[Truncated abstract] Traditional medicines are used by millions of people throughout the world as their primary source of medical care. A range of materials are in used traditional medicines including plant and animal parts. Even though the traditional medicine trade is estimated to be worth sixty billion dollars annually the trade remains largely unregulated. Unscrupulous practices by vendors to increase their profit margins such as substituting and adulterating expensive material with cheaper varieties go unchecked. This can be dangerous to consumers because some substitutions involve poisonous material. Also, animal parts from endangered species can find their way into traditional medicines, therefore there needs to be a way to identify them in traditional medicines to prosecute poachers. The traditional techniques used for the identification of material used in Traditional Chinese Medicine (TCM) include, morphological, histological, chemical and immunological analysis. However, these techniques have their limitations. This makes applying multiple techniques essential to provide thorough authentication of the material. DNA profiling provides a technique well suited to analysing material used in TCM. DNA profiling is advantageous over other techniques used to authenticate material used in TCM because it requires only a small sample amount, can determine the cultivator, be used on all forms of TCM and potentially distinguish the components of mixtures. ... Therefore, profiles of different species/individual are different and species? can be distinguished. Commercially sold traditional medicines are processed which is likely to degrade the DNA of the sample making extraction and amplification difficult. Here an organic Phenol:Chloroform extraction technique extracted DNA from commercial dried root samples. The extracted DNA was amplifiable using RAPD primers. The RAPD primers used here produced enough polymorphic bands to distinguish different plant species. They were used to distinguish commercial samples that were sold as three different species within the Panax genus, Panax ginseng, Panax quinquefolium and Panax notoginseng and genetically unrelated plant material; Potato and Eleutherococcus senticosus. Liquid samples and mixtures were also profiled with the RAPD primers to determine whether the RAPD primers provide enough distinguishing ability to analyse these forms of TCM. DNA was extracted from the liquid samples, one a ginseng drink and the other an ginseng extractum. However, there was no reliability in the production of PCR products. The analysis of the mixture samples found that not enough polymorphic bands were produced by the RAPD primers used here to identify Panax species within mixtures of two Panax species. While when P. ginseng was mixed with a genetically unrelated sample there was enough polymorphism to differentiate the two samples in the mixture. The results of this research show that RAPD analysis provides a simple and inexpensive technique to begin analysis of materials used in TCM. Using RAPD analysis it is possible to distinguish Panax plant species from each other. However, the RAPD primers used here did not provide enough reproducibility or polymorphism to analyse liquid and mixtures of Panax species plants.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

In this study, we study the polarization dependence, gain property, and amplified spontaneous emission in Cr4+: YAG crystal fibers. Cr4+: YAG crystal has an ultra-wide bandwidth of 300 nm. Cr4+: YAG crystal fibers fabricated through laser heated pedestal growth technique are suitable for the applications of fiber amplifiers, fiber lasers, and broadband light sources. The experiment results showed that the polarization-dependent loss has a severe variation as the optical wavelength change. The maximum polarization-dependent loss was up to 18 dB. The main reason of such a large polarization-dependent loss is the combination of multimode interference and the birefringence induced by the non-uniformity of optical waveguide structure and residue strain in Cr4+: YAG crystal fibers. Thus, the results of polarization-dependent loss can be used as a feedback parameter to improve the fabrication process. In the experiment of gain property, bi-directional pump and double-pass transmission scheme was adopted and a 0.2 dB net gain was obtained for the first time at signal wavelength of 1400 nm, pumping wavelength of 1060 nm, and total pumping power of 2.8 W. It shows that Cr4+: YAG crystal fiber has potential to be developed as a broadband fiber amplifier. In the measurement of amplified spontaneous emission spectrum, a wide bandwidth of amplified spontaneous emission of 300 nm with total power of 50 £gWwas obtained at 0.2W pumping power condition. The coupling efficiencies from amplified spontaneous emission to single mode fibers and multimode fibers were 1.5 % and 9.9 %, respectively. This result reveals that it has potential to be developed as a broadband light source. To improve the optical properties of Cr4+: YAG crystal fiber in the future, improving the uniformity of optical fiber waveguide and reducing the residue strain in Cr4+: YAG crystal fiber may suppress the polarization-dependent loss; increasing the fiber length, decreasing the mode number, and employing a cladding pump technique with a well-distributed pump power in the crystal fiber to alleviate the excited state absorption may raise the gain performance and the amplified spontaneous emission power.

Recently, with the escalating demands for optical communications, the need for bandwidth in optical communication network has increased. The technology breakthrough in dry fiber fabrication opens the possibility for fiber bandwidth from 1.3 to 1.6 £gm. Cr4+:YAG double-clad crystal fiber (DCF) grown by the co-drawing laser-heated pedestal growth method has a strong spontaneous emission spectrum from 1.3 to 1.6 £gm. Such fiber is, therefore, eminently suitable for broadband optical amplifier, amplifier spontaneous emission (ASE) light source, tunable solid-state laser, and optical coherence tomography (OCT) applications. In this thesis, multilayer dielectric thin films were directly deposited by E-gun coating onto the end faces of the heterostructure Cr4+:YAG DCF. In this way we have successfully improved the extracted ASE power by the high reflection (HR) coatings. The backward ASE in the fiber reflected and propagates with gain through the fiber in the forward direction. In dual-pump scheme, as much as 1.7 mW power (DCF length is 9.5 cm) of collimated output ASE was achieved. The dual-pump scheme and HR thin films provided 1.6 time improvements of the ASE output power. For broadband optical amplifier in dual-pump and double-pass scheme, a 3.7-dB gross gain and a 0.7-dB net loss (DCF length is 8.7 cm) at 1.4-£gm signal wavelength have been successfully developed with HR coatings onto one of the Cr4+:YAG DCF end faces. In addition, we have successfully developed the Cr4+:YAG DCF fiber laser by direct HR coatings onto fiber end faces. A record-low threshold of 96 mW (DCF length is 1.6 cm) with a slope efficiency of 6.9% was achieved at room temperature. It is more than four times lower than any previously reported Cr4+:YAG lasers.

The Cape parrot (Poicephalus robustus) is South Africa's only endemic parrot. It has become increasingly rare in recent years, with fewer than 500 birds left in the wild, and is now regarded as endangered. Possible factors contributing to this rapid decline in numbers include habitat loss, food shortage, disease and illegal trafficking and trading in the species. Habitat loss and food shortage have been brought about by the rapid destruction of the yellowwood trees in the afromontane forests in South Africa and have played a role in reducing the population numbers. The Psittacine beak and feather disease virus (PBFDV) has also contributed to the loss of some individuals, however it is the illegal trafficking of this rare and valuable species that has become of great concern. As the Cape parrot is becoming increasingly rare and therefore highly sought after, its commercial value has multiplied to the extent that illegal black market trapping is on the rise. The industry involved in breeding and conservation of endangered bird species, has a need for the proper establishment of studbooks, containing all available information on captive as well as tagged birds. Most of the information found in studbooks is based on morphological attributes of individual birds. Although this is useful, there is a need to add molecular information in order for complete identification of individuals, particularly in a species threatened by illegal trading and theft. A preliminary analysis of the amount of variation present in the population of interest is therefore required so that appropriate methods and techniques can be developed to identify individual birds. A RAPD analysis was conducted to assess the amount of variation in the Cape parrot and lay the foundations for the establishment of individual identification in the species. Blood samples from 30 parrots, consisting of both related and unrelated individuals, were obtained from three separate locations: Amazona in Assagay, Rehoboth Farm in Dargle, as well as from the Eastern Cape. 15 random primers were selected and used to conduct a randomly amplified polymorphic DNA (RAPD) analysis. RAPDs are extremely useful in situations where relatively inexpensive first approximations of the genetic variation are needed, such as in rare and endangered species. After successful optimisation of the technique in the species, the 15 primers were screened for all 30 individuals and the individual DNA fingerprints, analysed. Clear, distinctive and reliable DNA fingerprints were obtained for all individuals however, it was interesting to note despite the analysis of 85 loci using the 15 primers almost identical DNA fingerprints were produced between the individual birds. A population analysis into the amount of variation present between and within the three populations, as well as for the representative population as a whole, was conducted. Using various statistical programmes such as POPGENE and ARLEQUIN, heterozygosities, genetic distance measures, diversity indices, Wright's fixation index and AMOVAs were estimated. The amount of polymorphism detected in this investigation was 33 % and the heterozygosity, 0.37, which is a relatively high value for the uniformity displayed in the DNA profiles. The high GC content of the primers however, could be a possible explanation thereof. Relationship and kinship determination, sex determination as well as population assignment was possible despite not being able to identify each individual based on unique DNA fingerprints. The AMOVA analysis indicated significant variation on both the between (5.59 %) and within (94.41 %) levels of analysis. Little variation or differentiation was observed between the three subpopulations, which was confirmed with an FST value of 0.056. The variation experienced within each subpopulation was analysed using Shannon's index of phenotypic diversity. The Amazona population displayed the most variation with a value of 0.286 and the Rehoboth population, the least with 0.195. This was expected, with the individuals from the latter population comprising one extended family. Nei's measures of genetic identity revealed that the individuals from Amazona were more similar to the Eastern Cape population, which was again expected with regular exchanging of chicks between the two breeders. RAPD technology was successful in laying the foundations for individual identification in the Cape parrot. It was also successful in producing reproducible DNA fingerprints in the species that were able to determine relatedness to some extent, determine the sex of individuals and identify individuals from a particular subpopulation. Furthermore RAPD analysis gave a good indication of the variation found in the Cape parrot population, which is important for conservation purposes. In order to maximize conservation efforts and strategies in an endangered species, determining the level of genetic diversity and variation found in the remaining individuals of the population is of great importance. This information could provide powerful insight for conservation purposes and depending on the level of diversity detected, appropriate breeding programmes could be set up in order to increase the genetic variation and thereby reduce the chance of extinction of the species. The following important findings emerged from this investigation: • RAPD technology, once optimised for the species of interest, is successful in producing clear and reliable DNA fingerprints, provided the same protocol is followed carefully throughout the investigation. • An optimised protocol for fingerprinting the Cape parrot using RAPDs was established. • Possible sex identification, population assignment and a degree of kinship determination was determined using RAPDs. • Little variation was found within the representative Cape parrot population as a whole due to small population size and possible inbreeding. • As expected for an avian species, little genetic sub-division or differentiation was observed between the three populations analysed. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2004.

No abstract available. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2004.

A collection of 29 clinical streptococcal isolates obtained from the University of KwaZulu-Natal, Medical School, Durban Metro area (South Africa) were studied to establish their penicillin G susceptibility patterns often refered to as minimal inhibitory concentration (MIC) and to determine the genetic diversity among them using two genotyping methods, randomly amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) analysis. All isolates with MIC less than or equal to 0.12 µg/ml were considered susceptible, intermediate resistant if MIC was between 0.25 µg/ml and 4 µg/ml and resistant if greater than 4 µg/ml, The percentage of isolates with resistance was relatively high (75.9%), only 10.3% of isolates showed intermediate resistance and 13.8% of the isolates were completely susceptible to penicillin G. Some of the resistant isolates were highly resistant reaching penicillin G MIC levels of 5000 µ/ml. They were speculated to contain Path altered penicillin binding proteins and high level of crosslinking cell wall induced by the gene products of the MurMN operon. RAPD analysis was performed using three primers, MBPZ-1, MBPZ-2, and MBPZ-3, respectively. RAPD analysis allowed for the identification of 27 RAPD types with MBPZ-1 and MBPZ-3 and 26 RAPD types with MBPZ-2. Ninety-eight percent of these isolates were clustered into two groups, group I and group II, with 90% to 100% dissimilarity among them. Fifty two percent of the isolates of MBPZ-1 group I were in MBPZ-2 group I, 72% isolates of MBPZ-1 group I were in MBPZ-3 group I, and 72% of the isolates of MBPZ-2 group I were in MBPZ-3 group 1. This shows the discriminatory ability of the primers used in this study. Despite clustering of isolates, relatively high diversity was seen. PFGE analysis of macrorestriction fragments obtained after digestion of chromosomal DNA by restriction enzyme, SmaI showed 24 PFGE patterns. The 24 PFGE patterns were divided into three groups (I, II and III) of isolates, with an average of 85% dissimilarity (15% homology) among them. At 25% homology, four clusters, A (13 isolates), B (9 isolates), C (4 isolates), and D (4 isolates) were observed. Two pairs of isolates in group I, cluster A, showed 100% homology. This suggested that each represent the same strain. Four isolates of group I, cluster B, also exhibited 100% homology. This study showed that most of streptococcal isolates with the same penicillin G susceptibility patterns grouped together in a phylogenetic tree by both RAPD and PFGE analysis. There was also some similarity between the results obtained by RAPD analysis and PFGE analysis. Seventeen and nine of the 29 isolates grouped into group I and group II, respectively, two pairs of isolates were indistinguishable, and two pairs of islates were closely related by both RAPD (using MBPZ-3) and PFGE analysis. Although, RAPD analysis is sensitive, specific, faster and cost effective, the ease with which PFGE analysis can be performed, high discriminatory power, reproducibility of the results, and the polymorphism seen in the patterns, suggests that PFGE method has the potential to be very useful for epidemiological evaluations of nosocomial streptococcal infections in KwaZulu-Natal. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2004.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

The specificity of fungal isolates from endemic Western Australian orchid species and hybrids in the tribe Diurideae was investigated using symbiotic seed germination and analysis of the fungal DNA by amplified fragment length polymorphism (AFLP). The distribution of the fungal isolates in the field was also assessed using two different seed baiting techniques. The information from these investigations is essential for developing protocols for reintroduction and translocation of orchid species. Two groups of orchids in the tribe Diurideae were studied. Firstly, a number of Caladenia species, their natural hybrids and close relatives from the southwest of Western Australia were selected because orchid species from the genus Caladenia are considered to have among the most specific mycorrhizal relationships known in the orchid family – an ideal situation for the investigation of mycorrhizal specificity. Secondly, species of Drakaea and close relatives, from the southwest of Western Australia and elsewhere in Australia, which are never common in nature and occur in highly specialised habitats, were selected to investigate the influence of habitat on specificity. Seed from the common species Caladenia arenicola germinated on fungal isolates from adult plants of both C. arenicola and its rare and endangered relative C. huegelii, while seed from C. huegelii only germinated on its own fungal isolates. The AFLP analysis grouped the fungal isolates into three categories: nonefficaceous fungi, C. huegelii type fungi, and C. arenicola type fungi. The group of C. huegelii type fungi included some fungal isolates from C. arenicola. An analysis of the AFLP fingerprints of C. arenicola fungal isolates from different collection locations showed that some, but not all, populations were genetically distinct, and that one population in particular was very variable. Despite being thought to have very specific mycorrhizal relationships, Caladenia species hybridise frequently and prolifically in nature, often forming self-perpetuating hybrid lineages. Five natural hybrids within Caladenia and its closest relatives were investigated. Symbiotic cross-germination studies of parental and hybrid seed on fungi from the species and the naturally occurring hybrids were compared with AFLP analyses of the fungal isolates to answer the question of which fungi the hybrids use. The germination study found that, while hybrid seeds can utilise the fungi from either parental species under laboratory conditions, it is likely that the natural hybrids in situ utilise the fungus of only one parental species. Supporting these observations, the AFLP analyses indicated that while the parental species always possessed genetically distinct fungal strains, the hybrids may share the mycorrhizal fungus of one parental species or possess a genetically distinct fungal strain which is more closely related to the fungus of one parental species than the other. The work on Caladenia hybrids revealed that C. falcata has a broadly compatible fungus that germinated seeds of C. falcata, the hybrid C. falcata x longicauda, and species with different degrees of taxonomic affinity to C. falcata. In general, germination was greater from species that were more closely related to C. falcata: seeds from Caladenia species generally germinated well on most C. falcata isolates; species from same subtribe (Caladeniinae) germinated well to the stage of trichome development on only some of the fungal isolates and rarely developed further; and seeds from species from different subtribes (Diuridinae, Prasophyllinae, Thelymitrinae) or tribes (Orchideae, Cranichideae) either germinated well to the stage of trichome development but did not develop further, or did not germinate at all. The AFLP analysis of the fungal isolates revealed that the fungi from each location were genetically distinct. In situ seed baiting was used to study the introduction, growth and persistence of orchid mycorrhizal fungi. A mycorrhizal fungus from Caladenia arenicola was introduced to sites within an area from which the orchid and fungus were absent, adjacent to a natural population of C. arenicola. In the first growing season, the fungus grew up to 50 cm from its introduction point, usually persisted over the summer drought into the second season and even into the third season, stimulating germination and growth to tuber formation of the seeds in the baits. Watering the inoculated areas significantly increased seed germination. Mycorrhizal relationships in Drakaeinae were less specific than in Caladeniinae. A study of the species Spiculaea ciliata revealed that this species, when germinated symbiotically, develops very rapidly and has photosynthetic protocorms, unlike all other members of the Drakaeinae. An AFLP analysis of the fungal isolates of this species grouped the isolates according to whether they had been isolated from adult plants or reisolated from protocorms produced in vitro. Isolates were genetically distinct when compared before germination and after reisolation. A cross-species symbiotic germination study of seeds of three Drakaea species and one Paracaleana species against fungal isolates from the same species and several other Drakaeinae species revealed lower specificity in this group than previously thought. A number of fungal isolates from Drakaea and Paracaleana species germinated two or more seed types, while all seed types germinated on fungal isolates from other species and the seed of Drakaea thynniphila germinated to some extent on every fungal isolate tested. An AFLP analysis of the Drakaeinae fungal isolates supported this information, revealing little genetic differentiation between the fungi of different orchid species. An ex situ seed baiting technique was used to examine the role of mycorrhizal fungi in microniche specialisation in the narrow endemic Drakaea. Soil samples from within and outside two Drakaea populations were tested for germination of the relevant seed types. In both cases, germination was significantly higher on soil samples from within than outside the populations, suggesting that the relevant mycorrhizal fungi may be restricted to the same microniches as the Drakaea species. The presence of similar fungi at distant, disjunct locations may be related to the extreme age and geological stabilityof the Western Australian landscape. The information from these investigations is essential for developing protocols for reintroduction and translocation of orchid species. It appears that the mycorrhizal relationships in these groups of orchids are not as specific as was previously thought. For reintroduction work, a broad sampling strategy is necessary, as it cannot be assumed that the same orchid species has the same fungus at different locations. A broadly compatible fungus may be of considerable utility in conservation work, such as in situations where a specific fungus appears to have poor saprophytic competence or where soil conditions have been altered. Seed baiting studies provide additional data on fungal distribution in situ. In general, molecular data do not provide information about efficacy or fungal distribution, so research programs that combine symbiotic germination studies with seed baiting investigations and genetic analyses of the fungi will provide the maximum benefit for designing more effective conservation programs.