Food Chemistry Molecular Sciences最新文献

{"title":"A protocol for microRNA extraction from gastrointestinal digesta","authors":"Miguel Cifuentes Acebal ,&nbsp;Yvan Devaux ,&nbsp;Torsten Bohn","doi":"10.1016/j.fochms.2025.100245","DOIUrl":"10.1016/j.fochms.2025.100245","url":null,"abstract":"<div><div>MicroRNAs (miRNAs) are non-coding RNAs that influence gene-expression via post-transcriptional regulation of target protein-coding RNAs. With literature reports indicating survival of diet-derived miRNAs following their ingestion, it is important to study their stability and concentration during gastrointestinal digestion. The unique combination of chemicals and elevated RNAse content present in the gastrointestinal matrix may be a limiting factor for studying diet-derived miRNAs. First, chemical cross-reactivity with matrix constituents (e.g. bile salts) may interfere with the salt bridge interactions typically present during RNA extraction, reducing the efficiency of the column. Second, high RNAse content may not be fully inhibited during extraction and could continue degrading the miRNAs, as is observed for other tissues with high RNAse content. These combined issues may result in a reduced efficiency in yield and purity of RNA extracts, further limiting the study of diet-derived miRNAs (i.e. in downstream metabolism). In the present manuscript, we display a method based on silica column purification to extract and quantify diet-derived miRNAs from the bioaccessible phase of the gastrointestinal digesta. The proposed protocol provides a simple, quick (less than 2 h), reliable, and systematic method for miRNA purification from gastrointestinal digesta. The optimization showcased that the challenges caused by high RNAse activity, plant bioactive substances and bile-salt content within the gastrointestinal digesta have been overcome and the study of the miRNA fraction in a body fluid so far neglected is now available to researchers, allowing the use of miRNA as biomarkers of intake and potentially biomarkers of biological changes.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100245"},"PeriodicalIF":4.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143445291","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Semi-rational engineering of an α-L-fucosidase for regioselective synthesis of fucosyl-N-acetylglucosamine disaccharides","authors":"Peng Liu ,&nbsp;Xiaodi Chen ,&nbsp;Xueting Cao ,&nbsp;Yuying Wang ,&nbsp;Yafei Gao ,&nbsp;Li Xu ,&nbsp;Xukai Jiang ,&nbsp;Min Xiao","doi":"10.1016/j.fochms.2025.100244","DOIUrl":"10.1016/j.fochms.2025.100244","url":null,"abstract":"<div><div>α-L-Fucosidases are attractive biocatalysts for the production of bioactive fucosylated oligosaccharides, however, poor regioselectivity and activity for transglycosylation have significantly limited their applications. We have recently derived an α-L-Fucosidase, BF3242, from <em>Bacteroides fragilis</em> NCTC9343, which could efficiently synthesize a mixture of Fuc-α-1,3/1,6-GlcNAc, but its 1,3/1,6-regioselectivity was observably affected by reaction temperature. Here, we integrated loop-targeted random mutagenesis and site-directed mutagenesis to engineer the regioselectivity and transglycosylation activity of BF3242. Loop-targeted random mutagenesis revealed that L266 in the loop-4 (H242-S267) within the model of BF3242 was a key residue for the regioselectivity for transglycosylation, and the saturation mutagenesis at residue L266 uncovered a mutant L266H with a significantly increased 1,3-regioselectivity of 97 % from 69 % of WT BF3242. Subsequently, five designed single-site mutations at the putative aglycone subsites were performed, resulting in a double-site mutant L266H/M285C that increased the overall yield of Fuc-α-1,3/1,6-GlcNAc to 76 % from 68 % of WT BF3242. The saturation mutagenesis at residue M285 finally generated a double-site mutant L266H/M285T with the maximal overall yield of Fuc-α-1,3/1,6-GlcNAc of 85 % and 1,3-regioselectivity of 98 %. The <em>R</em>_<em>T/H</em> of L266H/M285T was approximately 2.7-fold higher than that of the WT BF3242. Molecular dynamics simulations revealed that the structural flexibility of the loop-4 was substantially reduced in mutant L266H, and the hydrogen bond formation and binding affinity between mutant L266H/M285T and Fuc-α-1,3-GlcNAc was significantly enhanced. The semi-rationally engineered enzyme L266H/M285T would be a promising biocatalyst for highly 1,3-regioselective synthesis of fucosyl-<em>N</em>-acetylglucosamine disaccharide.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100244"},"PeriodicalIF":4.1,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143420972","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of mammary glands and milk fat globule transcripts in lactating buffalo and goats","authors":"Hancai Jiang ,&nbsp;Xiaoxian Xu ,&nbsp;Shuwan Wang ,&nbsp;Xinhui Song ,&nbsp;Ling Li ,&nbsp;Qingyou Liu ,&nbsp;Kuiqing Cui ,&nbsp;Deshun Shi ,&nbsp;Jian Wang ,&nbsp;Hui Li ,&nbsp;Jieping Huang ,&nbsp;Zhipeng Li","doi":"10.1016/j.fochms.2025.100243","DOIUrl":"10.1016/j.fochms.2025.100243","url":null,"abstract":"<div><div>Gene expression and post-transcriptional regulation are key mechanisms affecting lactation performance in dairy animals. However, the difficulty of obtaining mammary gland tissue samples from lactating animals has significantly impeded lactation research. Milk fat globules may be a non-invasive way to obtain mammary transcripts. Here, we aimed to reveal the universal rule of the transcript profiles of the milk fat globules and mammary glands from buffaloes and goats by RNA-sequencing analysis. Results showed that, in buffalo, 97 % of mRNAs were expressed in both milk fat globules and mammary glands, with 45 % showing differential expression. Among 6086 lncRNAs and 7010 miRNAs identified, 35 % and 50 % were differentially expressed, respectively. Of 11,631 circRNAs, only 618 showed significant differences. In goat, more than 99 % of mRNAs and 87 % of ncRNAs (including lncRNAs, circRNAs, and miRNAs) were expressed in both milk fat globules and mammary glands, and over 91 % of mRNAs, 96 % of lncRNAs, 98 % of circRNAs, and 86 % of miRNAs showed no significant differences, suggests that the transcripts in milk fat globules exactly reflect that in the mammary gland. This study suggests that milk fat globules are an effective candidate for non-invasive acquisition of mammary gland transcripts, but their applicability needs further study.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100243"},"PeriodicalIF":4.1,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143351013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics and bioinformatics of peptides from natural and cultured sandfish (Holothuria scabra)","authors":"Pawitporn Daopa ,&nbsp;Chakkapat Aenglong ,&nbsp;Sittiruk Roytrakul ,&nbsp;Teerasak E-kobon ,&nbsp;Xue Zhao ,&nbsp;Wanwimol Klaypradit","doi":"10.1016/j.fochms.2025.100242","DOIUrl":"10.1016/j.fochms.2025.100242","url":null,"abstract":"<div><div>This study aimed to investigate the characteristics and bioinformatics identification of peptides in sandfish (<em>Holothuria scabra</em>) protein hydrolysate from natural and cultured sources, with the hypothesis that different sources of sandfish and enzymatic treatments would result in distinct peptide profiles. Sandfish from both sources were subjected to double enzymatic hydrolysis using neutral protease–alcalase (NA), papain–neutral protease (PN), and papain–alcalase (PA) to obtain protein hydrolysates. The hydrolysates were analyzed for amino acid composition, protein molecular weight distribution, functional groups using FTIR spectroscopy, LC-MSMS analysis coupled with bioinformatics for protein and peptide identification, and mineral profile. The resulting hydrolysates exhibited similar amino acid profiles, characterized by high levels of glycine, alanine, glutamic acid, and aspartic acid. The functional groups of the sandfish protein hydrolysates were primarily found at wavenumbers 1658 cm⁻¹ (amide I), 1541 cm⁻¹ (amide II), and 1246 cm⁻¹ (amide III). Peptides with molecular weights below 500 Da predominated in every sample, highlighting their small molecular size. LC-MSMS analysis, coupled with bioinformatics database comparisons, indicated that sandfish from natural and cultured sources, as well as different enzymes used in the hydrolysis process, significantly affect protein and peptide pattern. Of the 2132 identified proteins, 1258 exhibited significant differences (<em>p</em> &lt; 0.05, FDR &lt; 0.05). This study provides insights into how source and enzymatic treatment influence peptide profiles, which could be applied in the development of functional ingredients or bioactive peptides from sandfish.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100242"},"PeriodicalIF":4.1,"publicationDate":"2025-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143325417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A universal DNA microarray for rapid fish species authentication","authors":"Patrizia Bade ,&nbsp;Sebastian Stix ,&nbsp;Kristina Kappel ,&nbsp;Jan Fritsche ,&nbsp;Ilka Haase ,&nbsp;Andrew Torda ,&nbsp;Nils Wax ,&nbsp;Markus Fischer ,&nbsp;Dirk Brandis ,&nbsp;Ute Schröder","doi":"10.1016/j.fochms.2025.100241","DOIUrl":"10.1016/j.fochms.2025.100241","url":null,"abstract":"<div><div>DNA microarrays are now used in fields such as gene expression analysis, pathogen/virus detection and identification of biomarkers. Although they have been used in the food sector for species identification, they detect a limited number of species and are thus less suited for fishery products due to the large variety of traded species. Here, the aim of this proof-of-principle study was to design a universal DNA microarray that should be able to distinguish all fish species by comparing hybridization signal patterns from samples with patterns obtained from reference specimens. A universal set of 100 DNA probes (based on the genetic marker genes 16S ribosomal RNA and cytochrome <em>b</em>) generated species-specific DNA probe patterns for all 86 analyzed fish specimens. This new screening method shows potential to authenticate specimens from all fish species and by this could play an important role in fighting fraudulent practices and adulteration in the seafood sector.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100241"},"PeriodicalIF":4.1,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143160422","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Random antimicrobial peptide mixtures as non-antibiotic antimicrobial agents for cultured meat industry","authors":"Idan Yakir ,&nbsp;Einav Cohen ,&nbsp;Sharon Schlesinger ,&nbsp;Zvi Hayouka","doi":"10.1016/j.fochms.2025.100240","DOIUrl":"10.1016/j.fochms.2025.100240","url":null,"abstract":"<div><div>Antibiotics, commonly used in cell culture studies to prevent microbial contamination, cannot be employed in Cultured meat (CM) due to potential residues in the final food products. Hence, there is an urgent need to develop novel and safe non-antibiotic antimicrobial agents. Here, we investigated the potential of random antimicrobial peptide mixtures (RPMs) as non-antibiotic antimicrobial agents. RPMs are synthetic peptide cocktails that have previously shown strong and broad antimicrobial activity; however, their use in cell culture media and their effect on mammalian cells have not yet been explored. Here we show that RPMs had no significant impact on mesenchymal stem cells (MSCs) at concentrations that effectively inhibit bacterial growth. RPMs displayed strong bactericidal activity against Gram-positive bacteria, achieving a 6-log reduction of <em>L. monocytogenes</em> in cell culture medium without any cytotoxicity. Additionally, RPMs showed a low occurrence of resistance development with no significant resistance developed in compared with a combination of penicillin and streptomycin. Moreover, LK20 mixture was rapidly digested in a simulated digestion model. Our results indicate that RPMs have great potential to serve as safe and effective non antibiotic antimicrobial agents in cultured meat industry.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100240"},"PeriodicalIF":4.1,"publicationDate":"2025-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143161379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Application of bacterioruberin from Arthrobacter sp. isolated from Xinjiang desert to extend the shelf-life of fruits during postharvest storage","authors":"Wasim Sajjad ,&nbsp;Murad Muhammad ,&nbsp;Sayed Muhammad Ata Ullah Shah Bukhari ,&nbsp;Sumra Wajid Abbasi ,&nbsp;Osama Abdalla Abdelshafy Mohamad ,&nbsp;Yong-Hong Liu ,&nbsp;Wen-Jun Li","doi":"10.1016/j.fochms.2024.100239","DOIUrl":"10.1016/j.fochms.2024.100239","url":null,"abstract":"<div><div>Post-harvest losses and rapid fruit ripening at room temperature are major challenges in preserving fruit quality. This study aimed to reduce such losses by applying a red carotenoid pigment, bacterioruberin extracted from an <em>Arthrobacter</em> sp. The carotenoid was characterized as bacterioruberin and its derivative tetra anhydrous bacterioruberin (λmax 490 nm), and an <em>m</em>/<em>z</em> value of 675 and 742 (M+ 1H)⁺¹. The annotated LIPID MAP demonstrated the presence of over 360 isoprenoids annotated transcripts. The compound exhibited significant antioxidant activity, with an IC₅₀ of 22 μg/mL, iron chelation and antibacterial activities indicating its potential as a natural preservative. When applied to grapes, peaches, and apricots, bacterioruberin (2 %) effectively prevented spoilage for six days at room temperature. Statistical analysis using one-way ANOVA revealed a significant correlation <em>(p = 0.05)</em> between treated and control groups in subjective quality attributes. Computational investigation with phospholipase D and VQ22 motif protein further supported the preservative potential of bacterioruberin.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100239"},"PeriodicalIF":4.1,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11773480/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143060886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Mapping taste and flavour traits to genetic markers in lettuce Lactuca sativa” [Food Chem.: Mol. Sci. 9 (2024) 100215]","authors":"Martin Chadwick ,&nbsp;Jonathan R. Swann ,&nbsp;Frances Gawthrop ,&nbsp;Richard Michelmore ,&nbsp;Davide Scaglione ,&nbsp;Maria Jose-Truco ,&nbsp;Carol Wagstaff","doi":"10.1016/j.fochms.2024.100226","DOIUrl":"10.1016/j.fochms.2024.100226","url":null,"abstract":"","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"9 ","pages":"Article 100226"},"PeriodicalIF":4.1,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143129642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metagenomics-based tracing of genetically modified microorganism contaminations in commercial fermentation products","authors":"Jolien D’aes ,&nbsp;Marie-Alice Fraiture ,&nbsp;Bert Bogaerts ,&nbsp;Yari Van Laere ,&nbsp;Sigrid C.J. De Keersmaecker ,&nbsp;Nancy H.C. Roosens ,&nbsp;Kevin Vanneste","doi":"10.1016/j.fochms.2024.100236","DOIUrl":"10.1016/j.fochms.2024.100236","url":null,"abstract":"<div><div>Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermentation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final product is not authorized, contaminations occur frequently. Insight into the contamination source of a GMM is of crucial importance to allow the competent authorities to take appropriate action. The aim of this study was to explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, focusing on source tracing of GMM strains using innovative strain deconvolution and phylogenomic approaches. In most cases, analysis of 16 GMM-contaminated food enzyme products supported finding the same GM producer strains in different products, while often multiple GMM contaminations per product were detected. Presence of AMR genes in the samples was strongly associated with GMM contamination, emphasizing the potential public health risk. Additionally, a variety of other microbial contaminations were detected, identifying a group of samples with a conspicuously similar contamination profile, which suggested that these samples originated from the same production facility or batch. Together, these findings highlight the need for guidelines and quality control for traceability of these products to ensure the safety of consumers. This study demonstrates the added value of metagenomics to obtain insight in the microbial contamination profiles, as well as their underlying relationships, in commercial microbial fermentation products. The proposed approach may be applied to other types of microbial fermentation products and/or to other (genetically modified) producer strains.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100236"},"PeriodicalIF":4.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11743831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013004","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the complex molecular architecture of the genetically modified soybean FG72 through paired-end whole genome sequencing","authors":"Fan Wang ,&nbsp;Shengtao Lu ,&nbsp;Wenting Xu ,&nbsp;Litao Yang","doi":"10.1016/j.fochms.2024.100238","DOIUrl":"10.1016/j.fochms.2024.100238","url":null,"abstract":"<div><div>The clear molecular characterization of genetically modified (GM) plants and animals is a prerequisite for obtaining regulatory approval and safety certification for commercial cultivation. This characterization includes the identification of the transferred DNA (T-DNA) insertion site, its flanking sequences, the copy number of inserted genes, and the detection of any unintended genomic alterations accompanying the transformation process. In this study, we performed a comprehensive molecular characterization of the well-known GM soybean event FG72 using paired-end whole-genome sequencing (PE-WGS). We examined the T-DNA insertion site, flanking sequences, the entire structure and copy number of the T-DNA integration, the presence of plasmid backbone sequences, and genome-wide structural variations (SVs). Our analysis revealed that the T-DNA integrated into two distinct sites on chromosome 15 of the host genome, accompanied by a translocation of host genomic sequences. One site harbored a partial T-DNA integration, while the other site contained two tandem repeats of the full T-DNA. Importantly, no plasmid backbone sequences were detected in the host genome, indicating a clean T-DNA integration during the biolistic transformation process. Furthermore, we identified numerous genome-wide SVs, with chromosome 15 ranking second among all 20 chromosomes in terms of SV frequency, and most of these variations occurring within gene-coding regions. These results provide a refined and comprehensive molecular characterization of the FG72 soybean event, which could further support its commercial approval and cultivation. Our work highlights the utility of the PE-WGS approach as a sensitive and labor-efficient alternative to conventional molecular characterization techniques, generating comprehensive data to facilitate the safety assessment of GM crops during research and commercialization pipelines.</div></div>","PeriodicalId":34477,"journal":{"name":"Food Chemistry Molecular Sciences","volume":"10 ","pages":"Article 100238"},"PeriodicalIF":4.1,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11750281/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013003","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}