A novel duplex droplet digital PCR assay for simultaneous authentication and quantification of Panax notoginseng and its adulterants

Molecular quantification of herbs (Herb-Q): a pyrosequencing-based approach and its application in Pinellia ternata

Variations in herb dosage due to species adulteration and dosing inaccuracies can substantially affect clinical safety and efficacy. Accurate species quantification remains challenging, as current methods often yield inconsistent results. This study introduces a novel pyrosequencing-based technique, termed herb molecular quantification (Herb-Q), designed to precisely quantify herbal products. We evaluated its effectiveness using Pinellia ternata and five of its adulterants. Initially, we assessed commonly used DNA barcodes with sequences from a public database, identifying two candidate regions, Maturase K (matK) and internal transcribed spacer 2 (ITS2), for screening specific single nucleotide polymorphism (SNP) loci, allowing for species-specific identification. These loci were validated by amplifying and sequencing genomic material from collected samples. Our validation studies showed that Herb-Q demonstrated excellent linearity, accuracy, repeatability, and detection limits. We established quantitative standard curves with high R2 values (> 0.99) to enable precise species quantification, which were combined with external standards to provide clear and accurate visual quantification results. The average bias in quantifying the tuber of P. ternata was 2.38%, confirming that Herb-Q can accurately identify and quantify herbal product constituents. Moreover, the entire quantification process took less than 4 h. This study presents a novel, rapid method for accurately quantifying species in herbal products and advances the application of DNA barcoding from species identification to quantitative detection.

An integrated digital polymerase chain reaction chip for multiplexed meat adulteration detection

Meat adulteration detection is a common concern of consumers. Here, we proposed a multiplex digital polymerase chain reaction method and a low-cost device for meat adulteration detection. Using a polydimethylsiloxane microfluidic device, polymerase chain reaction reagents could be pump-free loaded into microchambers (40 × 40 chambers) automatically. Due to the independence of multiplex fluorescence channels, deoxyribonucleic acid templates extracted from different animal species could be distinguished by one test. In this paper, we designed primers and probes for four types of meat (beef, chicken, pork, and duck) and labeled each of the four fluorescent markers (hexachlorocyclohexane [HEX], 6-carboxyfluorescein [FAM], X-rhodamine [ROX], and cyanine dyes 5 [CY5]) on the probes. Specific detection and mixed detection experiments were performed on four types of meat, realizing a limit of detection of 3 copies/µL. A mixture of four different species can be detected by four independent fluorescence channels. The quantitative capability of this method is found to meet the requirements of meat adulteration detections. This method has great potential for point-of-care testing together with portable microscopy equipment.

Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations

Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.

Study of the suitable climate factors and geographical origins traceability of Panax notoginseng based on correlation analysis and spectral images combined with machine learning

INTRODUCTION

The cultivation and sale of medicinal plants are some of the main ways to meet the increased market demand for plant-based drugs. Panax notoginseng is a widely used Chinese medicinal material. The growth and accumulation of bioactive constituents mainly depend on a satisfactory growing environment. Additionally, the occurrence of market fraud means that care should be taken when purchasing.

METHODS

In this study, we report the correlation between saponins and climate factors based on high performance liquid chromatography (HPLC), and evaluate the influence of climate factors on the quality of P. notoginseng. In addition, the synchronous two-dimensional correlation spectroscopy (2D-COS) images of near infrared (NIR) data combined with the deep learning model were applied to traceability of geographic origins of P. notoginseng at two different levels (district and town levels).

RESULTS

The results indicated that the contents of saponins in P. notoginseng are negatively related to the annual mean temperature and the temperature annual range. A lower annual mean temperature and temperature annual range are favorable for the content accumulation of saponins. Additionally, high annual precipitation and high humidity are conducive to the content accumulation of Notoginsenoside R1 (NG-R1), Ginsenosides Rg1 (G-Rg1), and Ginsenosides Rb1 (G-Rb1), while Ginsenosides Rd (G-Rd), this is not the case. Regarding geographic origins, classifications at two different levels could be successfully distinguished through synchronous 2D-COS images combined with the residual convolutional neural network (ResNet) model. The model accuracy of the training set, test set, and external validation is achieved at 100%, and the cross-entropy loss function curves are lower. This demonstrated the potential feasibility of the proposed method for P. notoginseng geographic origin traceability, even if the distance between sampling points is small.

DISCUSSION

The findings of this study could improve the quality of P. notoginseng, provide a reference for cultivating P. notoginseng in the future and alleviate the occurrence of market fraud.

Digital PCR: A Tool to Authenticate Herbal Products and Spices

Authentication of herbal products and spices is experiencing a resurgence using DNA-based molecular tools, mainly species-specific assays and DNA barcoding. However, poor DNA quality and quantity are the major demerits of conventional PCR and real-time quantitative PCR (qPCR), as herbal products and spices are highly enriched in secondary metabolites such as polyphenolic compounds. The third-generation digital PCR (dPCR) technology is a highly sensitive, accurate, and reliable method to detect target DNA molecules as it is less affected by PCR inhibiting secondary metabolites due to nanopartitions. Therefore, it can be certainly used for the detection of adulteration in herbal formulations. In dPCR, extracted DNA is subjected to get amplification in nanopartitions using target gene primers, the EvaGreen master mix, or fluorescently labeled targeted gene-specific probes. Here, we describe the detection of Carica papaya (CP) adulteration in Piper nigrum (PN) products using species-specific primers. We observed an increase in fluorescence signal as the concentration of target DNA increased in PN-CP blended formulations (mock controls). Using species-specific primers, we successfully demonstrated the use of dPCR in the authentication of medicinal botanicals.

Droplet digital PCR for the identification of plant-derived adulterants in highly processed products

BACKGROUND

The high sensitivity of droplet digital PCR (ddPCR) contributes to its excellent performance in animal and microorganism identification, but the utilization of ddPCR is limited in plant adulterant identification of highly processed products for which effective methods are lacking.

PURPOSE

This study investigated the feasibility of ddPCR in the identification of plant adulterants in Chinese patent medicine (CPM) as groundwork to develop ddPCR assays for other highly processed goods.

METHODS

The original plant, processed and highly processed products of Mutong (Akebiae Caulis) and its two adulterants were used to analyze the specificity, sensitivity, and practical performance of the developed singleplex and triplex ddPCR assays.

RESULTS

The results revealed that the limit of detection (LOD) and limit of quantification (LOQ) for the selective ddPCR assays developed to identify Mutong and its adulterants were 0.00002 ng/μl and 0.00016 ng/μl, respectively, and that the regression equations representing the relationships between DNA concentration and target copy number all exhibited good linearity. Furthermore, the common adulterant of Mutong in three samples of Longdan Xiegan pills was successfully identified through ddPCR assays and confirmed by Sanger sequencing.

CONCLUSION

This work comprehensively revealed the great ability of ddPCR technology in detecting plant adulterants in traditional Chinese medicine (TCM), providing a method for the quality control of highly processed plant products with complex components for commonly used goods.

Rapid detection of adulteration in powder of ginger (Zingiber officinale Roscoe) by FT-NIR spectroscopy combined with chemometrics

•

Rapid detection of adulteration in GP was realized by NIR spectroscopy.

•

PCA and PLS-DA models were successfully explored to identify adulterants in GP.

•

Three algorithms achieved satisfactory results for discrimination of adulteration.

•

Adulteration levels in GP can be predicted by PLSR model.

•

The optimal pretreatment methods were compared and selected for modeling.

Ginger powder (GP) is a popular spice in the world. Duo to its nutritional value, GP is regarded as an attractive target for adulteration, which is not easily detected. In this study, chromaticity analysis and Fourier transform near-infrared (FT-NIR) spectroscopy combined with chemometrics were developed to identify and quantify of GP and its adulterants. The result showed that GPs and adulterated GPs cannot be completely distinguished by chromaticity analysis. While, the optimized NIR spectra could accurately distinguish the authentic GPs from those adulterated samples. Random forest and gradient boosting algorithms exhibited the highest accuracies (100%) in classification. Moreover, a quantitative model was successfully established to predict the adulteration level in GP. The optimal parameters of prediction to deviation were 8.92, 13.68, 14.61, and 4.30, for pure and adulterated GPs. Overall, FT-NIR spectroscopy is a promising tool, which can quickly identify potential adulteration in GP and track the types of adulterants.

DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

Rice (Oryza sativa L.) is one of the most cultivated and consumed crops worldwide. It is mainly produced in Asia but, due to its large genetic pool, it has expanded to several ecosystems, latitudes and climatic conditions. Europe is a rice producing region, especially in the Mediterranean countries, that grow mostly typical japonica varieties. The European consumer interest in rice has increased over the last decades towards more exotic types, often more expensive (e.g., aromatic rice) and Europe is a net importer of this commodity. This has increased food fraud opportunities in the rice supply chain, which may deliver mixtures with lower quality rice, a problem that is now global. The development of tools to clearly identify undesirable mixtures thus became urgent. Among the various tools available, DNA-based markers are considered particularly reliable and stable for discrimination of rice varieties. This review covers aspects ranging from rice diversity and fraud issues to the DNA-based methods used to distinguish varieties and detect unwanted mixtures. Although not exhaustive, the review covers the diversity of strategies and ongoing improvements already tested, highlighting important advantages and disadvantages in terms of costs, reliability, labor-effort and potential scalability for routine fraud detection.