Forensic & Investigative Sciences Program Theses and Dissertations

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Utilization of Blow Flies (Phormia regina) as Vertebrate Resource Diversity Indicators
(2022-08) Jones, Ashton Brooke; Picard, Christine; Walsh, Susan; Wells, Jeffrey
Blow flies are often utilized in the field of forensic science due to their ability to aid in the estimation of time since death. Currently, estimations of postmortem interval require assumptions to be made and are prone to a margin of error, prompting research that may contribute to more accurate postmortem interval estimations and help to fill in the gaps of unknown information. Blow flies are necrophagous, feeding on feces and carrion, and therefore, are constantly sampling the environment. This behavior can be exploited in order to monitor the biodiversity in an environment. Through analysis of DNA isolated from the guts of blow flies, information can be obtained regarding what animals have died in an environment, what animals are still living in that environment, and the abundance and diversity of the animals present in a specific environment. Using fly-derived ingested DNA is a viable method for vertebrate resource identification and biodiversity monitoring. Over the course of a two-summer sampling period, in and around two national parks, a total of 162 blow fly (Phormia regina) samples returned a positive vertebrate DNA identification, with 33 species identified from five animal orders. Of the total number of flies collected and analyzed, 23.58% returned a positive vertebrate species identification. The method detected both abundant and common species based on National Park surveys, as well as some uncommon or unknown to the park species. In the SE region, 9 individuals belonging to the Rodentia order, 12 individuals belonging to the Artiodactyla order, 21 individuals belonging to the Carnivora order, 1 individual belonging to the Cingulata order, and 3 individuals belonging to the Lagomorph order were detected. In the SE region, 63% of the individuals detected belonged to the common category, 14% of the individuals detected belonged to the uncommon category, and 23% of the individuals detected belonged to the not in park/unknown category. In the NW region, 42 individuals belonging to the Rodentia order, 46 individuals belonging to the Artiodactyla order, and 28 individuals belonging to the Carnivora order were detected. In the NW region, 52% of the individuals detected belonged to the abundant category, 36% of the individuals detected belonged to the common category, and 12% of the individuals detected belonged to the uncommon category. The relative biodiversity of the sampled environment can be inferred. In the SE region, the Shannon Biodiversity Index was calculated to be 2.28 with an evenness of 0.844, while in the NW region, the Shannon Biodiversity Index was calculated to be 2.79 with an evenness of 0.855. Unsurprisingly, there was greater biodiversity in the Northwest Park samples than in the Southeast Park samples. Additionally, the ideal weather conditions for blow fly collection were determined be at a temperature of between 60- and 80-degrees Fahrenheit, a relative humidity between 50% and 60%, no precipitation, and a wind speed between 2 and 8 miles per hour. This information has further implications in the field of forensic science, specifically dealing with wildlife forensics, pathogen distributions, and can help to improve accuracy in regards to postmortem interval (PMI) estimations.
The Detection and Identification of Explosives by Canines and Chemical Instrumentation
(2022-05) Reavis, Madison Dylan; Goodpaster, John V.; Manicke, Nicholas; Bors, Dana
With bombings in the United States on the rise for the first time since 2016, the detection and identification of explosives remains of pertinent interest to law enforcement agencies. This work presents two soon-to-be published research articles that focus on the detection and identification of explosives by both chemical instrumentation and canines. The first article, Quantitative Analysis of Smokeless Powder Particles in Post-Blast Debris via Gas Chromatography/Vacuum Ultraviolet Spectroscopy (GC/VUV), utilizes gas chromatography/vacuum ultraviolet spectroscopy (GC/VUV) to determine the difference in chemical composition of two smokeless powders in both pre- and post-blast conditions. The compounds of interest in this study were nitroglycerin, 2,4- dinitrotoluene, diphenylamine, ethyl centralite, and di-n-butyl phthalate. Concentration changes between pre- and post-blast smokeless powder particles were determined as well as microscopic differences between pre- and post-blast debris for both smokeless powders in all devices. To our knowledge, this is the first use of GC/VUV for the quantification of explosives. The second article, An Odor-Permeable Membrane Device for the Storage of Canine Training Aids, proposes the use of an odor-permeable membrane device (OPMD) as a standardized storage method for canine training aids. It is hypothesized that the OPMD would minimize cross-contamination between training aids, and that the OPMD could be used for canine training as well as storage. The goal of this research is to use flux and evaporation rate to quantify the explosive odor that escapes from the OPMD compared to unconfined explosives. Preliminary data suggests that there is an exponential relationship between relative boiling point and evaporation rate. It has been determined that compounds with higher boiling points have lower evaporation rates than compounds that have lower boiling points. The materials studied thus far are known odor compounds produced by explosive formulations. These include nitromethane, nitroethane, 1- nitropropane, r-limonene, and toluene.
Electrochemical Characterization of Fentanyl for Forensic Analysis
(2021-08) Sellnau, Natalie; Deiss, Frederique; Goodpaster, John; Manicke, Nicholas
The use and abuse of fentanyl has risen drastically over the last several decades. The abuse of this substance has created a hazardous situation for law enforcement and first responders because they could arrive at locations and not necessarily know that they will encounter fentanyl or a fentanyl analog. Fentanyl analogs are substances that have a similar structure to fentanyl, and while the analogs may have additional or altered groups on the molecule, the backbone structure remains similar. This work focus on the electrochemical characterization of fentanyl as a stepping stone for the detection of both fentanyl and later fentanyl analogs by electrochemistry. The metabolic reaction of fentanyl is an N-dealkylation to norfentanyl, occurring in the liver, and can be mimicked by electrochemistry through the irreversible oxidation of fentanyl. This electrochemical reaction is hypothesized to generate electroactive metabolites in solution. The combination of the visualization of both the irreversible oxidation with the development of the additional metabolic electrochemical peaks would constitute a unique electrochemical signature for fentanyl and fentanyl analogs towards a universal rapid screening assay. The electrochemical behavior of fentanyl was characterized in depth using multiple electrochemical techniques such as cyclic voltammetry (CV), square wave voltammetry (SWV) and differential pulse voltammetry (DPV). The optimization of the supporting electrolyte, the potential range, and methods to decrease the background current were explored with CV. To work towards a more portable system, screen printed electrodes were used. The observation of the metabolic peaks remained challenging, and different methods were attempted to achieve it. The quantification of fentanyl was successfully demonstrated using the different electrochemical systems proposed in this work. The electrochemical characterization of fentanyl and the optimization of multiple experimental parameters were the first step in developing a universal, rapid, electrochemical sensing method for the detection of fentanyl and fentanyl analogs.
Understanding the Relationship Between HERC2 and OCA2 Variants and Iris Pigmentation Genetics
(2021-08) Wallpe, Clarissa; Walsh, Susan; Picard, Christine J.; Marrs, Kathleen A.
Externally visible characteristics (EVCs) predicted from an unknown sample of DNA are particularly useful in forensics as they can provide information beyond that of an STR profile. Current EVCs which are highly studied and well-predicted include iris, hair, and skin color. Notably, models predicting iris color, such as IrisPlex, are the most accurate with up to ~95% accuracy; however, some inaccurate predictions occur, as is evidenced by the ~5%. Often, these are due to green or hazel eyes, which are frequently viewed as intermediate. Though, some of the inaccurate predictions are due to true-blue being predicted as brown and vice versa. Previous research has theorized the possibility of two SNPs, rs12913832 and rs1800407, acting as a functional haplotype affecting iris color. rs12913832 is recognized as the most predictive SNP for iris color and highly significant in other pigmentation phenotypes; presently, rs1800407 is the second-ranked SNP in the IrisPlex 6-SNP system. Both SNPs are highly variable in Europe, where the majority of variation in iris color originates. In the present study, we explore the SNP variation present in the genetic regions of OCA2-HERC2 as well as possible haplotypes. Our research centers around the functional haplotype and the addition of SNPs to the functional haplotype. In addition, three different ways of classifying the phenotype are assessed simultaneously. First, using a 4-point categorical phenotype—blue/blue grey, blue/green yellow, hazel/light brown, and dark brown. Second, calculating a continuous scale from a quantitative phenotype in which the percentage of each categorical color has been measured. Third, using the IrisPlex 6-SNP system to predict eye color and identify individuals which have been inaccurately predicted. Exploration of the SNP and haplotype variation resulted in two SNPs for both the categorical and quantitative phenotypes which were significantly correlated with hazel/light brown—rs1448484 and rs61335644, both as independent SNPs and when assessed in a haplotype with rs1800407-rs12913832. SNP rs1448484 has been associated with skin pigmentation previously and is located in a possible transcription factor binding site. SNP rs61335644 is not presently associated with pigmentation but is in complete LD with two SNPs in and around regulatory regions present in HERC2. Finally, the addition of rs1448484 and rs61335644 into the current IrisPlex 6-SNP system slightly improved each of the tested performance metrics for hazel/light brown and dark brown. Within the inaccurately predicted phenotypes, rs1800407 is confirmed to affect both inaccurately predicted groups and is the most significant SNP. Additionally, rs121918166, a missense variant in OCA2, is the second most significant SNP in true blue predicted as brown. Both SNPs were also the two most significant haplotypes with at least one allele being derived. Therefore, the next steps should include the addition of the functional haplotype and rs121918166 into the current IrisPlex model, and further testing of rs1448484 and rs61335644 on a molecular level. Consequently, the current IrisPlex model should also be reassessed on an independent test set using the 4-point categorical scale rather than the present 3-point scale.
Paper Spray - Mass Spectrometry: Investigation of Sampling Devices for Illicit Drug Detection and Quantification
(2021-07) Nguyen, Chau Bao; Manicke, Nicholas E.; Goodpaster, John V.; Deiss, Frederique T.
Paper spray - mass spectrometry (PS-MS) has been developed as a rapid and direct ionization method for qualitative and quantitative analysis of complex samples at trace levels. In this work, different sampling devices for PS-MS were investigated to improve the assay’s simplicity and sensitivity over traditional approaches. In particular, chapter two characterizes an alternate paper substrate to enhance drug detection on surfaces like asphalt, cloth, concrete, aluminum, and glass. Analysis occurs on a single spray ticket coated with pressure-sensitive adhesive (PSA), also known as Post-it notes to detect and quantify drug residues. A PS-MS method utilizing PSA paper was developed to detect a mixture of ten drugs off of various surfaces to evaluate the qualitative and quantitative capabilities of the aforementioned substrate. After the method development on a conventional linear ion trap mass spectrometer, the assay was translated for use on a portable mass spectrometer to evaluate the suitability of the pressure-sensitive adhesive paper substrate in the field in chapter three. Chapter four introduces a sampling device combined with a snap-in solid-phase extraction (SPE) column. The new cartridge design not only inherits the functions from the first iteration SPE cartridge, including extraction and preconcentration from complex samples, but also exhibits greater flexibility in volume control and ease of use for on-site sample collection.
Critical Comparison of Total Vaporization- Solid Phase Microextraction vs Headspace- Solid Phase Microextraction
(2021-05) Train, Alexandra; Goodpaster, John; Manicke, Nicholas; Picard, Christine
Solid Phase Microextraction (SPME) is a popular sampling technique that can be paired with Gas Chromatography/Mass Spectrometry (GC-MS). SPME-GC-MS is used in forensic chemistry due to its simplification of the sample preparation process. Headspace-Solid Phase Microextraction (HS-SPME) is a technique where the sample is heated to generate volatiles in the headspace of the vial. A SPME fiber is then inserted into the vial and the compounds in the headspace will bind to the fiber. Total Vaporization- Solid Phase Microextraction (TV-SPME) is a technique that is derived from the HS-SPME technique. In Chapter 1, the critical comparison of HS-SPME and TV-SPME is discussed. Samples including marijuana, essential oils, and CBD oil were utilized to compare the two techniques. The compounds of interest in marijuana are the three main cannabinoids: cannabinol (CBN), cannabidiol (CBD), and tetrahydrocannabinol (THC). The sample preparation and GC-MS parameters were kept the same for all samples to determine which SPME technique works best for these sample types and yielded the greatest sensitivity. It was found that HS-SPME shows greater sensitivity with CBN and equivalent sensitivity with essential oils, THC and CBD. In Chapter 2, the detection of synthetic cannabinoids utilizing liquid-liquid injection as well as HS-SPME and TV-SPME is discussed. The detection of these compounds is important because this type of drug has become more prevalent in the United States because they can be chemically altered slightly so they still have the effects of a drug but can evade drug legislation. The detection of synthetic cannabinoids using liquid injection was found to be successful but detection using HS-SPME and TV-SPME was found to be unsuccessful. In Chapter 3, the analyses of real and artificial saliva utilizing HS-SPME and TV-SPME is discussed. Determining the compounds present in real saliva and artificial saliva will be of importance for future research into determining if the presence of drugs in saliva can be analyzed with these techniques. The analyses of real and artificial saliva were found to be successful using HS-SPME, without derivatization, and TV-SPME, with and without derivatization. Many of the compounds present in the real saliva were detected and were confirmed to be compounds regularly found in saliva by other scientific literature.
An investigation of genetic variability in Lucilia cuprina and Musca domestica utilizing phylogenetic and population genetic approaches
(2020-08) Doll, Laura Catherine; Picard, Christine J.; Roper, Randall; Tarone, Aaron
Forensic entomology is a subdiscipline of entomology that involves the use of insect behavior and developmental data to aid in criminal investigations. Genetic data has become increasingly important to the field as there has been a push for DNA-based species identification methods of forensically relevant insects. Genetic data can also elucidate population structure and relatedness of these insects, and such knowledge can contribute to the development of more specific datasets for insects in different regions. The first study presented here investigated the phylogenetics of sister species Lucilia cuprina and Lucilia sericata to identify possible subspecies divisions and issues with DNA-based identifications in the United States. The initial aim of this study was to identify genetic differences between specimens of L. cuprina that preferred live versus carrion flesh. Flies collected from Indiana, USA and South Africa were sequenced and analyzed. Upon sequencing of the genes COI, Period, and 28s, our results indicated that L. cuprina from Indiana possess a unique combination of nuclear and mitochondrial haplotypes that suggest a unique lineage, possibly indicating modern hybridization with L. sericata. The inability of both nuclear and mitochondrial genes to distinguish between L. cuprina and L. sericata raises questions about the capabilities of DNA-based species identifications within this genus. Additionally, the inability of these genes to distinguish between specimens that preferred live versus carrion flesh highlights a need for continued research of these behavioral differences. The second study presented here investigated the population structure and relatedness of house flies in the American southwest in relation to a civil lawsuit where neighbors of a poultry farm alleged that flies were emanating from the farm to their homes. Musca domestica (house fly) specimens were collected from the chicken farm and from locations in varying directions and distances from the farm. Amplified fragment length polymorphism (AFLP) analysis was performed and the data were used in a number of analyses. Population reallocation simulations generally indicated that samples from different locations were not genetically different enough from other locations to allocate to their true origin population over others. Kinship analysis showed differences in samples collected in a later season that indicate a genetic bottleneck over time. Population structure analysis indicated the presence of two intermixing genetic populations in the dataset. AMOVA revealed that the majority of genetic variation laid within, rather than among, populations. A Mantel test revealed no significant correlation between genetic and geographic distances. These results indicate that the M. domestica population in this region of southwestern America is large and intermixing, with no clear genetic distinctions between specimens collected at the poultry farm versus the surrounding locations. In regard to the civil lawsuit, it was not possible to conclude that the flies did not emanate from the poultry farm. In a broader perspective, these data can be utilized to develop pest management strategies in this region. Overall, the data from both studies presented here will be useful to forensic investigations, development of more specific and detailed data and identification techniques, and pest control measures.
Optimization of Marker Sets and Tools for Phenotype, Ancestry, and Identity using Genetics and Proteomics
(2019-08) Wills, Bailey; Walsh, Susan; Picard, Christine; Skalnik, David
In the forensic science community, there is a vast need for tools to help assist investigations when standard DNA profiling methods are uninformative. Methods such as Forensic DNA Phenotyping (FDP) and proteomics aims to help this problem and provide aid in investigations when other methods have been exhausted. FDP is useful by providing physical appearance information, while proteomics allows for the examination of difficult samples, such as hair, to infer human identity and ancestry. To create a “biological eye witness” or develop informative probability of identity match statistics through proteomically inferred genetic profiles, it is necessary to constantly strive to improve these methods. Currently, two developmentally validated FDP prediction assays, ‘HIrisPlex’ and ‘HIrisplex-S’, are used on the capillary electrophoresis to develop a phenotypic prediction for eye, hair, and skin color based on 41 variants. Although highly useful, these assays are limited in their ability when used on the CE due to a 25 variant per assay cap. To overcome these limitations and expand the capacities of FDP, we successfully designed and validated a massive parallel sequencing (MPS) assay for use on both the ThermoFisher Scientific Ion Torrent and Illumina MiSeq systems that incorporates all HIrisPlex-S variants into one sensitive assay. With the migration of this assay to an MPS platform, we were able to create a semi-automated pipeline to extract SNP-specific sequencing data that can then be easily uploaded to the freely accessible online phenotypic prediction tool (found at https://hirisplex.erasmusmc.nl) and a mixture deconvolution tool with built-in read count thresholds. Based on sequencing reads counts, this tool can be used to assist in the separation of difficult two-person mixture samples and outline the confidence in each genotype call. In addition to FDP, proteomic methods, specifically in hair protein analysis, opens doors and possibilities for forensic investigations when standard DNA profiling methods come up short. Here, we analyzed 233 genetically variant peptides (GVPs) within hair-associated proteins and genes for 66 individuals. We assessed the proteomic methods ability to accurately infer and detect genotypes at each of the 233 SNPs and generated statistics for the probability of identity (PID). Of these markers, 32 passed all quality control and population genetics criteria and displayed an average PID of 3.58 x 10-4. A population genetics assessment was also conducted to identify any SNP that could be used to infer ancestry and/or identity. Providing this information is valuable for the future use of this set of markers for human identification in forensic science settings.
Automated derivatization and identification of controlled substances via total vaporization solid phase microextraction (Tv-Spme) and gas chromatography-mass spectrometry (Gc-Ms)
(2018) Hickey, Logan D.; Goodpaster, John
Gas chromatography-mass spectrometry (GC-MS) is one of the most widely used instrumental techniques for chemical analyses in forensic science laboratories around the world due to its versatility and robustness. The most common type of chemical evidence submitted to forensic science laboratories is seized drug evidence, the analysis of which is largely dominated by GC-MS. Despite this, some drugs are difficult or impossible to analyze by GC-MS under normal circumstances. For these drugs, derivatization can be employed to make them more suitable for GC-MS. In Chapter 1, the derivatization of primary amino and zwitterionic drugs with three different derivatization agents, trifluoroacetic anhydride (TFAA); N,O-bis(trimethylsilyl)trifluoroacetamide + 1% trimethylchlorosilane (BSTFA + 1% TMCS); and dimethylformamide dimethylacetal (DMF-DMA), is discussed. The chromatographic performance was quantified for comparison between the derivatives and their parent drugs. Peak symmetry was compared using the asymmetry factor (As), separation efficiency was measured by the number of theoretical plates (N), and sensitivity was compared by measuring the peak areas. In Chapter 2, derivatization techniques were adapted for an automated on-fiber derivatization procedure using a technique called total vaporization solid phase microextraction (TV-SPME). TV-SPME is a variation of SPME in which a small volume of sample solution is used which can be totally vaporized, removing the need to consider the equilibrium between analytes in the solution and analytes in the headspace. By allowing derivatization agent to adsorb to the SPME fiber prior to introduction to the sample vial, the entire derivatization process can take place on the fiber or in the headspace surrounding it. The use of a robotic sampler made the derivatization procedure completely automated. In Chapter 3, this on-fiber derivatization technique was tested on standards of 14 controlled substances as well as on realistic samples including simulated “street meth”, gamma-hydroxybutyric acid (GHB) in mixed drinks, and hallucinogenic mushrooms, and was also tested on several controlled substances as solid powders. Future work in this area is discussed in Chapter 4, including adapting the method to toxicological analyses both in biological fluids and in hair. Some of the expected difficulties in doing so are discussed, including the endogenous nature of GHB in the human body. The presence of natural GHB in beverages is also discussed, which highlights the need for a quantitative addition to the method. Additional method improvements are also discussed, including proposed solutions for complete derivatization of more of the analytes, and for decreasing analysis time.
Forensic applications of associating human scalp hair morphology and pigmentation analysis at the microscopic and molecular level
(2017-08) Stubbs, Wesli Kay; Walsh, Susan; Picard, Christine; Berbari, Nicholas
Criminal investigation and the science behind evidence analysis is an ever- growing niche, and forensic DNA phenotyping (FDP) is no exception. For years the only information given to authorities regarding DNA found at a crime scene was STR analysis and matching to a comparative DNA sample from a known source. However, what happens when there is no suspect to compare DNA profiles, or the case involves a missing person where the only available piece of evidence is a biological sample found at the scene? Before FDP, not much could be done with the DNA sample and the investigation would be stalled. Now it is becoming possible to statistically predict an individual’s visual characteristics using FDP. Currently, with the use of Irisplex, HIrisplex, and HIrisplex-S, statistical analyses and predictions can be done for categorical eye, hair, and skin color by looking at specific genes and their associative SNPs, such as HERC2 and OCA2. The more that is understood about trait-determining genes and their functional significance with regards to our physical traits, the more phenotypes can be added to these prediction tools. In an effort to discover additional genes associated with human phenotypes, this study looked at thirty-two pigmentation-associated candidate genes, and eleven hair structure and morphology associated genes in owl monkey pelage samples. Although the samples were not of human origin, it is important to point out the high conservation between humans and their non-human primate relatives. The owl monkeys used in this study were helpful for tracking expression levels of genes controlling differentpigmentation and hair structure types, because each monkey had intra-individual variation in thickness and in coat color which allowed the generation of potential candidate genes for human investigation. Of the 43 total candidate genes analyzed, 36 had successful amplification, and 28 showed a significant difference in expression when comparing the different samples. The second part of this study was to compare quantitative characteristics of human hair in physical samples and two-dimensional (2D) photos. A test set of 45 individuals had 3-5 hairs from the vertex of their head plucked and analyzed, and a 2D photograph was taken of their scalp hair. The idea was to be able to make quantitative phenotypes in hair (such as hair width, amount of curl) from 2D imagery, when physical samples are not available for analysis. This is due to the fact that the majority of genotype-phenotype databases consist solely of photographic imagery, and seldom have hairs that can be microscopically prepared for analysis. Defining measurable phenotypes from 2D photos that strongly correlate with their physical counterparts allow for the generation of a more accurate phenotype for future genome wide association studies (GWAS) within and outside this laboratory that study hair thickness and hair curl. Three different quantitative phenotypes were compared between the microscopic and 2D photo- analysis.

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