Discrimination of Soils at Regional and Local Levels Using Bacterial and Fungal T‐RFLP Profiling*

Abstract: DNA profiling of microbial communities has been proposed as a tool for forensic comparison of soils, but its potential to discriminate between soils from similar land use and/or geographic location has been largely unexplored. We tested the ability of terminal restriction fragment length polymorphism (T‐RFLP) to discriminate between soils from 10 sites within the Greater Wellington region, New Zealand, based on their bacterial and fungal DNA profiles. Significant differences in bacterial and fungal communities between soils collected from all but one pair of sites were demonstrated. In some instances, specific terminal restriction fragments were associated with particular sites. Patch discrimination was evident within several sites, which could prove useful for site‐specific matching (e.g., matching shoe/car tire print to an object). These results support the need for further understanding of the spatial distribution of soil microbial communities before DNA profiling of soil microbial communities can be applied to the forensic context.     

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.     

Assessing the potential of bacterial DNA profiling for forensic soil comparisons

A pilot study was undertaken to evaluate DNA profiling of the bacterial community in soil as an alternative to geological methods for forensic soil comparisons. Soil samples from three different ecosystems were compared, and the variation within and between ecologically different sites was determined by using terminal restriction fragment (TRF) analysis of 16S ribosomal DNA. Comparison of TRF profiles revealed that samples from within a specific ecosystem (e.g., a field) showed a significantly higher similarity to each other than to those from another ecosystem (e.g., a forest). In addition, some profile features were unique to specific ecosystems. These features may allow the determination of characteristic profiles that will facilitate identification of ecologically different sites, so that a given sample collected from a suspect could be identified as originating from, for example, a field, rather than a forest. The implications of these preliminary findings for forensic investigations are discussed.     

Molecular Identification of Indian Crocodile Species: PCR‐RFLP Method for Forensic Authentication*

Abstract: South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile‐based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA‐based identification of species using PCR‐RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species‐specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.     

Molecular Identification of Three Indian Snake Species Using Simple PCR–RFLP Method*

Abstract: Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR–restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431‐bp amplicon from cytochrome b gene was amplified using novel snake‐specific primers following restriction digestion with enzymes Mbo II and Fok I. The species‐specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor‐quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.     

Bacterial Profiling of Soil For Forensic Investigations: Consideration of Ex Situ Changes in Questioned and Known Soil Samples

Soil, being diverse and ubiquitous, can potentially link a suspect or victim to a crime scene. Recently scientists have examined the microbial makeup of soil for determining its origin, and differentiating soil samples is well-established. However, when soil is transferred to evidence its microbial makeup may change over time, leading to false exclusions. In this research, “known” soils from diverse habitats were stored under controlled conditions, while evidence soils were aged on mock evidence. Limited quantities of soil were also assayed. Bacterial profiles were produced using next-generation sequencing of the 16S rRNA gene. Overall, known soils stored open at room temperature were more similar to evidence soils over time than were known soils stored bagged and/or frozen. Evidence soils, even as little as 1 mg, associated with the correct habitat 99% of the time, accentuating the importance of considering ex situ microbial changes in soil for its successful use as forensic evidence.     

Evaluation of Postmortem Bacterial Migration Using Culturing and Real‐Time Quantitative PCR

Postmortem bacteriology can be a valuable tool for evaluating deaths due to bacterial infection or for researching the involvement of bacteria in various diseases. In this study, time‐dependent postmortem bacterial migration into liver, mesenteric lymph node, pericardial fluid, portal, and peripheral vein was analyzed in 33 autopsy cases by bacterial culturing and real‐time quantitative polymerase chain reaction (RT‐qPCR). None suffered or died from bacterial infection. According to culturing, pericardial fluid and liver were the most sterile samples up to 5 days postmortem. In these samples, multigrowth and staphylococci were not or rarely detected. RT‐qPCR was more sensitive and showed higher bacterial positivity in all samples. Relative amounts of intestinal bacterial DNA (bifidobacteria, bacteroides, enterobacter, clostridia) increased with time. Sterility of blood samples was low during the studied time periods (1–7 days). The best postmortem microbiological sampling sites were pericardial fluid and liver up to 5 days after death.     

Recovery and STR amplification of DNA from RFLP membranes

Restriction fragment length polymorphism (RFLP) techniques were utilized in the forensic DNA community until the mid 1990s when less labor-intensive polymerase chain reaction short tandem repeat (PCR STR) techniques became available. During the transition from RFLP technology to PCR-based STR platforms, a method for comparing RFLP profiles to STR profiles was not developed. While the preferred approach for applying new technology to old cases would be to analyze the original biological stain, this is not always possible. For unsolved cases that previously underwent RFLP analysis, the only DNA remaining may be restriction cut and bound to nylon membranes. These studies investigate several methods for obtaining STR profiles from membrane bound DNA, including removal of bound DNA with bases, acids, detergents, various chemicals, and conventional cell extraction solutions. Direct multiplex STR amplification of template in the membrane-bound state was also explored. A partial STR profile was obtained from DNA that was recovered from an archived membrane using conventional extraction buffer components, indicating promise for recovering useful STR information from RFLP membranes that have been maintained in long-term frozen storage.     

A Molecular Key for the Identification of Blow Flies in Southeastern Nebraska*

Abstract: Immature blow flies (Calliphoridae) are typically the first colonizers of cadavers. Identification of the early instars using traditional, morphology‐based keys is difficult because of their small size, similarity, and simplicity in external morphology. Information derived from molecular genetic data would augment the accurate identification of immature flies. Nine species of blow flies commonly found in southeastern Nebraska were used to examine the utility of molecular‐based keys. Polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLP) were investigated with 10 common, inexpensive, restriction enzymes from an amplicon of approximately 1500 bp spanning the mitochondrial cytochrome oxidase I gene. A simple molecular taxonomic key, comprising RFLP from the restriction enzymes HinfI and DraI, enabled the differentiation of all species used. Further development of PCR–RFLP, including more extensive and intensive examination of blow flies, would benefit forensic laboratories in the accurate identification of evidence consisting of immature blow flies.     

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.     

Individual Identification of Racehorses from Urine Samples Using a 26‐Plex Single‐Nucleotide Polymorphism Assay

To construct a system for identifying individual horses from urine samples that are submitted for postracing doping tests, we developed a genotyping assay based on 26‐plex single‐nucleotide polymorphisms (SNPs). DNA was isolated from urine using a commercially available DNA/RNA extraction kit, and SNP genotyping was achieved with a SNaPshot^? technique. DNA profiles including 26 SNPs were acquired from urine samples and blood/hair samples. Within the studied Thoroughbred population, the 26‐plex assay showed a probability of identity of 5.80 × 10^?11. Compared to the conventional short tandem repeat assay, the SNP assay used less DNA, and the rate of successful genotyping was improved to 97% using aliquots of horse urine as small as 140 μL. The urinary DNA could be successfully genotyped under proper storage concerning refrigeration or freeze–thawing. This SNP assay can be used for individual identification when suspicious results are obtained from horse doping tests.     

Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next‐Generation Sequencing,,

Previous research has revealed the potential of soil bacterial profiling for forensic purposes; however, investigators have not thoroughly examined fluctuations in microbial profiles from soil aged on evidence. In this research, soils collected from multiple habitats were placed on evidence items and sampled over time, and then bacterial profiles were generated via next‐generation sequencing of the 16S rRNA locus. Bacterial abundance charts and nonmetric multidimensional scaling plots provided visual representation of bacterial profiles temporally, while supervised classification was used to statistically associate evidence to a source. The ex situ evidence soils displayed specific, consistent taxonomic changes as they aged, resulting in their drift in multidimensional space, but never toward a different habitat. Ninety‐five percent of the 364 evidentiary profiles statistically classified to the correct habitat, with misclassification generally stemming from evidence type and increased age. Ultimately, understanding bacterial changes that occur temporally in ex situ soils should enhance their use in forensic investigations.     

Sexual Dimorphism of the Humerus in Contemporary Cretans—A Population‐Specific Study and a Review of the Literature*

Abstract: Sex determination is the first essential step for positive identification when a decomposed body is recovered. Taking into consideration the population aspect of sexual dimorphism of the skeleton, the present study aimed to create a sex identification technique using osteometric standards, derived from a contemporary Cretan population. A total of 168 left humeri were measured according to standard osteometric techniques. The differences between the means in males and females were significant (p < 0.0005). About 92.3% of cases were correctly classified when all measurements were applied jointly. Stepwise procedure produced an accuracy rate of 92.9%. The most effective single dimension was vertical head diameter (89.9%). The current study provides standards for a population that has not been represented so far in the existing databases. It demonstrates that the humerus is an effective bone for the estimation of sex because even in a fragmentary state it can give high classification accuracy.     

Enhancement of Aged and Denatured Fingerprints Using the Cyanoacrylate Fuming Technique Following Dusting with Amino Acid‐Containing Powders

We have carried out experiments to investigate the aging of latent fingerprints deposited on black PVC over a period of 4–15 weeks. A thumbprint was used in each case and before deposition of the print the donor rubbed their thumb around their nose to add sebaceous deposits. We have studied the effect of heat, light, and moisture and we find that moisture is the most significant factor in the degradation of the latent print. We have attempted to enhance these latent prints by dusting with valine powder or powders composed of valine mixed with gold or red fluorescent commercial fingerprint powders. To make a direct comparison between “treated” and “untreated” prints, the prints were cut in half with one‐half being “treated” and one‐half not. Our studies show the best results being obtained when powders of valine and red fluorescent powders are applied prior to cyanoacrylate fuming.     

High‐throughput Sequencing of Trace Quantities of Soil Provides Reproducible and Discriminative Fungal DNA Profiles

High‐throughput sequencing (HTS) offers improved resolution between forensic soil samples by characterizing individual taxa present; however, the heterogeneous distribution of taxa in soils, and limited quantity of material available, may hinder the reliability of HTS in casework. Using HTS of the internal transcribed spacer, we examined the effect of soil mass (50, 150, and 250 mg) on fungal DNA profiles, focusing on reproducibility and discriminatory power between close proximity soils, and samples with similar textural classification. The results show that reduced soil mass had no significant effect on sample differentiation and that 150 mg soil provides the most reproducible DNA profiles across different soil types. In addition, Ascomycota was identified as a robust fungal target for forensic intelligence as this phylum was detected consistently across all samples regardless of sample quantity. Overall, this study highlights the value of trace quantities of soil for use in forensic casework.     

Integrated DNA and Fingerprint Analyses in the Identification of 60‐Year‐Old Mummified Human Remains Discovered in an Alaskan Glacier

Abstract: This report describes the identification of a merchant mariner who perished in 1948 when Northwest Airlines Flight 4422, a DC‐4 carrying 24 seamen and six crew members crashed into Mount Sanford, Alaska. Fifty‐one years later, a human forearm and hand were found close by the wreckage of the plane, prompting identification efforts using DNA and fingerprints. There were significant challenges to both the fingerprint and DNA analyses. The hand was badly desiccated, making fingerprint friction‐ridge detail almost invisible and the remains had been embalmed upon discovery, making DNA amplification difficult. We present the results of an interdisciplinary approach that successfully addressed these challenges and ultimately led to the identification of the remains. These efforts relied on efficient fingerprint rejuvenation and imaging techniques that improved print resolution, as well as new DNA extraction techniques optimized for aggressively embalmed remains.     

Detection and Classification of Ignitable Liquid Residues Using a Fluorescence‐Based Vapor‐Sensitive Microsphere Array*

Abstract: This paper describes the application of microsphere vapor sensing arrays to the detection of ignitable liquid (IL) vapors as both pure vapors and as residues (ILRs) on simulated fire debris samples. The temporal fluorescence response profile of the microsphere array generated a reproducible pattern unique to each analyte that could be used to classify subsequent sensor responses. This system, together with a support vector machine pattern recognition algorithm, was used to address several different IL and ILR classification scenarios. High classification accuracy (98%) was maintained over more than 200 vapor responses and the array was able to identify ILs when presented to the pattern classification algorithm within a dataset containing 11 other volatile compounds. Both burned and unburned IL treated samples were classified correctly greater than 97% of the time. These results indicate that microsphere vapor sensing arrays may be useful for the rapid identification of ILs and ILRs.     

Validation of Half‐Reaction Amplification Using Promega PowerPlex® 16*

Abstract: DNA amplification is a fundamental yet costly process used in DNA analysis. This study evaluated half‐reaction amplification (12.5, 12, and 13 uL) using the Promega Powerplex^® 16 Kit with the hope of reducing sample analysis costs by half. A sensitivity study was completed, along with the testing of various blood stain samples including those with low (<0.40 ng) and high DNA concentrations (>3.0 ng), peak height imbalances, and allelic drop‐out. Also, 467 samples submitted to the MUFSC laboratory for testing were analyzed. Results indicate that half‐reaction amplification produced higher quality profiles than full‐reactions. Average peak heights increased by 85%, peak height imbalances improved, and drop‐out was eliminated in 75.8% of samples. Only eight of 467 case samples required re‐amplification, a success rate of 94% was observed, and the repeat rate decreased significantly. Finally, a DNA input of 0.25–1.0 ng is ideal for half‐reaction amplification.     

Development of a Real‐Time PCR‐Based Method for Analyzing Semen‐Specific Unmethylated DNA Regions and Methylation Status in Aged Body Fluid Stains

The detection of semen in forensic investigation is considered important evidence of sexual assault. In this study, we report the development of a real‐time polymerase chain reaction‐based method for identifying semen that can simply and rapidly analyze the semen‐specific unmethylated region of the DACT1 gene. Using two fluorescent probes designed for the methylated or unmethylated status, this method could perform quantitative analysis of the methylation status in this region. Furthermore, this method was used to analyze various body fluid samples, including 29‐year‐old semen and blood stains. The results showed that this method can detect almost exclusively semen or nonsemen signals even in highly decomposed samples, while a few semen or nonsemen samples showed slight signals of the other fluorescence probe. Although there is still a need for further analysis such as setting thresholds to analyze unknown samples, this method could be a useful supplementary tool for identifying semen, especially in old stains such as those in cold‐case investigations.     

Reliable and Robust Molecular Sexing of the Hen Harrier (Circus cyaneus) Using PCR‐RFLP Analysis of the CHD 1 Gene

The hen harrier (Circus cyaneus) is a bird of prey that is persecuted in the United Kingdom, and there is a need for a DNA‐based individual identification and sexing system for the use in forensic investigations. This study reports a new set of PCR primers for the chromo‐helicase‐DNA‐binding protein 1 gene, which allows sexing using PCR‐RFLP. Instead of exonic primers that amplify across a large intron, this set consists of a primer within the intron, enabling reduction in amplicon sizes from 356 to 212 bp and 565 to 219 bp in W and Z chromosomes. DNA degradation and dilution experiments demonstrate that this set is significantly more robust than one that amplifies across the intron, and sequencing of the intronic primer‐binding region across several individuals shows that it is highly conserved. While our objective is to incorporate this primer set into an STR‐based individualization kit, it may in the meantime prove useful in forensic or conservation studies.