Black wattle (Acacia mearnsii), which belongs to the genus Acacia, is one of the many species of trees or hardwoods grown commercially in South Africa. Black wattle is a species indigenous to Australia and was introduced into South Africa by the van der Plank brothers in 1864. These trees are grown in South Africa because of its tannin-rich bark, the extract of which is used by the leather tanning industry. Black wattle is also grown for its timber, timber products and pulp. The introduction and cultivation history of black wattle suggests that the South African plantations contain limited genetic variation with relatedness amongst groups estimated to be high, thus implying a narrow genetic base in the South African black wattle population. In this investigation, Random Amplified Polymorphic DNA (RAPD) was used to estimate the genetic variation between seven different black wattle groups. A total number of 34 individuals obtained from different areas in South Africa were examined; Piet Retief (group 47 and 50: half-sibs), Kumbula (group 85: unrelated individuals), Howick (group 400: unrelated individuals) and an unknown area (groups 88, 89, 91: full-sibs). As this investigation was the first of its kind, a DNA isolation method as well as a PCR-RAPD protocol had to be modified. Total genomic DNA was successfully extracted using the CTAB DNA extraction method. This method removed large amounts of tannin present in the cells of the black wattle leaves and extracted high quality DNA to conduct between 50-100 RAPD reactions. The DNA purities ranged from 0.1 to 1.8, with an average of 1.46. A total of fourteen 10-mer RAPD primer sequences were randomly selected from the Operon Technologies primer list A, and tested in this investigation. Of the 14 primers used, only nine primers produced clear, single and repeatable bands. Therefore nine primers were selected for subsequent analyses. Ninety one loci that generated bands ranging from 300-3050 base pairs were produced. Seven to 13 loci per primer were generated. A total of 95.6 % of the loci were polymorphic. The overall expected mean heterozygosity (H = 0.3) obtained in this study was high in comparison to other studies conducted on acacias. The high levels of genetic variation were attributed to mating systems, dissortative mating and geographic distribution. The statistical packages POPGENE and ARLEQUIN were used to analyse the RAPD fingerprints. The genetic measures, Nei's diversity and Shannon's Information Index, showed that there was greater diversity exhibited (Nei's gene diversity = 32.09 % and Shannon's = 48.31 %), in the whole population than in each of the groups (with average of Nei's gene diversity = 20.33 % and Shannon's = 34.64 %). With regards to individual group analyses, low levels of genetic variation was obtained in group 400 (unrelated), from the Howick region, and group 85 (unrelated), from the Kumbula region, (mean 0.14 and 0.17 respectively). The low genetic values were attributed to limited gene exchange occurring in these two areas, bottlenecks and selection pressures. Groups 88, 89 and 91, from the unknown region (full-sib groups), were the most variable in comparison to the other groups, with means of (0.27,0.24 and 0.18 respectively). These high genetic variation values could be due to the fact that gene migration could have occurred between these groups and others in the area. It is thought that most acacias are insect-pollinated and this could have lead to gene migration between groups or populations, thereby explaining the high mean values. The gene flow obtained for the seven groups (FST = 0.174) indicated that great genetic differentiation existed in this population of black wattle studied. This value is higher in comparison to other woody species; however it is similar to other acacia species. UPGMA cluster analysis using Nei's unbiased genetic distance, revealed four distinct clusters of groups corresponding to the distribution areas represented in this study. The Howick (group 400: unrelated) and Kumbula (group 85: unrelated) were more closely related to each other than to the other groups, since both these groups are from Natal. The Piet Retief groups (groups 47 and 50: half-sibs), branched-off together, indicating that they are distinct from the other groups. The pairwise analysis of identity showed that the relationship between the group from Howick (group 400: unrelated) and all the other groups from the other regions was the lowest, ranging from 64 % to 79 %. The relationship between all the groups beside the group from Howick (group 400: unrelated) was reasonably high, ranging from 78 % to 90 %. This distance displayed by group 400 (unrelated) from Howick in relation to the groups, is attributed to the fact that it is frost resistant and the other groups not. Genetic variation was also detected and partitioned, between and within groups, by Analysis of Molecular Variance (AMQVA). Majority of the variation existed within groups (82.65 %) but significant differentiation was recorded between groups (17.44 %). This high level of within group differentiation may be explained by many aspects, such as the species breeding system, genetic drift or genetic isolation of groups or populations. The application of RAPD fingerprinting in black wattle has provided a more in depth understanding of the genetic variation residing in the South African population. The results achieved implementing this technique has shown that significant genetic variation exists within the black wattle population in South Africa. The results obtained in this study are also important since it is contrary to the expectation that the black wattle population in South Africa has low genetic variation. This knowledge is of great value to genetically discriminate between individuals or groups, to improve the selection of superior genotypes and allowing improved quality control in breeding programmes and seed orchard management. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2005.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

Thesis (M.S.)--University of Tennessee, Knoxville, 2009. / Title from title page screen (viewed on Mar. 8, 2010). Thesis advisor: Frank T. van Manen. Vita. Includes bibliographical references.

As últimas décadas trouxeram grandes avanços tecnológicos às ciências forenses. Um dos marcos dessa evolução foram às pesquisas e os resultados obtidos com a aplicação da Biologia Molecular, como ferramenta de identificação humana a partir da década de 80. Desde então, novos estudos vêm sendo realizados nesta área. Vestígios encontrados em locais de crime são elementos que irão orientar na busca pela elucidação dos fatos. Existem dois tipos de vestígios: os macrovestígios, facilmente identificados e os microvestígios que demandam análises técnicas mais específicas. Dentre os microvestígios, tem-se a impressão digital, que se tornou uma possível fonte de extração de DNA, com um grande potencial de recuperação do material genético. Este trabalho objetivou analisar amostras coletadas em microvestígios de impressões digitais em vários objetos escolhidos como superfície de deposição sendo elas, vidro, metal, plástico, madeira e parede de alvenaria, demonstrando que é possível estabelecer uma ligação entre as amostras de DNA e as impressões digitais encontradas. As amostras foram coletadas de impressões latentes intactas e em esfregaço e impressões digitais intactas e em esfregaço com pó. Os resultados demonstraram a viabilidade de utilização deste tipo de amostra, tendo em vista a recuperação de DNA e o êxito da genotipagem. Os resultados obtidos nas diferentes matrizes analisadas evidenciaram maior êxito na superfície de metal, onde foi possível obter perfil genético íntegro em todas as amostras coletadas e analisadas. Com relação à matriz vidro, nas amostras “intacta latente” e “esfregaço latente” foi possível recuperar perfil genético com mais de 17 locos amplificados. Já nas amostras “intactas e esfregaço com pó”, mesmo com a confirmação da presença de DNA, as quantidades recuperadas foram insuficientes para gerar o eletroferograma. Na matriz madeira, assim como na matriz plástico, foi constatada a presença de DNA, mas em baixa concentração para gerar o eletroferograma. E, por último, as amostras coletadas da matriz parede de alvenaria “intacta latente” e “intacta com pó”, apresentaram respectivamente amplificação de 17 e 19 locos dos 24 presentes no kit. Estudos e experimentos já tornaram esta metodologia viável no Laboratório de Genética Molecular Forense da Polícia Científica do Estado do Paraná, com resultados positivos em diversos casos, identificando suspeitos e contribuindo com a Rede Integrada de Banco de Perfis Genéticos (RIBPG). Os resultados demonstraram a eficiência e a possibilidade de se obter um perfil genético quando se trabalha com este tipo de amostra, tornando esta mais uma ferramenta pericial. / The last decades have brought great technological advances to the Forensic Sciences. The Molecular Biology has been used as a tool for human identification since the 80´s, and it has bought fantastic results from this application, being a landmark in the evolution of Forensic Science. Since this decade, new studies have been carried out in this area. Traces found in crime scenes are elements that can guide the search for the elucidation of the facts. There are two types of traces: macro-traces, that are easily identified and micro-traces that requires more specific technical analysis. One of the traces is the digital fingerprint, that is a possible source of DNA extraction, with great potential for recovery of the genetic material. This research has the purpose to analyze samples collected from fingerprints on various objects chosen as deposition surface, such as glass, metal, plastic, wood and masonry wall. This research shows that it is possible to establish a connection between DNA samples and fingerprints. Samples have been collected from intact and intact smears and fingerprints intact and smeared with powder. The results showed the feasibility of using this type of sample, based on the DNA recovery and the success of the genotyping. The results obtained in the different matrices analyzed showed greater results in the metal surface, where it was possible to obtain a complete genetic profile in all the samples Collected and analyzed. In the glass matrix, either the samples "latent intact" or in "latent smear" it was possible to recover genetic profile with more than 17 amplified loci. In the "intact and powder smear" samples, even with confirmation of the presence of DNA, the quantities recovered were insufficient to generate the electropherogram. In the wood matrix, such as in the plastic matrix, the presence of DNA was observed, but at low concentration to generate the electropherogram. Finally, the samples collected from the "latent intact" and "intact with powder" masonry wall samples, respectively, showed amplification of 17 and 19 loci of the 24 present in the kit. Some Studies and experiments have been done in the Forensic Molecular Genetics Laboratory of Scientific Police in Paraná with positive results in many cases, identifying suspects and contributing to the Integrated Network of Gene Prolifiling Banks (RIBPG). These studies have made this methodology feasible. The results show the efficiency and the possibility of obtaining a genetic profile from this type of sample, making this one more important pericial tool.

As últimas décadas trouxeram grandes avanços tecnológicos às ciências forenses. Um dos marcos dessa evolução foram às pesquisas e os resultados obtidos com a aplicação da Biologia Molecular, como ferramenta de identificação humana a partir da década de 80. Desde então, novos estudos vêm sendo realizados nesta área. Vestígios encontrados em locais de crime são elementos que irão orientar na busca pela elucidação dos fatos. Existem dois tipos de vestígios: os macrovestígios, facilmente identificados e os microvestígios que demandam análises técnicas mais específicas. Dentre os microvestígios, tem-se a impressão digital, que se tornou uma possível fonte de extração de DNA, com um grande potencial de recuperação do material genético. Este trabalho objetivou analisar amostras coletadas em microvestígios de impressões digitais em vários objetos escolhidos como superfície de deposição sendo elas, vidro, metal, plástico, madeira e parede de alvenaria, demonstrando que é possível estabelecer uma ligação entre as amostras de DNA e as impressões digitais encontradas. As amostras foram coletadas de impressões latentes intactas e em esfregaço e impressões digitais intactas e em esfregaço com pó. Os resultados demonstraram a viabilidade de utilização deste tipo de amostra, tendo em vista a recuperação de DNA e o êxito da genotipagem. Os resultados obtidos nas diferentes matrizes analisadas evidenciaram maior êxito na superfície de metal, onde foi possível obter perfil genético íntegro em todas as amostras coletadas e analisadas. Com relação à matriz vidro, nas amostras “intacta latente” e “esfregaço latente” foi possível recuperar perfil genético com mais de 17 locos amplificados. Já nas amostras “intactas e esfregaço com pó”, mesmo com a confirmação da presença de DNA, as quantidades recuperadas foram insuficientes para gerar o eletroferograma. Na matriz madeira, assim como na matriz plástico, foi constatada a presença de DNA, mas em baixa concentração para gerar o eletroferograma. E, por último, as amostras coletadas da matriz parede de alvenaria “intacta latente” e “intacta com pó”, apresentaram respectivamente amplificação de 17 e 19 locos dos 24 presentes no kit. Estudos e experimentos já tornaram esta metodologia viável no Laboratório de Genética Molecular Forense da Polícia Científica do Estado do Paraná, com resultados positivos em diversos casos, identificando suspeitos e contribuindo com a Rede Integrada de Banco de Perfis Genéticos (RIBPG). Os resultados demonstraram a eficiência e a possibilidade de se obter um perfil genético quando se trabalha com este tipo de amostra, tornando esta mais uma ferramenta pericial. / The last decades have brought great technological advances to the Forensic Sciences. The Molecular Biology has been used as a tool for human identification since the 80´s, and it has bought fantastic results from this application, being a landmark in the evolution of Forensic Science. Since this decade, new studies have been carried out in this area. Traces found in crime scenes are elements that can guide the search for the elucidation of the facts. There are two types of traces: macro-traces, that are easily identified and micro-traces that requires more specific technical analysis. One of the traces is the digital fingerprint, that is a possible source of DNA extraction, with great potential for recovery of the genetic material. This research has the purpose to analyze samples collected from fingerprints on various objects chosen as deposition surface, such as glass, metal, plastic, wood and masonry wall. This research shows that it is possible to establish a connection between DNA samples and fingerprints. Samples have been collected from intact and intact smears and fingerprints intact and smeared with powder. The results showed the feasibility of using this type of sample, based on the DNA recovery and the success of the genotyping. The results obtained in the different matrices analyzed showed greater results in the metal surface, where it was possible to obtain a complete genetic profile in all the samples Collected and analyzed. In the glass matrix, either the samples "latent intact" or in "latent smear" it was possible to recover genetic profile with more than 17 amplified loci. In the "intact and powder smear" samples, even with confirmation of the presence of DNA, the quantities recovered were insufficient to generate the electropherogram. In the wood matrix, such as in the plastic matrix, the presence of DNA was observed, but at low concentration to generate the electropherogram. Finally, the samples collected from the "latent intact" and "intact with powder" masonry wall samples, respectively, showed amplification of 17 and 19 loci of the 24 present in the kit. Some Studies and experiments have been done in the Forensic Molecular Genetics Laboratory of Scientific Police in Paraná with positive results in many cases, identifying suspects and contributing to the Integrated Network of Gene Prolifiling Banks (RIBPG). These studies have made this methodology feasible. The results show the efficiency and the possibility of obtaining a genetic profile from this type of sample, making this one more important pericial tool.

The ability to identify germplasm and select traits accurately is fundamental to successful plant breeding. Pedigrees and molecular markers facilitate these processes; however misleading experimental results can occur when incorrect relationships and/or cultivar names are recorded. Molecular markers can identify these inconsistencies, and with advances in genotyping technology these diagnostics can be done faster and more objectively. This study aimed to develop molecular marker assays and graphical genotyping methodologies for cultivar identification, seed purity assessment and trait selection in oat (Avena sativa L.). KBioscience’s Allele-Specific PCR (KASP™) and genotyping-by-sequencing (GBS) technologies were applied to a set of current Canadian oat cultivars to evaluate their utility for identifying cultivars and detecting intra-cultivar variation. Both KASP™ and GBS detected different extents of heterogeneity among a set of 160 seeds that originated from four seed sources of four cultivars. In both cases, the detected variation did not appear to be limited to a specific cultivar or seed source, reinforcing that all cultivars are heterogeneous. Graphical genotyping localized heterogeneity to specific chromosome regions, thereby distinguishing physical contamination from true genetic heterogeneity and heterozygosity. Pre-existing genotype data for 700 oat cultivars and breeding lines were also used to construct graphical genotypes for pedigree validation and discovery of potential sources for favourable quantitative trait loci (QTL) alleles. This methodology used historical QTLs and anchoring markers to identify 25 putative “high oil” allele carriers. The results from this study will provide diagnostic tools for cultivar identification and pedigree validation, in addition to meaningful information about existing heterogeneity and possible QTL locations in current cultivars.

Indiana University-Purdue University Indianapolis (IUPUI) / Short tandem repeat (STR) analysis is currently the most common method for processing biological forensic evidence. STRs are highly polymorphic and allow for a strong statistical power of discrimination when comparing deoxyribonucleic acid (DNA) samples. Since sample testing and court proceedings occur months, if not years apart, samples must be stored appropriately in the event additional testing is needed. There are generally accepted methods to store DNA extracts long-term; however, one universally recognized method does not exist. The goal of this project was to examine various methods of storage and make recommendations for a universal storage method that maintained DNA integrity over time. Four variables were evaluated: storage buffer, storage temperature, initial storage concentration and the effects of repeated freeze-thaw cycles. DNA quantity was assessed using real-time polymerase chain reaction and DNA quality was evaluated using STR genotyping. Overall, the Tris-EDTA (TE) buffer outperformed nuclease free water as a long-term storage buffer for DNA extracts. Stock tubes stabilized concentration better than single use aliquots when eluted with TE while tube type was not significant when water was the buffer. For samples stored in TE, temperature had no effect on DNA integrity over time, but samples stored in water were largely affected at room temperature. Additionally, the greater the initial DNA concentration, the less likely it was to degrade in water. As a result of this research, DNA extracts from forensic samples should be stored long-term in TE buffer with a minimum concentration of 0.1 ng/μL. When water is the buffer, frozen storage is recommended.

Indiana University-Purdue University Indianapolis (IUPUI) / Forensic DNA profiling is widely used as an identification tool for associating an individual with evidence of a crime. Analysis of a DNA sample involves observation of data in the form of an electropherogram, and subsequently annotating a DNA “profile” from an individual or from the evidence. The profile obtained from the evidence can be compared to reference profiles deposited in a national DNA database, which may include the potential contributor. Following a match, a random match probability is calculated to determine how common that genotype is in the population. This is the probability of obtaining that same DNA profile by sampling from a pool of unrelated individuals. Each state has adopted various laws requiring suspects and/or offenders to submit a DNA sample for the national database (such as California’s law that all who are arrested must provide a DNA sample). These profiles can then be associated with past unsolved crimes, and remain in the database to be searched in the event of future crimes. In the case of database samples, a physical sample of the offender’s DNA must be kept on file in the laboratory indefinitely so that in the event of a database hit, the sample is able to be retested. Current methods are to collect a buccal swab or blood sample, and store the DNA extracts under strict preservation conditions, i.e. cold storage, typically -20° C. With continually increasing number of samples submitted, a burden is placed on crime labs to store these DNA extracts. A solution was required to help control the costs of properly storing the samples. FTA™ paper was created to fulfill the need for inexpensive, low maintenance, long term storage of biological samples, which makes it ideal for use with convicted offender DNA samples. FTA™ paper is a commercially produced, chemically treated paper that allows DNA to be stored at room temperature for years with no costly storage facilities or conditions. Once a sample is required for DNA testing, a small disc is removed and is to be used directly in a PCR reaction. A high quality profile is important for comparing suspect profiles to unknown or database profiles. A single difference between a suspect and evidentiary sample can lead to exclusion. Unfortunately, the DNA profile results yielded from the direct addition have been unfavorable. Thus, most crime laboratories will extract the DNA from the disc, leading to additional time and cost to analyze a reference sample. Many of the profiles from the direct addition of an FTA™ disc result in poor quality profiles, likely due to an increase in PCR inhibitors and high concentrations of DNA. Currently, standardized protocols regarding the recommended locations for removal of a sample disc from a bloodspot on an FTA™ card does not exist. This study aims to validate the optimal location by comparing DNA profiles obtained from discs removed from the center, halfway, and edge locations of a bloodspot from 50 anonymous donors. Optimal punch location was first scored on the number of failed, partial or discordant profiles. Then, profile quality was determined based on peak characteristics of the resulting DNA profiles. The results for all three disc locations were 5.3% failed amplifications, 4.2% partial amplifications, and one case of a discordant profile. Profile quality for the majority of the samples showed a high incidence of stutter and the absence of non-template adenylation. Of the three disc locations, the edge of the blood stain was ideal, due to a presumably lower concentration of DNA and likely more dilute amount of the PCR inhibitor heme. Therefore, based on the results of this study, there is a greater probability of success using a sample from the edge of a blood stain spotted in FTA™ paper than any other location of the FTA™ card.

This study analyses how DNA evidence can be distorted by the behaviour of criminal investigators and role-players within the Criminal Justice System (CJS). This has a negative impact on justice resulting in further criminality. The study has resulted in revelatory weaknesses owing to constitutional violations which cause sound evidence to become futile as it will not be admissible in court. Justice is aborted. The researcher has further explained the properties of the pertinent terms, such as: mental illness, psycho-social functioning, DNA, forensic investigator, forensic psychology, and courts. Concepts are building blocks, hermeneutical distortion leads to the frustrating of what justice intends and this, in turn, leads to poor criminal investigation performance. It is submitted that not only ineptness, but also deception possibly evolves from genotypic to phenotypic type which causes unwelcome behaviour within the criminal justice system to surface. The frequency of monitoring psychological behaviour amongst criminal investigations is low, and it, therefore, also contributes to delict and the miscarriage of justice occurs. / Police Practice / M.A. (Criminal Justice)

The State as the representative of the victims of crime is expected to protect those vulnarable group of people with due regard to the rights of the perpetrators’s of crime. It is imperative that the law of general application which is aimed at protecting victims of crime, be sufficiently effective to protect the victims. The Criminal Procedure Act 51 of 1977 is aimed at assisting the police to conduct pre-trial criminal procedure in order to bring perpetrators of crime to book. Sections 36A, 36B, 36C and 37 (both previous and as amended) of the Criminal Procedure Act including chapter 5A of the South African Police Act, 1995 are explored in this dissertation. This dissertation examines the areas in the Criminal Procedure Act that make it problematic for the police to conduct efficient and effective crime detection through the ascertainment of bodily features of the suspected or accused person. The law in three foreign jurisdictions relating to this topic are investigated and compared in order to make recommendations and suggest possible solutions. / Criminal & Procedural Law / LL.M.