Animal sexual abuse (ASA) involves the sexual molestation of animals by humans. The identification of semen provides a legally-accepted indicator that sexual activity occurred, while forensic DNA analysis provides a lead to a potential suspect. After conducting a systematic literature review, no previous research investigating semen and/or DNA recovery from animals over time was found. Therefore, this pilot study aimed to assess the recovery of human semen and DNA from animal fur over a two-week period to establish baseline data pertaining to evidence retention in the ASA context. This pioneer study also attempted to contribute towards the development of a suitable animal fur model on which to perform experiments. Daily swabbing and testing of semen from three fur models (unpreserved baboon fur, preserved nyala hides and faux fur) showed that semen could still be detected at 14 days using standard presumptive and confirmatory tests. Although DNA degradation showed a statistically significant increase over time, forensically usable DNA profiles (≥ 12 fully typed short tandem repeat loci) were consistently obtained. There was significantly higher DNA degradation in samples from the baboon fur compared to the others, while DNA concentrations were significantly different between each fur model. These differences highlight that future research must consider the choice of fur model to best represent the animal of interest; e.g. dissected fur from a recently deceased animal would best mimic a fatal ASA case. The insight regarding the choice of animal model hopes to be of benefit for future research, which should focus on the influence of more realistic variables (e.g. movement and body heat) on semen and DNA retention on animal fur. Overall, this study successfully generated baseline data, and provides a foundation for additional research, which hopes to eventually assist in the interpretation of forensic evidence in the global burden of ASA.

Very little chemical information is known about substances being abused in South-Africa. This can be attributed to the fact that possession of drugs constitutes a criminal offence. Not much research is done, and with the exception of self-reported, rehabilitation institution data, from the South African Community Epidemiology Network on Drug Use (SACENDU) and the South African Police drug related arrest data, no other data on drugs and drug use, is publically available. Drugs are being manufactured from legal and illegal chemicals in clandestine laboratories, not complying with any health, safety or quality standards causing a serious health risk in communities. The strategy for the fight against drug abuse in South Africa, the National Drug Master Plan 2013-2017 (NDMP), is compiled by the Central Drug Authority (CDA). Without proper research, data to base decisions and strategies on and proper measuring of achievements, the implementation of the plan suffers as a consequence. The Forensic Science Laboratory (FSL) of the South African Police Service (SAPS), is responsible for the chemical testing of substances, suspected of being illegal drugs, for identification purposes. This supports the prosecuting of suspects during criminal procedures. With the active ingredient known, the use of street names e.g. Tik, Choef or Speed (all referring to methamphetamine) can be abandoned and confusion and misconceptions eliminated. This pilot study investigates the arrest data, in combination with the charge laid against the arrestee and the chemically identified active ingredient in each case. Arrest data revealed a 400% increase in drug related arrests over the last 10 years, while the NDMP requires a 10% decrease. It further highlights the fact that the measurement of success (number of arrests) in the SAPS, resulted in a focus on arresting persons in possession of drugs. The dealers and manufacturers were not adequately addressed and prevention, through chemical monitoring, suffered as a result. This study also clearly revealed that international trends are not a definite indication of the extent and type of drug abuse in South African Communities. The study further attempts to contribute, and to better describe the situation of drugs and drug abuse in communities. This in turn, will provide data to develop evidence based strategies, designed to meet the defined needs of communities, one of the aspects highlighted by the minister in the NDMP, namely an intervention based on reality and local statistics. It is therefore clear that a scientific understanding of the composition of abused substances can direct treatment, policy, prevention measures and provide intelligence to combat drug abuse and illegal drug manufacturing in South Africa.

Background: Sudden unexpected death in infancy (SUDI) is among the most frequent causes of mortality in infants less than one year of age. Respiratory infections have been identified as the most frequent cause of death in these infants. Yet, the broad range of respiratory pathogen that might be involved in SUDI is poorly studied. This study aimed to investigate the incidence of the respiratory pathogens in SUDI. Methods: A prospective study was carried out on SUDI cases admitted to Salt River Forensic Pathology Laboratory from February 2015 through May 2015. Cerebrospinal fluid, pericardial fluid and lung biopsy were collected from each study participant during post-mortem examination. Total nucleic acids were extracted on the automated QIAsymphony platform. The microbial diversity was investigated using a commercialized multiplex real-time PCR assay, the "FTD Respiratory pathogens 33" kit. This assay is able to detect 21 viruses, 11 bacteria and one fungus. In each real-time PCR run, a positive and non-template sterile water were included as controls. Results: Thirty SUDI cases (median age, 3 (interquartile range (IQR): 2 - 8 months) were included in the study. Twenty participants were males. Positive microbiological results from at least one of the three samples were obtained in 28 cases (93%). According to the type of sample, respiratory pathogens were detected in almost all the lung biopsies (93%), while it was only detected in 60% and 50% of the cerebrospinal and the pericardial fluids, respectively. The median cycle threshold value was lower in lung biopsies (30 (IQR: 28 ‒ 35)) compared to both cerebrospinal (34 (IQR: 30 ‒ 36)) and pericardial fluids (35 (IQR: 33 ‒ 35)) (p= 0.039). In lung biopsies, the most commonly detected bacteria were K. pneumoniae (47%, 14/30) and M. catarrhalis (20%, 6/30). H. influenza (7%, 2/30) and M. pneumoniae (7%, 2/30) were the bacteria often detected in pericardial fluid and cerebrospinal fluid, respectively. Human Metapneumovirus was the most frequently virus detected in all three sample types assessed, accounting for 33% (10/30) in cerebrospinal fluid, 37% (11 /30) in pericardial fluid and 57% (17/30) in lung biopsy samples, respectively. A single type of pathogen was detected n seven of the 28 positive cases. Conclusion: This study highlights the potential implication of respiratory infection in SUDI and it reports one of the highest incidences of respiratory pathogens in SUDI cases. In addition, it is the first to report the high incidence rate of Human Metapneumovirus in SUDI cases. The findings also showed that the majority of SUDI cases are associated with synergetic interaction of multiple respiratory infections. However, data related to histopathology and bacterial culture were not available. A broad range of respiratory pathogens should be included in the routine investigation of SUDI cases with more sensitive diagnostic methods.

The burden of unresolved crime in South Africa highlights the need to improve methods of identifying perpetrators of crimes. One globally accepted method for human identification is forensic DNA profiling. Since trace evidence is often retrieved in small amounts, the optimal recovery of DNA from these samples is crucial. Methods for the recovery of touch DNA from swabs typically make use of a spin basket or filter, combined with a centrifugation step, to enhance the release of cells from the swab prior to DNA extraction. The NucleoSpin® Forensic Filter (Macherey-Nagel, Düren) is one such example, but it has not been thoroughly assessed on touch DNA samples. This study aimed to assess if the inclusion of the NucleoSpin® Forensic Filter significantly improved DNA recovery and DNA profiling success from cotton and flocked swabs used to collect touch DNA and buccal cells (control). Buccal cells and touch DNA samples were collected from 25 volunteers using each swab type (cotton and flocked) in duplicate. DNA was extracted from the samples using the NucleoSpin® DNA Forensic kit, one set with, and the other set without, NucleoSpin® Forensic Filters. DNA concentration was assessed using Qubit™ fluorometry and qPCR, and DNA profiling was done using the PowerPlex® ESX 16 system. The inclusion of the NucleoSpin® Forensic Filters significantly improved DNA concentration in buccal cells collected using flocked swabs (p = 0.035). However, no significant differences were noted for touch DNA samples, for either swab type. There was also no significant difference in DNA profiling success when NucleoSpin® Forensic Filters were used, regardless of swab and sample type. These results suggest that the NucleoSpin® Forensic Filters should not be included in the DNA extraction workflow, particularly for touch DNA samples. With only 16 % of touch DNA samples yielding full DNA profiles, there is the need to improve DNA recovery. Factors such as swab type and swab preservation buffers, should be investigated in future research.

This dissertation outlines the history of the discipline of forensic archaeology in South Africa, reviewing its development over the years. Forensic archaeology is an important discipline in the detection and recovery of human remains and related evidence. While forensic archaeology has been shown to be important, it’s existence is largely within the shadows of forensic anthropology. What is further evident is that it’s development has been significantly varied from one country to the next. I principally focused on four countries (Australia, the United Kingdom, the United States of America, and South Africa) to critically assess its historical development. Furthermore, two sets of respondents were interviewed through the use of questionnaires to provide the necessary insights. These were the students studying Physical Anthropology (ANA 315) and the professionals working directly and indirectly within the industry of forensic archaeology. I found that the discipline is in its embryonic stages in the country, with no one really identifying as a forensic archaeologist. There are no independent courses offered for one to train as a specialist in the field. Equally, there are no set of requirements for those who wish to practice as forensic archaeologists. / Dissertation (MA (Archaeology))--University of Pretoria, 2020. / Anthropology and Archaeology / MA (Archaeology) / Unrestricted

Tooth mark and gnaw damage modifications on bone from African carnivores have been extensively examined; however, there are little data on North American carnivores, especially on ursids. Tooth mark modifications include pits, punctures, scores, and furrows, while gnaw damage modifications include crenellated margins, edge polish, scalloping, scooping, and crushed margins. Forensically, tooth mark identification and measurements allow for easier identification of species involved in cases containing predator or scavenger alteration. The present study hypothesized that black bear (Ursus americanus) and grizzly bear (U. arctos) tooth marks will be able to be distinguished from one another and the two bear species will have different gnawing patterns. Further, the study hypothesized that ursid tooth marks and gnaw damage will be distinguishable from other documented carnivore alterations. In the present study, black bears and grizzly bears from the Oakland Zoo were fed 56 proximal and distal femoral epiphyses from cattle (Bos taurus). The skeletal remains were cleaned and analyzed at Boston University, School of Medicine for pits, punctures, scores, and furrows. Each tooth mark was photographed and then processed through the open-source software ImageJ (National Institutes of Health) in order to obtain the area, perimeter, length, and width of each tooth mark. The presence of certain gnaw damage characteristics were also recorded for each bone, such as crenellated margins, edge polish, scalloping, scooping, and deep furrows. Statistical analyses were used to distinguish if the epiphysis type (proximal or distal) or bear species were statistically significant factors in the type of tooth mark and gnaw damage. The results indicate a pattern distinctive to ursid scavenging with pits with an average length of 3.53 mm and width of 2.19 mm, an average score width of 1.47 mm, scalloping on the distal epiphysis especially on the patellar surface of the femur, scooping on the proximal epiphysis especially on the greater trochanter of the femur, and deep furrows primarily on the distal epiphysis along the patellar region and condyles of the femur. When comparing the present study to previous ursid studies (Arilla et al. 2014; Domínguez-Rodrigo and Piqueras 2003; Sala and Arsuaga 2013; Saladié et al. 2011) and previous other carnivore studies (Andrés et al. 2012; Delaney-Rivera et al. 2009; Pobiner 2007), there was a statistical significance between ursid pits and fox (Vulpes vulpes), skunk (Mephitis mephitis), and the combination of hyena (Crocuta crocuta) and lion (Panthera leo) pits. Scooping occurred in 35.2% of the entire sample, while scalloping occurred in 29.6% of the entire sample. Scooping has been observed in previous research but not as high of a percentage as the present study, and scalloping has been noted in a black bear study (Carson et al. 2000) and a wolf/dog study (Milner and Smith 1989), but with no numerical data for comparison. The high percentage of scooping and scalloping on long bones could be distinctive characteristics of ursid gnaw damage and could distinguish ursid scavenging from other carnivores.

A retrospective case review revealed an increase in sudden unexpected death (SUD) admittance at Salt River Mortuary (SRM) between 2014 and 2018, and that 40 % of SUD occurred in young individuals between the ages of 1 and 40 years old (SUDY). Despite extensive investigations, the cause of death remained undetermined in 26 % of SUDY cases. These dormant cases may benefit from retrospective post-mortem molecular autopsies for investigation into genetic causes of death. Often, formalin fixed paraffin embedded tissues (FFPETs) are the only archival sources of DNA available for retrospective analyses. This study aimed to optimise DNA recovery from FFPETs for potential use in molecular autopsies of unresolved SUDY cases. To this end, DNA was extracted from FFPET sections using the QIAamp® DNA FFPE tissue kit; the thickness and number of sections were varied. DNA was assessed using spectrophotometry, real-time PCR and digital capillary electrophoresis. Results showed that finer sectioning (1-µm thick as compared to 3-µm and 5-µm thick), improved DNA concentrations, purities and DNA fragment lengths. Increasing the number of 1-µm thick sections from 30 to 100, significantly improved DNA yield. DNA was not significantly more degraded for FFPETs stored for up to three years, which holds promise in the effectiveness of the technique for aged samples. The DNA extraction method developed in this study yielded a median of 320 ng (287 ng - 698 ng) of DNA with 55 % of DNA fragments being at least 400 bp in size. These results are especially informative for downstream molecular analyses, indicating that genotyping or sequencing assays need to be designed to target amplicons less than 400 bp in size. The degraded nature of the FFPET samples also suggests that massively parallel sequencing might be suited for downstream molecular analysis for determining cause of death in unresolved SUDY cases.

Road traffic collisions (RTCs) are a major contributor to unnatural death worldwide, but especially in low-to-middle-income countries (LMICs) where motorised transport has rapidly expanded. A literature review into RTCs and alcohol indicated that it is well recognised that alcohol intoxication is a key risk factor in RTCs and road traffic fatalities (RTFs). It also indicated that literature concerning the role of alcohol intoxication in RTFs in South Africa is limited. Hence, this study aimed to investigate alcohol in RTF victims in five of the major mortuaries (Salt River, Tygerberg, Paarl, Worcester and George) in the Western Cape Province between 1 January 2016 and 31 December 2017. Cases were extracted from the Western Cape Forensic Pathology Service (FPS) internal database, which included demographic and crash information, together with blood alcohol concentration (BAC) results. In total, 2079 cases over the two years were included in the study, with most cases admitted in the metropole of Cape Town (Salt River: n=838, Tygerberg: n=693). The proportion of unnatural deaths were greater outside the metropole (George, Worcester and Paarl) compared to the metropole (Salt River and Tygerberg) areas. The majority of fatalities were male individuals (male to female ratio of 3.52:1), with the average age of 35.2 ± 17.2 years. Most victims were pedestrians (n = 1106; 53.7%) and dark wet roads, and highways were noted as risk factors in RTFs. Blood was submitted for alcohol analysis in 1432 (68.9%) cases, and results were available for 1314 (91.8%) cases. Of the available results, 709 cases (54%) were positive for alcohol (BAC of ≥ 0.01g/100 mL). Of the positive cases, most had a BAC between 0.15 and 0.29 g/100mL and the overall average BAC was 0.20 g/100 mL. Pedestrians and drivers had the highest median BACs, and almost a third of all the positive BAC results were from pedestrian deaths. The findings of this dissertation can contribute to the growing research on alcohol and injury in South Africa, especially as it relates to RTFs. Insight into vulnerable populations within the province is highlighted, together with key risk factors associated with RTFs, as well as safety measures that may be targeted for improvement, especially with regards to driving and walking on the roads while intoxicated.

Homicide is one of the leading causes of death in South Africa. Homicides as a result of a firearm, sharp instrument or blunt object, may all potentially inflict severe cranial trauma. Often the lateral aspect of the cranium is fractured in homicidal assaults, however, the focus of head injury biomechanics has been the frontal bone. This is due to automotive-related incidents. Thus it is important for researchers to broaden their knowledge on lateral head impacts. This data could ultimately act as a tool in making cranial bone trauma analysis less subjective in nature. This minor dissertation discusses human cranial bones and explores different types of cranial fractures. It further provides an in depth discussion on the different types of experimental tests and specimens used in biomechanical testing. A current review on the literature surrounding head impacts is also provided. The research conducted for this minor dissertation uses the Cape (Chacma) Baboon as a model to attempt to simulate cranial blunt trauma observed in human bone. Fifteen Cape (Chacma) Baboon head specimens were subjected to a single temporo-parietal impact. These specimens were impacted with an aluminium striker bar that resembles the dimensions of a hammer (length: 23cm, circumference: 40cm and weight: 200g). The aim of these hammer tests were to characterise soft and hard tissue wound morphology as a result of blunt cranial impacts. Resulting data was analysed to determine if a significant correlation existed between impact velocity or energy and the extent of trauma observed. The remaining twelve Cape (Chacma) Baboon specimens were all subjected to a single impact in the temporo-parietal region. These specimens were impacted with a Hopkinson pressure bar, which is manufactured from the same material as the striker bar. The aim of the Hopkinson pressure bar tests was to attempt to determine the force of impact. The use of the Hopkinson pressure bar to determine fracture forces in baboon head specimens is novel. The fracture forces obtained in the current study compare well with literature investigating lateral impacts. Furthermore, the fracture patterns obtained in the current study realistically simulate cranial trauma seen in humans. It would therefore be beneficial to advance research using the baboon model and Hopkinson pressure bar apparatus.

The identification of bodily fluids for forensic purposes is typically classified as either presumptive or confirmatory. Presumptive tests (PT) are conducted first to screen for certain compounds which are relatively specific to particular fluids. Confirmatory tests are used to confirm the identity of a body fluid. Semen is one of the most common bodily fluids encountered in sexual assault cases and contains high concentrations of the acid phosphatase (AP) enzyme. The brentamine FB reagent reacts with the AP that is present in semen, and turns purple. If the colour change is observed within a specific time threshold, it is considered presumptively positive for semen. Cut-off time varies considerably between forensic laboratories, but in South Africa, the cut-off time is defined as 65 seconds. Additionally, semen may be considered to be from human origin if it reacts within 50 seconds. These cut off times have been arbitrarily defined, and there is little research in a local context to substantiate or inform the threshold time for the brentamine FB test for semen. Therefore this study assessed the sensitivity, specificity and kinetics of the brentamine FB test on semen from South African male volunteers (n=15), canines (n=2) and various fruit extracts and compared these results to purified human AP. Each semen sample was subjected to the PT in an indirect and direct method, and these tests were performed both on fresh and aged samples. The majority of fruit extracts yielded a distinctly different colour change compared to the purple that was produced from semen except for mushroom which also turned purple. Absorbance spectroscopy was used to determine the rate of the reaction at 525 nm. There were no significant differences between the rate of reaction for fresh and aged samples using both direct and indirect testing.