Forensic DNA barcoding and bio-response studies of animal horn products used in traditional medicine

Morpometric and molecular characterization of Surguli goat through CO1 gene in district Kohat

The present study was designed with the aim to study morphometric characterization as well as phylogeny and diversity of the local Surguli goat at their breeding tract district Kohat through mitochondrial DNA region, i.e., Cytochrome C Oxidase Subunit One (CO1) gene. Morphometric data and blood samples were collected from thirty (30) pure goats. Morphometric analysis showed that sex had significant effect (p < 0.05) on body weight, body length, hearth girth and horn length while no significant effect (p > 0.05) was observed for other characteristics. The results also indicated that age had significant effect (p < 0.05) on height at rump, ear length, horn length and tail length while no significant effect (p > 0.05) was observed for other characteristics. The phylogenetic analysis through CO1 nucleotide sequences within nucleotide range 1-767 showed nine polymorphic sites segregating into eight haplotypes. The mean intraspecific diversity and mean interspecific diversity were calculated as 0.23 and 2.36%, respectively. Phylogenetic tree revealed that Capra Ibex and native Surguli goat have common ancestors. The morphometric and molecular results obtained from the present study can be exploited as a selection tool for breeding and overall improvement.

Universal mtDNA fragment for Cervidae barcoding species identification using phylogeny and preliminary analysis of machine learning approach

The aim of the study was to use total DNA obtained from bone material to identify species of free-living animals based on the analysis of mtDNA fragments by molecular methods using accurate bioinformatics tools Bayesian approach and the machine learning approach. In our research, we present a case study of successful species identification based on degraded samples of bone, with the use of short mtDNA fragments. For better barcoding, we used molecular and bioinformatics methods. We obtained a partial sequence of the mitochondrial cytochrome b (Cytb) gene for Capreolus capreolus, Dama dama, and Cervus elaphus, that can be used for species affiliation. The new sequences have been deposited in GenBank, enriching the existing Cervidae mtDNA base. We have also analysed the effect of barcodes on species identification from the perspective of the machine learning approach. Machine learning approaches of BLOG and WEKA were compared with distance-based (TaxonDNA) and tree-based (NJ tree) methods based on the discrimination accuracy of the single barcodes. The results indicated that BLOG and WEKAs SMO classifier and NJ tree performed better than TaxonDNA in discriminating Cervidae species, with BLOG and WEKAs SMO classifier performing the best.

A method for determining the origin of crude drugs derived from animals using MinION, a compact next-generation sequencer

We evaluated whether MinION, an inexpensive portable sequencer, can be used to identify the origin of crude drugs derived from animals. Standard and nonstandard crude drugs with different species of origin were examined. In addition, standards mixed with nonstandard samples were used. As a target gene, cytochrome c oxidase I was amplified and sequenced. The fast mode results had a slightly lower match ratio than high-accuracy mode, but the animals of origin were correctly determined by BLAST for all samples. For antler velvet derived from Rangifer tarandus, even when the sequences were aligned based on Cervus elaphus, the animal of origin was determined correctly. Minor contents could be detected from mixtures of two animals, if the mixtures contained at least 19:1 mtDNA when the coverage allele-fraction threshold was 0.05. By contrast, in fast mode, two sequences could not be separated due to the low accuracy of the base-calling for each read. For fieldwork, the species of origin of crude drugs could be identified with only simple DNA extraction and library preparation. Therefore, MinION appears to be a convenient tool for identifying the origins of crude drugs derived from animals.

Pragmatic Applications and Universality of DNA Barcoding for Substantial Organisms at Species Level: A Review to Explore a Way Forward

DNA barcodes are regarded as hereditary succession codes that serve as a recognition marker to address several queries relating to the identification, classification, community ecology, and evolution of certain functional traits in organisms. The mitochondrial cytochrome c oxidase 1 (CO1) gene as a DNA barcode is highly efficient for discriminating vertebrate and invertebrate animal species. Similarly, different specific markers are used for other organisms, including ribulose bisphosphate carboxylase (rbcL), maturase kinase (matK), transfer RNA-H and photosystem II D1-ApbsArabidopsis thaliana (trnH-psbA), and internal transcribed spacer (ITS) for plant species; 16S ribosomal RNA (16S rRNA), elongation factor Tu gene (Tuf gene), and chaperonin for bacterial strains; and nuclear ITS for fungal strains. Nevertheless, the taxon coverage of reference sequences is far from complete for genus or species-level identification. Applying the next-generation sequencing approach to the parallel acquisition of DNA barcode sequences could greatly expand the potential for library preparation or accurate identification in biodiversity research. Overall, this review articulates on the DNA barcoding technology as applied to different organisms, its universality, applicability, and innovative approach to handling DNA-based species identification.

Mitochondrial phylogenetic and diversity analysis in Azi-Kheli buffalo

NOVELTY STATEMENT

The present study was conducted for the first time in Pakistan to investigate Cytochrome C Oxidase Subunit 1 (CO1) gene and full-length Displacement Loop (D-loop) region of mitochondrial DNA in Azi-Kheli buffalo breed native to northern hilly areas of Khyber Pakhtunkhwa Province of Pakistan. The present study was designed to investigate phylogeny and diversity in Azi-Kheli buffalo, through two mitochondrial DNA regions, i.e., Cytochrome C Oxidase Subunit-I (CO1) and Displacement Loop (D-loop) region. Thirty (30) blood samples were taken from Azi-Kheli pure breed animals from original breeding tract, i.e., Khwazakhela, Swat. Polymerase chain reactions using gene-specific primers were carried out for amplifying 709-bp region of CO1 gene and 1159-bp region of D-Loop for identification, phylogeny, and diversity in Azi-Kheli buffalo, respectively. The sequences of CO1 gene revealed four (04) haplotypes, whereas D-loop sequences revealed five (05) haplotypes. Mean interspecific diversity with related species was 2.56%, and mean intraspecific diversity within Azi-Kheli buffalo was 0.25%, estimated via Kimura-2 parameter. Phylogenetic tree (maximum likelihood) revealed clustering of Azi-Kheli haplotypes with river buffalo and is distinct from swamp buffalo and other related species of genus Bubalus. Mean haplotype and nucleotide diversity of D-loop were Hd = 0.9601 ± SD = 0.096 and π = 0.01208 ± SD = 0.00182, respectively. Phylogenetic tree (neighbor-joining) revealed two main clades, i.e., river buffalo and swamp buffalo clade. The haplotypes of Azi-Kheli clustered with haplotypes of different river buffalo breeds at different positions. The current study suggests that Azi-Kheli has common origin with other river buffalo breeds; hence, it is river buffalo which harbors high genetic diversity.

A review of the genus Rusa in the indo-malayan archipelago and conservation efforts

Genus Rusa, belonging to the deer family Cervidae is native to the Indo-Malaya Archipelago (IMA). However, detailed information on the Rusa genus in the IMA is limited. This review provides comprehensive information on the Rusa genus in the IMA including, threats and conservation efforts. There are four species of deer in Rusa genus, which is Sambar deer (Rusa unicolor), Javan deer (Rusa timorensis), Visayan spotted deer (Rusa alfredi) and Philippine deer (Rusa marianna). Despite their wide distribution in the South Asian and Southeast Asian regions, they are under serious threats. Some conservation efforts that are being done to protect and conserve them among others are; (1) facilities protection, (2) habitat enrichment programme, (3) Ex-situ conservation, (4) legislations, and (5) captive breeding. Conservation through genetics is also an important step in conserving these species. Recommendations for conservation of the genus are also discussed; 1. maintenance of ecosystem. 2. more effective monitoring system on the existing protected area. 3. ex-situ conservation, and 4. habitat monitoring.

Identification of the original species of cubilose based on DNA barcode

Cubilose, a valuable traditional Chinese medicine, is mainly composed of the saliva by several species of Aerodramus or Collocalia in the Apodidae. Due to rarity, high economic value and huge market demand, its fake or adulteration is frequently found in the market. Therefore, it is urgent to establish a simple and accurate method for authenticating cubilose. DNA barcoding, which is an easy, quick and reliable method, is widely used to trace the origin of traditional Chinese medicine. For identifying the original species of cubilose, cytb gene of 18 cubilose samples including 15 officer cubilose and 3 feather cubilose were amplified and entered into the GenBank database using the BLAST search tool. The genetic distances among 18 cubilose samples were calculated based on the Kimura two parameter (K2P) model. To construct the reference database, 18 cytb sequences of Aerodramus or Collocalia were downloaded from GenBank. The neighbor-joining (NJ) and unweighted pair group method with arithmetic average (UPGMA) trees were constructed based on sequences from GenBank and our dataset. Blast analysis showed that all cubilose samples had the highest similarity with A. fuciphagus, and the sequence similarity reached over 99%. Genetic distance of 18 cubilose samples ranged from 0.000-0.010. Trees constructed by NJ and UPGMA gave similar topology: all cubilose samples clustered together with A. fuciphagus. These result demonstrated that the original species of all 18 cubilose samples were A. fuciphagus, and cytb gene is a good candidate for identifying cubilose.

DNA barcoding of southern African crustaceans reveals a mix of invasive species and potential cryptic diversity

Globally, crustaceans represent one of the most taxonomically diverse and economically important invertebrate group. Notwithstanding, the diversity within this group is poorly known because most crustaceans are often associated with varied habits, forms, sizes and habitats; making species identification by conventional methods extremely challenging. In addition, progress towards understanding the diversity within this group especially in southern Africa has been severely hampered by the declining number of trained taxonomists, the presence of invasive alien species, over exploitation, etc. However, the advent of molecular techniques such as “DNA barcoding and Metabarcoding” can accelerate species identification and the discovery of new species. To contribute to the growing body of knowledge on crustacean diversity, we collected data from five southern African countries and used a DNA barcoding approach to build the first DNA barcode reference library for southern African crustaceans. We tested the reliability of this DNA barcode reference library to facilitate species identification using two approaches. We recovered high efficacy of specimen identification/discrimination; supported by both barcode gap and tree-base species identification methods. In addition, we identified alien invasive species and specimens with ‘no ID” in our DNA barcode reference library. The later; highlighting specimens requiring (i) further investigation and/or (ii) the potential presence of cryptic diversity or (iii) misidentifications. This unique data set although with some sampling gaps presents many opportunities for exploring the effect and extent of invasive alien species, the role of the pet trade as a pathway for crustacean species introduction into novel environments, sea food authentication, phylogenetic relationships within the larger crustacean groupings and the discovery of new species.

Investigating the genetic diversity and presence of forensically informative nucleotide sequences in Indian antelope (Antilope cervicapra) using multiple genes of the mitochondrial genome

Indian antelope or Blackbuck (Antilope cervicapra) is one of the widely distributed endemic species in India among wild bovids and a majority of preferred habitats are in human-dominated landscapes. Poaching threats and habitat degradation are major factors for the decline in Blackbuck population from its distribution range. Till date, there is no detailed study using molecular techniques in India on Blackbuck, except a few studies entailing phylogenetic scenario based on inadequate sampling and DNA sequences restricted over limited geographic areas. In view of this, the present study is aimed to screen the Blackbuck samples from a large part of its distribution range and to investigate the genetic diversity as well as to identify the forensically informative nucleotide sequences (FINS) for species identification. We relied on multi-genes approach using three genes of mtDNA genome viz. Cytochrome Oxidase I, Cytochrome b and 16S rRNA and identified the FINS in the Blackbuck population along with conspecific sequences divergence and genetic diversity indices. In all three genes, we observed 8 to 17 haplotypes with the intra-species sequence divergence of 0.004-0.016. Inter-species sequence divergence with the other closely related species of the Blackbuck was 0.0225-0.033. We report the presence of FINS across three genes from 12 to 18 and found more informative nucleotide sites using Cytochrome Oxidase I genes compared to Cytochrome b and 16S rRNA gene. We did not observe the presence of geographic-specific FINS amongst Blackbuck population that can be used to assign individuals to geographic origin. Besides, in the phylogenetic tree, samples from different locations did not cluster into geographic-specific clade and exhibited mixed homology for these sequences. We suggest exploring the feasibility of using nuclear markers for population assignment.

Molecular authentication of sika deer (Cervus nippon) based on allele-specific PCR

Sika deer (Cervus nippon) is listed as a tonic in many ancient Chinese pharmaceutical. Many adulterants of sika deer products have been found in Chinese medicinal materials markets, which led to detrimental impacts in clinical treatment. However, it is lack of the rapid and effective identification method for sika deer. This study amplified 574 bp fragment of mtDNA COI region of 19 samples from seven Cervidae species, and the relevant five sequences from reindeer (Rangifer tarandus) were downloaded from GenBank. It was found that there were two SNP loci for sika deer. Phylogenetic analysis indicated that individuals from sika deer clustered together. Based on SNP locus, one pair specific primer for allele-specific PCR identification of sika deer was designed, which could be used to rapidly and accurately identify sika deer.

Full-Length Multi-Barcoding: DNA Barcoding from Single Ingredient to Complex Mixtures

DNA barcoding has been used for decades, although it has mostly been applied to somesingle-species. Traditional Chinese medicine (TCM), which is mainly used in the form ofcombination-one type of the multi-species, identification is crucial for clinical usage.Next-generation Sequencing (NGS) has been used to address this authentication issue for the pastfew years, but conventional NGS technology is hampered in application due to its short sequencingreads and systematic errors. Here, a novel method, Full-length multi-barcoding (FLMB) vialong-read sequencing, is employed for the identification of biological compositions in herbalcompound formulas in adequate and well controlled studies. By directly sequencing the full-lengthamplicons of ITS2 and psbA-trnH through single-molecule real-time (SMRT) technology, thebiological composition of a classical prescription Sheng-Mai-San (SMS) was analyzed. At the sametime, clone-dependent Sanger sequencing was carried out as a parallel control. Further, anotherformula-Sanwei-Jili-San (SJS)-was analyzed with genes of ITS2 and CO1. All the ingredients inthe samples of SMS and SJS were successfully authenticated at the species level, and 11 exogenousspecies were also checked, some of which were considered as common contaminations in theseproducts. Methodology analysis demonstrated that this method was sensitive, accurate andreliable. FLMB, a superior but feasible approach for the identification of biological complexmixture, was established and elucidated, which shows perfect interpretation for DNA barcodingthat could lead its application in multi-species mixtures.

Buffalo species identification and delineation using genetic barcoding markers

Enrichment of barcode databases with mitochondrial cytochrome c oxidase subunit I (COI) barcode sequences in different animal taxa has become important for identification of animal source in food samples to prevent commercial fraud. In this study, COI barcode sequence in seventy one river buffalo samples were determined, analyzed and deposited in Genbank barcode database and barcode of life database (BOLD) to contribute for construction of public reference library for COI barcode sequence in river buffalo. Moreover COI barcode sequence was used to identify the closely related buffalo groups: river buffalo, swamp buffalo, lowland anoa and African buffalo. Results indicated the success of the COI barcode in the identification of each of the tested groups. Whereas a suggested sequence of other mitochondrial segment representing two successive transfer RNA (tRNA) genes; tRNA-Threonine (MT-TT) and tRNA-Proline (MT-TP) was failed to be used as a barcode marker for differentiation between the tested buffalo groups.

Establishment of widely applicable DNA extraction methods to identify the origins of crude drugs derived from animals using molecular techniques

We established widely applicable DNA extraction methods to identify the origins of crude drugs derived from animals. Twenty-one samples including 17 kinds of crude drug derived from animals were examined. DNA was extracted from most of the crude drugs by adjustment of the QIAamp^® DNA Mini Kit. DNA extraction was performed successfully using phenol to remove impurities after applying a proteinase treatment. DNA extraction was performed successfully by decalcification treatment using ethylenediaminetetraacetic acid (EDTA), before applying the proteinase treatment for crude drugs having high calcium content, such as those from oyster shell and cuttlefish bone. DNA could not be extracted from sea-ear shell using the EDTA decalcification treatment, but was extracted successfully using a TBONE EX KIT. The mitochondrial 16S ribosomal RNA (rRNA) gene region was amplified, and Basic Local Alignment Search Tool (BLAST) analysis was performed after sequencing. Polymerase chain reaction (PCR) products of approximately 600 bp in length were obtained from all samples except donkey glue, one of the two seahorses, and longgu. Drug origins were determined in all samples by sequence analysis based on the BLAST results, and match rates were >97 %. Moreover, 16 samples had a match rate >99 %. Our DNA extraction methods were widely applicable to evaluation of many crude drugs derived from animals, and proved very useful for identifying the origins of such drugs.

Sika deer (Cervus nippon)-specific real-time PCR method to detect fraudulent labelling of meat and meat products

Since game meat is more valuable and expensive than meat from domesticated animal species it is a potential target for adulteration. Analytical methods must allow the identification and quantification of meat species to be applicable for the detection of fraudulent labelling. We developed a real-time PCR assay for the authentication of sika deer (Cervus nippon) and products thereof. The primer/probe system amplifies a 71 bp fragment of the kappa-casein precursor gene. Since the target sequence contained only one sika deer-specific base, we introduced a deliberate base mismatch in the forward primer. The real-time PCR assay did not show cross-reactivity with 19 animal and 49 plant species tested. Low cross-reactivity was observed with red deer, fallow deer, reindeer and moose. However, with a ΔCt value of ≥11.79 between sika deer and the cross-reacting species, cross-reactivity will not affect the accuracy of the method. LOD and LOQ, determined by analysing serial dilutions of a DNA extract containing 1% (w/w) sika deer DNA in pig DNA, were 0.3% and 0.5%, respectively. The accuracy was evaluated by analysing DNA mixtures and DNA isolates from meat extract mixtures and meat mixtures. In general, recoveries were in the range from 70 to 130%.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

Single nucleotide polymorphism barcoding of cytochrome c oxidase I sequences for discriminating 17 species of Columbidae by decision tree algorithm

DNA barcodes are widely used in taxonomy, systematics, species identification, food safety, and forensic science. Most of the conventional DNA barcode sequences contain the whole information of a given barcoding gene. Most of the sequence information does not vary and is uninformative for a given group of taxa within a monophylum. We suggest here a method that reduces the amount of noninformative nucleotides in a given barcoding sequence of a major taxon, like the prokaryotes, or eukaryotic animals, plants, or fungi. The actual differences in genetic sequences, called single nucleotide polymorphism (SNP) genotyping, provide a tool for developing a rapid, reliable, and high‐throughput assay for the discrimination between known species. Here, we investigated SNPs as robust markers of genetic variation for identifying different pigeon species based on available cytochrome c oxidase I (COI) data. We propose here a decision tree‐based SNP barcoding (DTSB) algorithm where SNP patterns are selected from the DNA barcoding sequence of several evolutionarily related species in order to identify a single species with pigeons as an example. This approach can make use of any established barcoding system. We here firstly used as an example the mitochondrial gene COI information of 17 pigeon species (Columbidae, Aves) using DTSB after sequence trimming and alignment. SNPs were chosen which followed the rule of decision tree and species‐specific SNP barcodes. The shortest barcode of about 11 bp was then generated for discriminating 17 pigeon species using the DTSB method. This method provides a sequence alignment and tree decision approach to parsimoniously assign a unique and shortest SNP barcode for any known species of a chosen monophyletic taxon where a barcoding sequence is available.

An activity-calibrated chemical standardization approach for quality evaluation of Salvia miltiorrhiza Bge

Low content does not always represent low biopotency and vice versa.

Identification of marine traditional Chinese medicine dried seahorses in the traditional Chinese medicine market using DNA barcoding

Seahorse documented in Chinese pharmacopeia possess important medicinal efficacy and are used as an ingredient in traditional Chinese medicines. The growing international trade threatens the species. DNA barcoding holds a great application potentiality in wildlife conservation and might prevent the illegal trade of threatened species. The COI gene was used to identify seahorse, and nine Hippocampus species were found in the three large traditional Chinese medicines markets of China. All inter-specific genetic variations were larger than 2%. Mean genetic distances between species were 17-fold larger than those within the species. Phylogenetic tree showed that each species clustered in the appropriate branch. All results demonstrated that COI-based barcoding technique could be used to identify seahorse species and played a major role in monitoring the seahorse trade.

Available sustainable alternatives replace endangered animal horn based on their proteomic analysis and bio-effect evaluation

The use of endangered animal products in traditional Chinese medicine (TCM) and other ethno-medicines is culturally widespread across many regions of Asia. In the present study, traditional efficacies of seven types of animal horn including antipyretic, sedative and procoagulant activities were evaluated. Shotgun proteomic analysis was performed on material from horns following separation into soluble and insoluble fractions. Over 200 proteins were identified in each sample using nano LC-MS/MS, and these were classified according to their molecular function and cellular component using principal component analysis (PCA). The results indicated that seven horns showed antipyretic, sedative and procoagulant effect. Proteomic analysis showed that YH and WBH were similar to RH in terms of protein profile, and GH was similar to SAH. In addition, YH and GH were similar to RH in their cellular component classification profile. PCA based on the composition of keratin and keratin-associated proteins showed that constituents of WBH and GH were similar to RH and SAH, respectively. This is the first analysis of the protein content of animal horns used in TCM, and it is effective to substitute the horn of endangered animals with sustainable alternatives from domestic animals.

Application of DNA barcodes in wildlife conservation in Tropical East Asia

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.

From writing to reading the encyclopedia of life

Prologue 'As the study of natural science advances, the language of scientific description may be greatly simplified and abridged. This has already been done by Linneaus and may be carried still further by other invention. The descriptions of natural orders and genera may be reduced to short definitions, and employment of signs, somewhat in the manner of algebra, instead of long descriptions. It is more easy to conceive this, than it is to conceive with what facility, and in how short a time, a knowledge of all the objects of natural history may ultimately be acquired; and that which is now considered learning and science, and confined to a few specially devoted to it, may at length be universally possessed in every civilized country and in every rank of life'. J. C. Louden 1829. Magazine of natural history, vol. 1: This article is part of the themed issue 'From DNA barcodes to biomes'.

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for indels to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indels and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.

Species cross-amplification, identification and genetic variation of 17 species of deer (Cervidae) with microsatellite and mitochondrial DNA from antlers

Strong anthropogenic impact has caused 28 of the currently recognized 55 species of deer (Cervidae) to be listed on the IUCN Red List. Particular threats to vulnerable species include habitat deterioration and hybridization with alien, introduced species. The scarcity of many species has severely hampered genetic analyses of their populations, including the detection of loci for cross-species amplification. Because deer antlers are shed and re-grown annually, antlers offer the possibility for non-invasive genetic sampling of large individual numbers, and may provide material for reference genotyping from historical samples stored in zoos, museums and trophy collections of rare and extinct species/populations. In this paper, we report cross-species amplification of 19 nuclear microsatellite loci and the amplification of 16S mtDNA for barcoding from nearly a third of all deer species worldwide based on high quality DNA extracted from antler bone up to 40 years old. Phylogenetic analysis based on mtDNA of seventeen species and five subspecies corroborate previously published phylogenetic data, thus confirming the specific resolution of the DNA extraction methodology.

Biological ingredient analysis of traditional Chinese medicine preparation based on high-throughput sequencing: the story for Liuwei Dihuang Wan

Although Traditional Chinese Medicine (TCM) preparations have long history with successful applications, the scientific and systematic quality assessment of TCM preparations mainly focuses on chemical constituents and is far from comprehensive. There are currently only few primitive studies on assessment of biological ingredients in TCM preparations. Here, we have proposed a method, M-TCM, for biological assessment of the quality of TCM preparations based on high-throughput sequencing and metagenomic analysis. We have tested this method on Liuwei Dihuang Wan (LDW), a TCM whose ingredients have been well-defined. Our results have shown that firstly, this method could determine the biological ingredients of LDW preparations. Secondly, the quality and stability of LDW varies significantly among different manufacturers. Thirdly, the overall quality of LDW samples is significantly affected by their biological contaminations. This novel strategy has the potential to achieve comprehensive ingredient profiling of TCM preparations.

Authentication of animal signatures in traditional Chinese medicine of Lingyang Qingfei Wan using routine molecular diagnostic assays

Lingyang Qingfei Wan produced by Beijing TongRenTang is a long-standing and popular medicine in China and international pharmaceutical markets. Concerns continue to be raised about the legality of usage of saiga antelope, which was defined as endangered species by Convention on International Trade in Endangered Species of Wild Fauna and Flora legislation and internal legislation in China. Therefore, the alternative pill in which substitutes saiga antelope with goat in the formula of Lingyang Qingfei Wan was developed. In order to authenticate the origin of animal contents in Lingyang Qingfei Wan and its alternative pill, molecular diagnostic assay was utilized by mtDNA polymorphism analysis. Four universal primer pairs containing mtDNA 12SrRNA, 16SrRNA, cytochrome b gene and cytochrome oxidase I were employed to obtain species-specific sequences of saiga antelope and goat, and multiple species-specific primer pairs for saiga antelope and goat were used to identify the animal origin in patent pills according to nucleotide polymorphisms between the two species. In additions, alternative techniques were attempted surrounding dilemmas of low concentration of target DNAs and presence of PCR-inhibitory substances in organic ingredients within complex pill. Results revealed that all species-specific primers could be successfully used for authentication of animal origin within complex pill, and sample preprocessing was critical during experimental manipulation. Internal positive control was an efficient and cost-effective way to assist in monitoring the potential interference from inhibitory substances which existed in the highly processed pills.

Promotion of quality standard of herbal medicine by constituent removing and adding

To identify major active constituents and measure their levels in a typical medicinal herb-Rhizoma coptidis, we applied the concept of removing and adding, taking inspiration from functional genetic methods. As this herb has bacteriostatic properties and is used to treat bacterial diarrhea, we examined the effects of individual constituents (berberine, palmatine, coptisine, epiberberine, jateorrhizine and columbamine) on the growth of Shigella dysenteriae with microcalorimetry. The removing and adding procedures revealed that berberine and coptisine were the main antibacterial constituents of R. coptidis, with bacteriostatic activities of 54.10% and 39.75%, respectively. The relative levels of berberine and coptisine in R. coptidis were 8.08%-31.92% and 4.05%-14.45%, respectively. On the basis of whole effect, the method of constituents removing and adding, coupled with a bioassay, is a useful strategy to identify the active constituents and measure their levels in herbal medicines, which may provide reference to other natural products.