Search Results (41)

The detection of single-nucleotide variants (SNVs) is an important challenge in modern genomics, with broad applications in medicine, diagnostics, and agricultural biotechnology. Current detection approaches include PCR-based techniques with high-affinity probes, ligase-based strategies, and sequencing approaches, each with varying degrees of sensitivity, specificity, and practicality. Despite advances in SNV analysis in the medical field, their implementation in the official control and monitoring of genetically modified organisms (GMOs) remains limited. This challenge has gained priority with the advent of new genomic techniques (NGTs), such as CRISPR-Cas nucleases, which allow precise genome editing, including subtle changes at the nucleotide level without introducing foreign DNA. Therefore, traditional methods of GMO detection targeting transgene sequences may not be sufficient to monitor such GMOs. In the European Union, GMO legislation requires distinguishing between conventionally bred and genetically modified plants. The planned introduction of new regulatory categories of NGT plants (NGT1 and NGT2) with different surveillance requirements emphasizes the need for robust, sensitive, and cost-effective SNV detection methods suitable for distinguishing between GMOs, particularly in the context of food and feed safety, traceability, and compliance. Full article

The textile sector provides essential goods, yet it remains environmentally and socially intensive, driven by high water use, pesticide dependent monocropping, chemical pollution during processing, and growing waste streams. This review examines credible pathways to sustainability by integrating emerging plant-based fibres from hemp, abaca, stinging nettle, and pineapple leaf fibre. These underutilised crops combine favourable agronomic profiles with competitive mechanical performance and are gaining momentum as the demand for demonstrably sustainable textiles increases. However, conventional fibre identification methods, including microscopy and spectroscopy, often lose reliability after wet processing and in blended fabrics, creating opportunities for mislabelling, greenwashing, and weak certification. We synthesise how advanced molecular approaches, including DNA fingerprinting, species-specific assays, and metagenomic tools, can support the authentication of fibre identity and provenance and enable linkage to Digital Product Passports. We also critically assess environmental Life Cycle Assessment (LCA) and social assessment frameworks, including S-LCA and SO-LCA, as complementary methodologies to quantify climate burden, water use, labour conditions, and supply chain risks. We argue that aligning fibre innovation with molecular traceability and harmonised life cycle evidence is essential to replace generic sustainability claims with verifiable metrics, strengthen policy and certification, and accelerate transparent, circular, and socially responsible textile value chains. Key research priorities include validated marker panels and reference libraries for non-cotton fibres, expanded region-specific LCA inventories and end-of-life scenarios, scalable fibre-to-fibre recycling routes, and practical operationalisation of SO-LCA across diverse enterprises. Full article

Background/Objectives: Ergot alkaloids are mycotoxins produced mainly by fungi of the genus Claviceps, infecting a wide variety of plants, especially cereals. These toxins usually manifest as black, hardened sclerotia (ergots), though they may also be invisible when dispersed in grain. They pose a significant risk to animals and humans when present in contaminated cereals. They can cause ergotism, with vasoconstriction, ischemia, hallucinations, and in severe cases gangrene. This study was carried out in response to the European legislative actions which determine the permissible levels of ergot alkaloids in cereals. Historically, consumers manually removed visible sclerotia from grain, and farmers applied fertilizers or timed harvests to specific periods to mitigate contamination. However, these traditional methods have proven insufficient. We therefore explored advanced techniques for detecting and quantifying ergot-contaminated cereals, as well as methods for reducing ergot alkaloid concentrations. Methods: Searches were conducted in scientific databases including Google Scholar, PubMed, and Scopus to identify research articles, reviews, and experimental studies published mainly between 2012 and August 2025, including accepted or in-press manuscripts, with special attention to works from 2021 onward to capture the most recent advancements. Results/Conclusions: Ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC-MS/MS) is the reference method for confirmatory, epimer-aware quantification of ergot alkaloids, and is already standardized. Recent QuEChERS-UHPLC-MS/MS workflows in cereal matrices, including oat-based products, routinely achieve limits of quantification of about 0.5–1.0 µg/kg with single-run analysis times of about 5–15 min. Rapid screening options complement, rather than replace, confirmatory mass spectrometry: magnetic bead-based immunoassays that use magnetic separation and a smartphone-linked potentiostat provide sub-hour turnaround and field portability for trained quality-assurance staff, although external validation and calibration traceable to LC-MS/MS remain prerequisites for routine use. In practice, operators are adopting tiered, orthogonal workflows (e.g., immunoassay or electronic-nose triage at intake followed by DNA-based checks on grain washings and LC–MS/MS confirmation, or hydrazinolysis “sum parameter” screening followed by targeted MS speciation). Such combinations reduce turnaround time while preserving analytical rigor. Biotechnology also offers potential solutions for reducing ergot alkaloid concentrations at the source. Finally, to enhance consumer safety, artificial intelligence and blockchain-based food traceability appear highly effective. These systems can connect all stakeholders from producers to consumers, allowing for real-time updates on food safety and rapid responses to contamination issues. This review primarily synthesizes advances in analytical detection of ergot alkaloids, while mitigation strategies and supply chain traceability are covered concisely as supporting context for decision making. Full article

In a world of rapidly globalizing food markets, biodiversity, authenticity, and the safety of food products have become a universal concern. DNA barcoding is a widely used molecular-based method that can identify biological material and is used for the traceability of both raw materials and ingredients in processed food. In the present study, contacted within the framework of the BioValue Horizon Project, which promotes the role of agrobiodiversity in sustainable food systems, DNA barcoding using the ITS and rbcL markers was employed as a proof-of-concept approach to reveal the biodiversity and authenticity of ten commercial plant-based products. Following successful DNA amplification and sequencing using six products as a proof-of-concept, a diverse range of plant genera and species were identified, verifying biodiversity. A strong correlation between ITS and rbcL-based markers was demonstrated, supporting their combined use for reliable species-level biodiversity assessment. Finally, heat map analysis of label contents and sequencing-based genera identification confirmed high concordance between label claims and sequencing results in most cases, though undeclared species and absent labeled taxa were also detected, highlighting potential mislabeling or cross-contamination. Full article

Identifying the botanical origin of honey is essential for ensuring its quality, preventing adulteration, and protecting consumers. Traditional techniques, such as melissopalynology, physicochemical analysis, and PCR, are often labor-intensive, time-consuming, or limited to the detection of only known species, while advanced DNA sequencing remains prohibitively costly. In this study, we aim to develop a deep learning-based approach for identifying pollen grains extracted from honey and captured through microscopic imaging. To achieve this, we first constructed a dataset named VNUA-Pollen52, which consists of microscopic images of pollen grains collected from flowers of plant species cultivated in the surveyed area in Hanoi, Vietnam. Second, we evaluated the classification performance of advanced deep learning models, including MobileNet, YOLOv11, and Vision Transformer, on pollen grain images. To improve performances of these model, we proposed data augmentation and hybrid fusion strategies to improve the identification accuracy of pollen grains extracted from honey. Third, we developed an online platform to support experts in identifying these pollen grains and to gather expert consensus, ensuring accurate determination of the plant species and providing a basis for evaluating the proposed identification strategy. Experimental results on 93 images of pollen grains extracted from honey samples demonstrated the effectiveness of the proposed hybrid fusion strategy, achieving 70.21% accuracy at rank 1 and 92.47% at rank 5. This study demonstrates the capability of recent advances in computer vision to identify pollen grains using their microscopic images, thereby opening up opportunities for the development of automated systems that support plant traceability and quality control of honey. Full article

Bos frontalis (Mithun) and Bos grunniens (yak) are crucial to the culture, food security, and economy of Southeast Asia, especially in India and China, respectively. Their genetic closeness to Bos indicus (indicine cattle) and Bos taurus (taurine cattle) necessitates precise methods for meat origin authentication. This study introduces a DNA-based technique to distinguish Mithun and yak species using the alkaline lysis (AL) protocol for DNA extraction, followed by species-specific polymerase chain reaction (PCR) to amplify unique mitochondrial D-loop regions, yielding 489 bp and 422 bp amplicons, respectively. The AL-PCR method showed high specificity for both species, with no cross-amplification with other related species. The method’s effectiveness was validated across various sample preparations, including raw, cooked, autoclaved, microwaved, and fried samples. The AL-PCR assay is highly sensitive, detecting as little as 1 pg of Mithun DNA and 100 pg of yak DNA, and can identify down to 0.1% of these species in binary mixtures. This approach is rapid and cost-effective, offering significant benefits for consumer protection, promoting Mithun and yak farming, and addressing food safety and traceability issues. Full article

Genome editing (GE) technologies have the potential to completely transform breeding and biotechnology applied to crop species, contributing to the advancement of modern agriculture and influencing the market structure. To date, the GE-toolboxes include several distinct platforms able to induce site-specific and predetermined genomic modifications, introducing changes within the existing genetic blueprint of an organism. For these reasons, the GE-derived approaches are considered like new plant breeding methods, known also as New Breeding Techniques (NBTs). Particularly, the GE-based on CRISPR/Cas technology represents a considerable improvement forward biotech-related techniques, being highly sensitive, precise/accurate, and straightforward for targeted gene editing in a reliable and reproducible way, with numerous applications in food-related plants. Furthermore, numerous examples of CRISPR/Cas system exploitation for non-editing purposes, ranging from cell imaging to gene expression regulation and DNA assembly, are also increasing, together with recent engagements in target and multiple chemical detection. This manuscript aims, after providing a general overview, to focus attention on the main advances of CRISPR/Cas-based systems into new frontiers of non-editing, presenting and discussing the associated implications and their relative impacts on molecular traceability, an aspect closely related to food safety, which increasingly arouses general interest within public opinion and the scientific community. Full article

A significant part of our stone heritage is made of limestone. Researchers are increasingly concerned about the risk of biodeterioration of these important objects. In this article, we present an up-to-date review of the microbial diversity of biodeteriorated limestone cultural heritage (CHL). This is based on an extensive bibliographic search of the literature investigating biodiversity using culture-dependent (CD) and culture-independent (CI) techniques. In the case of the former, only articles in which microorganisms were identified using molecular tools that generate DNA sequences were selected, with the aim of providing traceable identification based on the sequences submitted to public databases. The literature search resulted in the selection of 50 articles published between 2004 and 2023. The biodiversity data obtained from the CHL were organized into the following groups: fungi (626 records), bacteria and cyanobacteria (786 and 103 records, respectively), algae (51 records), and archaea (27 records). Within each group, the microbial diversity studied was compared according to results obtained using CD and CI techniques. Of all the articles selected, 12 used both approaches, demonstrating the growing effort to discover the total microbiome of biodeteriorated cultural heritage assets. Full article

Rice (Oryza sativa) varieties are generated through breeding programs focused on local requirements. In Chile, the southernmost rice producer, rice productivity relies on the use and generation of temperate japonica germplasms, which need to be adapted to the intensifying effects of climate change. Advanced biotechnological tools can contribute to these breeding programs; new technologies associated with precision breeding, including gene editing, rely on procedures such as regeneration and gene transfer. In this study, the local rice varieties Platino, Cuarzo, Esmeralda, and Zafiro were evaluated for somatic embryogenesis potential using a process that involved the combined use of auxins and cytokinins. An auxin-based (2,4-D) general medium (2N6) allowed for the induction of embryogenic masses in all the genotypes. After induction, masses required culturing either in N6R (kinetin; Platino) or N6RN (BAP, kinetin, IBA, and 2,4-D; Cuarzo, Esmeralda, and Zafiro) to yield whole plants using regeneration medium (N6F, no hormone). The sprouting rates indicated Platino as the most responsive genotype; for this reason, this variety was evaluated for gene transfer. Fifteen-day-old embryo masses were assayed for Agrobacterium-mediated transformation using the bacterial strain EHA105 harboring pFLC-Myb/HPT/GFP, a modified T-DNA vector harboring a geminivirus-derived replicon. The vector included the green fluorescent protein reporter gene, allowing for continuous traceability. Reporter mRNA was produced as early as 3 d after agroinfiltration, and stable expression of the protein was observed along the complete process. These achievements enable further biotechnological steps in these and other genotypes from our breeding program. Full article

Nowadays, traceability is the main issue in many businesses, particularly for coffee. The advantages of keeping it at a high degree are that it provides a guarantee for consumers, provides increased power in the value chain, helps quality monitoring, and, last but not least, can be used a marketing tool. In the coffee business, it means verifying the history and the area of origin of green coffee beans (now moving to geolocation) and being able to identify them throughout all the logistic supply chain up to the last customer; to help this, we conceived an innovative service model of traceability and integration through a technique that recognizes the connection between genetic characteristics of coffee varieties and chemical and sensory analysis results, shared on a dedicated platform and linked to a QR code. By linking shipping documents with the results of chemical, genetic, and sensory analysis, users can verify the compliance of all declared data with the quality of the product received. Genetic analysis is based on DNA fingerprinting, detecting the presence of short and repetitive sequences (microsatellites) and characteristics of beans’ genetic code; thanks to a rich Coffea Arabica library that was built, DNA analysis identifies different varieties of green coffee beans which are also linked to the production countries. Chemical–physical analyses consist precisely of the determination of moisture, caffeine, 5-hydroxytrypdamides, and OTA, and sensory analyses are performed through the SCA cupping protocol. Gathered using a blockchain system, all the documents are available in sample cards to guarantee the transparency to both buyer and seller, from bean to cup. Full article

(1) Background: With an advanced technique, third-generation sequencing (TGS) provides services with long deoxyribonucleic acid (DNA) reads and super short sequencing time. It enables onsite mobile DNA sequencing solutions for enabling ubiquitous healthcare (U-healthcare) services with modern mobile technology and smart entities in the internet of living things (IoLT). Due to some strict requirements, 6G technology can efficiently facilitate communications in a truly intelligent U-healthcare IoLT system. (2) Research problems: conventional single user–server architecture is not able to enable group conversations where “multiple patients–server” communication or “patient–patient” communication in the group is required. The communications are carried out via the open Internet, which is not a trusted channel. Since heath data and medical information are very sensitive, security and privacy concerns in the communication systems have become extremely important. (3) Purpose: the author aims to propose a dynamic group-based patient-authenticated key distribution protocol for 6G-aided U-healthcare services enabled by mobile DNA sequencing. In the protocol, an authenticated common session key is distributed by the server to the patients. Using the key, patients in a healthcare group are allowed to securely connect with the service provider or with each other for specific purposes of communication. (4) Results: the group key distribution process is protected by a secure three-factor authentication mechanism along with an efficient sequencing-device-based single sign-on (SD-SSO) solution. Based on traceable information stored in the server database, the proposed approach can provide patient-centered services which are available on multiple mobile devices. Security robustness of the proposed protocol is proven by well-known verification tools and a detailed semantic discussion. Performance evaluation shows that the protocol provides more functionality and incurs a reasonable overhead in comparison with the existing works. Full article

Fish tissue samples from 203 adult individuals were collected in the main ports and markets of the Pacific coast of Panama. Molecular identification based on a cytochrome oxidase I gene segment of all species was verified by GENBANK reference sequences. A total of 34 species from 14 families (Ariidae, Caranjidae, Centropomidae, Gerreidae, Haemulidae, Lobotidae, Lutjanidae, Malacanthidae, Mugilidae, Scianidae, Scombridae, Serranidae, Sphyraenidae, Stromateidae) were identified at the species level from 164 sequences. Additionally, three Caribbean species were molecularly identified among the analyzed samples (Mycteroperca xenarcha, Paralonchurus brasilensis and Lobotes surinamensis). Species diversity was slightly higher in the Gulf of Panama than in the Gulf of Chiriquí. For species with five or more individual sequences, genetic diversity and genetic connectivity parameters such as total number of haplotypes (H), haplotype diversity (Hd), and nucleotide diversity (π) were calculated. Overall, pelagic-migratory species showed higher values of genetic diversity than coastal and estuarine species with some exceptions. Connectivity between Gulf areas was compared using values of genetic distances and genetic differentiation (Fst). The high level of connectivity observed between the Gulf of Chiriqui and the Gulf of Montijo indicates the existence of a single stock in that area for the following species: Scomberomorus sierra, Caranx caninus and Lutjanus guttatus. The demographic history of the most common species was examined using Tajima’s D values, suggesting population expansion for two snapper species, L. peru and L. argentiventris, having significant and higher values. Another important contribution from this research was the production of primers and dual-labeled probes for environmental DNA detection using qPCR for the five most abundant species (spotted rose snapper, yellow snapper, green jack, Pacific crevalle jack and the Pacific sierra fish). These markers represent a new set of tools for environmental DNA (eDNA) detection and molecular traceability of three commercially important fish species along the supply chain including landing sites and markets of the main fishery areas. Full article

The recent increase in international fish trade leads to the need for improving the traceability of fishery products. In relation to this, consistent monitoring of the production chain focusing on technological developments, handling, processing and distribution via global networks is necessary. Molecular barcoding has therefore been suggested as the gold standard in seafood species traceability and labelling. This review describes the DNA barcoding methodology for preventing food fraud and adulteration in fish. In particular, attention has been focused on the application of molecular techniques to determine the identity and authenticity of fish products, to discriminate the presence of different species in processed seafood and to characterize raw materials undergoing food industry processes. In this regard, we herein present a large number of studies performed in different countries, showing the most reliable DNA barcodes for species identification based on both mitochondrial (COI, cytb, 16S rDNA and 12S rDNA) and nuclear genes. Results are discussed considering the advantages and disadvantages of the different techniques in relation to different scientific issues. Special regard has been dedicated to a dual approach referring to both the consumer’s health and the conservation of threatened species, with a special focus on the feasibility of the different genetic and genomic approaches in relation to both scientific objectives and permissible costs to obtain reliable traceability. Full article

Honey is a widely consumed natural product, and its entomological origin can significantly influence its market value. Therefore, traceability of the entomological origin of honey should also be considered in honey quality control protocols. Although several methods exist, such as physicochemical characterization and bioactivity profiling of honey of different entomological origins, the most promising three methods for entomological authentication of honey include protein-based identification, chemical profiling, and a DNA-based method. All of these methods can be applied for reliable identification of the entomological origin of honey. However, as the honey is a complex matrix, the inconsistency of the results obtained by these methods is a pragmatic challenge, and therefore, the use of each method in all the cases is questionable. Most of these methodologies can be used for authentication of newly harvested honey and it is worth understanding the possibility of using these methods for authentication of relatively old samples. Most probably, using DNA-based methods targeting small fragments of DNA can provide the best result in old samples, however, the species-specific primers targeting short fragments are limited and not available for all species. Therefore, using universal primers in combination with a DNA metabarcoding approach can be a good solution that requires further investigation. This present article describes the applications of different methods, their pros, and their cons to identify honey based on entomological origin. Full article

Economically motivated or accidental species substitutions lead to economic and potential health damage to consumers with a loss of confidence in the fishery supply chain. In the present study, a three–year survey on 199 retail seafood products sold on the Bulgarian market was addressed to assess: (1) product authenticity by molecular identification; (2) trade name compliance to the list of official trade names accepted in the territory; (3) adherence of the list in force to the market supply. DNA barcoding on mitochondrial and nuclear genes was applied for the identification of whitefish (WF), crustaceans (C) and mollusks (cephalopods—MC; gastropods—MG; bivalves—MB) except for Mytilus sp. products for which the analysis was conducted with a previously validated RFLP PCR protocol. Identification at the species level was obtained for 94.5% of the products. Failures in species allocation were reconducted due to low resolution and reliability or the absence of reference sequences. The study highlighted an overall mislabeling rate of 11%. WF showed the highest mislabeling rate (14%), followed by MB (12.5%), MC (10%) and C (7.9%). This evidence emphasized the use of DNA–based methods as tools for seafood authentication. The presence of non–compliant trade names and the ineffectiveness of the list to describe the market species varieties attested to the need to improve seafood labeling and traceability at the national level. Full article