Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies.

The opium poppy acts as an important natural pain reliever but is also responsible for increased rates of severe drug abuse and addiction owing to its characteristic psychoactive effect. Non-medical illicit use of the poppy plant is markedly increasing worldwide, thereby highlighting the need for a robust species identification strategy. In this study, we identified SNPs within the region of two universal DNA barcodes, matK (maturase K) and the trnL-trnF (tRNA-Leu [3'exon]-tRNA-Phe [exon] intergenic spacer, that are forensically applicable for distinguishing opium poppy species based on a genetic analysis of 164 samples of family Papaveraceae obtained from locations spanning Jeolla-do and Jeju Island, Republic of Korea. A comparative analysis of the DNA barcode sequences for two narcotic types of the Papaver species (Papaver somniferum, Papaver somniferum subs. setigerum) to eight non-narcotic species revealed three unique nucleotide substitution events. Newly identified SNPs were located at position 255 of matK and at positions 305 and 306 of trnL-trnF; the narcotic species contained C, A, and T, whereas non-narcotic species contained T, G, and C at these positions. Phylogenetic analysis demonstrated that newly identified SNPs, which we named PsMAT255 and PsLF305/306, could be used to clearly differentiate between the narcotic and non-narcotic types of Papaver species based on the patterns of nucleotide variation. These results indicate that the nucleotide differences between the narcotic and non-narcotic species may influence genetic markers. We, therefore, developed a novel SNP-based allelic genotyping assay using the RT-PCR system that can reliably differentiate the narcotic type of the Papaver species. In summary, our findings suggest that the newly identified species-specific SNPs of both matK and trnL-trnF can be used as identification markers of narcotic Papaver species. Furthermore, a newly developed TaqMan allelic discrimination assay may be used as a practically applicable diagnostic method to survey several illicit narcotic specimens carrying the type-specific SNP.

A new minisatellite VNTR marker, Pscp1, discovered for the identification of opium poppy.

Opium poppy, a member of the Papaveraceae family, is an ancient herbaceous plant and well-known medical resource in the pharmaceutical industry. However, opium poppies are grown worldwide for producing illicit drugs, significantly increasing the incidence of narcotic drug abuse. Since the narcotic poppy has not yet been genetically investigated, we characterized a novel variable number tandem repeat (VNTR) marker of forensically important poppy species based on the genetic analysis of 164 samples collected from two locations spanning the Jeolla province and Jeju island of South Korea. Comparing analysis of the chloroplast (cp) genome sequences for four representative species of Papaver (Papaver somniferum, Papaver somniferum subs. setigerum, Papaver orientale, and Papaver rhoeas) revealed a unique region with 1-3 repeats for 16 nucleotide motifs in the genome inverted repeat A (IRA, positions 128,651 to 128,698) region. For 16 nucleotide motifs, 3 repeats were found in P. somniferum, and 2 repeats were found in P. somniferum subs. setigerum. Therefore, 10 known and the 133 unknown, seized Papaver species were compared to determine whether the species could be identified via variations in the repeat units. The sizes of a novel VNTR ranged from 181 to 252 bp between the species. Phylogenetic analysis confirmed that a novel VNTR, which we named Pscp1, could clearly distinguish between the narcotic and non-narcotic types of Papaver species based on the patterns of sequence variation. Interestingly, we found that Pscp1 could also distinguish between P. somniferum and P. somniferum subs. setigerum. The regions of eight non-narcotic species displayed similar patterns and also differences were found due to the nucleotide substitution and deletion events. The structural differences of Pscp1 were observed within the two narcotic species or between the narcotic and non-narcotic species, suggesting that these variations may act as a genetic marker. We, therefore, developed a new Pscp1 PCR-capillary electrophoresis (CE) method that can reliably identify the narcotic type of Papaver species. Taken together, our findings suggest that the newly developed Pscp1 can be used as an identification marker of opium poppy, and establish that the Pscp1 genotyping method by PCR-CE is an effective primary screening tool that can also contribute to species discrimination in the field of forensic diagnosis and applications.

Construction of an in-house allelic ladder for Canine Genotypes™ Panel 2.1 Kit.

Dogs (Canis lupus familiaris) are among the most common companion animals in the Republic of Korea. Recently, there have been many criminal cases of dog cruelty, injury, and theft, among others. This has increased the importance of dog-related biological evidence at crime scenes. The National Forensic Service of the Republic of Korea conducts short tandem repeat (STR) analysis using the Thermo Scientific Canine Genotypes™ Panel 2.1 Kit (Canine Kit) to identify individual dogs through forensic analysis. The Canine Kit was developed as a forensic STR kit for the identification of individual dogs. However, an allelic ladder was neither developed nor included in the commercial kit, leaving an issue of accurate genotyping. Primer details for the 18 markers used in the Canine Kit are proprietary information, and thus, unavailable to end-users. In this study, an allelic ladder was constructed with 160 fragments by combining 158 fragments of STR alleles obtained by nested PCR and two fragments artificially obtained from the sex-determination marker. By including the new allelic ladder in analysis of samples amplified with the Canine Kit, the accuracy and reliability of data analysis were improved. Application of this allelic ladder would be helpful for interlaboratory data sharing and standardization of canine genotype databases.

Novel C-arm based planning spine surgery robot proved in a porcine model and quantitative accuracy assessment methodology.

BACKGROUND: We assessed pedicle screw accuracy utilizing a novel navigation-based spine surgery robotic system by comparing planned pathways with placed pathways in a porcine model. METHODS: We placed three mini screws per vertebra for accuracy evaluation and used a reference frame for registration in four pigs (46 screws in 23 vertebrae). We planned screw paths and performed screw insertion under robot guidance. Using C-arm and CT images, we evaluated accuracy by comparing the 3D distance of the placed screw head/tip from the planned screw head/tip and 3D angular offset. RESULTS: Mean registration deviation between the preoperative 3D space (C-arm) and postoperative CT scans was 0.475 ± 0.119 mm. The average offset from preoperative plan to final placement was 4.8 ± 2.0 mm from the head (tail), 5.3 ± 2.3 mm from the tip and 3.9 ± 2.4 degrees of angulation. CONCLUSIONS: Our spine surgery robot showed good accuracy in executing an intended planned trajectory and screw path. This faster and more accurate robotic system will be applied in future studies, first in cadavers and subsequently in the clinical field.

Single Nucleotide Polymorphism Assay for Genetic Identification of Lophophora williamsii.

Lophophora is a member of the Cactaceae family, which contains two species: Lophophora williamsii and L. diffusa. Lophophora williamsii is an illegal plant containing mescaline, a hallucinogenic alkaloid. In this study, a novel method based on a single nucleotide polymorphism (SNP) assay was developed for identifying L. williamsii; this assay reliably detects SNPs within chloroplast DNA (rbcL, matK, and trnL-trnF IGS) and was validated for identifying Lophophora and L. williamsii simultaneously. The chloroplast DNA sequences from four L. williamsii and three L. diffusa plants were obtained and compared using DNA sequence data from approximately 300 other Cactaceae species available in GenBank. From this sequence data, a total of seven SNPs were determined to be suitable for identifying L. williamsii. A multiplex assay was constructed using the ABI PRISM® SNaPshot™ Multiplex Kit (Applied Biosystems, Forster City, CA) to analyze species-specific SNPs. Using this multiplex assay, we clearly distinguished the Lophophora among 19 species in the Cactaceae family. Additionally, L. williamsii was distinguished from L. diffusa. These results suggest that the newly developed assay may help resolve crimes related to illegal distribution and use. This multiplex assay will be useful for the genetic identification of L. williamsii and can complement conventional methods of detecting mescaline.

The identification of elephant ivory evidences of illegal trade with mitochondrial cytochrome b gene and hypervariable D-loop region.

DNA analysis of elephant ivory of illegal trade was handled in this work. The speciation and geographical origin of nine specimens of elephant ivory were requested by the police. Without national authorization, the suspect had purchased processed ivory seals from January to May, 2011 by Internet transactions from a site in a neighboring country. The DNA of decalcified ivory evidences was isolated with QIAGEN Micro Kit. The total 844-904 base pair sized sequences of mitochondrial cytochrome b and D-loop region could be acquired using direct sequencing analysis. They were compared with the sequences registered in GenBank. It was confirmed that most specimens were likely from African forest elephants (Loxodonta cyclotis), one from African savanna elephant (Loxodonta africana) and one from Asian elephant (Elephas maximus). Analysis of the mitochondrial hypervariable D-loop region sequence of elephants verified that one African savanna elephant might be from South Africa and one Asian elephant from Laos. Cytochrome b and D-loop region located in the mitochondrial DNA resulted in the successful determination of elephant DNA from nine processed ivory specimens.

Cap-independent protein translation is initially responsible for 4-(N-methylnitrosamino)-1-(3-pyridyl)-butanone (NNK)-induced apoptosis in normal human bronchial epithelial cells.

Evidences show that eukaryotic mRNAs can perform protein translation through internal ribosome entry sites (IRES). 5'-Untranslated region of the mRNA encoding apoptotic protease-activating factor 1 (Apaf-1) contains IRES, and, thus, can be translated in a cap-independent manner. Effects of changes in protein translation pattern through rapamycin pretreatment on 4-(methylnitrosamino)-1-(3-pyridyl)-butanone(NNK, tobacco-specific lung carcinogen)-induced apoptosis in human bronchial epithelial cells were examined by caspase assay, FACS analysis, Western blotting, and transient transfection. Results showed that NNK induced apoptosis in concentration- and time-dependent manners. NNK-induced apoptosis occurred initially through cap-independent protein translation, which during later stage was replaced by cap-dependent protein translation. Our data may be applicable as the mechanical basis of lung cancer treatment.

Four-week inhalation toxicity, mutagenicity and immunotoxicity studies of Keum-Yeon-Cho (NosmoQ), tobacco substitute composition, in mice.

Safety of Keum-Yeon-Cho (NosmoQ), a tobacco substitute composition, was evaluated in terms of acute- and 4 weeks repeated-inhalation toxicity, mutagenicity, and immunotoxicity using Balb/c mice. The air inside the inhalation chamber was collected and analyzed by GC-MS. In acute inhalation toxicity test, male and female mice were exposed to 40 Keum-Yeon-Cho cigarettes. The 50% lethal concentration (LC(50)) of NosmoQ was considered to be much higher than 40 cigarettes in both sexes. In 4-week repeated inhalation toxicity test, male and female mice were exposed for 6 h/day, 5 days/week for 4 weeks to 10 and 20 cigarettes per day, while control mice were exposed to filtered air. Our data indicated that no observed adverse effect level (NOAEL) of Keum-Yeon-Cho should be over 20 cigarettes per day. Results of Salmonella typhimurium reversion assay with/without histidine moiety, in vivo chromosomal aberration and in vivo micronucleus assays using mouse bone marrow cells revealed that Keum-Yeon-Cho has no mutagenicity. Evaluation of peripheral cellular immunity of mice treated with Keum-Yeon-Cho using in vitro lymphocyte proliferation assay showed no significant difference in mean stimulation index (SI) between mice exposed to Keum-Yeon-Cho and control mice. Mean CO concentrations and total particulate matter contents of 10 and 20 cigarettes were 21.1±1.23 and 40.7±1.21 ppm (mean±S.D., n=5), and 25.7±3.09 and 59.0±4.0 mg dry weight (mean±S.D., n=5), respectively. Although at negligible concentration (less than ppb level) several polycyclic aromatic hydrocarbons (PAHs) were also detected, these results indicate that NosmoQ has no toxic effect on mice.