Assessing three soil removal methods for environmental DNA analysis of mock forensic geology evidence

Soil is useful in criminal investigations as it is highly variable and readily transferred. Forensic geologists use several different techniques to removal soil from evidence prior to the analysis of inorganic components. There has been recent interest from the forensic science community to analyze environmental deoxyribonucleic acid (eDNA) associated with soil to augment existing forensic analyses. Notably however, limited research has been conducted to compare commonly used soil removal methods for downstream eDNA analysis. In this study, three soil removal methods were assessed: picking/scraping, sonication, and swabbing. Three mock evidence types (t-shirts, boot soles, and trowels) were sampled in triplicate with each removal method (n = 27). Soil samples underwent DNA isolation, quantification, and amplification of four genomic barcode regions: 16S for bacteria, ITS1 for fungi, ITS2 for plants, and COI for arthropods. Amplicons were prepared into libraries for DNA sequencing on an Illumina^® MiniSeq. DNA concentrations were highest in picked/scraped samples and were statistically significant compared with swabbed and sonicated samples. Amplicon sequence variants (ASVs) were identified, and removal methods had no impact on the recovery of the total number of target ASVs. Additionally, when assessing each sample in multidimensional space, picked/scraped samples tended to cluster separately from swabbed and sonicated samples. The soil core used a reference in this study also clustered with the picked/scraped samples, indicating that these samples may be more reflective of the communities collected from soil cores. Based on these data, we identified that picking/scraping is an acceptable soil removal method for eDNA analysis.     

An Improved Method for the Diatom Test Utilizing DNA Binding Ability of Silica

In order to devise a better forensic test for diatoms, the DNA binding ability of the diatom frustule constructing by silica, in the presence of chaotropic ions were utilized. It was proved that the diatoms were able to be captured via λDNA using silica‐coated magnetic beads (Mag beads), followed by isolation and purification from the Mag beads as a solid phase by substituting the chaotropic agent with ultrapure water. Five cases of drowning, three in freshwater and two in seawater, were applied to the present method and similar results as the usual diatom test were obtained. Specimens of lung and other organs were rendered clearly visible, with elimination of foreign impurities. The present method appears applicable for detection of diatoms indirectly using PCR amplification of bound DNA or directly staining of the DNA.     

Persistence of Biological Traces at Inside Parts of a Firearm from a Case of Multiple Familial Homicide

Backspatter from wounds caused by contact shots against a biological target had before been shown to be propelled into firearms' barrels where they can persist and be retrieved from as relevant forensic evidence. Herein, that insight was applied to the investigation of a case of multiple familial homicide with a firearm. Samples of backspatter were collected from the firearm using DNA‐free swabs. DNA was extracted from the swabs, and 16 STR systems were PCR‐amplified to generate DNA profiles of all victims shot by the firearm. The quality of the resulting DNA profiles was sufficient to exclude the perpetrator as donor and to differentiate the three closely related victims thereby proving that all three victims had been shot by the same firearm from very close or contact distance. A key insight gained from this case was that not only a firearms' barrel inside but other inner surfaces may be charged with profilable DNA.     

Simultaneous Detection of Human Mitochondrial DNA and Nuclear‐Inserted Mitochondrial‐origin Sequences (NumtS) using Forensic mtDNA Amplification Strategies and Pyrosequencing Technology

Next‐generation sequencing technologies enable the identification of minor mitochondrial DNA variants with higher sensitivity than Sanger methods, allowing for enhanced identification of minor variants. In this study, mixtures of human mtDNA control region amplicons were subjected to pyrosequencing to determine the detection threshold of the Roche GS Junior^® instrument (Roche Applied Science, Indianapolis, IN). In addition to expected variants, a set of reproducible variants was consistently found in reads from one particular amplicon. A BLASTn search of the variant sequence revealed identity to a segment of a 611‐bp nuclear insertion of the mitochondrial control region (NumtS) spanning the primer‐binding sites of this amplicon (Nature 1995;378:489). Primers (Hum Genet 2012;131:757; Hum Biol 1996;68:847) flanking the insertion were used to confirm the presence or absence of the NumtS in buccal DNA extracts from twenty donors. These results further our understanding of human mtDNA variation and are expected to have a positive impact on the interpretation of mtDNA profiles using deep‐sequencing methods in casework.     

单管一步甲基化可变位点分析技术

目的建立单管一步甲基化可变位点（methylationvariableposition,MVP）分析技术一单管消化后PCR链融解曲线分析（post—digestionPCR—meltingcurveanalysis,PDP—MCA）。方法以文献报道的差异甲基化区（differentiallymethylatedregion,DMR）为模型,在MVP两侧设计一组解链温度各不相同的引物。应用FastDigest甲基化敏感性限制酶（methylation—sensitiverestrictionenzyme,MSRE）,在同一反应管内顺次进行DNA的酶切、复合扩增和MCA检测．生成MCA图谱。同时用该方法和传统的MSRE—PCRMCA技术检测相同样品（外周静脉血、精液、阴道液各5份）,比较两种方法检测结果,验证其可行性,并分析比较不同样品的MCA／HRM图谱。结果解链温度相差2℃以上的片段,MCA峰分离良好,复合扩增后可以用MCA技术检测。应用单管PDP—MCA技术,可以集酶切、扩增和检测三步于一管,在2h内得到与传统方法一致的特异性图谱和数据,并实现样品的快速分类鉴别。结论单管PDP-MCA技术可以实现多个MVP的单管、闭管检测,具有简便、快速、易于自动化等优点,可用于样品DNA甲基化差异的检测。     

二乙酰吗啡盐酸盐标准物质的研制（1）—均匀性和稳定性检验

目的研制二乙酰吗啡盐酸盐标准物质,并检验其均匀性和稳定性。方法采用中压快速纯化制备系统分离纯化海洛因样品得到二乙酰吗啡盐酸盐,确认其结构后,采用统计学方法进行均匀性检验和稳定性检验。结果二乙酰吗啡盐酸盐标准物质含有0.88个结晶水,其瓶间不均匀性产生的标准不确定度为0.29%,短期和长期稳定性的标准不确定度分别为0.04%和0.46%。结论研制的二乙酰吗啡盐酸盐标准物质均匀性和稳定性良好。     

DNA IQ^TM SYSTEM在疑难指甲DNA检验中的应用

目的探索DNA IQTMSYSTEM在疑难指甲DNA提取中的应用。方法 15份疑难指甲采用Chelex方法检验没有成功获得STR分型图谱,采用DNA IQTMSYSTEM提取法并纯化,采用Identifiler PLUS试剂盒进行复合扩增,产物经ABI3130XL型DNA基因分析仪检测。结果成功获得15例疑难指甲的STR基因座DNA分型。结论 DNA IQTMSYSTEM方法能快速、有效提取疑难指甲DNA进行STR分型。     

Population genetic data of 38 autosomal InDels in San Basilio de Palenque,the first free town in America

In order to increase the information about Indels, we report allele frequencies and statistical parameters of forensic efficiency obtained typing a sample of 114 unrelated healthy individuals living in San Basilio de Palenque – Colombia using a panel of 38 autosomal InDels. No significant deviations from Hardy–Weinberg expectations were found except in the marker rs10629077 (p = 0.0002). The present database will be useful for forensic and paternity purposes for the region studied. Moreover, these additional markers can help forensic laboratories to solve parentage testing as well as to improve the analysis of degraded DNA samples.     

To destroy snail mail: Is this the sole solution for anthrax contaminated letters?

Suspicious packages, strange addresses on envelopes and/or the presence of particular powders: these are the most popular aspects of letters containing Bacillus anthracis. Since the World Trade Center tragedy, alarmism about chemical or biological attacks is always in force. The Italian Ministry of Foreign Affairs introduced new procedures to be followed in case suspected anthrax letters are identified (Ministry of Health PROT. 400.3/120.33/4786 of 23/10/2001). Scientists have to collect samples from surfaces and infectious waste have to be placed in autoclavable bags for decontamination. After the sterilization, mails and packages are burnt thus eliminating every biological trace present on their surface. As a matter of fact, after sterilization, DNA is still present and can be analyzed for forensic purposes: for this reason, here we report on the importance of preserving sterilized substrates. We recreated false infected mails with biological traces on their surfaces, sterilized them and, subsequently, we took samples of biological stains and processed them for DNA quantification and typing. We recreate different time conditions consistent with those of the postal service too. Real-Time PCR and DNA typing showed that, even if sterilization destroys the bacillus, human genomic traces still persist and we obtained both complete and partial profiles of samples’ donors. To conclude, the problem of anthrax contaminated letter call for peculiar and standardized procedures; nonetheless, we show that burning evidences after the sterilization process does not appear to be the best solution since there is a loss of biological material which could be decisive for forensic purposes.     

Combined analysis of two different ancestry informative assays using SNPs and Indels in Eurasian populations

In the absence of a suspect or DNA database match, small multiplex assays with ancestry informative markers (AIMs) provide an alternative to comparative DNA analysis as the knowledge of an unknown stain donor's biogeographic ancestry can be helpful in guiding criminal investigations. AIMs can provide valuable information in such cases. The research focus for AIMs has been on multiplex assays of single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (Indels). This work presents a combined analysis of two different AIM assays to increase differentiation between Eurasian populations.