Distinguishing between burnt human and non-human bone fragments using macroscopic methods has proved challenging and it was seen in the literature review that the previous research did not all come to the same conclusions. The aim of the research was to determine if, using histological methods, it was possible to distinguish between burned human and nonhuman bone fragments. A literature review was compiled to provide an overview of the anatomy of bones, morphological characteristics of bone, general bone histology, a comparison between human and non-human bones and the effect of temperature on bones. Bones of five different species (human, baboon, wildebeest, pig and cow) were burned in a muffle furnace for twenty minutes at either 600ᵒC or 800ᵒC. Following the burning procedure, thin ground bone sections of the burned and unburned bone specimens were prepared for microscopic analysis and the minimum canal diameter, maximum canal diameter, minimum Haversian system diameter, maximum Haversian system diameter, area of canal, and area of the Haversian system were measured. A comparative analysis was then done across species and temperature. A total of 523 osteons in unburned bone and 147 in the burned bone samples were analysed. ANOVA testing found overall significance (p < 0.0001) for all parameters measured, which suggests that temperature does affect the size of microstructures. Most parameter sizes increased with an increase in temperature. A greater increase was seen at 600 degrees than 800 degrees. Qualitatively, carbonation within the burned bone, made the measurement of parameters difficult in some samples. Human bone can easily be differentiated from pig, cow or wildebeest bone due to no or very few osteons present. Pig bone consisted almost entirely of plexiform bone, while the cow and wildebeest presented with only a few osteons in some parts of the bone. Human and baboon bone appeared similar on a microscopic level. The study revealed that temperature did not, in general, hamper the ability to differentiate between burned human and non-human bone, but it did impact on the number of measurable data points for each parameter.

In South Africa, little is known about the presence of drugs in infant cases admitted for post-mortem medico-legal examinations,as toxicological investigations are not routinely performed. It was hypothesised that drugs would be detected in sudden and unexpected death ofinfant (SUDI) cases admitted to Salt River Mortuary (SRM), as infantsform a vulnerable population. Biological samples (blood, vitreous humour, urine and hair) were collected from 30 infants who were admitted as SUDIcasesto Salt River Mortuary,Cape Town,between 28 May 2019 and 17 October 2019. Samples were screened for at least 750 common drugs using a SCIEX X500R QTOF. Demographic variables, social circumstances and clinical historywere recorded from the medico-legal case folder. Of the 30 SUDI cases, drugs were detected in 25 (83 %) cases, with acetaminophen (61 %) and caffeine (54 %) being most prevalent. Methaqualone (32 %) and methamphetamine (11 %),two commonly abused drugs in the Western Cape,werealsoidentified, with the former only present in hair. There were significantly more drugs detected in hair samples compared to the other samples (p < 0.0001). Therefore, while challenging in its interpretation, hair analyses provideda wealth of information concerningpossiblelonger-termdrug exposure in infants.This was particularly valuable inrevealingmethaqualoneexposure, which may have otherwise gone undetected, and which may indicate an environment of neglect. While the cause of death in most cases was natural (infectious causes) (63 %), next-of-kin seldom declared that their infant exhibited symptoms of illness orthat medication was administeredprior to death. Therefore, theresults of this study illustrate the valueof toxicological testing in SUDIcases at SRM, as well as the need to analyse multiple samples. This study provides empirical data to motivate for the SUDI investigation protocolatSRM toinclude routine toxicological analysis. This is anticipated toadd value to the medico-legal investigation as well as add social value to the lives of siblings who may also be at risk for neglect.

The large number of unidentified, decomposed and skeletonised remains found in South Africa (SA) necessitates relevant and reliable methods to assist in victim identification. Ancestry estimation from unknown skeletal remains is essential when reconstructing a demographic profile of a missing person. In the SA population, estimating ancestry is problematic as standards developed internationally rarely apply to the local, biologically heterogenous population. Craniofacial morphology is known to be ancestrally distinct and studies are yet to explore shape and size variation in the zygomatic bone of the SA population. The aim of this study was to assess ancestral variation in zygomatic shape and size in a SA population using three-dimensional geometric morphometric analyses. A sample of 158 individuals were analysed from Bantu-speaking (BA), European (EA) and Mixed Ancestral (MA) South African groups. Males were larger in size than females, but no size differences were observed between ancestral groups. Significant shape differences were observed between ancestral groups, while none were observed between males and females. BA and MA individuals had narrower, shorter and more anteriorly projecting zygomas than EA individuals. The zygoma was shown to accurately distinguish EA (84%) from BA (81%), and MA (80%) from EA (68%) individuals, but unreliably distinguished BA (60%) from MA (66%) individuals. This is likely correlated to the historical peopling of SA and historical forced racial classification. Age-related changes and antemortem tooth loss did not confound the ancestral variation in size, despite minor changes in zygomatic shape being associated with these two factors. These confounders did not impact ancestry estimation accuracies, further suggesting a minor impact on overall zygomatic shape. Furthermore, the patterning of ancestral variation in the zygoma revealed the need for further research to distinguish between the biologically heterogenous ancestral groups in SA.

A retrospective study of deaths attributable to anaphylaxis at the Salt River Forensic Pathology Laboratory was undertaken, with a view to determine if eosinophilia was present in tissue samples of the spleen, in accordance with previously published research. Suitable cases of non-anaphylactic death were used as controls. Use was made of two commonly available fabric dyes as alternative stains to the traditional Haematoxylin -Eosin ["H&E"].

The aim of this project is to develop a single quantification method for certain benzodiazepines, opiates and antidepressants in whole blood, serum and urine by LC-MS/M5 and to consequently validate the analytical method for official use in the Division of Pharmacology at the University of Cape Town.

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.

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.