Bibliography: leaves 172-197. / xvii, 197 leaves : ill. (chiefly col.) ; 30 cm. / Title page, contents and abstract only. The complete thesis in print form is available from the University Library. / Thesis (Ph.D.)--University of Adelaide, Dept. of Soil and Water, 2002?

Maize (Zea mays L.) is an important agronomic crop with the maize industry forming an important component of the South African economy. Considerable effort has been directed towards the genetic improvement of maize through both conventional breeding and biotechnology. Genotype identification by DNA fingerprinting is becoming an important activity in plant breeding. A widely used molecular based and relatively inexpensive method for DNA fingerprinting is the randomly amplified polymorphic DNA (RAPD) technique. The RAPD technique was tested in this study for its potential use in maize breeding programmes. Initial results using the technique showed a low degree of reproducibility, therefore both the DNA isolation and RAPD protocols were extensively optimised. DNA quality and quantity, and choice of Taq polymerase buffer were three of the variables found to be influential in ensuring reproducibility. The ability of the RAPD technique to characterise seven maize genotypes was evaluated. Sixty random oligonucleotide primers were screened. Forty two primers scored a total of 233 fragments (an average of 5.5 per primer), but not all primers gave reproducible profiles. Eighteen primers scored a total of 110 loci for the presence (1) and absence (0) of DNA fragments. RAPD markers were able to distinguish between all seven genotypes with five primers producing specific fragments for four genotypes. Genetic similarity matrices were calculated using two software programmes i.e. Genstat 5™ release 4.1 (1993) and PAUP (Phylogenetic Analysis Using Parsimony) 4.0 beta version (Swafford, 1998). Cluster analysis was used to generate dendrograms to visualise the genetic relationships of the seven maize genotypes (only minor differences were observed between the Genstat or PAUP method of analysis). Genetic diversity ranged from 0.62 to 0.96. The estimation of genetic relationship was in accordance with the presumed pedigree of the genotypes showing that the RAPD technique demonstrates potential for genome analysis of maize. The applicability of the technique for marker assisted selection was also evaluated. Near-isogenic lines (NILs) for leaf blight (Helminthosporium spp.) were screened for polymorphisms using a total of 120 primers. Ten primers identified polymorphisms between the NILs. Four primers produced five polymorphic fragments present in the resistant inbred K0315Y and absent in the susceptible inbred D0940Y. A small F2 population of 14 individuals was produced by selfing the F1 of a cross between K0315Y and D0940Y. To speed up the generation time, the F1 and F2 plants were cultured by embryo rescue from 18d old harvested seed. One fragment of 627 base pairs produced by primer OPB-01 (5' GTTTCGCTCC 3') showed a 3: 1 segregation in the small F2 population and was considered putatively linked to the HtN gene for leaf blight resistance. This study shows that the RAPD technique does have application in maize breeding programmes. / Thesis (M.Sc.)-University of Natal, Pietermaritzburg, 2000.

The purpose of this project was to determine if the human skeletal remains of two distinct Native American cemeteries, found in close geographic proximity, represent the same population. These archaeological sites are similar in location and artifacts. Burial practices, however, vary between the sites. These differences may represent class distinction or a difference in the times the cemeteries were used. Radiocarbon techniques have given dates of AD 230±300 and AD 635±105 for these two sites. Several methods of DNA isolation were compared for their ability to yield PCR amplifiable DNA. DNA isolation using a combination of CTAB and phenol/chloroform/isoamyl alcohol (24:24:1) provided the best results and yielded amplifiable DNA form two individuals, Hn I (8F-410) and Hn 10 ( 27F-8-14 b). Purification of the DNA by extraction from low melting agarose gel was required prior to PCR, and PCR conditions were optimized to maximize the DNA yields. Regions of the mitochondrial DNA (mtDNA) genome of isolated DNA were amplified by PCR using primers which are specific for the HincII region of the mtDNA genome. Inability of restriction enzyme HincII to digest the amplified DNA of these two individuals suggested that they belong to the Native American mtDNA lineage C characterized by the loss of this restriction site. / Department of Anthropology

The purpose of this experiment was to examine changes in strength and power measures accompanying traditional and ballistic training during in-season competition. Fourteen collegiate women volleyball players were trained for 11 weeks with periodized traditional and ballistic resistance training. There was a 5% decrease (p<0.05) in approach jump and reach height during the traditional training period (pre to mid), and a 5% increase (p<0.05) during the ballistic training period (mid to post), but values were not different from pre to post. There were significant decreases (p<0.05) in contact time during drop jumps (15% mid to post) and minimum dip height in countermovement jumps (7% mid to post and 16% pre to post) during ballistic training. Traditional resistance training displayed significant decreases in speed related measures, while ballistic training displayed significant increases in these same variables. A combination of traditional and ballistic training can maintain jump height over the competitive season. / Department of Biology

DNA profiling has ignited public interest and consequently their expectations for the capabilities of forensic criminal and science investigations. The prospect of characterising the genetic makeup of individuals or trace samples from a wide variety of depositional and post-mortem circumstances raises the question of how reliable the methods are given the potential for prolonged exposure to variation in environmental factors, i.e. temperature, pH, UV irradiation and humidity, that are known to induce damage to DNA. Thus, it is crucial to verify the validity of the DNA profiling for characterising the genetic makeup of post-mortem tissues. This project aimed to assess the reliability of sequence and microsatellite based genotyping of tissues (muscle, hair and bone) sampled from carcasses over a two year post-mortem period. This assessment investigated the impact of environment induced DNA degradation in the local geographic region that is typical of the circumstances that confront forensic practitioners in southern Australia and to utilise rigorous controls by studying animals whose time of death and burial was known and for which we had pre-decay tissue samples available. A ‘body farm’ with 12 pig carcasses on the northern Adelaide plains, ~60km north of Adelaide, which has a typical southern Australian Mediterranean climate, i.e. cold wet winters and hot dry summers. Pigs (Sus scrofa) were used as an experimental analogue for human subjects because of the logistical and ethical reasons. The pig carcasses were allocated among three treatments: four were left on the surface, four were buried at 1m depth, and four were buried at 2 m depth. These ‘burial’ conditions mimic a range of conditions encountered typically in forensic and archaeological studies. Cortical bone samples were taken from each pig carcass at one week, one month, three months, six months, one year and two years post-mortem and muscle and hair over the same sampling period for as long as those tissue types were present. A set of PCR primers to amplify two (short and a long) fragments from the hypervariable part of the mitochondrial control region (HVRI) that is used in forensic and evolutionary studies of humans and many other mammal species were developed. Also a panel of four pig microsatellite loci with fluorescent labels to facilitate automated multiplex genotyping. These loci matched as closely as possible the core motifs and allele lengths typical of the commercially available microsatellite marker kits used in Australian forensic science labs so that our experiments were as good a model as possible of the human forensic DNA technology. In this study it was possible to retrieve samples from muscle tissue up to 90 days, hair up to one year and bone at two years post-mortem. The analyses showed that the long and short HVRI region PCR fragments were only amplifiable up to 30 days from muscle tissue and that these fragments were amplifiable up to one year from hair. In contrast, in cortical bone both PCR fragments were amplifiable up to two years. The long fragment disappeared in muscle tissue completely after 30 days and in hair after six months. However, the long fragment was present in cortical bone even at two years. Overall, there was a general trend of loss of concentration of both the long and short fragments over time. Comparisons of the HVRI nucleotide sequences among tissues sampled from individual animals showed substitution changes in muscles as early as 30 days (3 out of 6 individuals) and hair at six months (1 out of 6 individuals). In contrast, in cortical bone substitutions first appeared at 365 days (1 out of 6 individuals). The most common substitution observed in all tissues types was the C-T transition, with A-G transversions observed in two episodes and C-A transversion observed in one episode. Analyses of microsatellite genotypes in muscle tissues showed high allele peaks on chromatograms up to day seven samples. However, by three months PCR was not successful from muscle tissue. While, bone tissue had lower allele peak heights compared to the muscle tissues, alleles were detectable up to six months. Allele drop out occurred for one animal (at 2 meters) in muscle tissue at the dinucleotide locus and for another animal (kept on surface) also in muscle tissue at a tetranucleotide locus. Stuttering was observed for a single animal at dinucleotide locus in muscle tissue (buried sample 2 meter depth). No stuttering or allele drop outs were seen in the bone tissue. Overall the four loci completely disappeared after 30 days in muscle tissue and after 180 days in bone tissue. In summary, analyses showed that post-mortem DNA degradation was present in all the three tissue types (muscle, hair and bone). The types of damage identified were DNA fragmentation, nucleotide substitutions and DNA loss, which resulted in a diminished frequency of successful PCR for mitochondrial and nuclear markers over time and stuttering and allele drop out in microsatellite genotyping. In addition, two nucleotide substitutions were concentrated in ‘hotspots’ that correlate with sites of elevated mutation rate in vivo. Also the frequency of successful PCR of longer nuclear and mitochondrial PCR products declined markedly more quickly than for shorter products. These changes were first observed at much shorter post mortem intervals in muscle and much longer post mortem intervals in hair and bone tissue. When considering the carcass deposition treatments, tissues that were retrieved from buried carcases showed higher levels of DNA degradation compared to tissues retrieved from carcases left on the surface. Overall, muscle tissue is a good source for DNA analysis in immediate post mortem samples, whereas hair and bone tissue are good source for DNA analysis from older samples. When comparing the microsatellite genotyping and mtDNA analyses, mtDNA is a reliable source for DNA analysis from tissue recovered from bodies that had decayed for longer post-mortem durations such as months to years, whereas microsatellite genotyping gives reliable results for tissue from shorter post mortem intervals (hours to few days). Therefore it is recommended that when analysing mtDNA sequences, cloning and sequencing PCR products can help to identify the base pair substitutions especially for tissue retrieved from longer post mortem intervals. In addition, increasing the template DNA concentrations and "neutralising" co-extracted DNA inhibitors should be considered when dealing with tissue from longer post mortem intervals. Finally, the more stringent protocols used in ancient DNA studies should be considered when dealing with tissue with much longer post mortem intervals in forensic settings. / Thesis (Ph.D.) -- University of Adelaide, School of Medical Sciences, 2009

Diss. (sammanfattning) Uppsala : Uppsala universitet, 2007. / Härtill 5 uppsatser.

The Criminal Law (Forensic Procedures) Amendment Act 37 of 2013 came into operation in January 2015. The Act makes provision for the establishment of a National Forensic DNA Database, which will store DNA profiles of certain groups of people. This research will discuss the establishment of a forensic DNA database in South Africa. The legal position in the United States of America will also be considered, with specific reference to the states of Maryland, California and New York. This research will focus predominantly on the collection of DNA samples and profiles from arrestees. When such samples are allowed to be collected, what offences warrant the collection of such samples and the period within which the DNA samples need to be destroyed. Collecting DNA samples and profiles from certain persons could potentially violate particular rights in the Bill of Rights. The rights to privacy, bodily integrity, equality and human dignity are discussed as well as the approach the courts have adopted in dealing with such infringements or possible infringements. This research furthermore deals with the historical developments of DNA evidence and contains a brief discussion on expert evidence. This research also deals with the evidential value of DNA evidence, as well as possible problems faced by prosecutors and defence attorneys when dealing with DNA evidence. The Criminal Law (Forensic Procedures) Amendment Act is still very new, and therefore, there is not yet much case law in South Africa specifically dealing with the sections of the said Act. This research makes submissions and recommendations regarding certain sections of the Act, as well as the overall constitutionality of the Act.

The primary objectives of this project were: 1. to develop improved methods for extraction of DNA from human skeletal remains, 2. to improve STR profiling success of low-copy DNA samples by employing whole genome amplification to amplify the total pool of DNA prior to STR analysis, and 3. to improve STR profiling success of damaged DNA templates by using DNA repair enzymes to reduce the number/severity of lesions that interfere with STR profiling. The data from this study support the following conclusions. Inhibitory compounds must be removed prior to enzymatic amplification; either during bone section pretreatment or by the DNA extraction method. Overall, bleach outperformed UV as a pretreatment and DNA extraction using silica outperformed microconcentration and organic extraction. DNA repair with PreCR™ A outperformed both whole genome amplification and repair with PreCR™ T6. Superior DNA extraction results were achieved using the A6 PMB columns (20 ml capacity column with 6 layers of type A glass fiber filter), and DNA repair with PreCR™ A led to an overall improvement in profile quality in most cases, although whole genome amplification was unsuccessful. Rapid, robust DNA isolation, successful amplification of loci from the sample-derived DNA pool, and an elimination of DNA damage and inhibitors may assist in providing sufficient genetic information from cases that might otherwise lie on the fringe of what is possible to obtain today.

The utility of hypervariable DNA polymorphisms as a general population genetics method was studied in three fish species by the use of multilocus DNA fingerprinting. Laboratory lines and field caught specimens from Belize and Florida of the clonal species <i>Rivulus marmoratus</i> were examined to determine the relative contributions of mutation and migration to genetic variation in the species. Specimens of <i>Poecilia latipinna</i>, the sailfin molly, from Florida and Georgia were used to explore the properties of hypervariable markers in the context of an outbred and abundant species that exhibits typical levels of genetic variability at nuclear loci. The results were compared to those of a previous allozyme survey of the same populations. Samples of <i>Morone saxatilis</i> from the Chesapeake Bay system were used to investigate the utility of hypervariable markers in the description of genetic variation of an outbred species depauperate in other measures of genetic variation. The results of this study indicate that variation observed among among <i>R. marmoratus</i> clones characterized by hypervariable loci may be the result of natural selection; based on the analyses of mutation rates and population structure. Results from the work with <i>P.latipinna</i> showed that hypervariable loci could have general utility as a method for studying population structure. This utility was demonstrated in the examination of Chesapeake Bay populations of <i>M. saxatilis</i>. Large degrees of interindividual variation at hypervariable loci permitted the characterization of population structure within Chesapeake Bay populations of this species. / Ph. D.

Pigeonpea (Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family in the order Fabales and the only cultivated species in the genus Cajanus. It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, one of the top producers of pigeonpea in Africa, it is grown by small scale farmers as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant yield losses for farmers. In this study, 48 polymorphic SSR markers were used to assess diversity in all pigeonpea varieties cultivated in Malawi with the aim of developing a genetic fingerprint to distinguish the released varieties. SSR alleles were separated by capillary electrophoresis on an ABI 3700 automated sequencer and allele sizes determined using GeneMapper 4.0 software. Allelic data was analysed with PowerMarker. A total of 212 alleles were revealed averaging 5.58 alleles per marker with a maximum number of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC) ranged from 0.03 to 0.89 with an average of 0.30. DARwin software was used to generate a neighbour-joining tree that displayed three major clusters with two sub clusters in Cluster I. The released varieties were scattered across all the clusters observed, indicating that they generally represent the genetic diversity available in Malawi, although it was observed that there is substantial variation that can still be exploited through further breeding. Screening of the allelic data associated with five popular pigeonpea varieties for which a DNA fingerprint was to be developed, revealed 6 markers – CCB1 (Marker 1), CCB7 (Marker 2), Ccac035 (Marker 7), CCttc003 (Marker 15), Ccac026 (Marker 37) and CCttc019 (Marker 40)– which gave unique allelic profiles for each of the five varieties. With further tests needed for its robustness, this genetic fingerprint can be used for seed certification to ensure only genetically pure seeds are delivered to Malawi farmers. / Agriculture and  Animal Health / M. Sc. (Agriculture)