Pub Date : 2025-09-06DOI: 10.1016/j.fochms.2025.100297
Hong Xu , Xueting Bi , Junjie Xing , Mengqian Guo , Haoran Zhang , Xuejie Zhang , Wei Li , Bingfu Lei
Hydrogen sulfide (H₂S) has been demonstrated to delay ripening and senescence in various fruits, offering great capability for postharvest preservation. However, existing application methods face several limitations, such as unstable release, difficulty in dosage control, and safety concerns, and its regulatory mechanisms in fruit systems remain unclear. In this study, calcium sulfide (CaS) was used as a slow-release H₂S donor that gradually releases H₂S through reactions with airborne moisture and carbon dioxide to treat bananas. CaS treatment significantly downregulated key ethylene biosynthetic genes and corresponding enzymes (ACO and ACS), thereby reducing ethylene production. The expression of starch-degrading and cell wall-modifying genes was also suppressed, delaying starch breakdown and cell wall disassembly. Enzyme assays and transcriptomic analyses confirmed that CaS delays banana ripening through coordinated regulation at both transcriptional and biochemical levels. As a result, CaS treatment effectively extended shelf life and maintained fruit quality of bananas. These findings reveal the potential of CaS as a novel H₂S-releasing agent for postharvest preservation.
{"title":"Regulatory role of calcium sulfide in ripening delay of postharvest bananas","authors":"Hong Xu , Xueting Bi , Junjie Xing , Mengqian Guo , Haoran Zhang , Xuejie Zhang , Wei Li , Bingfu Lei","doi":"10.1016/j.fochms.2025.100297","DOIUrl":"10.1016/j.fochms.2025.100297","url":null,"abstract":"<div><div>Hydrogen sulfide (H₂S) has been demonstrated to delay ripening and senescence in various fruits, offering great capability for postharvest preservation. However, existing application methods face several limitations, such as unstable release, difficulty in dosage control, and safety concerns, and its regulatory mechanisms in fruit systems remain unclear. In this study, calcium sulfide (CaS) was used as a slow-release H₂S donor that gradually releases H₂S through reactions with airborne moisture and carbon dioxide to treat bananas. CaS treatment significantly downregulated key ethylene biosynthetic genes and corresponding enzymes (ACO and ACS), thereby reducing ethylene production. The expression of starch-degrading and cell wall-modifying genes was also suppressed, delaying starch breakdown and cell wall disassembly. Enzyme assays and transcriptomic analyses confirmed that CaS delays banana ripening through coordinated regulation at both transcriptional and biochemical levels. As a result, CaS treatment effectively extended shelf life and maintained fruit quality of bananas. These findings reveal the potential of CaS as a novel H₂S-releasing agent for postharvest preservation.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100297"},"PeriodicalIF":4.7,"publicationDate":"2025-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145059964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-02DOI: 10.1016/j.fochms.2025.100296
Haijie Huang , Li Zhao , Weijian Huang , Xuejie Feng , Fuchu Hu , Ya Zhao , Huiliang Li , Yunlu Peng , Yuhan Wang , Zhongrun Zhang , Yijun Liu
Metabolite changes during the ripening process of cashew apples are crucial for their quality development. A total of 2379 metabolites were isolated and identified from fresh cashew apples at four different ripening stages using UHPLC-MS. Metabolite set enrichment analysis (MSEA) revealed that the differential metabolites in CA2_vs_CA1, CA3_vs_CA2, and CA4_vs_CA3 comparisons were mainly enriched in amino acids and peptides, steroids, pyrimidines, and fatty acids and conjugates, etc. Volcano plot analysis identified 631, 384, and 392 upregulated metabolites, and 625, 923, and 392 downregulated metabolites in CA2_vs_CA1, CA3_vs_CA2, and CA4_vs_CA3 comparisons, respectively. KEGG pathway enrichment analysis demonstrated that these differential metabolites were primarily involved in aminoacyl-tRNA biosynthesis, purine metabolism, and glycine, etc. Notably, the differential metabolites in CA4_vs_CA3 showed the highest enrichment in d-glutamine and D-glutamate metabolism, as well as phenylalanine. The metabolic profile of cashew apples revealed stage-specific patterns during ripening, offering key insights for optimizing harvest, storage, and processing.
{"title":"Deciphering the metabolic patterns of cashew apple ripening process: A comprehensive non-targeted metabolomics analysis","authors":"Haijie Huang , Li Zhao , Weijian Huang , Xuejie Feng , Fuchu Hu , Ya Zhao , Huiliang Li , Yunlu Peng , Yuhan Wang , Zhongrun Zhang , Yijun Liu","doi":"10.1016/j.fochms.2025.100296","DOIUrl":"10.1016/j.fochms.2025.100296","url":null,"abstract":"<div><div>Metabolite changes during the ripening process of cashew apples are crucial for their quality development. A total of 2379 metabolites were isolated and identified from fresh cashew apples at four different ripening stages using UHPLC-MS. Metabolite set enrichment analysis (MSEA) revealed that the differential metabolites in CA2_vs_CA1, CA3_vs_CA2, and CA4_vs_CA3 comparisons were mainly enriched in amino acids and peptides, steroids, pyrimidines, and fatty acids and conjugates, etc. Volcano plot analysis identified 631, 384, and 392 upregulated metabolites, and 625, 923, and 392 downregulated metabolites in CA2_vs_CA1, CA3_vs_CA2, and CA4_vs_CA3 comparisons, respectively. KEGG pathway enrichment analysis demonstrated that these differential metabolites were primarily involved in aminoacyl-tRNA biosynthesis, purine metabolism, and glycine, etc. Notably, the differential metabolites in CA4_vs_CA3 showed the highest enrichment in <span>d</span>-glutamine and D-glutamate metabolism, as well as phenylalanine. The metabolic profile of cashew apples revealed stage-specific patterns during ripening, offering key insights for optimizing harvest, storage, and processing.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100296"},"PeriodicalIF":4.7,"publicationDate":"2025-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145018842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mustard greens are gaining global popularity, but preservation methods like salting and pickling raise specific concerns related to high sodium content and microbial safety. This study conducted a proteomics analysis to identify health-beneficial proteins in mustard greens.
Objective
To explore protein profiles associated with health benefits in fresh and preserved mustard greens.
Methods
Shotgun proteomics combined with LC-MS/MS was applied to identify proteins, followed by statistical analysis using Welch's t-test with Benjamini–Hochberg false discovery rate correction. Unique proteins were visualized with a Venn diagram, annotated using the Gene Ontology (GO) database, and mapped to functional categories with Sankey diagrams. In silico validation of protein stability and gastrointestinal digestion was performed to assess the release of bioactive peptides.
Results
A total of 118 high-confidence proteins were identified, including 27 unique to fresh, 23 to salted, and 22 to pickled mustard greens. Unique proteins in fresh mustard greens were associated with carbohydrate, amino acid, and nucleotide metabolism. Pickled mustard greens had proteins linked to carbohydrate, lipid, glycerol, vitamin, and cofactor metabolism, while salted mustard greens had proteins involved in amino acid, nucleotide, lipid, and glycerol metabolism. In silico digestion revealed that approximately 19–20 % of peptide fragments contained bioactive motifs, predominantly angiotensin-converting enzyme (ACE) and dipeptidyl peptidase-IV (DPP-IV) inhibitory sequences.
Conclusion
Preserved mustard greens contain unique proteins associated with health benefits based on GO annotations, distinguishing their protein profiles from fresh mustard greens. This study provides insights into their functional properties, addressing concerns related to their consumption.
芥菜在全球越来越受欢迎，但腌制和酸洗等保存方法引起了人们对高钠含量和微生物安全的具体担忧。本研究对芥菜中有益健康的蛋白质进行了蛋白质组学分析。目的探讨新鲜和腌制芥菜中与健康益处相关的蛋白质谱。方法采用shotgun蛋白质组学联合LC-MS/MS对蛋白质进行鉴定，采用Welch’st检验进行统计学分析，并进行Benjamini-Hochberg错误发现率校正。使用Venn图可视化独特的蛋白质，使用基因本体（GO）数据库进行注释，并使用Sankey图映射到功能类别。通过计算机验证蛋白质稳定性和胃肠道消化来评估生物活性肽的释放。结果共鉴定出118个高信度蛋白，其中新鲜芥菜特有27个，腌制芥菜特有23个，腌制芥菜特有22个。新鲜芥菜中的独特蛋白质与碳水化合物、氨基酸和核苷酸代谢有关。腌制芥菜中含有与碳水化合物、脂质、甘油、维生素和辅助因子代谢有关的蛋白质，而腌制芥菜中含有与氨基酸、核苷酸、脂质和甘油代谢有关的蛋白质。硅酶切结果显示，约19 - 20%的肽片段含有生物活性基序，主要是血管紧张素转换酶（ACE）和二肽基肽酶- iv （DPP-IV）抑制序列。结论根据GO注释，保存的芥菜含有与健康有益的独特蛋白质，其蛋白质谱与新鲜芥菜不同。这项研究提供了对其功能特性的见解，解决了与消费相关的问题。
{"title":"Proteomic changes associated with health benefit properties in fresh and preserved mustard greens","authors":"Charanya Saekampang , Vipawan Pimpak , Poowadol Promwat , Pongsakorn Kruaweangmol , Narumon Phaonakrop , Sittiruk Roytrakul , Ulaiwan Withayagiat , Paiboon Tunsagool","doi":"10.1016/j.fochms.2025.100295","DOIUrl":"10.1016/j.fochms.2025.100295","url":null,"abstract":"<div><h3>Background</h3><div>Mustard greens are gaining global popularity, but preservation methods like salting and pickling raise specific concerns related to high sodium content and microbial safety. This study conducted a proteomics analysis to identify health-beneficial proteins in mustard greens.</div></div><div><h3>Objective</h3><div>To explore protein profiles associated with health benefits in fresh and preserved mustard greens.</div></div><div><h3>Methods</h3><div>Shotgun proteomics combined with LC-MS/MS was applied to identify proteins, followed by statistical analysis using Welch's <em>t</em>-test with Benjamini–Hochberg false discovery rate correction. Unique proteins were visualized with a Venn diagram, annotated using the Gene Ontology (GO) database, and mapped to functional categories with Sankey diagrams. In silico validation of protein stability and gastrointestinal digestion was performed to assess the release of bioactive peptides.</div></div><div><h3>Results</h3><div>A total of 118 high-confidence proteins were identified, including 27 unique to fresh, 23 to salted, and 22 to pickled mustard greens. Unique proteins in fresh mustard greens were associated with carbohydrate, amino acid, and nucleotide metabolism. Pickled mustard greens had proteins linked to carbohydrate, lipid, glycerol, vitamin, and cofactor metabolism, while salted mustard greens had proteins involved in amino acid, nucleotide, lipid, and glycerol metabolism. In silico digestion revealed that approximately 19–20 % of peptide fragments contained bioactive motifs, predominantly angiotensin-converting enzyme (ACE) and dipeptidyl peptidase-IV (DPP-IV) inhibitory sequences.</div></div><div><h3>Conclusion</h3><div>Preserved mustard greens contain unique proteins associated with health benefits based on GO annotations, distinguishing their protein profiles from fresh mustard greens. This study provides insights into their functional properties, addressing concerns related to their consumption.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100295"},"PeriodicalIF":4.7,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911971","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Curcuminoids are the active compounds richest in turmeric rhizomes (Curcuma longa L.), comprising curcumin I, demethoxycurcumin (curcumin II), and bisdemethoxycurcumin (curcumin III). This study hypothesized that particular curcumin derivatives could mitigate oxidative stress and inflammation response by targeting specific inflammatory mediators. Therefore, this study aimed to quantify the concentrations of these curcuminoid forms in local turmeric extracts from Thailand. Subsequently, the study analyzed their in vitro antioxidant properties, alongside molecular docking and dynamics simulations targeting key oxidative stress- and inflammation-related proteins. Samples were collected from three representative cultivated areas in Thailand: the eastern, southern, and northern regions. The ethanolic extracts from all samples exhibited relatively high total curcuminoid content (eastern: 15.1 %, southern: 25.9 %, and northern: 31.6 % w/w in extract), as determined by high-performance liquid chromatography. Curcumin I emerged as the predominant variant, followed closely by curcumin II and III. The ethanolic extracts from the three cultural areas demonstrated significant antioxidant activity, as assessed by ORAC, FRAP, and DPPH assays. Among the three curcuminoids, curcumin III exhibited the strongest predicted binding affinities in molecular docking studies toward antioxidant and anti-inflammatory targets, including 5-LOX, NRF2, IKK1, NF-κB, and NOX4. Molecular dynamics simulations corroborated these findings, revealing that curcumin III formed the most stable complexes, particularly with IKK1, as indicated by low RMSD values (2–3 Å), and high hydrogen bond occupancy. Thus, curcumin III exhibits potential in silico inhibition of inflammatory mediators, supporting its promise as a natural compound for antioxidant and anti-inflammatory nutraceutical development.
姜黄素是姜黄根茎（Curcuma longa L.）中最丰富的活性化合物，包括姜黄素I、去甲氧基姜黄素（姜黄素II）和双去甲氧基姜黄素（姜黄素III）。本研究假设特定的姜黄素衍生物可以通过靶向特定的炎症介质来减轻氧化应激和炎症反应。因此，本研究旨在量化泰国当地姜黄提取物中这些姜黄素形式的浓度。随后，该研究分析了它们的体外抗氧化性能，以及针对关键氧化应激和炎症相关蛋白的分子对接和动力学模拟。样本采集自泰国三个具有代表性的种植区：东部、南部和北部地区。通过高效液相色谱法测定，所有样品的乙醇提取物均具有较高的姜黄素总含量（东部：15.1%，南部：25.9%，北部：31.6% w/w）。姜黄素I是主要的变体，其次是姜黄素II和III。通过ORAC、FRAP和DPPH检测，三个培养区的乙醇提取物显示出显著的抗氧化活性。在三种姜黄素中，姜黄素III在抗氧化和抗炎靶点（包括5-LOX、NRF2、IKK1、NF-κB和NOX4）的分子对接研究中表现出最强的预测结合亲和力。分子动力学模拟证实了这些发现，显示姜黄素III形成了最稳定的复合物，特别是与IKK1，正如低RMSD值（2-3 Å）和高氢键占用所表明的那样。因此，姜黄素III显示出对炎症介质的硅抑制潜力，支持其作为抗氧化和抗炎营养品开发的天然化合物的前景。
{"title":"Comparative analysis of curcuminoid content, antioxidant capacity, and target-specific molecular docking of turmeric extracts sourced from Thailand","authors":"Shisanupong Anukanon , Komgrit Saeng-ngoen , Yawanart Ngamnon , Ngamnetr Rapan , Weerasak Seelarat , Pannraphat Takolpuckdee , Nisa Pakvilai , Yaiprae Chatree","doi":"10.1016/j.fochms.2025.100291","DOIUrl":"10.1016/j.fochms.2025.100291","url":null,"abstract":"<div><div>Curcuminoids are the active compounds richest in turmeric rhizomes (<em>Curcuma longa</em> L.), comprising curcumin I, demethoxycurcumin (curcumin II), and bisdemethoxycurcumin (curcumin III). This study hypothesized that particular curcumin derivatives could mitigate oxidative stress and inflammation response by targeting specific inflammatory mediators. Therefore, this study aimed to quantify the concentrations of these curcuminoid forms in local turmeric extracts from Thailand. Subsequently, the study analyzed their <em>in vitro</em> antioxidant properties, alongside molecular docking and dynamics simulations targeting key oxidative stress- and inflammation-related proteins. Samples were collected from three representative cultivated areas in Thailand: the eastern, southern, and northern regions. The ethanolic extracts from all samples exhibited relatively high total curcuminoid content (eastern: 15.1 %, southern: 25.9 %, and northern: 31.6 % <em>w</em>/w in extract), as determined by high-performance liquid chromatography. Curcumin I emerged as the predominant variant, followed closely by curcumin II and III. The ethanolic extracts from the three cultural areas demonstrated significant antioxidant activity, as assessed by ORAC, FRAP, and DPPH assays. Among the three curcuminoids, curcumin III exhibited the strongest predicted binding affinities in molecular docking studies toward antioxidant and anti-inflammatory targets, including 5-LOX, NRF2, IKK1, NF-κB, and NOX4. Molecular dynamics simulations corroborated these findings, revealing that curcumin III formed the most stable complexes, particularly with IKK1, as indicated by low RMSD values (2–3 Å), and high hydrogen bond occupancy. Thus, curcumin III exhibits potential <em>in silico</em> inhibition of inflammatory mediators, supporting its promise as a natural compound for antioxidant and anti-inflammatory nutraceutical development.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100291"},"PeriodicalIF":4.7,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This pilot study explores the relationship between the genetic profiles of olive cultivars and monounsaturated fatty acid (MUFA) content of their oils, with emphasis on oxidative stability and phenolic integrity. Our working hypothesis was that cultivar-specific genetic variation in MUFA content, directly affects the oxidative stability of key phenolics, particularly oleocanthal and oleacein. To examine the association between genetic clustering and oleic acid content, eighty Greek olive cultivars cultivated under controlled nursery conditions were genotyped using eleven genomic simple sequence repeat (SSR) markers, and their fatty acid composition was determined by 1H NMR. Phenolic stability was tested using oils with contrasting MUFA levels. Genetic analysis identified three clusters. Chemical cluster analysis, by dividing cultivars into three MUFA classes, revealed significant differences among divisions. Linking genetic and lipid profile groups highlighted notable overlap. This study reveals a clear experimental association between MUFA abundance in the olive matrix and its capacity to preserve phenolic integrity. By confirming the role of MUFA content in phenolic stability, our results provide a baseline reference for early-stage cultivar selection and for future breeding programs targeting enhanced olive oil quality.
{"title":"Genetic and chemical analysis of olive oil produced by Greek olive cultivars: Linking genetic profiles with fatty acid composition and phenolic stability","authors":"Annia Tsolakou , Kostas Ioannidis , Sofia Lymperopoulou , Panagiotis Diamantakos , Georgios Kostelenos , Eleni Melliou , Prokopios Magiatis","doi":"10.1016/j.fochms.2025.100292","DOIUrl":"10.1016/j.fochms.2025.100292","url":null,"abstract":"<div><div>This pilot study explores the relationship between the genetic profiles of olive cultivars and monounsaturated fatty acid (MUFA) content of their oils, with emphasis on oxidative stability and phenolic integrity. Our working hypothesis was that cultivar-specific genetic variation in MUFA content, directly affects the oxidative stability of key phenolics, particularly oleocanthal and oleacein. To examine the association between genetic clustering and oleic acid content, eighty Greek olive cultivars cultivated under controlled nursery conditions were genotyped using eleven genomic simple sequence repeat (SSR) markers, and their fatty acid composition was determined by <sup>1</sup>H NMR. Phenolic stability was tested using oils with contrasting MUFA levels. Genetic analysis identified three clusters. Chemical cluster analysis, by dividing cultivars into three MUFA classes, revealed significant differences among divisions. Linking genetic and lipid profile groups highlighted notable overlap. This study reveals a clear experimental association between MUFA abundance in the olive matrix and its capacity to preserve phenolic integrity. By confirming the role of MUFA content in phenolic stability, our results provide a baseline reference for early-stage cultivar selection and for future breeding programs targeting enhanced olive oil quality.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100292"},"PeriodicalIF":4.7,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144922748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-25DOI: 10.1016/j.fochms.2025.100294
Dengke Fu , Yuanzhong Wang , Jinyu Zhang
To improve the quality and efficiency of cultivating Amomum tsaoko (AT), a non-model plant, it is crucial to understand the intrinsic molecular mechanisms underlying its growth. This review summarizes the significance of multi-omics in the study of plant molecular mechanisms and illustrates how multi-omics technology can solve the practical problems of non-model plants using AT as an example. In this review, we argue that nonlinear dimensionality reduction is more suitable for data organization in multi-omics because it is compatible with the nonlinear relationship between the components of systems biology. Subsequently, researchers have verified the strong vitality of multi-omics from three perspectives: the natural communication, breeding, and shade tolerance mechanisms of AT. Finally, we summarized some of the current commonly used plant genome databases and analyzed their utility for such research. We believe that our study makes a significant contribution to the literature because this review summarizes the multi-omics research process in detail, from data processing to application to the use of public databases, and illustrates the potential for the application of multi-omics with the example of a non-model plant, AT.
{"title":"Omics landscapes in molecular mechanisms with Amomum tsaoko as an example","authors":"Dengke Fu , Yuanzhong Wang , Jinyu Zhang","doi":"10.1016/j.fochms.2025.100294","DOIUrl":"10.1016/j.fochms.2025.100294","url":null,"abstract":"<div><div>To improve the quality and efficiency of cultivating <em>Amomum tsaoko</em> (AT), a non-model plant, it is crucial to understand the intrinsic molecular mechanisms underlying its growth. This review summarizes the significance of multi-omics in the study of plant molecular mechanisms and illustrates how multi-omics technology can solve the practical problems of non-model plants using AT as an example. In this review, we argue that nonlinear dimensionality reduction is more suitable for data organization in multi-omics because it is compatible with the nonlinear relationship between the components of systems biology. Subsequently, researchers have verified the strong vitality of multi-omics from three perspectives: the natural communication, breeding, and shade tolerance mechanisms of AT. Finally, we summarized some of the current commonly used plant genome databases and analyzed their utility for such research. We believe that our study makes a significant contribution to the literature because this review summarizes the multi-omics research process in detail, from data processing to application to the use of public databases, and illustrates the potential for the application of multi-omics with the example of a non-model plant, AT.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100294"},"PeriodicalIF":4.7,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-25DOI: 10.1016/j.fochms.2025.100293
Jiajia Wang , Jiayu Liao , Kaisen Zhao , Na Shen , Yulin Xu , Jie Wang , Xianbo Jia , Wenqiang Sun , Songjia Lai
We hypothesized that the differences in meat quality stem from breed-specific regulation of muscle metabolic pathways. To explore the molecular mechanisms underlying meat quality differences between Liangshan cattle and Simmental crossbred cattle, we conducted metabolomic and transcriptomic analyses of the longissimus dorsi. Metabolomics revealed that Liangshan cattle exhibited higher l-carnitine levels, which may contribute to enhanced energy metabolism and improved meat quality, as well as a more favorable fatty acid composition. Integrated transcriptomic and metabolomic analysis suggested potential regulatory mechanisms: FASN may enhance fat deposition and tenderness by promoting butanoyl-CoA biosynthesis. Additionally, ALDOC, PFKL, PGAM1, and SDS may modulate citrulline metabolic flux, thereby influencing protein synthesis and promoting lipogenesis. These findings support our hypothesis by clarifying how coordinated gene–metabolite interactions influence meat quality. A potential regulatory model for the genetic-metabolic interaction of beef quality was established, providing a candidate framework for molecular breeding targeting beef quality traits.
{"title":"Integrated multi-omics reveals potential regulatory mechanisms of meat quality","authors":"Jiajia Wang , Jiayu Liao , Kaisen Zhao , Na Shen , Yulin Xu , Jie Wang , Xianbo Jia , Wenqiang Sun , Songjia Lai","doi":"10.1016/j.fochms.2025.100293","DOIUrl":"10.1016/j.fochms.2025.100293","url":null,"abstract":"<div><div>We hypothesized that the differences in meat quality stem from breed-specific regulation of muscle metabolic pathways. To explore the molecular mechanisms underlying meat quality differences between Liangshan cattle and Simmental crossbred cattle, we conducted metabolomic and transcriptomic analyses of the <em>longissimus dorsi</em>. Metabolomics revealed that Liangshan cattle exhibited higher <span>l</span>-carnitine levels, which may contribute to enhanced energy metabolism and improved meat quality, as well as a more favorable fatty acid composition. Integrated transcriptomic and metabolomic analysis suggested potential regulatory mechanisms: <em>FASN</em> may enhance fat deposition and tenderness by promoting butanoyl-CoA biosynthesis. Additionally, <em>ALDOC</em>, <em>PFKL</em>, <em>PGAM1</em>, and <em>SDS</em> may modulate citrulline metabolic flux, thereby influencing protein synthesis and promoting lipogenesis. These findings support our hypothesis by clarifying how coordinated gene–metabolite interactions influence meat quality. A potential regulatory model for the genetic-metabolic interaction of beef quality was established, providing a candidate framework for molecular breeding targeting beef quality traits.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100293"},"PeriodicalIF":4.7,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-24DOI: 10.1016/j.fochms.2025.100290
Haoran Shen , Hong Quan , Yixi Cai , Yazhou Lu , Peiyao Yu , Xiaozhong Lan , Xinbo Guo
This study investigated the antioxidant capacity and molecular mechanisms of lily bulb polyphenols using zebrafish (Danio rerio) embryos subjected to AAPH-induced oxidative stress. Two extraction methods—cold (CE) and hot (HE) water extraction—were compared. HE exhibited significantly higher total phenolic content (31 ± 4 %, p < 0.05) and polyphenol abundance (9.8 ± 0.6-fold increase, p < 0.05), particularly regaloside A and p-coumaric acid, than CE. Heat-assisted extraction of lily bulbs liberated more polyphenols (both in terms of content and variety), which translated into measurably greater antioxidant protection in vivo. In vivo assays revealed that both extracts improved embryo survival, restored SOD activity, and reduced ROS accumulation, lipid peroxidation, and cell death, with HE demonstrating superior efficacy. Mechanistically, regaloside A and p-coumaric acid reversed AAPH-induced dysregulation of key oxidative stress-related genes. Specifically, they downregulated keap1a, rela, erk2, and p38 expression while restoring nrf2, sod1, and sod2 levels, indicating modulation of Nrf2, NF-κB, and MAPK pathways. The data support the hypothesis that heating increases polyphenol yield and that lily polyphenols exert antioxidant effects via the stated pathways. These findings provide a mechanistic basis for developing lily-based antioxidant ingredients for functional foods.
{"title":"The potential regulation mechanism of lily extracts responds to AAPH induced oxidative stress in zebrafish","authors":"Haoran Shen , Hong Quan , Yixi Cai , Yazhou Lu , Peiyao Yu , Xiaozhong Lan , Xinbo Guo","doi":"10.1016/j.fochms.2025.100290","DOIUrl":"10.1016/j.fochms.2025.100290","url":null,"abstract":"<div><div>This study investigated the antioxidant capacity and molecular mechanisms of lily bulb polyphenols using zebrafish (<em>Danio rerio</em>) embryos subjected to AAPH-induced oxidative stress. Two extraction methods—cold (CE) and hot (HE) water extraction—were compared. HE exhibited significantly higher total phenolic content (31 ± 4 %, <em>p</em> < 0.05) and polyphenol abundance (9.8 ± 0.6-fold increase, <em>p</em> < 0.05), particularly regaloside A and <em>p-</em>coumaric acid, than CE. Heat-assisted extraction of lily bulbs liberated more polyphenols (both in terms of content and variety), which translated into measurably greater antioxidant protection in vivo. In vivo assays revealed that both extracts improved embryo survival, restored SOD activity, and reduced ROS accumulation, lipid peroxidation, and cell death, with HE demonstrating superior efficacy. Mechanistically, regaloside A and <em>p-</em>coumaric acid reversed AAPH-induced dysregulation of key oxidative stress-related genes. Specifically, they downregulated <em>keap1a</em>, <em>rela</em>, <em>erk2</em>, and <em>p38</em> expression while restoring <em>nrf2</em>, <em>sod1</em>, and <em>sod2</em> levels, indicating modulation of Nrf2, NF-κB, and MAPK pathways. The data support the hypothesis that heating increases polyphenol yield and that lily polyphenols exert antioxidant effects via the stated pathways. These findings provide a mechanistic basis for developing lily-based antioxidant ingredients for functional foods.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100290"},"PeriodicalIF":4.7,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144911969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Coconut flesh, the solid endosperm, of coconut, which is rich in fat, protein and polyphenols. To investigate the impact of ultrasound treatment on the biosynthesis of polyphenols in tender coconut flesh during storage, the targeted metabolomic and transcriptomic analyses were employed. A total of 36 phenolic compounds were identified, of which catechin, epicatechin, gossypol and vanillic acid were the most abundant ones in ‘Hainan Tall’ coconut flesh. Ultrasound treatment maintained the levels of syringic acid, catechin and epicatechin, while suppressing the expression of most associated genes. Correlation analysis revealed that, downregulation expressions of FLS, 4CL2, F3′5′H, CHS2 and CHS3 decreased kaempferol, isoliquiritigenin and luteoloside content but increased catechin content. Furthermore, downregulation of CSE, DFR and CHI reduced contents of luteolin, whereas downregulation of LAR and ANS elevated the contents of catechin and epicatechin. Unraveling the effect of ultrasound on phenolic biosynthesis in the tender coconut flesh at metabolite and transcript levels provides technical and theoretical support for the high-value development and utilization of Hainan coconut resources.
{"title":"Targeted metabolomic and transcriptomic reveal the regulatory network of ultrasound on polyphenol biosynthesis in tender coconut flesh during storage","authors":"Cheng Fang , Xie Huang , Yanpei Huang , Ming Zhang , Haiming Chen , Weijun Chen , Qiuping Zhong , Jianfei Pei , Ying Lv , Rongrong He , Wenxue Chen","doi":"10.1016/j.fochms.2025.100289","DOIUrl":"10.1016/j.fochms.2025.100289","url":null,"abstract":"<div><div>Coconut flesh, the solid endosperm, of coconut, which is rich in fat, protein and polyphenols. To investigate the impact of ultrasound treatment on the biosynthesis of polyphenols in tender coconut flesh during storage, the targeted metabolomic and transcriptomic analyses were employed. A total of 36 phenolic compounds were identified, of which catechin, epicatechin, gossypol and vanillic acid were the most abundant ones in ‘Hainan Tall’ coconut flesh. Ultrasound treatment maintained the levels of syringic acid, catechin and epicatechin, while suppressing the expression of most associated genes. Correlation analysis revealed that, downregulation expressions of <em>FLS</em>, <em>4CL2</em>, <em>F3′5′H</em>, <em>CHS2</em> and <em>CHS3</em> decreased kaempferol, isoliquiritigenin and luteoloside content but increased catechin content. Furthermore, downregulation of <em>CSE</em>, <em>DFR</em> and <em>CHI</em> reduced contents of luteolin, whereas downregulation of <em>LAR</em> and <em>ANS</em> elevated the contents of catechin and epicatechin. Unraveling the effect of ultrasound on phenolic biosynthesis in the tender coconut flesh at metabolite and transcript levels provides technical and theoretical support for the high-value development and utilization of Hainan coconut resources.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100289"},"PeriodicalIF":4.7,"publicationDate":"2025-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144907420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-20DOI: 10.1016/j.fochms.2025.100288
Jiaxiang Luo, Zilian Deng, Keye Ru, Juntao Zhu, Ji Yu, Guoying Qian, Caiyan Li
The calipash, a collagen-rich tissue in Pelodiscus sinensis, undergoes structural degradation during Aeromonas hydrophila infection, compromising its economic value. This study investigates the underlying collagen alterations. Turtles were challenged with A. hydrophila, and samples were collected at 0 h, 6 h, 1d, 3d, 6d, and 10d post-infection. Results showed progressive collagen degradation, peaking at 10d. Early infection increased collagen content, type I collagen proportion, and collagen-related gene expression, but these declined over time. Essential amino acids decreased, while non-essential amino acids (e.g., glycine, proline) increased. iTRAQ proteomics identified 517 differentially expressed proteins (227 up-, 290 down-regulated), including collagen metabolism regulators (ITGB4, TIMP2, LTBP1 up; COL6A6, FKBP7, COL28A1 down). Protein network analysis revealed ECM stabilization and oxidative stress regulation balances collagen turnover. These findings indicated that P. sinensis modulates collagen biosynthesis and degradation under A. hydrophila stress, altering collagen structure and mitigating oxidative damage.
{"title":"Proteomic insights into collagen remodeling of the calipash in Chinese soft-shelled turtle (Pelodiscus sinensis) under Aeromonas hydrophila challenge: Implications for nutritional quality and oxidative stress response","authors":"Jiaxiang Luo, Zilian Deng, Keye Ru, Juntao Zhu, Ji Yu, Guoying Qian, Caiyan Li","doi":"10.1016/j.fochms.2025.100288","DOIUrl":"10.1016/j.fochms.2025.100288","url":null,"abstract":"<div><div>The calipash, a collagen-rich tissue in <em>Pelodiscus sinensis</em>, undergoes structural degradation during <em>Aeromonas hydrophila</em> infection, compromising its economic value. This study investigates the underlying collagen alterations. Turtles were challenged with <em>A. hydrophila</em>, and samples were collected at 0 h, 6 h, 1d, 3d, 6d, and 10d post-infection. Results showed progressive collagen degradation, peaking at 10d. Early infection increased collagen content, type I collagen proportion, and collagen-related gene expression, but these declined over time. Essential amino acids decreased, while non-essential amino acids (e.g., glycine, proline) increased. iTRAQ proteomics identified 517 differentially expressed proteins (227 up-, 290 down-regulated), including collagen metabolism regulators (ITGB4, TIMP2, LTBP1 up; COL6A6, FKBP7, COL28A1 down). Protein network analysis revealed ECM stabilization and oxidative stress regulation balances collagen turnover. These findings indicated that <em>P. sinensis</em> modulates collagen biosynthesis and degradation under <em>A. hydrophila</em> stress, altering collagen structure and mitigating oxidative damage.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"11 ","pages":"Article 100288"},"PeriodicalIF":4.7,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144907421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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