运用分子生物学方法鉴定生物检材种属的研究进展

生物检材的种属鉴定在法医、海关和食品行业中均有较多应用。当前,用于鉴定种属的分子生物学方法发展迅猛。本文结合文献,从用于种属鉴定的目的基因及筛选标准、主要分子生物学方法、鉴定存在的主要问题等方面进行综述,并结合Real-time PCR和SNP技术对未来种属鉴定的发展方向进行了预测。     

Utilization of paw prints for species identification in the Canidae family

In this report, the bodies of six skinned animals were submitted to the Oklahoma Animal Disease Diagnostic Laboratory for necropsy examination as authorities were concerned these animals were domestic dogs. Given the condition of the animals, identification of the animal species could not be based on traditional physical characteristics such as size, fur characteristics, and ear characteristics. The paw prints from these animals were characterized based on size, heel pad architecture, and claw characteristics. The length of the forepaws measured 3-3.25 in., four toes were observed and only the claws of digits 3 and 4 were identified, and the heel pad had a pronounced three-lobed rear margin. The rear margin of the heel pad of the hind foot was of circular shape with two slightly forward-pointing crescents laterally. Based on the features of the paw print it was determined that the animals necropsied were coyotes.     

Resurrecting the Dodo: Positive control DNA for species identification

Positive controls are necessary standards for inclusion in forensic tests. When working as expected they demonstrate that methods have been applied correctly, and therefore results can be interpreted with confidence. However, the requirement for positive controls can also introduce problems. For species identification in wildlife DNA forensic testing, it is possible that the DNA sequence of the case sample will be a 100% match to the positive control. Whilst clear results for negative controls will indicate that cross-contamination is unlikely, it would be preferable to have a positive control that will not appear in casework. In addition, for many endangered species, obtaining positive control DNA for species-specific testing can be problematic. Here we present a simple method to use artificially generated positive control DNA from the extinct Dodo, Raphus cucullatus, for four species-identification tests run routinely in UK wildlife forensic casework.     

The analysis of biological samples from crime scene for a future human DNA profile confrontation. Effects of presumptive test reagents on the ability to obtain STR profiles for human identification

Because of the increase of evidence of blood stains, that have been washed or cleaned in an attempt to mask the analysis of DNA profiles, there is also an increase in the use of presumptive tests on samples sent to laboratories. Some of the presumptive tests, used to identify blood and semen stains, could potentially affect the recovery of high molecular weight DNA from the samples, or extinguish them, especially those already present in small quantities. After the presumptive tests, often these samples are discarded. This study aimed to examine the possibility of obtaining a DNA profile from samples submitted for presumptive testing and cleaned with bleaches with and without chlorine. Two different protocols were conducted: (a) A unique sample of human blood in natura (5 μL), already typed through the DNA techniques with the genetic profile previously known (control), was distributed onto cotton fabrics and dried at room temperature. Four samples of fabric were macerated in saline solution and Coombs serum and then stored for three months (room temperature and freezer −20 °C). (b) Another sample of human blood, type A, in natura, already typed through the techniques of DNA (control) was used. Aliquots of 200 μL were distributed in: cotton, denim and synthetic fabric. The samples were dried at room temperature for 24 h. The blood stains in those fabrics (cotton, denim and synthetic) were then divided into three groups: unwashed, cleaned with chlorine bleach and cleaned with chlorine bleach and soap powder. The samples were again dried at room temperature for 24 h, before the use of luminol. The DNA were extracted with Chelex 100 and amplified with the Identifiler Kit (Applied Biosystems). The blood stains exposed to saline and Coombs serum had DNA profiles consistent with untreated samples (controls). This result shows that the experts should keep and store the samples treated with saline and Coombs serum for future DNA confrontation when necessary. Also discussed in this paper the pattern of blood stains after washing with bleaching solutions, as well as the quantity of DNA obtained from these samples.     

The harms of human trafficking: demonstrating the applicability and value of a new framework for systematic,empirical analysis

This article uses human trafficking in Belgium to test a newly developed framework for assessing the harms of crime that has been applied previously to cocaine trafficking in the same country. We chose this criminal activity because of its policy relevance and to address apparent needs for systematic, evidence-based analysis. The framework uses quantitative and qualitative evidence to assess harms to individuals, private-sector entities, and others and to establish crime control priorities. The assessment process models the activity, evaluates the severity and incidence of harms, ranks priorities, and considers causality. We highlight three findings. First, trafficking victims can experience catastrophic harms, but the overall dimensions of human trafficking in Belgium appear to be modest. Second, the evidence suggests significant recent declines in the degree of exploitation and use of violence. Third, most harms to individual victims result directly from the activity, which sets it apart from other forms of trafficking.     

Standardization of Histological Procedures for the Detection of Toxic Substances by Immunohistochemistry in Dipteran Larvae of Forensic Importance

Immunohistochemistry (IHC) technique is an alternative toxicological analysis to detect drugs in insects of forensic importance, but it requires thorough histological procedures. In this study, we tested different fixatives—phosphate‐buffered paraformaldehyde 4% (PP), Carnoy's fluid (CF), Kahle's solution (KS), ethanol in different concentrations, and ethanol associated to PP and CF, time of fixation and histological processes for dipteran larvae's tissue, aiming to develop a sample preparation protocol for IHC application. A suitable fixation was achieved using PP for 12 and 24 h, CF for 3 h, 70% ethanol for 19 days, and 70% ethanol/CF for 2 h/3 h. Postfixation using negative pressure, two immersions in xylene for 30 min each, and one in xylene plus paraffin for 45 min increased tissue preservation. An immunohistochemical test for cocaine detection was performed using monoclonal benzoylecgonine antibody from mouse, peroxidase‐conjugated anti‐mouse IgG and visualized by 3,3′‐diaminobenzidine method showed these histological procedures didn't compromise antigenicity.     

线粒体16SrRNA和Cytb基因复合扩增进行种属鉴定

目的 建立一种用于种属鉴定的线粒体DNA16SrRNA基因和细胞色素b基因荧光标记复合扩增检测体系。方法 利用引物设计软件Primer 5．0对mtDNA序列的16SrRNA基因和细胞色素b基因各设计一对引物,建立复合扩增体系,分别扩增人和牛、猪、狗、鸡、草鱼5种常见动物,用310遗传分析仪对产物进行分析。结果 人和5种动物DNA扩增产物均出现两个峰。Cytb通用引物的扩增产物为人与动物的共有峰,为358bp;16SrRNA基因的扩增产物为人与动物间存在位置差异的特异峰,位于231～256bp之间。结论 该复合扩增体系可以明确区分人和5种动物样本,可用于种属鉴定。     

线粒体16srRNA和ND4基因在种属鉴定中的应用研究

目的构建一种用于种属鉴定的线粒体DNA(m tDNA)16 srRNA和ND4基因荧光标记复合扩增检测体系。方法利用引物设计软件(Prim er 5)对两个m tDNA序列ND4基因和16 srRNA基因设计两对引物,每对引物中的一条在5’端标记荧光素(6-FAM)。按传统复合扩增技术建立复合扩增体系,用AB I PR ISM 310基因分析仪对产物进行分析。结果人类DNA扩增产物出现两个峰,片段大小分别为110bp的人类特异片段和149bp的人与动物共有片段,而动物DNA扩增产物出现一个峰,片段大小为149bp。对30个实验室存放5~15年的陈旧人血痕也能明确判断其种属来源。结论该体系可以明确区分人源性生物检材与其它常见动物样本,对实验室长期存放的陈旧检材也具有较好的检测能力。     

Differences among species in compact bone tissue microstructure of mammalian skeleton: use of a discriminant function analysis for species identification

In order to develop an identification key for distinguishing between several mammalian species, bone structure of their compact bone tissue was analyzed using qualitative and quantitative characteristics. Ninety femora of adult male humans, pigs, cows, sheep, rabbits, and rats were studied. The average area, perimeter, minimum, and maximum diameter of 1863 Haversian canals and 1863 secondary osteons were measured using a digital image device. The observed data were first used to evaluate inter- and intraspecies diversity. After that, we applied a discriminant function analysis for differentiation of the species by these variables. Classification functions for investigated species give cross-validated correct classification rates for 76.17% of cases. This percentage value can be increased by integrating conclusions from the qualitative analysis.     

不同染色组织切片及不同组织固定方法对检测STR基因座的影响

目的探讨不同染色组织切片及不同组织固定方法对DNA检验的影响。方法采用Chelex100法及浓缩纯化方法提取DNA,PCR扩增后310型遗传分析仪检测。结果福尔马林固定4天以内或70%乙醇、无水乙醇分别固定1年及15年的HE染色切片可以检见Amel及9个STR基因座。PTAH等5种特殊染色未能检出相应基因座DNA谱带。结论70%乙醇或无水乙醇固定组织,石腊包埋组织及HE染色切片可以作为DNA?STR检验鉴定的样本材料。     

Development of a DNA-based macroarray for the detection and identification of Amanita species

A DNA-based macroarray was designed to quickly and accurately identify certain Amanita mushroom specimens at the species level. The macroarray included probes for Amanita phalloides and Amanita ocreata, toxic species responsible for most mushroom poisonings, and Amanita lanei and Amanita velosa, edible species sometimes confused with toxic species, based on sequences of the highly variable internal transcribed spacer (ITS) region of rDNA. A cryptic species related to A. ocreata and one related to A. lanei, identifiable by ITS sequences, were also included. Specific multiple oligonucleotide probes were spotted onto nylon membranes and the optimal hybridization temperatures were determined. The Amanita DNA array was highly specific, sensitive (0.5 ng DNA/μL and higher were detected), and reproducible. In two case studies, the method proved useful when only small amounts of mushroom tissue remained after a suspected poisoning. An identification could be completed in 12 h.     

Validation of the barcoding gene COI for use in forensic genetic species identification

The application of forensics to wildlife crime investigation routinely involves genetic species identification based on DNA sequence similarity. This work can be hindered by a lack of authenticated reference DNA sequence data resulting in weak matches between evidence and reference samples. The introduction of DNA barcoding has highlighted the expanding use of the mtDNA gene, cytochrome c oxidase I (COI), as a genetic marker for species identification. Here, we assess the COI gene for use in forensic analysis following published human validation guidelines. Validation experiments investigated reproducibility, heteroplasmy, mixed DNA, DNA template concentration, chemical treatments, substrate variation, environmental conditions and thermocycling parameters. Sequence similarity searches using both GenBank BLASTn and BOLD search engines indicated that the COI gene consistently identifies species where authenticated reference sequence data exists. Where misidentification occurred the cause was attributable to either erroneous reference sequences from published data, or lack of primer specificity. Although amplification failure was observed under certain sample treatments, there was no evidence of environmentally induced sequence mutation in those sequences that were generated. A simulated case study compared the performance of COI and cytochrome b mtDNA genes. Findings are discussed in relation to the utility of the COI gene in forensic species identification.     

A molecular genetic approach for species identification of mammals and sex determination of birds in a forensic case of poaching from South Korea

DNA-based analysis was performed using partial mitochondrial cytochrome b genes of five mammalian specimens and Chromo-Helicase-DNA-binding (CHD) genes of five pheasants to determine whether specimens were from illegally hunted animals. Mammalian specimens were identified as being those of horse, roe deer, and cow through gene amplification using cytb981f and cytb981r primer set and sequencing. CHD genes were revealed to be those of three male and two female pheasants through polymerase chain reaction amplification. Because hunting of roe deers and female pheasants is prohibited in Korea, these results provided forensic evidences of illegal wild animal hunting.     

mtDNA—HVⅠ和细胞色素b片段的复合扩增及其法医学应用

目的探讨复合扩增mtDNA D环HV I和细胞色素b片段进行种属鉴定和个体识别的方法及mtDNA-HV I多态性。方法用两对引物同步扩增HV I片段与细胞色素b片段,银染显带检测扩增产物,ABI377测序仪及荧光测序技术分析扩增产物序列多态性。结果人类有279bp,358bp两条带,动物只有358bp一条带。通过对131例随机广东汉族人群个体进行mtDNA控制区(15997～16236))序列测定统计,得出此区域的序列多态性。共发现69个位点变异,平均每个个体存在2.679个碱基突变,检出67个单倍型,基因多样性为97.92％。结论mtDNA控制区(15997—16236)具有较高的序列多态性。为良好的个体识别标记。复合扩增mtDNA D环HV I与细胞色素b片段进行测序分析可以同步进行种属鉴定和个体识别。     

Routine forensic use of the mitochondrial 12S ribosomal RNA gene for species identification

Since July 2004, Mitotyping Technologies has been amplifying and sequencing a approximately 150 base pair fragment of mitochondrial DNA (mtDNA) that codes for 12S ribosomal RNA, to identify the species origin of nonhuman casework samples. The approximately 100 base pair sequence product is searched at http://www.ncbi.nlm.nih.gov/BLAST and the species match is reported. The use of this assay has halved the number of samples for which no mtDNA results are obtained and is especially useful on hairs and degraded samples. The availability of species determination may aid forensic investigators in opening or closing off lines of inquiry where a highly probative but challenging sample has been collected.     

The effectiveness of various strategies to improve DNA analysis of formaldehyde-damaged tissues from embalmed cadavers for human identification purposes

Formalin-fixed tissues provide the medical and forensic communities with alternative and often last resort sources of DNA for identification or diagnostic purposes. The DNA in these samples can be highly degraded and chemically damaged, making downstream genotyping using short tandem repeats (STRs) challenging. Therefore, the use of alternative genetic markers, methods that pre-amplify the low amount of good quality DNA present, or methods that repair the damaged DNA template may provide more probative genetic information. This study investigated whether whole genome amplification (WGA) and DNA repair could improve STR typing of formaldehyde-damaged (FD) tissues from embalmed cadavers. Additionally, comparative genotyping success using bi-allelic markers, including INDELs and SNPs, was explored. Calculated random match probabilities (RMPs) using traditional STRs, INDEL markers, and two next generation sequencing (NGS) panels were compared across all samples. Overall, results showed that neither WGA nor DNA repair substantially improved STR success rates from formalin-fixed tissue samples. However, when DNA from FD samples was genotyped using INDEL and SNP-based panels, the RMP of each sample was markedly lower than the RMPs calculated from partial STR profiles. Therefore, the results of this study suggest that rather than attempting to improve the quantity and quality of severely damaged and degraded DNA prior to STR typing, a more productive approach may be to target smaller amplicons to provide more discriminatory DNA identifications. Furthermore, an NGS panel with less loci may yield better results when examining FD samples, due to more optimized chemistries that result in greater allelic balance and amplicon coverage.     

DNA analysis in perpetrator identification of terrorism-related disaster: Suicide bombing of the Australian Embassy in Jakarta 2004

We report the strategy that we employed to identify the perpetrator of a suicide car bombing in front of the Australian Embassy in Jakarta, Indonesia, on 9 September 2004. The bomb was so massive that only small tissue pieces of the perpetrator could be recovered, preventing conventional approach to the identification of the bomber, necessitating the introduction of DNA analysis as the primary means for perpetrator identification. Crime scene investigation revealed the trajectory of the bomb blast, which was used to guide the collection of charred tissue fragments of the perpetrator. Mitochondrial DNA analysis was first conducted on 17 tissue fragments, recovered over large areas of the trajectory to, (a) confirm that they are of a common source, i.e. the perpetrator, and thus (b) establish the mtDNA HV1 sequence profile of the perpetrator. The mtDNA of the perpetrator matches that of a maternally related family member of one of four suspects. Standard autosomal STR analysis confirmed the identification. This case is of interest as an illustration of a successful application of DNA analysis as the primary means of disaster perpetrator identification.     

DNA human identification for the family rights: One year of agreement between UNESP/Laboratory of Paternity and Public Defender Service in São Paulo State

The universities have realized the importance of extending their knowledge to the population through the provision of services. Thus, this paper presents the data obtained in an agreement between UNESP/Laboratory of Paternity and Public Defender Service in São Paulo State to make DNA paternity tests.     

A simple and inexpensive molecular method for sexing and identification of the forensic samples of elephant origin

The population of the Asian elephant is being dramatically reduced due to poaching of the ivory from the male. As poaching occurs in remote forests, it often takes weeks or longer for it to be discovered and it is therefore often very difficult to determine the sex of the decomposed body. Data suggest that in the recent past, over 2000 male elephants have been poached in South India. We have developed a technique based on molecular markers to determine that the carcass is an elephant and that it is a male. Using DNA sequence information from Genbank, we have developed two primer pairs: one for the mitochondrial DNA (mtDNA) and the other for the sex-determining region of Y chromosome (SRY) gene of the Indian elephant. After PCR amplification of known elephant DNA, we found that the mtDNA was common in both males and females, whereas the SRY-specific amplicon was observed only in the male.