A novel real time PCR assay using melt curve analysis for ivory identification

African and Asian elephant ivory discrimination using a portable strip test

Currently, the global elephant population has significantly declined due to the poaching of elephants for their ivory, and this is the reason why elephants are listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). However, Thailand allows the legal trade of ivory from registered, domesticated Asian elephants, leading to the smuggling of African elephant ivory, and passing them off as Asian elephant ivory. Therefore, this research aims to develop and validate a portable strip test to discriminate between Asian and African elephants DNA, using Recombinase Polymerase Amplification (RPA) and Lateral Flow Dipstick assay (LFD) according to international standards. The results showed that the strip test can be successfully developed with 100% accuracy (n = 105). This kit is specific to elephants, has a detection limit of 0.125 ng of DNA, and can effectively discriminate a variety of elephant ivory, including raw ivory, ivory products, and aged ivory over 25 years old, which had been damaged by fire, all with 100% accuracy (n = 117). Additionally, the developed strip test is designed to be portable and cost-effective. It does not require expensive laboratory equipment and provides a faster analysis process compared with conventional PCR-based methods. This will expedite the legal process and enforcement of laws related to elephant conservation, reducing the opportunities for illegal activities, and enabling timely prosecution under relevant wildlife conservation laws in Thailand and internationally.

A new multiplex qPCR assay to detect and differentiate big cat species in the illegal wildlife trade

All species of big cats, including tigers, cheetahs, leopards, lions, snow leopards, and jaguars, are protected under the Convention on the International Trade in Endangered Species (CITES). This is due in large part to population declines resulting from anthropogenic factors, especially poaching and the unregulated and illegal trade in pelts, bones, teeth and other products that are derived from these iconic species. To enhance and scale up monitoring for big cat products in this trade, we created a rapid multiplex qPCR test that can identify and differentiate DNA from tiger (Panthera tigris), cheetah (Acinonyx jubatus), leopard (Panthera pardus), lion (Panthera leo), snow leopard (Panthera uncia), and jaguar (Panthera onca) in wildlife products using melt curve analysis to identify each species by its unique melt peak temperature. Our results showed high PCR efficiency (> 90%), sensitivity (detection limit of 5 copies of DNA per PCR reaction) and specificity (no cross amplification between each of the 6 big cat species). When paired with a rapid (< 1 h) DNA extraction protocol that amplifies DNA from bone, teeth, and preserved skin, total test time is less than three hours. This test can be used as a screening method to improve our understanding of the scale and scope of the illegal trade in big cats and aid in the enforcement of international regulations that govern the trade in wildlife and wildlife products, both ultimately benefiting the conservation of these species worldwide.

A novel approach to combatting proboscidean ivory trafficking using a multiplex High-Resolution Melt (M-HRM) assay

To support efforts in prosecuting wildlife crimes, we developed and validated a multiplex High-Resolution Melt (M-HRM) assay for the identification of proboscidean taxa commonly required to be identified or excluded in ivory seizures and forensic casework: Asian elephant (Elephas maximus), African elephant (Loxodonta spp.), mammoth (Mammuthus spp.), and mastodon (Mammut spp.). Five hundred and fifty (550) blood, tissue, and ivory samples from individuals of these 4 proboscidean taxa were used to develop and validate the 2 proboscidean-specific mitochondrial sites targeted by this assay. The 28-basepair (bp) 16S ribosomal RNA (rRNA) and 54-bp cytochrome b (Cytb) gene segments yield a combination of melt peaks that create composite melt profiles unique to each of the 4 proboscidean taxa. Wildlife forensic laboratories can use this sensitive, rapid, and cost-effective assay to assist efforts to combat the unlawful commercialization of proboscidean ivory and to stop the poaching crisis leading to the decline of these ivory-bearing species in the wild.

Discrimination of highly degraded, aged Asian and African elephant ivory using denaturing gradient gel electrophoresis (DGGE)

BACKGROUND

Elephant populations have greatly reduced mainly due to illegal poaching for their ivory. The trade in elephant products is protected by national laws and CITES agreements to prevent them from further decline. For instance, in Thailand, it is illegal to trade ivory from African elephants; however, the law allows possession of ivory from Asian elephants if permission has been obtained from the authorities. As such, means of enforcement of legislation are needed to classify the legal status of seized ivory products. Many DNA-based techniques have been previously reported for this purpose, although all have a limit of detection not suitable for extremely degraded samples.

AIM

We report an assay based on nested PCR followed by DGGE to confirm the legal or illegal status of seized ivory samples where it is assumed that the DNA will be highly degraded.

METHOD AND RESULTS

The assay was tested on aged ivory from which the assay was tested for reproducibility, specificity, and, importantly, sensitivity. Blind testing showed 100% identification accuracy. Correct assignment in all 304 samples tested was achieved including confirmation of the legal status of 227 highly degraded, aged ivories, thus underlining the high sensitivity of the assay.

CONCLUSION AND RECOMMENDATION

The research output will be beneficial to analyze ivory casework samples in wildlife forensic laboratories.

Current issues for mammalian species identification in forensic science: a review

Mammalian species identification is one of the important issues in forensic science. Determining the origins of non-human biological material found at crime scenes can increase the possibility of identifying the true culprit by narrowing down the range of suspects. Although many techniques based on mitochondrial DNA (mtDNA) have been developed, challenges remain to cost-effectively identify species from degraded samples containing a mixture of DNA from multiple species and to standardize procedures for mammalian species identification. This review evaluates the reliability and versatility of mtDNA-based techniques to reveal obstacles to the establishment of standard analytical methods, with a particular focus on DNA mixtures. When samples contain a mixture of DNA from multiple species, the interpretation of sequencing analysis results is difficult. Although DNA metabarcoding using next-generation sequencing (NGS) technologies can overcome the DNA mixture problem, DNA metabarcoding is not suitable for the type of small-scale analysis routinely performed by local forensic laboratories, primarily because it is costly and time-consuming. By contrast, fluorescent multiplex PCR analysis enables cost-effective and simultaneous species identification from suboptimal samples, although the number of identifiable species is currently limited in comparison with sequencing techniques. The advantages and limitations of current techniques presented in this review indicate that multiplex PCR analysis will continue to be important for mammalian species identification in forensic casework analysis. Further developments in multiplex PCR analysis that enable the identification of an increased number of species will play a key step for standardization efforts among forensic laboratories.

Peptide Nucleic Acid Based Molecular Authentication for Identification of Four Medicinal Paeonia Species Using Melting Array Analysis of the Internal Transcribed Spacer 2 Region

Accurate taxonomic identification of plant materials in herbal medicines is important for product quality control. The genus Paeonia (Saxifragales) is the source of the herbal preparations Paeoniae Radix (Paeoniae Radix Alba and Paeoniae Radix Rubra) and Moutan Radicis Cotex. However, confusion has arisen regarding their contents due to linguistic and taxonomic ambiguities, similar morphologies and different definitions of Paeoniae Radix in the Korean and Chinese national pharmacopoeias, leading to the distribution of adulterated products. To develop a method for identifying the four Paeonia species used in these medicines, three fluorescently-labeled peptide nucleic acid (PNA) probes were designed against ITS2 sequences containing single nucleotide polymorphisms (SNPs) and used in a real-time PCR melting curve assay. Each of the four Paeonia species was accurately identified using this analysis. The accuracy and analytical stability of the PNA melting curve assay was confirmed using commercially available samples of the four Paeonia species. This assay is a reliable genetic tool to distinguish between different Paeonia-derived herbal medicines and identify the botanical origins of Paeoniae Radix and Moutan Radicis Cortex. This technique may also contribute to quality control and standardization of herbal medicines by providing a reliable authentication tool and preventing the distribution of inauthentic adulterants.