Search Results (302)

Background: The genus Anchusa L. includes plants used in Uyghur medicine for their anti-inflammatory and analgesic effects. However, in China, the botanical origin of HERBA ANCHUSAE (Niushecao, a Uyghur medicinal herb) is severely confused. Traditional identification methods and standard DNA barcodes do not work well for these close relatives. Chloroplast genomes are known to contain variable regions that can help distinguish species, yet no such study has been done for Anchusa. Therefore, We compared the complete chloroplast genomes of six Anchusa species and the main adulterants of Niushecao. Methods: We analyzed genome structure, repeat sequences, codon usage bias, and nucleotide diversity (Pi), as well as conducted comparative and phylogenetic analyses. Results: All genomes shared a typical ring-shaped quadripartite structure, ranged from 150,178 to 150,844 bp in size, and contained the same set of genes. Despite this overall conservation, we identified several highly variable spots, mostly located in non-coding intergenic spacer regions. Using two complementary approaches—sliding window analysis and mVISTA-based sequence visualization—we identified three overlapping regions (rbcL-psaI, petA-psbJ, and trnC-GCA-petN) as candidate DNA barcodes for species identification. Our phylogenetic tree showed that Anchusa strigosa Banks & Sol. is most closely related to the true medicinal species Anchusa azurea Mill. (Bootstrap support (BS) = 100%), while other look-alikes formed separate branches. Conclusions: These findings provide the first chloroplast genomic resources for this genus and offer potential molecular markers for authenticating Anchusa medicinal materials, laying a foundation for future development of molecular authentication methods. Full article

Accurate identification of Fritillaria taxa is essential for quality control of Fritillariae Cirrhosae Bulbus. This study evaluated morphological analysis, chloroplast DNA barcoding, and steroidal alkaloid profiling across 40 individuals from four taxa (F. unibracteata, F. unibracteata var. wabuensis, F. cirrhosa, and F. taipaiensis) from Sichuan province, China. Among five chloroplast markers, ycf1 and rps4 were the most polymorphic, with nucleotide diversity of 0.065 to 0.116 and 0.035 to 0.120, respectively, and generally distinguished the four taxa into well-supported clades, though two F. unibracteata nested within the F. cirrhosa group. Morphologically, F. unibracteata var. wabuensis produced the largest bulbs, with a mean fresh weight of 26.99 g, approximately 24-fold greater than that of F. unibracteata at 1.12 g, whereas F. unibracteata and F. cirrhosa overlapped substantially in all measured traits. PCA revealed that biomass traits were slightly more discriminative, while central bud height contributed the least. Among the samples analyzed, alkaloid profiles provided the most distinct diagnostic signals: F. unibracteata var. wabuensis accumulated the highest sipeimine at 298.40 μg/g and sipeimine-3-β-D-glucoside at 156.30 μg/g; F. taipaiensis was richest in peimine and peiminine; F. unibracteata uniquely contained sipeimine-3-β-D-glucoside without detectable sipeimine; and F. cirrhosa showed the lowest levels across all five compounds. The integration of chloroplast markers with alkaloid profiling improved species discrimination for the samples examined. Chloroplast markers for initial screening followed by the alkaloid profiling of the ambiguous sample might offer a practical framework for the authentication and quality control of Fritillariae Cirrhosae Bulbus, but this strategy requires validation across broader geographic scales and with larger sample sizes. Full article

Probiotics play an important role in maintaining human gastrointestinal health and immune function, driving a rapidly expanding global market for probiotic-fortified foods. Lacticaseibacillus paracasei is one of the most widely applied probiotic strains in functional foods and dairy formulations, with well-documented health-promoting properties. For probiotic foods, authenticity requires rigorous verification for efficacy and compliance, which depends on rapid strain-specific identification. However, conventional culture-based methods are time-consuming and cannot distinguish closely related Lacticaseibacillus species, while PCR-based assays require expensive thermal cyclers and trained personnel, barring deployment in resource-limited settings. Here, we report the development and validation of a MIRA-CRISPR/Cas12a fluorescence assay for rapid, species-specific, and highly sensitive on-site detection of Lacticaseibacillus paracasei. This integrated workflow combines 8 min rapid crude DNA extraction, 30 min isothermal MIRA pre-amplification, and 20 min CRISPR/Cas12a signal amplification with naked-eye fluorescence readout under blue light excitation, and requires only miniaturized portable equipment. The assay achieved a reliable limit of detection of 100 CFU/mL in milk-matrix spiked samples, showing no cross-reactivity across 17 tested lactic acid bacteria strains. In a validation set of 48 food samples, our method demonstrated 100% concordance with the gold-standard species-specific qPCR assay. This field-deployable method is appropriate for on-site quality control in probiotic manufacturing, label compliance verification, and frontline market regulatory inspections. Full article

Ngueak Pla Mo is a Thai medicinal crude drug derived from the pharmacopoeial Acanthus species A. ebracteatus Vahl and A. ilicifolius L.; however, morphological similarity and the occurrence of non-pharmacopoeial substitutes such as A. montanus (Nees) T. Anderson may complicate authentication and quality control. This study aimed to develop an integrated molecular–chemical approach for differentiating pharmacopoeial Ngueak Pla Mo species from A. montanus. Twenty authenticated Acanthus samples were analyzed using ITS2 DNA barcoding, including nucleotide variation, pairwise genetic distance, barcode gap, haplotype network, phylogenetic analysis, and predicted ITS2 secondary structure. Representative samples were further examined by untargeted LC–QTOF/MS metabolite profiling combined with hierarchical clustering, PCA, PLS-DA, VIP analyses, fold-change evaluation, and specificity scoring. ITS2 analyses clearly separated A. montanus from A. ebracteatus and A. ilicifolius, supported by diagnostic sequence variation, positive barcode gaps, distinct haplotypes, phylogenetic clustering, and secondary-structure differences, whereas A. ebracteatus and A. ilicifolius could not be reliably differentiated from each other at the species level using ITS2. LC–QTOF/MS profiling revealed species-consistent metabolite patterns and prioritized gallic acid, catechol, 3,4-dihydroxybenzoic acid, trigonelline, and ursolic acid as preliminary candidate markers for A. montanus discrimination. These results indicate that combining ITS2 barcoding with metabolite profiling provides complementary evidence for Ngueak Pla Mo authentication and supports future quality-control development. Full article

Food products containing plant ingredients are particularly vulnerable to economically motivated adulteration (EMA), which poses risks to consumer trust and regulatory compliance. While traditional methods—such as microscopy, chemical profiling or targeted PCR—struggle to detect adulterants in processed food products or complex mixes, DNA metabarcoding offers a non-targeted, high-throughput alternative. This study presents a nanopore sequencing-based technique that is easy to implement, cost-effective and sufficiently sensitive to detect substitutions, with a focus on spices and herbal teas as model matrices. The method was evaluated using eight single-species reference samples and five commercial multi-ingredient products. It reliably detected undeclared contaminants (e.g., mint in oregano) and species substitutions. Compared to single-barcode approaches, the combination of ITS2 + matK + trnH-psbA markers achieved higher sensitivity. The proposed workflow requires minimal infrastructure and a 2–4-day turnaround time. However, factors such as DNA degradation in highly processed foods, database gaps, and biological diversity limited detection in some cases. These findings demonstrate the workflow’s potential as a first-line screening tool for food authenticity testing, aligning with requirements such as EU regulation 1169/2011 on food labelling or the FDA’s Economically Motivated Adulteration (EMA) program. Future work should validate the method against regulatory thresholds and expand testing to a broader variety of species and matrices. Full article

The high commercial value and the increasing demand for caviar make it susceptible to illegal trade and fraudulent activities, while mislabelling can occur both deliberately and unintentionally. Therefore, reliable methods are urgently needed to distinguish even closely related sturgeon species for the authentication of declared species in caviar products. In this study, we explore the effectiveness of ONT sequencing combined with nanopore adaptive sampling (NAS) to recover mitochondrial genomes from genomic DNA extracted from two caviar samples. NAS yielded similar percentages of mitochondrial reads as sequencing experiments without using the NAS option. However, NAS substantially increased the percentage of bases that could be mapped against a mitochondrial reference genome, demonstrating its effectiveness in enriching ONT sequencing data for mitochondrial sequences. The percentage of mapped mitochondrial reads varied between two samples in our sequencing experiments, ranging between 2.37% and 10.46%, which is exceptionally high compared to previous studies focusing on the recovery of mitochondrial genomes from genomic DNA. This increase may be attributed to the extraction of genomic DNA from individual fish eggs. To determine the taxonomic identities of the two caviar samples, a phylogenetic analysis was performed that included all available acipenseriform mitochondrial genomes from GenBank, as well as the newly recovered mitochondrial genomes. During this process, four problematic mitochondrial genomes obtained from GenBank were identified, which were characterized by either suggestively low sequence quality, chimeric sequence information, or potential misidentification. This underscores the need for reviewing sequencing data before database submission to avoid negative impacts on research and DNA-based species authentication. Full article

Pepper breeding in China faces challenges including narrow genetic backgrounds, variety homogenization, and authenticity issues in the seed market. The original SSR-based variety identification system (NY/T 2475-2013) has limitations such as low polymorphism and uneven marker distribution, failing to meet current efficiency requirements. In this study, 240 pepper varieties were used. Fluorescent capillary electrophoresis was employed to analyze issues in the original system. A total of 150 SSR primer pairs was screened using eight phenotypically distinct varieties, followed by rescreening with 96 varieties from different origins. After marker optimization, a new identification system was established, validated using 144 varieties, and a DNA fingerprint database was constructed. Phenotypic experiments were conducted to evaluate applicability. The new system comprises 26 core primer pairs: 12 newly selected and 14 retained from the original standard. These primers are evenly distributed across chromosomes, with annealing temperatures optimized to 57 °C and grouped into seven multiplex panels. Across 240 pepper varieties, the 26 primer pairs detected 153 allelic variants and 293 genotypes. Average polymorphism information content (PIC) increased from 0.43 to 0.49 compared to the original system, and the discrimination efficiency reached 99.975% among 28,680 pairwise variety combinations. Phylogenetic and population structure analyses divided the 240 pepper varieties into six groups. Varieties with molecular genetic distance approaching zero showed high phenotypic similarity. The newly developed SSR-based system demonstrated excellent performance and strong applicability. It can be used for authenticity and purity identification, parentage testing, and auxiliary selection in DUS testing, supporting new variety rights protection and providing technical support for standardized management of the pepper seed industry. Full article

Forensic biotechnology is a rapidly evolving interdisciplinary field integrating molecular biology, genomics, and data science to address complex investigative challenges. Its applications span diverse domains, including criminalistics, food authentication, environmental monitoring, and bioterrorism preparedness. Advanced technologies such as Next-Generation Sequencing (NGS), CRISPR-Cas biosensors, and Artificial Intelligence (AI) play pivotal roles in modern diagnostics. NGS and eDNA revolutionize genetic profiling and ecological tracking, while microbiome analysis provides crucial insights into post-mortem intervals, cause of death, and geolocation. Simultaneously, CRISPR-based methods enable ultra-rapid pathogen detection, nanobiotechnology facilitates portable Lab-on-a-Chip (LOC) DNA analysis, and AI-driven algorithms optimize the interpretation of complex genomic mixtures and epigenetic age estimation. Despite these breakthroughs, significant challenges persist, including the strict legal admissibility of novel methodologies, the “black-box” dilemma in AI, ethical concerns regarding genetic privacy, and the critical need for global standardization. This review critically examines current biotechnological progress and future prospects, emphasizing the necessity of interdisciplinary collaboration to ensure reliable, accurate, and ethically sound forensic practices. Full article

The authentication of Algerian honey represents a critical challenge for the valuation of national biological patrimony. The present review provides a comprehensive synthesis of existing literature regarding Algerian honeys, emphasizing their diverse botanical origins and complex chemical profiles across seven distinct biogeographical regions, while proposing an innovative Foodomics and AI-driven roadmap to secure geographic authenticity and sustainable rural development. Such evidence underscores the necessity of transitioning from this classical analytical framework toward the emerging ‘Foodomics’ paradigm. By integrating advanced technologies like DNA metabarcoding and molecular fingerprinting, the establishment of a proposed ‘digital passport’ is proposed as a strategic solution to secure Protected Geographical Indications (PGI). Beyond technical innovation, this evolution is presented as a vital socio-economic necessity to ensure the sustainability of rural beekeeping and the international competitiveness of the industry. Ultimately, bridging established data with a molecular roadmap ensures that the biological prestige of this natural heritage is preserved for future generations. Beyond chemical and botanical analyses, this roadmap also incorporates Chemometric Modeling as a cognitive system. By applying techniques such as self-organizing maps (SOMs) and principal component analysis (PCA). This combination ensures highly accurate classification and supports the implementation of a sustainable digital passport system for the local honey industry. Full article

DNA must be efficiently extracted from samples to accurately test the authenticity of food, particularly from processed matrices in which DNA integrity may be compromised. We systematically evaluated the efficiency of extracting DNA from dairy and blood products by four methods, namely SDS-CTAB, SDS-isopropanol precipitation, guanidine isothiocyanate magnetic beads, and a commercial kit. The guanidine isothiocyanate-magnetic bead method yields high quantities and purity of DNA; for example, the yield obtained from chicken blood samples was 318.34 ± 4.77 ng/µL, with an A260/A280 ratio ranging from 1.8 to 2.0. The processing time of this method was compared with the DNA Extraction Kit shorter by 40% and unlike methods such as the SDS-CTAB protocol, does not require the use of toxic reagents such as phenol or chloroform, meeting green chemistry requirements. Among the dairy and blood samples tested, it enables the extraction of DNA in quantities comparable to those obtained using commercial kits; moreover, the DNA yield achieved is 20–30% higher than that of these kits. Furthermore, this method is free from the limitations associated with protein contamination and amplification instability often encountered in protocols such as the CTAB-SDS and SDS-isopropanol methods. The magnetic bead approach was adaptable for complex matrices and demonstrated strong tolerance to coexisting contaminants, thereby improving extraction performance in challenging food samples. The magnetic bead surface functionalization and buffer systems could be improved to further increase their versatility. This method enables reliable DNA extraction and advanced technical support for DNA analysis. Full article

This study examines the impact of a National Institute of Health (NIH)-funded STEM project on high school students’ STEM self-efficacy and perceptions of future STEM careers across two academic years in Western New York. The intervention engaged students in authentic scientific practices, including environmental sampling, microbial DNA analysis, and presenting research posters at a Capstone event. Pre- and post-surveys were administered to intervention and control groups, measuring STEM self-efficacy and perceived future in STEM. Data from 313 students were analyzed using explanatory factor analysis (EFA), confirmatory factor analysis (CFA), and structural equation modeling (SEM) with multiple imputation. EFA results supported a one-factor structure, which was confirmed by CFA results showing a good model fit for both constructs. SEM findings indicated that program participation significantly improved STEM self-efficacy, while effects on perceived future in STEM were nonsignificant, though potentially moderated by cohort. No race-based interaction effects emerged, suggesting consistent program benefits. The findings imply that schools should incorporate authentic STEM learning experiences to strengthen students’ confidence and broaden equitable engagement in STEM. Limitations include the bias on self-report measures. Future longitudinal and mixed-methods research is needed to examine how early gains in self-efficacy translate into sustained STEM pathways. Full article

Crete, a major Mediterranean biodiversity hotspot, hosts many local endemic, threatened and/or protected plant taxa (species and subspecies). Besides their ecological and conservation significance, these unique phytogenetic resources hold significant economic potential for sustainable utilization. Since DNA barcoding is critical for conservation, taxonomy, and plant-derived product authentication, we studied 15 local Cretan endemic taxa using three chloroplast DNA (cpDNA) regions (rbcL, trnL, trnH-psbA). A comparative analysis against GenBank (NCBI) records revealed significant new data: (i) the first genetic information for five taxa (Centaurea redempta subsp. redempta, Galium fruticosum, Micromeria hispida, Salix kaptarae, Teucrium cuneifolium); (ii) new marker-specific sequences for seven taxa (Helichrysum heldreichii, Scutellaria hirta, Sesleria doerfleri, Staehelina petiolata, Teucrium alpestre, Campanula pelviformis, Phlomis lanata); and (iii) novel genotypes of already represented markers for three species (Phlomis lanata, Scutellaria sieberi, Staehelina petiolata). Phylogenetic analyses were performed for all three molecular markers across selected members of Scutellaria section Scutellaria, Teucrium section Polium, and Campanula section Quinqueloculares. The overall results indicated that, amongst the studied species, the trnH-psbA marker is more suitable for species-level identification, whereas the rbcL and trnL markers were more helpful to genus-level identification within Lamiaceae and Campanulaceae. These results enrich the DNA barcoding reference library and form a concrete contribution towards the protection, conservation and traceability of Crete’s unique botanical heritage. Full article

Ensuring the authenticity of origin labeling is a challenge for brown algae products such as kelp, wakame, and hijiki. While conventional DNA analysis has high discriminatory capabilities, it is not necessarily suitable for routine screening of large quantities of samples due to time and cost considerations. This study aimed to identify the species (variety) and geographical origin of brown algae (kelp, wakame, and hijiki), with both variety and origin evaluated for kelp and geographical origin evaluated for wakame and hijiki. To achieve this, classification methods were developed for each of three spectroscopic analysis techniques—excitation emission matrix (EEM), Fourier transform infrared spectroscopy (FT-IR), and near-infrared spectroscopy (NIR)—using machine learning algorithms, and their classification performance was systematically compared and evaluated. Six classification models, k-nearest neighbors (KNN), convolutional neural networks (CNN), LightGBM, XGBoost, random forest, and support vector machines, were constructed to distinguish varieties and origins based on EEM, NIR, and FT-IR data. Depending on the combination of methods, high-precision identification was obtained (>99%), especially for kelp variety identification using NIR + KNN (≈100%). These results suggest that each spectral dataset contains characteristic information specific to each sample and that selecting a model suited to these characteristics is effective for highly accurate identification of variety (in kelp) and geographical origin. The selected method can serve as a rapid and simple identification tool that contributes to verifying the authenticity of brown algae products and improving raw material traceability. Full article

Background: Piper is one of the largest genera in the family Piperaceae, with approximately 2100 species. Most Piper species are used as spices or as medicinal plants. Piper methysticum G. Forst., popularly known as kava-kava (or kava), is widely used to treat anxiety disorders. Due to similar morphological features, P. auritum Kunth (known as “false kava”) is sometimes mistakenly or intentionally used as an alternative botanical source for “kava” extracts. The false kava extracts do not contain active kavalactones but contain safrole, which is hepatotoxic. It is important to verify the component botanical materials in order to evaluate the quality and safety attributes of a potential botanical drug. Some studies have evaluated genetic variation in Piper sp. using the chloroplast regions matK, rbcL, rpoC1 and trnH-psbA and the nuclear ITS2 markers. However, none has focused on the identification of P. methysticum using DNA barcodes. In the present investigation, the ITS2 DNA barcode region from the nuclear genome was tested to confirm the identification and authentication of kava-kava samples. Methods: Seven P. methysticum samples were collected from three different geographic lo-cations and two P. auritum samples were collected and the ITS2 region from the nuclear genome, was amplified, sequenced and aligned to determine their genetic distances. Results: The ITS2 locus showed high amplification and sequence output with a discriminating barcode gap. A distance-based phylogenetic tree and BLAST confirmation (using blastn) revealed the ITS2 locus as a diagnostic DNA barcode for the accurate identification of kava-kava species. Discussion: In conclusion, the ITS2 region proves to be an effective and reliable DNA barcode for distinguishing P. methysticum from closely related species such as P. auritum. Its application can significantly improve the safety, quality, and traceability of kava-containing products, addressing a critical need in the standardization of botanical drugs. Full article

Background: This case report presents a 12-year-old male with vertically transmitted chronic hepatitis B virus (HBV) infection, exhibiting a rare pan-reactive serological profile (concurrent HBsAg, HBsAb, HBeAg, HBeAb, and HBcAb positivity) alongside fluctuating low-level viremia (HBV DNA: 1.06 × 10² IU/mL to undetectable). Rigorous exclusion of technical artifacts confirmed the authenticity of this atypical serologic pattern, observed in <0.001% of the general population. Methods: Liver biopsy and immunohistochemical staining were performed to evaluate hepatic inflammation and fibrosis. HBV serological markers and viral load were quantified using commercial diagnostic kits, with longitudinal monitoring for 18 months. Results: Liver biopsy revealed Grade 2 inflammation with focal HBsAg/HBcAg expression, supporting immune-active chronic hepatitis B (CHB) despite partial seroconversion. The patient’s clinical course highlights key challenges in pediatric HBV management: (1) delayed immune reconstitution (18-month longitudinal HBeAg/HBeAb dynamics), (2) non-linear virologic-ALT correlation, and (3) diagnostic ambiguity in pan-positive serology—potentially reflecting S-gene escape mutants or transitional immune responses. Initiation of tenofovir disoproxil fumarate (TDF) achieved sustained virologic suppression, underscoring the importance of early antiviral therapy in pediatric CHB with atypical markers. Conclusions: This case provides preliminary insights into the complex interplay between viral evolution and immature host immunity, advocating for refined monitoring protocols integrating high-sensitivity HBV DNA, quantitative serology, and non-invasive fibrosis assessment in pediatric HBV care. Full article