A Study of PCR Inhibition Mechanisms Using Real Time PCR*,†

Abstract: In this project, real time polymerase chain reaction (PCR) was utilized to study the mechanism of PCR inhibition through examination of the effect of amplicon length, melting temperature, and sequence. Specifically designed primers with three different amplicon lengths and three different melting temperatures were used to target a single homozygous allele in the HUMTH01 locus. The effect on amplification efficiency for each primer pair was determined by adding different concentrations of various PCR inhibitors to the reaction mixture. The results show that a variety of inhibition mechanisms can occur during the PCR process depending on the type of co‐extracted inhibitor. These include Taq inhibition, DNA template binding, and effects on reaction efficiency. In addition, some inhibitors appear to affect the reaction in more than one manner. Overall we find that amplicon size and melting temperature are important in some inhibition mechanisms and not in others and the key issue in understanding PCR inhibition is determining the identity of the interfering substance.     

Determining the Source of Equine Bloodstains by Dinucleotide Repeats*

Abstract: A novel multiplex of independent dinucleotide tandem repeat (DTR) loci was previously described that is capable of not only discriminating human and equine DNA, but of identifying a single equine source. We report a case in which a bloodstained syringe and two needles were found during inspection of a barn by inspectors of the Pennsylvania Racing Commissions. Using the multiplex and single‐locus detection, all 21 equine DTR markers were detected in a suspect horse and two evidence samples, indicating the evidence samples came from the suspect animal. Only six markers were detected in the third evidence sample because the volume of blood was limited. Following whole‐genome amplification and single‐locus PCR, the third evidence sample detected a total of 17 markers and the likelihood of identity (probability from suspect horse/probability from a random pacer) was 7.0 × 10⁶. The DTR multiplex has some technical limitations, but it is already practical for casework.     

Investigation of Reproducibility and Error Associated with qPCR Methods using Quantifiler® Duo DNA Quantification Kit*

Abstract: Reproducibility of quantitative PCR results is dependent on the generation of consistent calibration curves via accurate volume transfers and instrument performance. A review of 14 standard curves, using two different QuantDuo^® standard DNA lots, showed variability of cycle threshold values between assays were larger than those of the Internal PCR Control (IPC). This prompted a set of experiments designed to determine the source of variability. Results showed that error introduced during DNA addition to the plate resulted in little variation. A comparison of seven independent series demonstrated cycle threshold variation between dilutions was larger than the variation expected from repeated samples. Modeling the influence of pipette errors on dilution series accuracy indicated that a more rigorous approach to external calibration curve production is required and showed that improvement in calibration curve stability is expected if the pipette conditions are carefully chosen and/or a single validated curve is utilized as the calibrator.     

Multicolor Real-Time PCR Genotyping of ABO System Using Displacing Probes

Abstract:  Rapid and informative ABO genotyping has become increasingly popular in forensic use. We developed a multiplex real-time polymerase chain reaction (PCR) approach to genotype ABO major groups and subgroups. Seven differently fluorophor-labeled displacing probes for O¹(261delG), A(261G), A(796C/803C), B(796A/803C), O² (802G>A), A² (1059delC), and A² (1009A>G) were combined in one or two PCRs to determine either ABO major groups or subgroups. The method correctly detected 13 reference DNA samples. A blind test of 237 samples resulted in complete agreement with their phenotypes, and 110 of these 237 samples as well as with PCR-SSP method. The whole analysis could be finished in less than 100 min at substantially low material cost and the template DNA ranging from 0.16 to 500 ng per reaction could be quantitatively detected. Despite the limited informativeness of ABO genotyping, the developed methods could find application in rapid and inexpensive screening of forensic settings.     

Study: The Lack of Significant Association of the Catechol-O-Methyl Transferase (COMT) Gene Polymorphism in Violent Offenders with Mental Retardation

Abstract:  Little is known about criminality of cognitively impaired people and also there have been no reports on the relationship between catechol- O -methyl transferase (COMT) and committed Mental Retardation (MR) subjects. In the present study, the association between committed (violent offences) MR subjects and genetic variants of COMT were investigated by using polymerase chain reaction and based restriction fragment length polymorphism methods. During 6 years of follow-up, 36 violent offenders with mild MR were investigated. Thirty-six control volunteers were included in the study as a control group. H/L polymorphism of the COMT gene was investigated in these two groups. In conclusion, the COMT gene genotype distribution and allele frequency is not significantly different between the two groups ( p  > 0.05). This result suggests that the H/L polymorphism of the COMT gene does not show an association with the potential of "commits-violent offense" of Turkish subjects with mental retardation, compared with control group.     

Evaluation of Tamm‐Horsfall Protein and Uroplakin III for Forensic Identification of Urine

Abstract: In this study, Tamm‐Horsfall protein (THP), a major component of urinary protein, and uroplakin III (UPIII), a transmembrane protein widely regarded as a urothelium‐specific marker, were evaluated for forensic identification of urine by ELISA and/or immunohistochemistry. THP was detected in urine, but not in plasma, saliva, semen, vaginal fluid, or sweat by the simple ELISA method developed in this study. In addition, most aged urine stains showed positive results. The urine specificity of THP was confirmed by gene expression analysis. Therefore, as reported previously, ELISA detection of THP can be used as a presumptive test for urine identification. UPIII was specific for immunohistochemical staining of cells in centrifuged precipitate of urine. However, ELISA and RT‐PCR for UPIII were not specific for urine. UPIII may be applicable for forensic urine identification by immunohistochemistry.     

InDel_typer30:用于中国5个主要民族DNA鉴定的多重PCR系统

目的采用插入/缺失(Insertion/Deletion,InDel)多态性遗传标记,建立一种可用于中国汉族、回族、维吾尔族、蒙古族、藏族5个主要民族法医DNA鉴定的多重PCR系统。方法采用人类基因组浏览器和dbSNP数据库筛选具有高度遗传多态性的人类常染色体InDel标记,采用Primer 3软件设计多重PCR引物,通过复合荧光标记系统建立多重PCR扩增体系,采用该体系对汉、回、维、蒙、藏5个民族进行多态性调查。结果成功建立了一个包含30个InDel位点和Amelogenin性别鉴定位点的复合荧光多重PCR扩增体系,命名为InDel_typer30。多态性调查显示这30个InDel位点在上述5个主要民族中均呈高度遗传多态性,平均期望杂合度分别为:0.464、0.460、0.453、0.466和0.469,平均个人识别率分别为:0.595、0.585、0.586、0.589和0.595。该系统在5个民族中的累积个人识别率(CDP)均达到0.999999999996以上。结论 InDel_typer30是一种适用于中国汉、回、维、蒙、藏5个主要民族的法医DNA鉴定系统。     

小鼠肝组织GAPDH mRNA降解与死亡时间关系

目的探讨小鼠在不同的死亡方式下肝组织管家基因甘油醛-3-磷酸脱氢酶(glyceraldehyde-3-phosphate dehydrogenase,GAPDH)mRNA降解与死亡时间(postmortem interval,PMI)的关系。方法将60只NIH小鼠分别采用窒息法和断颈法处死,分别置于10℃和25℃温控系统内,利用两步法RT-PCR技术和核酸蛋白测定仪检测小鼠肝组织中GAPDH mRNA在死后0～48h的降解情况。结果在10℃温控系统内的小鼠死后0～48h及25℃温控系统内的小鼠死后0～36h肝组织均可检测到GAPDH mRNA,且其扩增产物呈规律性下降趋势。结论小鼠死亡后肝组织GAPDH mRNA降解与PMI呈负相关,可为PMI推断提供一种新的观测指标。     

“三鹿奶粉”系列案定性探疑

"三鹿奶粉"系列案涉及的、含有三聚氰胺的所谓"蛋白粉"是有害物质而不是有毒物质,添加者故意将其添加到原牛奶中并卖给"三鹿集团"的行为,在性质上属于生产、销售有害食品。制造并销售"蛋白粉"的行为不应当如法院判决的那样构成以危险方法危害公共安全罪,而应当与添加者的行为构成生产、销售有害食品罪的"连锁共犯"。"三鹿集团"的行为,应当以2008年8月1日检测报告出具明确结论为界分为两个阶段:在前一阶段,其直接负责的主管人员构成重大责任事故罪,在后一阶段,"三鹿集团"的行为在性质上属于生产、销售有害食品,与生产销售伪劣产品罪存在法条竞合;根据《刑法》第149条关于择一重罪处罚的规定,应按第140条的规定构成生产、销售伪劣产品罪;对"三鹿集团"直接负责的主管人员两个阶段的罪行应当数罪并罚。     

Detection and Identification of Psilocybe cubensis DNA Using a Real‐Time Polymerase Chain Reaction High Resolution Melt Assay,

Psilocybe cubensis, or “magic mushroom,” is the most common species of fungus with psychedelic characteristics. Two primer sets were designed to target Psilocybe DNA using web‐based software and NBCI gene sequences. DNA was extracted from eighteen samples, including twelve mushroom species, using the Qiagen DNeasy^® Plant Mini Kit. The DNA was amplified by the polymerase chain reaction (PCR) using the primers and a master mix containing either a SYBR^® Green I, Radiant? Green, or LCGreen Plus^® intercalating dye; amplicon size was determined using agarose gel electrophoresis. The PCR assays were tested for amplifiability, specificity, reproducibility, robustness, sensitivity, and multiplexing with primers that target marijuana. The observed high resolution melt (HRM) temperatures for primer sets 1 and 7 were 78.85 ± 0.31°C and 73.22 ± 0.61°C, respectively, using SYBR^® Green I dye and 81.67 ± 0.06°C and 76.04 ± 0.11°C, respectively, using Radiant? Green dye.