovics, Z.; Harmath, A.; University of Debrecen Biotechnology BSc class of 2026, ; Sipiczki, M.; Pocsi, I.; Pfliegler, W. P.

2026-02-28 microbiology 10.64898/2026.02.27.708468 medRxiv
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We present a comparative analysis of 13 yeasts available for mead (honey wine) fermentation, a source of Saccharomyces cerevisiae diversity that has not yet been analyzed in detail. Using genomic, phenotyping, and analytic methods, we show that currently available mead yeasts belong to various clades of the species, most commonly to the Commercial Wine clade (5 of 13 samples). Mead yeasts in this group displayed genome structure variations and occasional loss of killer activity, despite being closely related. Historic European and traditional African mead isolates with sequenced genomes were found not to be closely related to any contemporary mead yeast product. The 13 yeasts tested here displayed high variability in oenological characteristics and in aroma production. Maximum ethanol tolerance ranged from 15 to 22% v/v, however, the most tolerant strain produced lower ethanol levels and retained high fructose content in experimental meads. The most abundant aroma components produced in meads were ethyl acetate, ethyl caprylate, isoamyl alcohol, and ethyl caprate, with similar aroma profiles in members of the Commercial Wine clade, and pronounced differences among other yeasts. Our results contribute to the knowledge of Saccharomyces yeasts in various fermentation environments, adding mead to the list of alcoholic beverages with a known diversity of starter cultures. Our results may aid strain selection for honey wine fermentations and inspire strain improvement.

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Quantification of Phytohormones in Plants - Optimized Extraction, Separation and Detection

Wewer, V.; Dyballa-Rukes, N.; Metzger, S.

2026-03-18 biochemistry 10.64898/2026.03.17.712349 medRxiv
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Phytohormones are key players in the regulation of plant development and metabolism. The different phytohormone classes comprise numerous chemically very diverse compounds, which are often present at very low concentrations. The chemical properties of phytohormones range from acidic to basic and from polar to non-polar. Furthermore, concentration varies strongly among different phytohormones, between plant species, tissues and developmental stages. Challenges often arise when only small amounts of plant material are available and when plant species are investigated in which the phytohormone profile has not yet been characterized. To establish a method for comprehensive phytohormone analysis we addressed these challenges by choosing and optimizing a suitable extraction method followed by optimized HPLC separation. We compared the most widely-used mass spectrometric detection methods, multiple reaction monitoring (MRM) on a triple quad instrument with high-resolution mass spectrometry (HRMS) on a Q-TOF instrument, and discuss the advantages of both methods and their limitations. O_LIWe compared various methods described in literature for the extraction of six phytohormone classes by liquid-liquid extraction and solid phase extraction purification and describe our optimizations to the selected method. C_LIO_LIWe optimized HPLC separation for 50 different phytohormones. C_LIO_LIWe evaluated the application of MRM and HRMS detection strategies. C_LI

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Production of Mixed Fruits (Watermelon, Banana, and Pineapple) Wine Using Saccharomyces cerevisiae Isolated from Palm Wine.

Egbelo, J. E.; Edeghor, U. O.; Nwokpuru, J. C.; Achokwu, C. O.; Igwe, V. C.

2026-03-02 microbiology 10.64898/2026.02.28.708690 medRxiv
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Postharvest losses and rapid nutrient degradation due to fruit spoilage necessitate alternative preservation methods. Wine production presents a viable approach to minimizing fruit waste while retaining essential nutrients. In this study, mixed fruit wines (watermelon, banana, and pineapple) were produced using Saccharomyces cerevisiae isolated from palm wine as a starter culture. After secondary fermentation, the wines maintained an acidic pH range (2.29{+/-}0.1 to 3.25{+/-}0.2), a stable fermentation temperature (26.50{+/-}1.1{degrees}C to 27.00{+/-}1.1{degrees}C), specific gravity values of 1.021{+/-}0.02 kg/L and 1.027{+/-}0.03 kg/L, and total acidity levels of 1.57{+/-}0.2% and 2.11{+/-}0.1% for Wines A and B, respectively. The final alcohol content was 8.40{+/-}2.9% in Wine A and 9.84{+/-}3.6% in Wine B. Proximate analysis demonstrated the retention of key nutrients post-clarification and maturation, and sensory evaluation indicated a higher consumer preference for Wine B (P>0.05). These findings highlight the potential of indigenous S. cerevisiae strains from palm win for efficient wine fermentation and support the utilization of mixed fruits as a sustainable raw material for value-added wine production. This approach not only mitigates fruit wastage but also provides an economic avenue for enhancing fruit utilization.

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DEDuCT 3.0: An enhanced and expanded FAIR-compliant resource and toxicology knowledge graph for endocrine disrupting chemicals

Chivukula, N.; Vashishth, S.; Kandasamy, P.; Madgaonkar, S. R.; Samal, A.

2026-01-26 pharmacology and toxicology 10.64898/2026.01.23.701267 medRxiv
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Endocrine disrupting chemicals (EDCs) are of particular regulatory and research interest due to the increasing incidence of endocrine-related disorders, such as declining fertility rates and reproductive health problems. The Database of Endocrine Disrupting Chemicals and their Toxicity Profiles (DEDuCT) has gained importance in both academic and regulatory settings by systematically curating data from published literature to characterize these chemicals. Given the growing body of EDC literature, this study aimed to consolidate the latest research and update this critical database. First, more than 14000 research articles were screened through an extensive four-stage manual process, and integrated with the earlier version to create the updated DEDuCTv3.0, comprising 1043 unique EDCs and 796 unique endocrine-related endpoints curated from 3269 published articles. Thereafter, human- and rodent-specific biological endpoint data including interacting genes/proteins, phenotypes, diseases, and adverse outcome pathways (AOPs) were curated from toxicology-relevant databases and systematically integrated with DEDuCTv3.0 to construct a large-scale toxicology knowledge graph for EDCs, termed DEDuCT-KG. DEDuCT-KG was then hosted on a Neo4j database and made easily accessible through a novel interactive user interface. The utility of DEDuCT-KG was demonstrated by exploring potential mechanisms of action associated with obesogenic EDCs within DEDuCTv3.0. Furthermore, the constructed EDC-AOP network, linking 949 EDCs to 381 AOPs within AOP-Wiki, revealed diverse toxicity mechanisms associated with EDCs. Integration with consumer product database and regulatory chemical lists showed that some of these EDCs are present in food contact materials, personal care products, and daily use items, highlighting potential exposure pathways. Overall, all data compiled in this study have been integrated into the DEDuCT webserver, which has been further enhanced to align with FAIR principles. In sum, this study provides a much-needed update to DEDuCT and offers a single point of access to EDC-relevant data to accelerate research and regulation of EDCs.

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The role of two GLYCOALKALOID METABOLISM genes in α-tomatine biosynthesis and basal defense in tomato

You, Y.; Balaji, A.; Herrera Valderrama, A. L.; Denarie, M.-E.; Hassan Muralidhar, S.; Ramirez Gaona, M.; Hanika, K.; Verstappen, F.; Kappers, I. F.; van Kan, J. A. L.

2026-02-17 plant biology 10.64898/2026.02.16.705890 medRxiv
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Steroidal glycoalkaloids and saponins are plant cholesterol-based steroid metabolites with antimicrobial activities and potential pharmacological value. The saponin uttroside B from black nightshade (Solanum nigrum) plays an important role in defense against herbivorous insect and exhibits anti-hepatocellular carcinoma activity. The tomato (S. lycopersicum) glycoalkaloid -tomatine has been studied because of its antinutritional effects, however, its role in protecting plants from fungal pathogens remains understudied. The biosynthetic pathway of -tomatine involves multiple clustered genes designated as glycoalkaloid metabolism (GAME) genes. In this study, we generated single knockout mutants of SlGAME4 and SlGAME2 by CRISPR/Cas9-based genome editing. The SlGAME4 mutants did not accumulate glycoalkaloids but instead redirected resources towards steroidal saponin (uttroside B) synthesis. SlGAME2 mutants contained unaltered -tomatine contents indicating that the SlGAME2 gene, previously reported to catalyze the transfer of xylose to {beta}1-tomatine, is not involved in -tomatine biosynthesis. Infection assays with four fungal tomato pathogens demonstrated that the SlGAME4 mutant plants were slightly more susceptible to Botrytis cinerea, but equally susceptible to the other three fungi. Up-regulation of -tomatine-responsive genes in B. cinerea was observed during infection on SlGAME4 mutant tomato, as well as on S. nigrum suggesting that uttroside B induces a fungal transcriptional response similar to -tomatine. Furthermore, we observed that tolerance mechanisms to plant saponins mediated by glycosyl hydrolases and a glycosyltransferase contribute to virulence of B. cinerea on SlGAME4 mutant plants and S. nigrum. This indicates that also uttroside B contributes to defense against fungal pathogens and can be detoxified by B. cinerea.

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Prebiotic Potential of Non-digestible Oligosaccharides Isolated from Barnyard Millet (Echinochloa frumentacea ) Grain

MAJI, S.; BISWAS, P.; AGRAWAL, S.; SHIT, S.; DEY, S.

2026-02-26 microbiology 10.64898/2026.02.26.708187 medRxiv
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It is encouraging to see the growing acceptance of millet among the general public, driven by its numerous health benefits. Various research efforts have focused on the many non-digestible oligosaccharides (NDOs) in millets, given their significant nutraceutical potential. Barnyard millet is a viable candidate for extracting NDOs owing to its superior nutritional value and affordability. In the present study, crude oligosaccharides were extracted from barnyard millet under optimized conditions: 80% aqueous ethanol (v/v) at a 1:5 sample-to-solvent ratio for 1 h at 60 {degrees}C, yielding 3.61{+/-}0.24%. Extracted oligosaccharides were further purified through adsorption chromatography and dialyzed through dialysis membranes (500 Da). Several significant peaks at m/z values of 527, 689, 852, 1014, and 1338 were detected in the MALDI-TOF mass spectrum, indicating that barnyard millet oligosaccharides (BMOs) comprise various oligosaccharides with degrees of polymerization (DP) from 3 to 8. BMOs were treated with digestive enzymes (porcine pancreatic and salivary -amylase) and an artificial acidic solution, and results showed that approximately 91% of BMOs were not digested. The positive prebiotic scores and the generation of lactic and short-chain fatty acids (SCFAs) upon fermentation by various probiotic strains indicate the prebiotic potential of BMOs. In this study, the results also showed that the presence of BMOs increased auto-aggregation of lactobacilli and enhanced the adhesion of probiotics to HCT116 cells. Our findings indicate that, with its nutritional benefits, barnyard millet may serve as a viable reservoir of beneficial carbohydrates, including NDOs. HighlightsO_LIExtraction of BMOs under optimized parameters. C_LIO_LIPartial purification of BMOs through charcoal column chromatography and dialysis. C_LIO_LIA positive prebiotic activity score conferred the prebiotic potential of BMOs. C_LIO_LIProduction of short-chain fatty acids by fermentation of BMOs. C_LIO_LIBMOs increased the auto-aggregation percentage of different probiotics. C_LI

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The significance of sukumo (composted indigo leaves) as a microbial source for traditional Japanese indigo dyeing

Kato, S.; Igarashi, K.; Kanie, S.; Yamamoto, K.; Kitagawa, W.; Narihiro, T.; Watanabe, K.; Fujii, K.; Yumoto, I.; Ueno, Y.

2026-01-29 microbiology 10.64898/2026.01.29.702489 medRxiv
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A critical process in traditional Japanese indigo dyeing is the microbial reduction of indigo within the dye suspension, which consists solely of sukumo (fermented indigo leaves), wood ash lye, and microbial nutrients such as wheat bran. Although sukumo has long been recognized as a potential microbial source, the microbial community dynamics during its production is still largely unexplored, and its contribution to dyeing performance via microbial supply remains poorly characterized. In this study, we investigated the significance of sukumo as a microbial source, in addition to its established role as a pigment source. We conducted a time-series analysis of microbial communities throughout the four-month fermentation process of sukumo, using weekly samples collected from two geographically distinct indigo dyeing studios. Microbial profiling revealed similar successional patterns between the two sites. Notably, in the later stages of fermentation, known indigo-reducing bacteria, such as the genus Oceanobacillus and the family Tissierellaceae, emerged at both locations. Laboratory-scale dyeing experiments using immature sukumo demonstrated that supplementation with a small amount of mature sukumo restored dyeing activity and increased the abundance of Oceanobacillus and Tissierellaceae. Furthermore, the addition of the indigo-reducing isolate Tissierellaceae strain TU-1 to the immature sukumo-based dye suspension led to a marked enhancement in dyeing performance. These findings highlight the critical role of sukumo as a microbial source in traditional indigo dyeing and suggest that prolonged fermentation is essential for nurturing functional indigo-reducing bacteria. This insight provides a foundation for improving dye suspension performance through targeted microbial community management.

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A Multicopper Oxidase from Paenibacillus polyethylenelyticus JNU01 Oxidizes Polyethylene

Yun, S.-D.; Kim, S.; An, S. J.; Kim, H.-W.; Cho, J.-H.; Son, H. F.; Yun, C.-H.; Sung, B. H.; Beckham, G. T.; Chi, W. S.; Park, C.; Yeom, S.-J.

2026-02-24 microbiology 10.64898/2026.02.24.707384 medRxiv
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Polyethylene (PE) is a widely used plastic that persists in the environment and resists breakdown via microbial degradation. In this work, we discovered a new bacterium, Paenibacillus polyethylenelyticus JNU01, that grows on a PE-like wax (PELW, 4 kDa) as its sole carbon source, causing chemical modifications to the substrate and releasing small-molecule products. Genomic and transcriptomic analyses identified a multicopper oxidase (PpMmcO) as a key enzyme candidate for this observed activity. PpMmcO caused surface oxidation, increased hydrophilicity, and the release of oxygenated products such as ketones, alkanes, and alkenoic acids. Scanning electron microscopy confirmed surface damage on both PELW and post-use greenhouse PE films. Weight loss analysis showed mass losses of 5.2% for the PELW powder and 1.6% for the greenhouse PE film after treatment with wild-type PpMmcO. We propose a radical-mediated pathway catalyzed by PpMmcO. These findings identify a new bacterium and enzyme capable of initiating PE oxidation and provide insight into biological processes that may act on polyethylene.

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Benchmarking Artificial Intelligence Models for Predicting Nuclear Receptor Activity from Tox21 Assays

Chivukula, N.; Karthikeyan, J.; Thangavel, H.; Madgaonkar, S. R.; Samal, A.

2026-03-24 pharmacology and toxicology 10.64898/2026.03.20.713297 medRxiv
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Tox21 assays compile extensive chemical bioactivity data across diverse biological targets, making them widely utilized resources for in silico model development. Nuclear receptor-specific assays within this dataset are particularly valuable for screening potential endocrine disrupting chemicals. This study presents a comprehensive benchmarking of diverse machine learning (ML), deep learning (DL), and transformer-based architectures with varied chemical feature representations across nuclear receptor assays. First, 43 datasets associated with 18 nuclear receptors within Tox21 assays were systematically curated from ToxCast invitrodb v4.3. Upon testing across these datasets, model performance was found to be dependent on the degree of class imbalance. Tree-based ML models such as random forest (RF) and extreme gradient boosting (XGBoost) trained on descriptors, or combination of descriptors and fingerprints, consistently outperformed in datasets with higher proportions of active chemicals (>10%), while DL models showed greater robustness for those with moderate proportions (5-10%). Further analysis revealed that approximately 40% of misclassified active chemicals occupied structurally isolated regions of the chemical space, suggesting absence of close structural analogues in the training set potentially contributed to their misclassification. External validation using in vitro and in vivo androgen and estrogen receptor bioactivity data showed generally good concordance. Finally, a systematic literature review revealed that the models in this study span wider range of architectures, feature representations, and assay endpoints, and are broadly comparable to or better than existing work. Overall, insights from this study can inform the development of more reliable in silico tools supporting new approach methodologies for nuclear receptor bioactivity predictions.

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Genome-wide analysis of Heavy metal ATPase (P1B-type ATPase) gene family in Mung bean and their expression analysis under heavy metal (Zn, Cd and Cu) stress

Panigrahi, J.; Panigrahy, D.; Rath, B.; Gupta, K.

2026-03-27 molecular biology 10.64898/2026.03.25.713876 medRxiv
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Heavy metal ATPases (HMAs) are important group of transmembrane proteins involved in homeostasis of metal ions in plant systems. In this study, a comprehensive analysis of genome assembly (VC1973A v7.1) resulted in the identification of nine HMA genes (VrHMA) and their corresponding proteins in Mungbean, an agronomically important legume crop known for its nutritional values. VrHMA proteins were also characterized based on their biomolecular features, conserved domains and motifs arrangement, transmembrane helices, pore-line helices, subcellular location and occurrence of signal peptides. Based on sequence homology, nine VrHMAs were clustered into two major substrate-specific groups: VrHMA1, VrHMA5 and VrHMA7 were categorized under the Zn/Co/Cd/Pb ATPase group, whereas the remaining six VrHMAs belong to the Cu/Ag subgroup. Gene structure analysis and promoter scanning revealed the structural divergence and presence of various stress-responsive cis-acting elements, respectively. The expression analysis of VrHMA genes in root and leaf tissues, in response to heavy metal (Zn, Cd and Cu) stress, indicates their role in the uptake, transport and sequestration of metal ions. Interestingly, VrHMA5 showed incremental upregulation in roots in response to all three heavy metal stresses, whereas its expression was only upregulated in the leaf tissues under Zn stress, which indicates its role in vascular transport in V. radiata. In addition, this study provides valuable insights into the functional roles of VrHMA genes and will lay a foundation for future genetic improvement in mung bean aimed at enhanced heavy metal stress tolerance and micronutrient homeostasis.

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Prebiotic ALPINA GOS produced from whey permeate has a bifidogenic effect on the adult fecal microbiota in vitro, including stimulation of organic acids production

Orrego, D.; Kortman, G. A. M.; Hester, E. R.; Sierra-Zapata, L.; Blel-Jubiz, S.; Caro-Miranda, V.; Klotz-Ceberio, B.

2026-01-29 microbiology 10.64898/2026.01.26.701770 medRxiv
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Functional oligosaccharides, such as galacto-oligosaccharides (GOS), are valued for modulating gut microbiota and promoting health. This study aimed to produce a high-purity GOS ingredient (ALPINA GOS) via nanofiltration/diafiltration and assess its prebiotic efficacy using an in vitro fermentation model. GOS-rich syrup was obtained from transgalactosylation of lactose in concentrated whey permeate (30% lactose) and processed by diafiltration/nanofiltration to reduce monosaccharides and enrich oligosaccharide content. Carbohydrate composition was analyzed by HPAEC-PAD. Prebiotic activity was evaluated using a MicroColon model with fecal inocula from healthy adults, measuring pH, short-chain fatty acids (SCFAs), and microbiota shifts. Membrane processing increased oligosaccharides from 55.5% to 70.2% (dry basis) and reduced monosaccharides from 25.2% to 5.1%. ALPINA GOS induced a dose-dependent pH reduction and significantly enhanced lactate and acetate production, with stronger effects at 10 mg/mL. Microbiota profiling showed increased abundance of beneficial bacteria, especially Bifidobacterium, versus control. The findings confirm that GOS can be sustainably produced from whey permeate and exhibits potent prebiotic activity, supporting its application in functional foods aimed at gut health.

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In vivo pharmacokinetics and tissue distribution profile of a Wnt/β-catenin pathway-targeting anticancer cassane diterpene isolated from Caesalpinia pulcherrima

De Vass Gunawardane, S.; Epitawala Arachchige, O. V.; Wijerathne, S. K.; Punyasiri, P. A. N.; Murugananthan, A.; Samarakoon, S. R.; Senathilake, K. S.

2026-04-01 pharmacology and toxicology 10.64898/2026.03.30.715187 medRxiv
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A cassane diterpene, 6{beta}-cinnamoyl-7-hydroxyvouacapen-5-ol (6{beta}CHV), isolated from Caesalpinia pulcherrima, has emerged as a promising anticancer drug lead with reported Wnt/{beta}-catenin pathway inhibitory activity and in vivo safety. The present study reports the in vivo pharmacokinetics and tissue distribution of 6{beta}CHV in Wistar rats following a single oral dose of 200 mg/kg. A reproducible RP-HPLC-UV method was developed and validated for quantifying 6{beta}CHV in rat plasma and tissues. Chromatographic separation was achieved using a gradient elution of methanol and water. The method was subsequently applied to investigate the pharmacokinetics and tissue distribution of 6{beta}CHV. Plasma pharmacokinetic analysis revealed delayed and moderate absorption, with a Tmax of 4 h and a Cmax of 1314.12 ng/mL. Following absorption, 6{beta}CHV is distributed widely across peripheral tissues, including the liver, heart, lungs, spleen, and kidneys, as well as pharmacological sanctuary sites such as the brain and testes. The highest concentrations were observed in the stomach, small intestine, and liver, with detectable levels persisting up to 24 h, reflecting extensive tissue partitioning and retention. Overall, these findings demonstrate that oral administration of 6{beta}CHV is feasible. However, the delayed absorption suggests that further optimization of formulation or alternative administration routes may enhance systemic exposure. This study provides the first comprehensive pharmacokinetic and tissue distribution profile of 6{beta}CHV, supporting its continued preclinical development as a potential anticancer therapeutic. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/715187v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@4ae86forg.highwire.dtl.DTLVardef@1e1e51aorg.highwire.dtl.DTLVardef@1881c43org.highwire.dtl.DTLVardef@f7789f_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Characterization of ovine follicular fluid and granulosa cell-derived extracellular vesicles and their miRNA cargo following in vitro exposure to bisphenols A and S.

Desmarchais, A.; Uzbekova, S.; Maillard, V.; Papillier, P.; Douet, C.; Duret, T.; Uzbekov, R.; Piegu, B.; Lefort, G.; Teixido, N.; Carvalho, A.; Roger, S.; elis, S.

2026-03-31 molecular biology 10.64898/2026.03.27.713654 medRxiv
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Bisphenol A (BPA) and Bisphenol S (BPS) exposure disrupt ovarian function and granulosa cell (GC) steroidogenesis. Extracellular vesicles (EVs) and their miRNA cargo, as mediators of cellular response to environmental stimuli, might be involved in fertility and folliculogenesis. This study explored modulation of microRNA expression after 48h BPA or BPS exposure (10 {micro}M) in ovine primary GC and EVs from corresponding conditioned medium (CM EVs). Small RNA sequencing of control (0h) and 48h treated GC, CM EVs as well as follicular fluid EVs allowed identification of 533 ovine miRNAs, including 129 new sequences. BPA did not alter miRNA expression in GC, while BPS decreased cellular oar-24b miR. In contrast, BPA modified expression of 4 miRNAs in CM-EVs, including 3 new sequences, and two miRNAs were modified by BPS. Both compounds reduced expression of sequence homologous to miR-1306. Further studies are required to decipher their roles in bisphenol toxicity in GC.

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A comprehensive resource on chemicals used in aquaculture and their ecotoxicity

Madgaonkar, S. R.; Vashishth, S.; Chivukula, N.; Garisetti, V.; Marigoudar, S. R.; Sharma, K. V.; Samal, A.

2026-01-28 pharmacology and toxicology 10.64898/2026.01.26.701529 medRxiv
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Sustainable aquaculture requires comprehensive chemical oversight, as compounds used in aquaculture can persist in ecosystems, bioaccumulate through food chains, and affect aquatic life and human health. This study presents ReCAnt (Resource on Chemicals used in Aquaculture and their Ecotoxicity), which compiles information on 690 aquaculture chemicals, with data on toxic effects and therapeutic potential curated from published literature. It was observed that only a fraction of the 690 chemicals are currently regulated, revealing gaps in existing regulations. Integration of data from the Comparative Toxicogenomics Database revealed associations with genes, phenotypes, and diseases, while ECOTOX data provided toxicity and bioconcentration information. Predicted biotransformation pathways and partition coefficients indicated microbial degradation potential and fate across environmental media. Further, food web network analysis identified species vulnerable to trophic transfer and common entry points for chemicals into aquatic ecosystems. This resource can aid in developing evidence-based regulatory frameworks and promoting sustainable chemical management.