The persistence of human DNA in soil following surface decomposition

The effect of insect excretions/secretions and decomposition fluid on DNA quantity and quality in human bloodstains

The larval excretions/secretions (ES) of blowflies contain proteolytic enzymes and bacteria that assist with tissue breakdown. Decomposition fluid (DF) contains organic and inorganic waste products from cell death. This study investigated if human DNA recovery from blood was impacted by exposure to ES and DF over time. Lucilia sericata ES were collected daily from 50 larvae, and all available DF was collected from two fetal piglets left to decompose for 2 weeks. Daily for 3-5 days, 28 μL-30 μL of ES, DF, or a 1:1 mixture of the fluids was added to 30 μL of blood on cotton. Three bloodstains per treatment were sampled every 12 h up to 3 days and at 1 and 2 weeks after initial addition of fluid. No PCR inhibition was detected, but DNA degradation increased over time, primarily in samples exposed to ES and ES/DF mixtures. The amount of DNA recovered decreased over time, but generally more DNA was recovered from DF samples than other samples. Full profiles, or partial profiles suitable for routine database searching (14-39 alleles), were generated from all DF and ES samples and at least one mixture sample at all timepoints. Partial profiles of between 1 and 13 alleles were obtained from all other mixture samples, except one mixture sample which generated no profile. These findings indicate bloodstain evidence recovered from maggot-infested and/or decomposing bodies may generate forensically useful DNA evidence and should be analyzed as quickly as possible after collection or stored appropriately to prevent further degradation.

A review of the contributions of forensic archaeology and anthropology to the process of disaster victim identification

Forensic archaeology and anthropology have developed significantly over past decades and now provide considerable assistance to the investigation process of disaster victim recovery and identification. In what are often chaotic death and crime scenes, the formal process of utilizing archaeological methods can bring control, order, and ensure systematic search. Procedures assist in defining scene extent, locating victims and evidence, rule out areas for consideration, and provide standardized recording and quality assurance through dedicated use of standardized forms (pro formas). Combined archaeological and anthropological search methods maximize opportunities to recovery the missing through identifying remains, mapping distributions, and providing accounting of victims at the scene. Anthropological assistance in examinations contributes to individual assessment, resolving commingling and fragmentation issues, and utilizing DNA sampling methods and matching data to reassociate and account for the missing. Utilization of archaeology, anthropology, and DNA matching data provides scope to review crime scene recovery and determine requirements and potential for further survey and retrieval. Adopting the most suitable methods for a particular context can maximize recovery, efficiency, and resource use. Case studies demonstrate the utility of archaeological methods in a range of scenarios. They exemplify the success of multidisciplinary analysis in providing evidence of the sequence of events, the timing of events, the impact of taphonomic processes, the location and accounting of victims, and the demonstration of systematic scene search. The considerations provided in this article, utilizing archaeology and anthropology processes, may assist investigators in planning and implementing responses to mass fatalities.

Utilization of qPCR to Determine Duration and Environmental Drivers Contributing to the Persistence of Human DNA in Soil

Little is known about the underlying mechanisms that contribute to the persistence and degradation of DNA within soil. The goals of this study are to determine the duration of mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) persistence in soils enriched by surface-level human decomposition and to better understand the contribution of environmental factors. The surface-level decomposition of three human cadavers was documented over 11 weeks. Based on quantitative PCR results, we found nuDNA to persist in soils six weeks post-placement, while mtDNA was recoverable for the entire 11-week decomposition period. Principle components analyses and Spearman's rank correlations revealed that (1) time, (2) total body score, and (3) weekly average air temperature were significantly correlated with concentrations of nuDNA and mtDNA in soil, suggesting these factors play a role in the degradation of DNA in soils.

Persistence of touch DNA on commonly encountered substrates in different storage conditions

The persistence of touch DNA deposited after realistic handling of items typically encountered in forensic investigations has been the subject of few studies. Understanding the long-term persistence of touch DNA on different substrates in varying conditions can be central to the effective triage of samples for further processing. As the time between an alleged incident and collection of evidence may vary from a few days to years after an alleged event, this study assessed three different common substrates for the persistence of touch DNA over a time span up to 9 months. These substrates included fabric, steel, and rubber, each of which were handled in a way to imitate what may happen during a criminal act. The three substrates were exposed to two different environments for up to 9 months: inside a dark cupboard with no traffic to act as a control and an outside semi-exposed environment. Ten replicates from each of the 3 substrates were tested at 5 time points to create 300 samples. All samples were processed using a standard operating workflow to provide genotype data after exposure to different environments. It was found that the fabric samples produced informative STR profiles (defined here as 12 or more alleles) up to the 9 month timepoint for either environment. The rubber and steel substrates for the inside condition produced informative STR profiles up to the 9 month timepoint, but only generated informative STR profiles for the outside condition up to 3 and 6 months, respectively. These data add to our understanding of the external factors that affect DNA persistence.

Effects of decomposition on the recoverability of biological fluid evidence

The present research assessed how the physical and chemical changes associated with decomposition affect the detection and identification of blood and semen evidence, as well as subsequent DNA analysis. A feeder pig (postmortem interval (PMI) < 3 h) was placed within the Boston University Outdoor Research Facility for a period of 22 days. Human blood and semen were individually dispensed onto multiple areas of two cotton t-shirts; one layer of fabric was placed above and below the pig and a control. One of each sample type was collected per day for a period of 22 days from each location. It was observed that both sample types when collected from beneath the pig exhibited the greatest decline in enzymatic activity over the course of testing, followed by samples from beneath the control, which can be inferred from the increase in negative screening results compared to the other samples. Spermatozoa were observed in nearly all semen samples, even when all screening results were negative, which lead to the generation of comparable DNA profiles for nearly all semen samples typed. Genetic typing of the blood samples beneath the pig and control rarely yielded comparable data while the samples from above yielded full profiles for all but a few samples tested.

About the influence of environmental factors on the persistence of DNA - a long-term study

DNA persistence and DNA transfer are important features in the assessment of a crime scene. The question how long DNA may persist at a certain location is similarly important as the one how the DNA has been transferred to this location. Depending on the source of the DNA as well as the conditions at the crime scene, the answer to this question is quite difficult. In this study, persistence of DNA from epithelial abrasions, blood cells, and saliva cells in indoor and outdoor scenarios has been investigated with regard to exposure time and exposure conditions including sunlight, temperature, and humidity in summer and winter scenarios. Overall, we generated 338 epithelial samples, 572 blood samples, and 572 saliva samples. A complete profile of the cell/DNA donor after exposure could be obtained in 47%, 65%, and 58% of epithelial abrasions, blood samples, and saliva samples, respectively. Regarding blood samples, there were no differences between supporting materials cloth and plastic; however, the percentage of complete profiles was higher for saliva samples on plastic and for epithelial samples on cloth. In indoor scenarios, complete profiles could be recovered from nearly all blood and saliva samples up to 9 months, whereas the amount of epithelial complete profiles already started to decline after 3 months. In outdoor scenarios, we observed a tipping point at an exposure time of 3 months. Blood and saliva samples collected after this period displayed complete profiles in less than 25% of samples. After 12 months, no outdoor sample showed a complete profile. The results of this study facilitate decisions on the relevance of recovered DNA from crime scenes.

Improved Protocol for DNA Extraction from Subsoils Using Phosphate Lysis Buffer

As our understanding of soil biology deepens, there is a growing demand for investigations addressing microbial processes in the earth beneath the topsoil layer, called subsoil. High clay content in subsoils often hinders the recovery of sufficient quantities of DNA as clay particles bind nucleic acids. Here, an efficient and reproducible DNA extraction method for 200 mg dried soil based on sodium dodecyl sulfate (SDS) lysis in the presence of phosphate buffer has been developed. The extraction protocol was optimized by quantifying bacterial 16S and fungal 18S rRNA genes amplified from extracts obtained by different combinations of lysis methods and phosphate buffer washes. The combination of one minute of bead beating, followed by ten min incubation at 65°C in the presence of 1 M phosphate buffer with 0.5% SDS, was found to produce the best results. The optimized protocol was compared with a commonly used cetyltrimethylammonium bromide (CTAB) method, using Phaeozem soil collected from 60 cm depth at a conventional agricultural field and validated on five subsoils. The reproducibility and robustness of the protocol was corroborated by an interlaboratory comparison. The DNA extraction protocol offers a reproducible and cost-effective tool for DNA-based studies of subsoil biology.

Predicting the fate of eDNA in the environment and implications for studying biodiversity

Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.

Mitochondrial DNA Extraction from Burial Soil Samples at Incremental Distances: A Preliminary Study

Preservation variance of soil DNA is neglected in the literature, and exceptional cases exaggerate amplification capabilities. This study sought to amplify a short mitochondrial fragment (212 bp) specific to Sus scrofa domesticus from the soil surrounding decomposing pig remains from an open-air locale. Samples collected above the body at incremental distances after 145 days of initial placement yielded pig DNA. A secondary sampling was collected in 2017, approximately 768 days after burial. Inhibition tests corroborated that pig DNA was no longer present in the soil resulting in a loss of original DNA between 145 and 768 days. The results provide evidence that genetic material leaches out radially from the source and DNA fragments longer than 200 bp do not persist in soil for a relatively short timeframe in western Montana. The conclusions support the collection of soil in crime scene investigation procedures within the first few months of decomposition.