A comparison of six adhesive tapes as tape lifts for efficient trace DNA recovery without the transfer of PCR inhibitors

Tape-lifting is a non-destructive method employed in the laboratory to recover and collect trace DNA evidence from crime scene exhibits with porous surfaces. The success of tape-lifting is a balance between capturing the biological material and compatibility with downstream DNA extraction processes to ensure efficient release of the tape-lifted material during DNA extraction. In this study, six commercially available low-, regular- and high-tack adhesive tapes were evaluated. The low-tack S183 tape and the highly adhesive S-Hold tape were compared for DNA recovery efficiency from different materials commonly encountered in casework. All tape-lifts were processed using PrepFiler Express™ BTA and AutoMate Express™ Forensic DNA extraction systems, DNA samples quantitated by Quantifiler TRIO, amplified using Powerplex® 21 and VeriFiler™ PLUS (VFP), and analysed on a 3500xl genetic analyser to evaluate the quality of the resultant STR profiles obtained. The more adhesive S-Hold tape recovered comparable or more DNA than the low-tack S183 tape from the majority of materials tested. However, STR profiles obtained from S183 tape-lifts were of markedly higher quality compared to S-Hold tape-lifts. This was most evident for towel, denim and printed chiffon, where S-Hold samples exhibited severe PCR inhibition, with VFP internal quality markers confirming the presence of inhibitors. The findings suggest that strong adhesion is not necessarily beneficial for tape-lifting, as the low tack S183 tape was able to efficiently recover cellular material from the surface of porous substrates commonly encountered in casework, while avoiding the co-transfer of PCR-inhibitory substances from the sampled material.

The impact of substrate characteristics on the collection and persistence of biological materials, and their implications for forensic casework

This study assessed the level of nucleic acid persistence on the substrate pre-, and post-swabbing, in order to assess whether biological materials (touch, saliva, semen, and blood) are collected differently depending on the substrate characteristics. A total of 48 samples per deposit and substrate variety (n = 384) were assessed by tracking the persistence of nucleic acid using Diamond™ Nucleic Acid Dye (DD) staining and Polilight photography. The number of DD nucleic acid fluorescent complexes formed post-staining were counted (fluorescent count) and in conjunction with the fluorescence signal intensity (DD nucleic acid complex accumulation) used to estimate the level of nucleic acid persistence on substrates. Touch deposits have shown to be the most persistent deposit with strong adhesion capabilities on both substrate verities. Saliva displayed a higher persistence than semen and/or blood. Semen displayed a high collection efficiency as well as a high fluorescence signal intensity. Blood displayed a low persistence on both substrates with a superior collection efficiency that may also indicate a higher probability to become dislodged from surfaces given a particular activity. Our research has shown that the persistence and recovery of biological deposits is not only measurable but more importantly, may have the potential to be estimated, as such, may build an understanding that can provide valuable guidance for collection efficiency evaluations, and the assessing of the probability of particular profiles, given alternate propositions of means of transfer occurring.

Salmon sperm DNA increases sample recovery from cotton swabs

Forensic samples with low DNA template amounts are difficult to analyze and interpret. There is a large body of research demonstrating that adding carrier nucleic acid to storage tubes, solid phase extractions, or filtering devices can improve yields of target DNA. However, the addition of carrier nucleic acid to sampling substrates, like cotton swabs, has not yet been attempted. In this proof-of-concept study, carrier nucleic acids in the form of either Poly (A) RNA or salmon sperm DNA were spotted onto cotton swabs, followed by human genomic DNA, to determine if introducing the carrier prior to sample collection would increase recovery from the swabs post-extraction. Extracts were also evaluated to determine whether adding the carrier nucleic acids to human DNA would interfere with downstream forensic DNA analysis processes such as real-time PCR quantitation, PCR amplification of STR loci, or capillary electrophoresis. The RNA carrier did not improve human sample recovery from cotton swabs. The extraction efficiency of human DNA from cotton swabs was increased when the DNA carrier was applied to the swabs prior to sample deposition, and the scale of the increase depended on the amount of carrier DNA used. When applying the salmon sperm DNA carrier to cotton swabs, with each increase from no carrier to 0.001-1-10 µg, human DNA recovery went from ∼29 % to ∼50 % to ∼75 % to ∼100 %. Additionally, no inhibitory effects from the carrier DNA were observed post-extraction with quantitation or in the DNA profile after amplification. Therefore, salmon sperm DNA carrier will increase human DNA yield from cotton swabs without negative effects on downstream forensic DNA profiling methods, with the optimal carrier amount being 10 µg.

Comparison of swabbing and cutting-out DNA collection methods from cotton, paper, and cardboard surfaces

Choosing an inappropriate method of sample collection can often have a detrimental impact on DNA recovery. Multiple studies highlight the importance of selecting the recovery method based on the type of surface the DNA sample is located on. This study aimed to investigate the efficacy of sample collection via the single cotton swabbing method in comparison to recovery directly from the material cut from the surface. The three types of surfaces included cotton, paper, and cardboard. DNA sources comprised cell-free and cellular DNA, as well as blood and saliva as examples of body fluids commonly encountered at crime scenes. The data analysis revealed that the cutting-out method resulted in higher DNA recovery from all but cardboard surfaces, making it the more efficient collection method. Despite its limitations, the cutting-out method should be considered as the DNA recovery method of choice when suitable.

Collection techniques of touch DNA deposited on human skin following a strangulation scenario

Trace DNA is a significant type of evidence for its ability to be collected from touched items or surfaces at crime scenes to link suspects to their crimes. In cases of violent crimes like assault, sexual offences, or even homicide, often touch DNA is collected from the victim's skin. However, the collection of touch DNA from the victim's skin can be complex because of the mixture of DNA present, as there is likely to be a small quantity of the offender's DNA compared to the victim's DNA. Validating different collection methods or techniques can improve touch DNA sampling; therefore, this study investigated three collection techniques involving cotton and nylon swabs to test their efficiency for the collection of touch DNA from the human neck. There was a significant difference between the three recovery techniques used to recover touch DNA with a cotton swab (CS) (p < 0.05) and nylon swab (NS) (p < 0.05), with more alleles observed when the neck skin was moistened with 100 μL of distilled water using a spray bottle before collection with both swabs.

Effects of solvent-based adhesive removal on the subsequent dual analysis of fingerprint and DNA

The combined approach of classical fingerprinting and DNA profiling is a powerful tool in forensic investigations of latent "touch" traces. However, little attention has been paid to the organic solvents frequently used in dactyloscopic laboratories to facilitate the separation of adhesive evidence prior to fingerprint development and downstream effects on subsequent DNA profiling. In the present study, we tested a selection of adhesive removers (n = 9) and assessed their potential impact on DNA recovery and amplification by PCR. Thereby, we identified and characterized novel PCR inhibitors. All investigated chemicals contain volatile organic compounds that evaporate under normal indoor atmospheric conditions. Exposure to certain solvents resulted in increased DNA degradation, but only if evaporation was prevented. A series of adhesive-removal experiments were conducted with prepared mock evidence (self-adhesive postage stamps affixed to paper envelope) to investigate the impact of treatment time and the location of applied traces on DNA recovery and dactyloscopy, respectively. Due to the early onset of print decomposition, we found that only a short treatment time was compatible with the development of fingerprints on the adhesive side of a stamp. Solvents also removed DNA from the adhesive surface, thus resulting in a marked shift in the substrate distribution of recovered DNA from the stamp to the envelope, but not in the reverse direction. Furthermore, we observed that treatment with conventional fingerprint reagents lead to a significant reduction in the amounts of DNA recovered from stamps, while the additional use of adhesive removers did not significantly enhance this effect.

Presence of Human DNA on Household Dogs and Its Bi-Directional Transfer

Awareness of the factors surrounding the transfer of DNA from a person, item, or surface to another person, item, or surface is highly relevant during investigations of alleged criminal activity. Animals in domestic environments could be a victim, offender, or innocent party associated with a crime. There is, however, very limited knowledge of human DNA transfer, persistence, prevalence, and recovery (DNA TPPR) associated with domestic animals. This pilot study aimed to improve our understanding of DNA TPPR associated with domestic dogs by collecting and analysing samples from various external areas of dogs of various breeds, interactions with humans, and living arrangements, and conducting a series of tests to investigate the possibility of dogs being vectors for the indirect transfer of human DNA. Reference DNA profiles from the dog owners and others living in the same residence were acquired to assist interpretation of the findings. The findings show that human DNA is prevalent on dogs, and in the majority of samples, two-person mixtures are present. Dogs were also found to be vectors for the transfer of human DNA, with DNA transferred from the dog to a gloved hand during patting and a sheet while walking.

Improvements, factors, and influences on DNA recovery from firearms

Touch DNA recovery from firearms can be central to many criminal investigations, yet the generation of DNA profiles from these items remains poor. Currently in Australia, published casework data highlights extremely poor DNA success from samples recovered from firearms. Only between 5% and 25% of samples result in useful DNA data and therefore increasing the success of DNA recovered from firearms is highly important but has not yet been explored in-depth. This study focused on increasing the recovery of DNA from ten firearm components that were held for 15 s. Multiple recovery methods were used, and the resulting genetic data compared. DNA evidence may be deliberately removed from firearms after discharge to hamper forensic investigations, therefore this study examined the effect of wiping down the components or handling them with gloves. A standard double swab and rinse swab recovery method resulted in an average of 73% cellular recovery. A cumulative swab process had the highest average recovery at 86%, although it was found that increasing the DNA yield led to an increase in mixture complexity. Wiping over the components was observed to remove on average 69% of cellular material, compared with 33% when handed with gloves. However, the size and texture of the components affected the efficiency of cellular material removal. The results from this study allow for prioritisation of areas to sample on firearms, as well as suggesting techniques that can be applied for the optimum process of cellular recovery and subsequent generation of STR DNA data.

An improved rapid method for DNA recovery from cotton swabs

We present a novel rapid method for the recovery of cellular and free DNA from cotton swabs based on a simple elution buffer containing a high molecular weight polymer and detergent combined with a short proteinase K digestion to release cellular DNA. This method shows increased yields approaching 80% recovery of the input DNA compared to the QIAamp DNA Mini kit standard extraction protocol for swabs which has a recovery of 20-30%. The buffer components in the described method are compatible with direct PCR analysis of the isolated DNA without further purification. Recovery efficiencies were estimated by qPCR.

Pulse Lavage System (PLS) versus forensic wet-vacuum collection of biological material

Wet-vacuum collection of forensic biological material has been shown to recover greater total DNA yields compared to traditional methods, such as wet swabbing. The Pulse Lavage System (PLS), an orthopedic surgical instrument, was evaluated in comparison to a forensic wet-vacuum device for the DNA collection and recovery of diluted bloodstains from seven substrates of varying porosity. Three different PLS models were evaluated, and each model yielded DNA concentrations which were comparable to the forensic wet-vacuum system, recovering 79-99 % relative to the wet-vacuum, which were overall not statistically different. Our results suggest that the PLS, though intended for medical use, has the potential to serve as an affordable alternative to the forensic wet-vacuum system. However, additional evaluation and modification to the PLS collection method may be warranted for complete optimization.

Preliminary investigation into isolation and extraction of DNA recovered from drug residues

It is a commonly held belief that drug residues may affect the integrity of DNA and/or interfere with DNA analysis, and therefore DNA on drug paraphernalia and the associated drugs may be overlooked as a source of evidence. This study investigated whether DNA could be isolated from a drug residue-bearing surface to ascertain whether a forensically useful DNA profile could be obtained. Human blood and pre-extracted "naked" DNA were deposited on samples of acetaminophen, codeine, morphine, oxycodone, ketamine, and synthetic cannabinoids and left for an hour before DNA extraction using DNA-IQ™. To investigate DNA integrity, the absolute amount of DNA recovered, degradation index, and number of PCR cycles required for the IPC to reach threshold (Ct), number of reportable alleles and average peak height (APH) in the DNA profile, were examined. The samples were also qualitatively analysed using LC:MS to determine if any residual drugs were present in the samples post-DNA extraction. Overall, the drugs had no to minimal degradation or inhibitory effects on the DNA with sufficient DNA recovered to generate a partial or full DNA profile in 80% of naked DNA samples and 100 % of blood samples. The amount of DNA collected was sufficient for further analysis in 86% of naked DNA samples, and 100% of blood samples, with all median APH values being over the 175 RFU standard. Chemical analysis showed that traces of the drug were still present in the samples after DNA extraction was performed. Therefore, this study demonstrates forensically useful DNA can be recovered from surfaces bearing drug residues, even when sampling directly from the samples of drugs.

Optimization of DNA extraction and sampling methods for successful forensic microbiome analyses of the skin and saliva

Microbiome studies have contributed to many fields, such as healthcare and medicine; however, these studies are relatively limited in forensics. Microbiome analyses can provide information, such as geolocation and ancestry information, when short tandem repeat (STR) profiling fails. In this study, methods for DNA extraction and sampling from the skin and saliva were optimized for the construction of a Korean Forensic Microbiome Database (KFMD). DNA yields were estimated using four DNA extraction kits, including two automated kits (Maxwell® FSC DNA IQ™ Casework Kit and PrepFiler™ Forensic DNA Extraction Kit, updated) and two manual kits (QIAamp DNA Mini Kit and QIAamp DNA Micro Kit) commonly used in forensic DNA profiling laboratories. Next-generation sequencing of the 16S rRNA V4 region was performed to analyze microbial communities in samples. The Bacterial Transport Swab with Liquid Media (NobleBio), two cotton swabs (PoongSung and Puritan), and nylon-flocked swabs (NobleBio and COPAN) were tested for DNA recovery. The PrepFiler and Maxwell kits showed the highest yields of 3.884 ng/μL and 23.767 ng/μL from the scalp and saliva, respectively. With respect to DNA recovery, nylon-flocked swabs performed better than cotton swabs. The relative abundances of taxa sorted by DNA extraction kits were similar contributions; however, with significant differences in community composition between scalp and saliva samples. Lawsonella and Veillonella were the most abundant genera in the two sample types. Thus, the Maxwell® FSC DNA IQ™ Casework Kit and nylon-flocked swab (NobleBio) were optimal for DNA extraction and collection in microbiome analyses.

DNA Transfer in Forensic Science: Recent Progress towards Meeting Challenges

Understanding the factors that may impact the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR), and the availability of data to assign probabilities to DNA quantities and profile types being obtained given particular scenarios and circumstances, is paramount when performing, and giving guidance on, evaluations of DNA findings given activity level propositions (activity level evaluations). In late 2018 and early 2019, three major reviews were published on aspects of DNA-TPPR, with each advocating the need for further research and other actions to support the conduct of DNA-related activity level evaluations. Here, we look at how challenges are being met, primarily by providing a synopsis of DNA-TPPR-related articles published since the conduct of these reviews and briefly exploring some of the actions taken by industry stakeholders towards addressing identified gaps. Much has been carried out in recent years, and efforts continue, to meet the challenges to continually improve the capacity of forensic experts to provide the guidance sought by the judiciary with respect to the transfer of DNA.

Comparison of swab types for collection and analysis of microorganisms

The human microbiome has begun to emerge as a potential forensic tool, with varied applications ranging from unique identification to investigative leads that link individuals and/or locations. The relative abundance of the combined DNA of the microbiome, compared to human nuclear DNA, may expand potential sources of biological evidence, especially in cases with transfer or low-copy number DNA samples. This work sought to determine the optimal swab type for the collection and analysis of microorganisms. A bacterium (Proteus mirabilis) was deposited by pipette onto four swab types (cotton, flocked, dental applicators, and dissolvable), and extraction and real-time PCR quantitation of the bacterial DNA were performed, which allowed for absolute microbial DNA recovery and comparison of yields across the four sampling substrates. Flocked swabs had the highest yield (~1240 ng) compared to the cotton swabs (~184 ng), dental applicators (~533 ng), and dissolvable swabs (~430 ng). The collection efficiency was further evaluated for cotton and flocked swabs using dried microbial samples spotted onto non-porous surfaces (treated wood, glass, plastic, and tile). Flocked swabs performed consistently better across wood, glass, and tile, but showed decreased recovery from plastic. The cotton swabs failed in the recovery of P. mirabilis DNA across all surfaces. Knowing the appropriate sampling substrate will be useful as others continue to investigate the use of the microbiome as a forensics tool.

Comparison of Isohelix™ and Rayon swabbing systems for touch DNA recovery from metal surfaces

A previous study evaluating two swabbing systems found that DNA was best recovered from sterile metal substrates using an Isohelix™ swab wetted with isopropyl alcohol rather than a Rayon swab with water as the wetting agent. We tested the same swabbing systems on metal (aluminum, brass, and stainless steel) and plastic substrates in a regularly touched environment to simulate the non-deliberate transfer of touch evidence likely seen in a casework scenario, to ascertain the performance of these swabs in an uncontrolled situation. Higher amounts of touch DNA were recovered with Isohelix™ swabs (0.5 – 3.3 ng) compared to Rayon swabs (0.13 – 1.2 ng). The Isohelix™ swabbing system was found to significantly recover more touch DNA (p = 0.04) from the metal substrates than the Rayon swabbing system, consistent with the findings of our previous work. The results contribute to our understanding of the impact of sample collection techniques on touch DNA recovery from problematic metal surfaces and suggest that supplemental cleaning of substrates as a precautionary step against the spread of infections may affect touch DNA persistence and the recovery efficiency of swabs.

Back to Amido Black: Uncovering touch DNA in blood-contaminated fingermarks

Blood-contaminated fingermarks (FMs) found in violent crime scenes may directly connect the suspect to the crime by linking the FM to the suspect and the DNA from the blood to the victim. However, marks that are incomparable are considered "dead-evidence" as the link to the suspect is lost. In this study, a novel approach was attempted to uncover the trace amount of touch DNA of the suspect in such marks. We examined the effect of two enhancement methods, ninhydrin (NIN) and amido black (AB), on DNA recovery from blood-contaminated FMs. A total of 108 fingerprints were deposited in three sets of depleted blood prints, blood-contaminated FMs, and latent FMs. All FMs were developed by either NIN or AB, or left undeveloped as reference followed by the quantification of the total DNA amount. This work shows that while AB had a detrimental effect on the quantity of blood-derived DNA specifically, reducing it by half, no similar effect was observed for touch DNA in latent FMs. This reduction led to the alteration of the major-to-minor DNA profile ratio to 70:30, thus enabling to obtain two distinct DNA profiles of the suspect from the touch DNA as well as the victim's profile from the blood. From an operational perspective, the use of AB in crime scenes may have an added value to retrieve the crucial DNA profile of the suspect, thus resurrecting a "dead-evidence."

Non-destructive DNA recovery from handwritten documents using a dry vacuum technique

Investigations of many crimes such as robberies, kidnappings, and terrorism are often associated with the recovery of a paper document which has been written by the perpetrator. Paper can provide a variety of forensic evidence such as DNA, latent fingermarks, and indented writing. The focus of this study was DNA recovery from handwritten notes through a vacuum suction device while preserving the other evidence types and the integrity of the document. Copy paper was used to create handwritten documents and sheets with deliberate fingerprints, and indentations. The homemade vacuum device consists of a glass pipette blocked with a moistened swab and attached to a vacuum source. The method collected sufficient DNA amounts for DNA typing analysis with 80% of the 11 copy paper samples tested giving probative DNA profiles with five being eligible for DNA database entry. DNA recovery was also tested on other commonly encountered paper types. DNA quantities would have been sufficient for STR typing for approximately 50% of manila envelopes and notebook paper samples, but not for magazine pages and bank deposit slips. Deliberate sebaceous and eccrine latent fingermarks placed onto copy paper and developed with magnetic fingerprint developer or 1,2 indanedione were not affected by the vacuum swabbing technique. Simulated robbery notes with indented writing and processed using an Electrostatic Detection Apparatus (ESDA) demonstrated no interference through the DNA collection. This vacuum-based collection method enables laboratories to reverse the current questioned document workflow and start with DNA collection.

Comparison of DNA typing success in compromised blood and touch samples based on sampling swab composition

Sample collection at the crime scene can introduce variations in DNA recovery based upon the substrate from which a sample is collected, the material of the collection device used, or the storage conditions after collection. There are many factors during this process that can degrade the sample during drying and storage, and before DNA extraction can be performed. The purpose of this study was to evaluate and compare the performance of standard cotton swab collection with the Bode BioSafe^® swab, which includes both a desiccant at the swab head and proprietary compounds to prevent degradation of the sample during sample collection and preservation. Blood and touch DNA samples were collected from porous and nonporous substrates and stored at elevated temperatures to simulate accelerated time. DNA quantification and STR profile data were used to assess the performance of the swabs. BioSafe^® swab collection resulted in similar DNA yields from blood samples and significantly higher DNA yields from touch samples when compared to collection with cotton swabs. BioSafe^® swabs also resulted in higher DNA integrity during long-term storage, increased STR profile success and improved retention of low-level contributor alleles.

Prevalence of DNA of regular occupants in vehicles

People will deposit, redistribute and remove biological traces when they interact with their environment. Understanding the dynamics of trace DNA is crucial to assess both the optimal sampling strategy to recover traces and the relevance of DNA evidence in the context of a case. This paper addresses the prevalence of DNA of drivers, passengers, and unknown individuals in vehicles. Five vehicles with a regular driver only, and five vehicles with a regular driver and regular passenger have each been sampled at twenty locations. Based on the findings, we propose a sampling strategy for investigative purposes as well as for evaluative purposes when evaluating the findings given scenarios that propose the person-of-interest as either the driver or passenger in a vehicle.

Comparison of five membrane filters to collect bioaerosols for airborne microbiome analysis

AIMS

Recovering DNA of airborne micro-organisms (AM) from air is a challenging task. We compared five membrane filters for bioaerosol sampling-mixed cellulose ester (MCE), polyethersulfone (PES), polyamide (PA), polytetrafluorethylene (PTFE) and polyvinylidene fluoride (PVDF)-based on their bacterial, fungal and eukaryotic DNA recoveries.

METHODS AND RESULTS

Bacterial, fungal and eukaryotic populations were quantified using quantitative PCR. With a bacterial consortium, PTFE exhibited the best recovery efficiency (113%), followed by PA (92%), PES (86%), MCE (48%) and PVDF (1%). When filters were compared with air, PA was used as a control to normalize results from the others. The bacterial, fungal and eukaryotic DNA recovery ratios were markedly greater in PES (9·3, 11·5 and 10·3 respectively) than in the remaining. Eukaryotic MiSeq sequencing revealed that PES recovered a more diverse and considerably richer assemblage (richness ratios, 4·97 vs ≤ 1·16 for PES vs the others). Rank abundance distribution analysis showed that distribution tails were longer (>4 times) in PES, but these did not differ between the remaining and PA. Community comparison showed that PES exhibited a lower variation across trials than the PA, while the remaining did not.

CONCLUSIONS

PES filter markedly outperformed the other filters in quantitative and qualitative recovery of AM.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our findings demonstrated the importance of filter selection for sampling AM.

Investigation into the prevalence of background DNA on flooring within houses and its transfer to a contacting surface

When sampling an item or surface for DNA, the collection of 'background' DNA (bDNA) from previous use poses an issue as it may impact the detectability of 'target' DNA and the interpretation of the DNA results given alleged activities. This study investigates the prevalence and transferability of bDNA on flooring surfaces within occupied houses under conditions similar to those that are encountered in casework. To assess bDNA presence and transferability, and the impact of how and who contacts the surface, areas used frequently and infrequently were targeted in the kitchen, living room, bedroom and bathroom of five houses, and two samples taken from each area; one directly from the floor and another from a cotton surface after contacting the floor. DNA was detected in 97 % (of 39) of samples collected directly from flooring, with 92 % providing interpretable profiles. DNA was detected in 85 % (of 39) samples collected from cotton swatches after contacting the floors, with 79 % providing interpretable profiles. The overall quantity, number of contributors, and likelihood of observing a major contributor was greater for samples obtained directly from the floor compared to the cotton. In 80 % of samples recovered from cotton, the quantity of DNA recovered was less than 20 % of that which was recovered directly from the floor. Overall, no trend was observed between the level of reported activity by occupants within areas of the same room and the quantity of DNA recovered directly from the flooring, the quantity of DNA transferred to and recovered from the cotton, or the number of contributors in resulting DNA profiles. In contrast, greater quantities of DNA were generally obtained from houses with a greater number of occupants. Profile composition was similar for samples collected from different areas of the same room, irrespective of the level of activity and from where the sample was obtained (i.e. directly from the floor or contacting surface). Occupants were often not detected in DNA profiles collected from rooms they were known to use and could be observed in profiles collected from rooms they reportedly did not use. The findings of this preliminary investigation provide an understanding of the complexities of transfer, persistence, prevalence and recovery of DNA traces in houses occupied by multiple people and highlights the need to consider how and who uses a space, in the investigation of criminal activities where DNA traces are recovered from, or have been in contact with, flooring.

A comparison of crystal structure in fresh, burned and archaic bone - Implications for forensic sampling

Standard protocols for extracting DNA from bone are variable and are largely dependent on the state of preservation. In archaic samples, endogenous DNA is believed to be tightly bound to crystal aggregates in the Hydroxyapatite (HAp) matrix requiring prolonged demineralisation to allow its release. By comparison, fresh bone contains abundant cellular material, discounting the need for demineralisation. Recommendations for incinerated bone, specifically how viable sampling sites should be selected and the ideal techniques for DNA recovery are unclear, and the protocol used is often selected based on macroscopic sample appearance. It has been postulated that like archaic bone, burned bone is 'highly degraded' and therefore aDNA techniques may present better results for DNA recovery than using fresh protocols. However, little research has been undertaken comparing the crystal structure of burnt, fresh and archaic bone. This study uses a combination of XRPD and SEM analysis to compare the crystalline profile and microscopic appearance of burned bone subjected to temperatures ranging from 100-1000°C, with archaic and fresh samples. Although macroscopically visually different, fresh samples and samples heated up to 500°C showed no microscopic differences or significant changes in crystallinity. By comparison, samples heated above 500°C became significantly more crystalline, with HAp crystal size increasing dramatically. Archaic samples were different again, more closely resembling the amorphous fresh samples than the highly crystalline incinerated samples. These results suggests that, potentially, samples burned at 500°C or lower can be treated as fresh samples, whilst samples exposed to higher temperatures may require adapted protocols. Whether or not these highly burned samples require demineralisation needs to be investigated.

Evaluating the persistence of laundered semen stains on fabric using a forensic light source system, prostate-specific antigen Semiquant test and DNA recovery-profiling

Semen stains on the clothes of victims of sexual assault can remain as evidence even after garments have been laundered. In this study, we aimed to investigate the effectiveness of commonly preferred methods to detect semen stains in two different fabric types that were laundered with different washing machine programmes and washing powders, and to obtain a DNA profile from the semen stains. For this purpose, a comprehensive study was performed on semen-stained underwear using three different methods for stain detection, confirmation and identification: a forensic light source (FLS) system, the prostate-specific antigen (PSA) test and DNA recovery profiling. With FLS applications, stronger fluorescence was achieved in wash protocols performed at a low temperature (30°C) on semen-stained cotton underwear. DNA recovery between 13.45 and 55.00 ng/µl was obtained by modifications in the DNA extraction step when the effect of temperature and washing powder on DNA recovery was evaluated, and these were enough for short tandem repeat (STR) typing in all samples. This study shows that when semen-stained underwear is washed after a month, some semen stains can be determined by FLS and PSA, and all stains can be identified by STR analyses.

DNA detection of a temporary and original user of an office space

There is a need to improve our awareness of the transfer, persistence, prevalence and recovery of DNA (DNA-TPPR) from items/surfaces, and within different spaces and circumstances, to assist sample targeting during collection and activity level assessments. Here we investigate DNA-TPPR within office spaces. Specifically, to what extent DNA, left by a temporary user of an office space that has been occupied by a regular user for an extended period, is detectable when the duration of their temporary occupancy and their general activities are known. Also, how readily the DNA of the regular user is still detectable after a known period of occupancy by another person, and to what extent DNA of others is present. Samples were collected from 18 core items/surfaces within eight single use office spaces that had been used temporarily by another occupant for 2.5-7 h. Four of these offices were within one forensic laboratory and four within another. Each lab collected and processed the samples to generate DNA profiles using their own set of methodologies. The owner/regular user of an office space was found to be the major/majority contributor to profiles from most items within the space, even after temporary use by another person. The detectability of the temporary occupier of an office space varied among offices and items. The temporary occupier was not observed on all items touched. In most instances, when detected, the temporary occupier was known to have touched the surface at some stage. Therefore, where one is seeking to collect samples that may detect a temporary user of a space, it is advisable to target several potentially touched sites. A difference in methodologies applied from collection through to profiling appears to impact DNA yields and profile types. Ascertaining the impact of using different methodologies on the profiles generated from collected samples, requires further research. More research is also needed to generate data to help determine frequency estimates for different types of profiles given different user histories of an item or space.

An Internal Control for Evaluating Bisulfite Conversion in the Analysis of Short Stature Homeobox 2 Methylation in Lung Cancer

Objective: The methylation status is considered as powerful diagnostic, prognostic, and predictive biomarkers. However, the limited DNA amount and conversion efficiency after bisulfite treatment are considerable hindrances in quantitative methylation analysis. In this study, we designed an artificial internal control (IC) system that contained the cytosine-free fragment (CFF) following CpG sequences of the SHOX2 promoter whose methylation status has been described as a valuable biomarker of lung cancer. Its performance in quantifying DNA recovery and bisulfite conversion efficiency as well as in detecting false-positive SHOX2 methylation was determined on samples from lung cancer patients. Material and Methods: The IC system is composed of two pConIC and pUnIC plasmids that both contain a cytosine-free (CF) sequence derived from the CFF and the CpG containing SHOX2 sequences. They are identical in sequence, except that in the ConIC insert, all cytosines have been converted into thymines. Thus, the ConIC can be used as calibrator of 100% bisulfite conversion efficiency, while the UnIC is the indicator in order to evaluate the DNA recovery, bisulfite conversion efficiency of the SHOX2 promoter sequence by quantitative real time PCR. Results: The copy number of the target sequences impacted on both DNA recovery rates and bisulfite conversion efficiency. An amount of 0.005 ng pUnIC (106 copies) showed recovery rate of 18%, similar to that of pConIC, and a bisulfite conversion efficiency of the SHOX2 reaching 98.7%. On the contrary, higher copy number of pUnIC showed incomplete conversion (<85%) and over recovery (~42%). Using this calibrator/indicator couple, we were able to detect false-positive SHOX2 methylation (3.77% instead of 0.03%) due to incomplete bisulfite conversion.Conclusion: Our results proposed a customizable internal control using the ConIC/UnIC as calibrator/indicator to quantify simultaneously and accurately the DNA recovery and bisulfite conversion efficiencies of individual sequence as well as whole genome in methylation assays, thus promoting the validation of standardized clinical DNA methylation biomarker values to progress toward clinical applications

Sharing data on DNA transfer, persistence, prevalence and recovery: Arguments for harmonization and standardization

Sharing data between forensic scientists on DNA transfer, persistence, prevalence and recovery (TPPR) is crucial to advance the understanding of these issues in the criminal justice community. We present the results of a collaborative exercise on reporting forensic genetics findings given activity level propositions. This exercise outlined differences in the methodology that was applied by the participating laboratories, as well as limitations to the use of published data on DNA TPPR. We demonstrate how publication of experimental results in scientific journals can be further improved to allow for an adequate use of these data. Steps that can be taken to share and use these data for research and casework purposes are outlined, and the prospects for future sharing of data through publicly accessible databases are discussed. This paper also explores potential avenues to proceed with implementation and is intended to fuel the discussion on sharing data pertaining to DNA TPPR issues. It is further suggested that international standardization and harmonization on these topics will benefit the forensic DNA community as it has been achieved in the past with the harmonization of STR typing systems.

Acetone facilitated DNA sampling from electrical tapes improves DNA recovery and enables latent fingerprints development

Electrical tapes (ETs) are a common component of improvised explosive devices (IEDs) used by terrorists or criminal organizations and represent a valuable forensic resource for DNA and latent fingerprints recovery. However, DNA recovery rates are typically low and usually below the minimal amount required for amplification. In addition, most DNA extraction methods are destructive and do not allow further latent fingerprints development. In the present study a cell culture based touch DNA model was used to demonstrate a two-step acetone-water DNA recovery protocol from ETs. This protocol involves only the adhesive side of the ET and increases DNA recovery rates by up to 70%. In addition, we demonstrated partially successful latent fingerprints development from the non-sticky side of the ETs. Taken together, this protocol maximizes the forensic examination of ETs and is recommended for routine casework processing.

A Modified SDS-Based DNA Extraction Method for High Quality Environmental DNA from Seafloor Environments

Recovering high quality genomic DNA from environmental samples is a crucial primary step to understand the genetic, metabolic, and evolutionary characteristics of microbial communities through molecular ecological approaches. However, it is often challenging because of the difficulty of effective cell lysis without fragmenting the genomic DNA. This work aims to improve the previous SDS-based DNA extraction methods for high-biomass seafloor samples, such as pelagic sediments and metal sulfide chimney, to obtain high quality and high molecular weight of the genomic DNA applicable for the subsequent molecular ecological analyses. In this regard, we standardized a modified SDS-based DNA extraction method (M-SDS), and its performance was then compared to those extracted by a recently developed hot-alkaline DNA extraction method (HA) and a commercial DNA extraction kit. Consequently, the M-SDS method resulted in higher DNA yield and cell lysis efficiency, lower DNA shearing, and higher diversity scores than other two methods, providing a comprehensive DNA assemblage of the microbial community on the seafloor depositional environment.