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.     

The Diagnostic Value of Quantitative Assessment of Diatom Test for Drowning: An Analysis of 128 Water‐related Death Cases using Microwave Digestion‐Vacuum Filtration‐Automated Scanning Electron Microscopy

The value of diatom test for the diagnosis of drowning remains controversial. The conventional forensic diatom test with low sensitivity is not a useful tool to provide accurate information about diatom in the tissues and organs. To improve the sensitivity of the diatom test, we developed a novel method called the Microwave Digestion‐Vacuum Filtration‐Automated Scanning Electron Microscopy (MD‐VF‐Auto SEM) method which resulted in a high recovery of diatoms. In this article, we analyzed 128 water‐related death cases. Our results showed that the MD‐VF‐Auto SEM method could achieve a much higher positive rate (0.97) in drowning cases. Large amounts of diatoms are retained, even concentrated, in the lung tissues during the intense breathing movement in drowning process. This might be useful for the diagnosis of drowning. Our research indicates that the MD‐VF‐Auto SEM method would be a valuable methodology in the study of diatom test for the forensic community.     

A Simple Digestion Method with a Lefort Aqua Regia Solution for Diatom Extraction

Presence of diatoms in tissues has been considered as a significant sign of drowning. However, there are limitations in the present extraction methods. We developed a new digestion method using the Lefort aqua regia solution (3:1 nitric acid to hydrochloric acid) for diatom extraction and evaluated the digestive capability, diatom destruction, and diatoms' recovery of this new method. The kidney tissues from rabbit mixed with water rich in diatoms were treated by the Lefort aqua regia digestion method (n = 10) and the conventional acid digestion method (n = 10). The results showed that the digestive capability of Lefort aqua regia digestion method was superior to conventional acid digestion method (p < 0.01); the structure of diatom remained almost intact; and the recovery of diatom was comparable to the conventional acid digestion method (p > 0.05). The Lefort aqua regia reagent is an improvement over the conventional acid digestion for recovery of diatoms from tissue samples.     

硅藻硝酸消化法与浮游生物16S rDNA PCR法在溺死鉴定中的比较

目的比较和探讨硅藻硝酸消化法与浮游生物16S rDNA PCR法在溺死鉴定中的应用价值。方法收集40例温州医科大学法医学系2010—2011年受理并证实溺死的鉴定案件,每例案件标本包括肺、肾、肝及现场水样4份样本,分别运用硅藻硝酸消化法与浮游生物16S rDNA PCR法对标本进行检验,硅藻硝酸消化法和浮游生物16S rDNA PCR法所需各器官检材量分别为约20g和2g,现场水样分别为15mL和1.5mL,从所需检验时间以及检出率等方面进行比较分析。结果硅藻硝酸消化法检出硅藻主要为中心硅藻纲和羽纹硅藻纲,浮游生物16S rDNA PCR法可扩增出一条162 bp的条带。平均检验每例案件所需的检验时间,硅藻硝酸消化法为(95.30±2.78)min,少于浮游生物16S rDNA PCR法(325.33±14.18)min(P0.05)。两种方法对现场水样及肺样本的检出率均为100%,而对肝及肾样本的检出率,浮游生物16S rDNA PCR法均为80%,高于硅藻硝酸消化法40%和30%(P0.05)。结论在溺死的法医学鉴定中,应根据具体情况来挑选合适的实验室检验方法。与硅藻硝酸消化法相比,浮游生物16S rDNA PCR法具有检材用量少、信息量大、特异性高等特点,有一定的推广和实践价值。     

Identification of forensically important sarcophagid flies (Diptera: Sarcophagidae) in China, based on COI and 16S rDNA gene sequences

Insects attracted to cadavers may provide important indications of the postmortem interval (PMI). However, use of the flesh flies (Diptera: Sarcophagidae) for PMI estimation is limited as the species are often not morphologically distinct, especially as immatures. In this study, 23 forensically important flesh flies were collected from 13 locations in 10 Chinese provinces. Then, a 278-bp segment of the cytochrome oxidase subunits one (COI) gene and a 289-bp segment of the 16S rDNA gene of all specimens were successfully sequenced. Phylogenetic analysis of the sequenced segments showed that all sarcophagid specimens were properly assigned into four species (Boerttcherisca peregrina [Robineau-Desvoidy, 1830], Helicophagella melanura [Meigen, 1826], Parasarcophaga albiceps [Meigen, 1826], and Parasarcophaga dux [Thompson, 1869]) with relatively strong supporting values, thus indicating that the COI and 16S rDNA regions are suitable for identification of sarcophagid species. The difference between intraspecific threshold and interspecific divergence confirmed the potential of the two regions for sarcophagid species identification.     

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.     

Spatial and temporal influences on bacterial profiling of forensic soil samples

Bacterial content may be helpful in differentiating forensic soil samples; however, the effectiveness of bacterial profiling depends on several factors, including uniqueness among different habitat types, the level of heterogeneity within a habitat, and changes in bacterial communities over time. To examine these, soils from five diverse habitats were tested over a 1 year period using terminal restriction fragment length polymorphism (TRFLP) analysis. Soil samples were collected at central locations monthly, and 10 feet in cardinal directions quarterly. Similarity indices were found to be least related among habitats, while the greatest bacterial similarities existed among collection locations within a habitat. Temporally, however, bacterial content varied considerably, and there was substantial overlap in similarity indices among habitats during different parts of the year. Taken together, the results indicate that while bacterial DNA profiling may be useful for forensic soil analysis, certain variables, particularly time, must be considered.     

Next‐Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study

Soil has the potential to be valuable forensic evidence linking a person or item to a crime scene; however, there is no established soil individualization technique. In this study, the utility of soil bacterial profiling via next‐generation sequencing of the 16S rRNA gene was examined for associating soils with their place of origin. Soil samples were collected from ten diverse and nine similar habitats over time, and within three habitats at various horizontal and vertical distances. Bacterial profiles were analyzed using four methods: abundance charts and nonmetric multidimensional scaling provided simplification and visualization of the massive datasets, potentially aiding in expert testimony, while analysis of similarities and k‐nearest neighbor offered objective statistical comparisons. The vast majority of soil bacterial profiles (95.4%) were classified to their location of origin, highlighting the potential of bacterial profiling via next‐generation sequencing for the forensic analysis of soil samples.     

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。     

Comparison of two methods for isolating DNA from human skeletal remains for STR analysis

Abstract: The quality and efficiency of a standard organic DNA isolation method and a silica‐based method using the QIAGEN Blood Maxi Kit were compared to obtain human DNA and short tandem repeats (STRs) profiles from 39 exhumed bone samples for paternity testing. DNA samples were quantified by real‐time PCR, and STR profiles were obtained using the AmpFlSTR^® Identifiler^® PCR amplification kit. Overall, the silica‐based method recovered less DNA ranging from 0 to 147.7 ng/g (average 7.57 ng/g, median = 1.3 ng/g) than did the organic method ranging from 0 to 605 ng/g (average 44.27 ng/g, median = 5.8 ng/g). Complete profiles (16/16 loci tested) were obtained from 37/39 samples (95%) using the organic method and from 9/39 samples (23%) with the silica‐based method. Compared with a standard organic DNA isolation method, our results indicate that the published silica‐based method does not improve neither the quality nor the quantity of DNA for STR profiling.     

Development and validation of the AmpFlSTR MiniFiler PCR Amplification Kit: a MiniSTR multiplex for the analysis of degraded and/or PCR inhibited DNA

DNA typing of degraded DNA samples can be a challenging task when using the current commercially available multiplex short tandem repeat (STR) analysis kits. However, the ability to type degraded DNA specimens improves by redesigning current STR marker amplicons such that smaller sized polymerase chain reaction (PCR) products are generated. In an effort to increase the amount of information derived from these types of DNA samples, the AmpFlSTR MiniFiler PCR Amplification Kit has been developed. The kit contains reagents for the amplification of eight miniSTRs which are the largest sized loci in the AmpFlSTR Identifiler PCR Amplification Kit (D7S820, D13S317, D16S539, D21S11, D2S1338, D18S51, CSF1PO, and FGA). Five of these STR loci (D16S539, D21S11, D2S1338, D18S51, and FGA) also are some of the largest loci in the AmpFlSTR SGM Plus kit. This informative nine-locus multiplex, which includes the gender-identification locus Amelogenin, has been validated according to the FBI/National Standards and SWGDAM guidelines. Our results demonstrate significant performance improvements in models of DNA degradation, PCR inhibition, and nonprobative samples when compared to the AmpFlSTR Identifiler and SGM Plus kits. These data support that the MiniFiler kit will increase the likelihood of obtaining additional STR information from forensic samples in situations in which standard STR chemistries fail to produce complete profiles.