Dissertations / Theses on the topic 'Detector species'

Although protected areas have been used as principal conservation tools, most of them are suffering from human-induced threats. Consequently, a good understanding of such human-driven threats on biodiversity and identifying early warning systems for habitat change in protected areas is necessary for effective conservation of natural resources. To examine the impact of human disturbance on avifaunal assemblages and to assess the potential application of birds as bioindicators of forest health monitoring in the Afromontane forest of the Bale Mountains of Ethiopia, I recorded birds and habitat variables in three protected and three unprotected forests using a point transect method in 2009 and 2012. The two land use types differ in disturbance levels (higher in the unprotected areas), vegetation structure and bird assemblages. Species richness of entire bird guild, open woodland and open land habitat guilds, granivore and insectivore feeding guilds, and shrub layer and ground layer foraging substrate guilds of birds were significantly higher in the unprotected areas than the protected areas. Abundances of guilds of birds mostly followed a similar trend with species richness. However, densities of overall and forest-specialist bird guilds were higher in the protected area and vice versa for the other guilds. In general, the protected area assemblages were dominated by forest-specialist species, while those of the unprotected areas were dominated by openland and shrubland species. The implication is that disturbance had caused encroachment of non-native species (openland, open woodland and shrub land species) while negatively affecting native species (forest species, particularly tree canopy foragers). These assemblage differences are linked to changes in vegetation structure caused by disturbance. Thus, further forest degradation in the protected area should be avoided in order to maintain native/forest-specialist species. Given the differences in bird assemblages between the two land use types, there is a high likelihood that bioindicator species (i.e. indicator species - those 'characteristic' of a particular habitat - and detector species - those occurring in the different habitats considered but with moderate indication value) can be identified, therefore providing a useful tool to monitor ecosystem health of the forests. Four and nine species were identified as appropriate indicator species (i.e. species with indicator values > 60% and fulfilling biological and niche history criteria used in selection) in the protected and unprotected areas, respectively. In addition, nine species were identified as detectors of habitat change in the protected areas. These bioindicators provide a useful tool for managers of Afromontane forest in the Bale Mountains, as well as similar habitats elsewhere, for long term monitoring of ecosystem health of the forests.
Dissertation (MSc)--University of Pretoria, 2013.
DST/NRF Centre of Excellence
Zoology and Entomology
MSc
Unrestricted

I utilized a design science approach to create an automated kiosk that uses embodied intelligent agents to interview individuals and detect changes in arousal, behavior, and cognitive effort by using psychophysiological information systems. This dissertation achieves three primary purposes.First, I describe the creation of this new Information Technology artifact, discuss design choices, and show the completed prototype.Second, related to this new system, I propose a unique class of intelligent agents, which are described as Special Purpose Embodied Conversational Intelligence with Environmental Sensors (SPECIES). I outline a system model that frames the conceptual components of SPECIES agents, provide design principles for developing SPECIES agents, and discuss some of the research implications of the various components in the model.Third, based on the SPECIES paradigm, I present five studies that evaluate different parts of the model. These studies form the foundational research for the development of the automated kiosk. In the first study, participants interacted with an automated interviewing agent via a chat-based modality (108 participants). The study clearly demonstrates the strong, positive correlation of both response time and the number of times a message is edited to deceitful responses. The software developed became the heart of the kiosk. The second study evaluated changing human decision-making by including influence tactics in decision aids (41 participants). This paper-based decision experiment showed that framing decision aids as appeals to individuals' values possibly change individuals' decisions and was the basis for study 4. The third study examined human-computer interaction and how SPECIES agents can change perceptions of information systems by varying appearance and demeanor (88 participants). Instantiations that had the agents embodied as males were perceived as more powerful, while female embodied agents were perceived as more likeable. Similarly, smiling agents were perceived as more likable than neutral demeanor agents. The fourth study assessed how incorporating impression management techniques into embodied conversational agents can influence human perceptions of the system (88 participants). The impression management techniques proved to be very successful in changing user perceptions. Specifically, agents that performed self-promotion were perceived as more powerful, trustworthy and expert. Agents that performed ingratiation were perceived as more attractive. In the fifth study, I used an embodied agent to interview people who had either constructed a fake bomb and packed it into a bag or had only packed clothes into a bag (60 participants). The agent used eye-tracking technology to capture pupil dilation and gaze behavior. When combined with vocal measurements, the kiosk technology was able to achieve over 93% accuracy in one trial.

The identification and classification of yeasts has been based on morphological, physiological and biochemical properties. In recent years, different molecular biological techniques have been developed for yeast identification. A simple �·widely used but sUfficiently sensitive method is restriction analysis of amplified fragments (PCR-RFLP). Previous studies have produced reference records for Candida species and other yeast. However this reference library is not complete. In this study, PCR using ITS1 and ITS4 primers to amplify the ITS1, ITS2 and the 5.88 rRNA gene, and RFLP using C'ol, Haelll and Hinfl were used with 19 yeasts isolated from 21 soil and grass samples. Among these yeasts, PCR products varied between 400 bp to 650 bp. The restriction patterns could not all be identified due to limitations in the siz~ of the reference . database. Real-time PCRbased methodology has proved to be a sensitive detection system to both identify and quantify the level of microorganisms. In this study, real-time PCR using the F152 and R152 primer pair, targeting amplification of the 188 rONA, allowed for the differentiation of Candida and Saccharomyces, based on the Tm peak of the resultant products whilst the sensitivity of real-time PCR was as low as 500 femtogram of DNA whereas the sensitivity of conventional PCR was 500 picogram of DNA. Real-time PCR could be used to rapidly detect the presence of Candida species in environmental samples to a concentration of approximately 5 cellslcm3 �� The real-time PCR assay described detects Candida species in about 3 hours, which is faster than conventional culture methods. DNA isolation kits proved to be able to get rid of inhibitors in dirty samples but also inhibit the probe function in this study. The kits were only applicable for use with SYBR Green assay. By using DNA isolation kits, there were less positive real-time PCR results for Candida than cultivation followed by manual DNA extraction methodology. This investigation illustrates that the Tm values from SYBR Green assay may act as useful screening technique for Candida identification. The Cp value from probe assay is a confirmation technique as Cp values above 24 can be eliminated. The samples with Cp values below 24 were iden.tified as Candida species whilst those with Cp values above 24 were identified as other yeasts. PCR-RFLP can be used as an identification method for a number of Candida species but for Candida albicans and Candida tropicalis the results are inconclusive. Candida albicans and Candida tropicalis cannot be distinguished by RFLP or real-time PCR whilst morphological test such as germ tube production were also inclusive. However, sequence results clearly distinguished between these two species.

The importance of single-tree-based information for forest management and related industries in countries like Sweden, which is covered in approximately 65% by forest, is the motivation for developing algorithms for tree detection and species identification in this study. Most of the previous studies in this field are carried out based on aerial and spectral images and less attention has been paid on detecting trees and identifying their species using laser points and clustering methods. In the first part of this study, two main approaches of clustering (hierarchical and K-means) are compared qualitatively in detecting 3-D ALS points that pertain to individual tree clusters. Further tests are performed on test sites using the supervised k-means algorithm in which the initial clustering points are defined as seed points. These points, which represent the top point of each tree are detected from the cross section analysis of the test area. Comparing those three methods (hierarchical, ordinary K-means and supervised K-means), the supervised K-means approach shows the best result for clustering single tree points. An average accuracy of 90% is achieved in detecting trees. Comparing the result of the thesis algorithms with results from the DPM software, developed by the Visimind Company for analysing LiDAR data, shows more than 85% match in detecting trees. Identification of trees is the second issue of this thesis work. For this analysis, 118 trees are extracted as reference trees with three species of spruce, pine and birch, which are the dominating species in Swedish forests. Totally six methods, including best fitted 3-D shapes (cone, sphere and cylinder) based on least squares method, point density, hull ratio and slope changes of tree outer surface are developed for identifying those species. The methods are applied on all extracted reference trees individually. For aggregating the results of all those methods, a fuzzy logic system is used because of its good reputation in combining fuzzy sets with no distinct boundaries. The best-obtained model from the fuzzy system provides 73%, 87% and 71% accuracies in identifying the birch, spruce and pine trees, respectively. The overall obtained accuracy in species categorization of trees is 77%, and this percentage is increased dealing with only coniferous and deciduous types classification. Classifying spruce and pine as coniferous versus birch as deciduous species, yielded to 84% accuracy.

The detection and identification of bio-threat agents and study of host-pathogen interactions require a high-resolution detection platform capable of discerning closely related species. This dissertation addresses the completion of the development of an array based platform and provides a robust pipeline for the discovery of unique bio-signatures for pathogens and their host. Our collection (library) of host and pathogen signatures has been greatly expanded to improve robustness and identification accuracy of an 'unknown' sample. The library containing measured bio-signatures for each species/isolate is complemented with computational methodologies to resolve the identity of the unknown sample as well as a mixture of organisms or a pathogen in a host background. Current approaches for pathogen detection rely on prior genomic sequence information. This research targets use of a broad based platform for identification of pathogens from field or laboratory samples on a high density Universal Bio-signature Detection Array (UBDA). This array is genome independent and contains all possible (49 combinations) 9-mer probes which are mathematically computed and genome independent. It works by comparing signal intensity readout to a library of readouts established by interrogating a wide spectrum of organisms. Each genome has a unique pattern of signal intensities corresponding to each of these probes. These signal intensities were used to generate un-biased cluster analysis patterns that can easily distinguish organisms into accepted and known phylogenomic relationships. Classification methods such as hierarchical clustering, Pearsonâ s correlation matrix, principal component analysis and curve fitting regression methods were tested for pathogen specific use cases. Hierarchical clustering and Pearsonâ s correlation matrix methods can establish phylogenomic relationships between highly diverse genomes. However, in order to assign a given sample to one or more groups, such as a pure isolate of a single species or composite mixture of multiple species, principal component analysis (PCA) was used. The test cases included identification of mixed samples, case study of field samples from state diagnostic labs and finally a surveillance method for viral and parasite carrying insect host vectors. Completion of these application challenges is meant to demonstrate the power and confirm confidence in the Universal Bio-signature Detection Array.
Ph. D.

Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau...
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau...
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau. Deuxième étude : des durées d’échantillonnage intermédiaires d’une à deux semaines (l’échelle des traitements allant d’un jour à un mois) étaient la durée optimale de déploiement de la plaque de fixation pour la détection des espèces « rares » (c’est-à-dire, des le début du recrutement). Une analyse au niveau de l’assemblage montre toutefois que l’augmentation de la durée et de la fréquence de l’échantillonnage augmentait logarithmiquement le nombre total d’espèces rares observées. Ces résultats espèce par espèce et au niveau de l’assemblage démontrent que la modification des éléments temporels de l’échantillonnage, tels que la durée et la fréquence, peut affecter considérablement la détection d’espèces. Troisième étude : après avoir évalué plusieurs sources spatiales et temporelles (le site, la région, la saison, et l’année), le moment choisi pour le déploiement des plaques est apparu comme étant la plus grande source de variabilité du recrutement benthique d’espèces rares. En particulier, le moment optimal pour la détection précoce serait en automne (a) lorsque le recrutement saisonnier d’espèces envahissantes établies tend à atteindre un pic et (b) lorsque la détection au niveau du site d’espèces envahissantes rares tend à se produire. Quatrième étude : l’échelle spatiale dominante dans le recrutement d’espèces rares est la plus petite (centaine de mètres). Cette échelle dominante peut être interprétée comme étant la bonne échelle spatiale pour la détection d’espèces rares. Une analyse plus poussée a montré que si l’échantillonnage a été structuré de manière aléatoire, l’échantillonnage à des échelles intermédiaires (millier de mètres) devient l’échelle optimale pour la détection d’espèces rares. Ces résultats élucident les différences de variabilité naturelle de la population benthique entre multiples échelles d’espace et de temps pour des espèces rares et communes. Ces études écologiques font partie d’une boîte à outils de détection précoce nécessaire à la gestion des espèces envahissantes marines en renseignant sur la manière dont l’échantillonnage des espèces rares doit être faite à multiples échelles spatio-temporelles. Des expériences de terrain similaires optimisant la détection d’espèces rares (au-delà de l’utilisation de plaques de fixation pour détecter les organismes benthiques dans les provinces Maritimes canadiennes) devraient être réalisées pour d’autres taxons, régions, t outils d’échantillonnage—en particulier, les envahisseurs à haut risque prévus, les invasions futures, et les outils récemment développés.
Les activités anthropiques causent des invasions biologiques qui sont devenues un problème mondial susceptible de causer des dommages écologiques (p. ex., sur la biodiversité et l’habitat), économiques (sur les industries) et sociaux (sur le bien-être humain). La prévention et la détection précoce des nouvelles invasions sont des éléments essentiels pour la gestion des risques et des impacts sur les écosystèmes et les économies. Bien sûr, la prévention est préférable, mais la détection précoce est une étape cruciale pour enrayer la propagation ultérieure des espèces envahissantes, car elle offre la possibilité de les éradiquer avant les phases d’établissement de la population et de propagation. Bien qu’il s’agisse d’une option de gestion efficace en matière de coût et de temps, la détection précoce exige un effort d’échantillonnage considérable pour détecter les populations envahissantes aux tout premiers stades de leur invasion. En utilisant le système benthique marin comme modèle, quatre études interdépendantes ont été menées pour identifier des stratégies d’échantillonnage susceptibles d’améliorer notre capacité à détecter des populations envahissantes rares et à comprendre les patrons et processus écologiques de recrutement benthique à multiples échelles spatiales et temporelles. Plus précisément, ces études expérimentales sur le terrain visaient à (1) évaluer la relation entre l’approvisionnement en larves et la fixation dans une population envahissante isolée, (2) déterminer la durée de l’échantillonnage et de la fréquence à l’aide de plaques de fixation pour la détection d’espèces rares, (3) déterminer l’importance relative aux sources de variations spatiales et temporelles du recrutement benthique, et (4) examiner l’effet de l’échelle spatiale de l’échantillonnage sur la détection des espèces en analysant les patrons de recrutement à de multiples échelles sur quatre ordres de grandeur allant de la dizaine de mètres à la dizaine de kilomètres. Première étude : contrairement à l’hypothèse originale d’une relation étroite entre l’approvisionnement et la fixation initiale, l’approvisionnement en larves était plutôt un facteur déterminant de la fixation aux échelles moyennes. Ces résultats suggèrent que la force de cette relation s’affaiblit avec l’augmentation de l’échelle spatiale des observations de terrain. Néanmoins, un quart de la variation de la fixation à moyenne échelle peut encore être expliqué par l’approvisionnement sur des courtes échelles de temps (une semaine). Par conséquent, cette relation confirme l’utilité des plaques de fixation en tant qu’outil efficace pour la détection précoce aux échelles moyennes dans une marina, car une faible densité de recrutement sur les plaques correspond à une faible abondance de propagules envahissantes dans la colonne d’eau. Deuxième étude : des durées d’échantillonnage intermédiaires d’une à deux semaines (l’échelle des traitements allant d’un jour à un mois) étaient la durée optimale de déploiement de la plaque de fixation pour la détection des espèces « rares » (c’est-à-dire, des le début du recrutement). Une analyse au niveau de l’assemblage montre toutefois que l’augmentation de la durée et de la fréquence de l’échantillonnage augmentait logarithmiquement le nombre total d’espèces rares observées. Ces résultats espèce par espèce et au niveau de l’assemblage démontrent que la modification des éléments temporels de l’échantillonnage, tels que la durée et la fréquence, peut affecter considérablement la détection d’espèces. Troisième étude : après avoir évalué plusieurs sources spatiales et temporelles (le site, la région, la saison, et l’année), le moment choisi pour le déploiement des plaques est apparu comme étant la plus grande source de variabilité du recrutement benthique d’espèces rares. En particulier, le moment optimal pour la détection précoce serait en automne (a) lorsque le recrutement saisonnier d’espèces envahissantes établies tend à atteindre un pic et (b) lorsque la détection au niveau du site d’espèces envahissantes rares tend à se produire. Quatrième étude : l’échelle spatiale dominante dans le recrutement d’espèces rares est la plus petite (centaine de mètres). Cette échelle dominante peut être interprétée comme étant la bonne échelle spatiale pour la détection d’espèces rares. Une analyse plus poussée a montré que si l’échantillonnage a été structuré de manière aléatoire, l’échantillonnage à des échelles intermédiaires (millier de mètres) devient l’échelle optimale pour la détection d’espèces rares. Ces résultats élucident les différences de variabilité naturelle de la population benthique entre multiples échelles d’espace et de temps pour des espèces rares et communes. Ces études écologiques font partie d’une boîte à outils de détection précoce nécessaire à la gestion des espèces envahissantes marines en renseignant sur la manière dont l’échantillonnage des espèces rares doit être faite à multiples échelles spatio-temporelles. Des expériences de terrain similaires optimisant la détection d’espèces rares (au-delà de l’utilisation de plaques de fixation pour détecter les organismes benthiques dans les provinces Maritimes canadiennes) devraient être réalisées pour d’autres taxons, régions, t outils d’échantillonnage—en particulier, les envahisseurs à haut risque prévus, les invasions futures, et les outils récemment développés.
As a consequence of anthropogenic activities, biological invasions have become a global problem that can cause ecological (e.g., biodiversity and habitat), economic (industries), and social (human wellbeing) harm. Prevention and early detection of new invasions are vital components of managing risks and impacts to ecosystems and economies. Prevention is, of course, preferred but early detection is a critical step that can ultimately stop future spread of invasive species because it provides an opportunity for eradication before population growth and spread. Despite being a cost- and time-effective management option, early detection requires considerably high sampling effort to detect incipient invasive populations at the early stages of their invasion. Using the marine benthic system as a model, four inter-related studies were carried out to identify sampling strategies that could enhance our ability to detect rare invasive populations and to understand ecological patterns and processes of benthic recruitment across multiple scales of space and time. Specifically, these experimental field studies aimed to (1) evaluate the relationship between propagule supply and settlement in a closed invasive population, (2) determine the optimal sampling duration and frequency using settlement plates to detect rare species, (3) ascertain the relative importance of spatial and temporal sources of variation in benthic recruitment, and (4) examine how the spatial scale of sampling affects species detection by analyzing recruitment patterns at multiple scales across four orders of magnitudes ranging from tens of metres to tens of kilometres. First study: Contrary to the expectation of a strong relationship between supply and initial settlement, larval supply was instead a limited determinant of settlement at mesoscales. This finding suggests that the strength of this relationship weakens as the spatial scale increased from previously reported small-scale field observations to mesoscales of the present study. Nonetheless, a quarter of the variation in settlement can still be explained by supply over short timescales (one week). Therefore, this relationship supports the utility of settlement plates as an effective tool for early detection at mesoscales within a marina because low densities of recruitment on plates correspond to low abundances of invasive propagules in the water column...
As a consequence of anthropogenic activities, biological invasions have become a global problem that can cause ecological (e.g., biodiversity and habitat), economic (industries), and social (human wellbeing) harm. Prevention and early detection of new invasions are vital components of managing risks and impacts to ecosystems and economies. Prevention is, of course, preferred but early detection is a critical step that can ultimately stop future spread of invasive species because it provides an opportunity for eradication before population growth and spread. Despite being a cost- and time-effective management option, early detection requires considerably high sampling effort to detect incipient invasive populations at the early stages of their invasion. Using the marine benthic system as a model, four inter-related studies were carried out to identify sampling strategies that could enhance our ability to detect rare invasive populations and to understand ecological patterns and processes of benthic recruitment across multiple scales of space and time. Specifically, these experimental field studies aimed to (1) evaluate the relationship between propagule supply and settlement in a closed invasive population, (2) determine the optimal sampling duration and frequency using settlement plates to detect rare species, (3) ascertain the relative importance of spatial and temporal sources of variation in benthic recruitment, and (4) examine how the spatial scale of sampling affects species detection by analyzing recruitment patterns at multiple scales across four orders of magnitudes ranging from tens of metres to tens of kilometres. First study: Contrary to the expectation of a strong relationship between supply and initial settlement, larval supply was instead a limited determinant of settlement at mesoscales. This finding suggests that the strength of this relationship weakens as the spatial scale increased from previously reported small-scale field observations to mesoscales of the present study. Nonetheless, a quarter of the variation in settlement can still be explained by supply over short timescales (one week). Therefore, this relationship supports the utility of settlement plates as an effective tool for early detection at mesoscales within a marina because low densities of recruitment on plates correspond to low abundances of invasive propagules in the water column...

Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 ìg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 ìg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.

Phytophthora diseases have caused worldwide economic, social and environmental impacts for decades. Once their presence is confirmed, they are difficult to eradicate. To reduce and manage the damage inflicted by the pathogen, fast and reliable disease management protocols are required. Tests that enable the rapid and reliable identification of the pathogen assist greatly in disease management. Phytophthora species are traditionally not only detected by baiting but also by plating of symptomatic tissue on selective media. Species can be identified by the characteristics of the mycelium growing out of the bait. However, the method is low throughput, labour intensive, and prone to false negatives. An alternative approach would be to detect the pathogen by the presence of its DNA. This involves amplification of the pathogen DNA using Polymerase Chain Reaction (PCR) and detection of the amplification product. Detection is usually by agarose gel electrophoresis. However, this is also a labour intensive process involving pouring, loading, running, and staining of the gels. The aim of this thesis is to explore the use of Matrix Assisted Laser Desorption/ Ionisation Time-of-Flight (MALDI-TOF) mass spectrometry for detection of PCR products. This procedure enables the analysis of large numbers of samples within a very short time-frame as the average time for analysis of each sample is in the order of milliseconds. The assay involves annealing an extension (genotyping) primer to the PCR product and its extension by a single nucleotide. The nature of the nucleotide added differentiates species as does the site to which the primer anneals. Multiple extension (genotyping) primers can be used together in a single reaction for detection of multiple species. In this project four genotyping primers (GPs) were designed from the ITS regions of Phytophthora palmivora, Phytophthora cinnamomi, Phytophthora citricola, and Phytophthora cambivora. The extension primers were tested for their specificity on the DNA of the target species. The four primers designed were specific for their intended targets except for GPpalm3 which in addition to being extended by ddT when tested with DNA from P. palmivora, was also extended by ddC when tested with DNA from other species of Phytophthora or Pythium. These primers were also tested for their ability to detect multiple Phytophthora species in a single reaction (multiplexing). Mixtures of primers were added to mixed DNA templates and the primer extension reaction carried out. The primers were designed so that their masses were sufficiently different for them to be identified from a mixture. Six replicates were analysed for each reaction. In general only about 1-3 of the six replicates gave a positive reaction. This indicates that there may be some interference between primers, or that the presence of all four nucleotides interfered with the primer extension reaction. Increasing either the amount of enzyme, the amount of nucleotides or both did not improve the results. The sensitivity of detection was tested by the addition of different amounts of mycelium to soil. The detection sensitivity depended on the primer pair used for PCR amplification. The ITS1/2 primer pair was more sensitive than the ITS1/4 pair. The limit of detection was 1 mcg mycelium g soil-1. However using nested PCR, levels of sensitivity comparable to those obtained using the ITS1/2 primer pair could be achieved. Primers to other regions of the genome such as the beta cinnamomin elicitin gene gave very low levels of sensitivity compared to the ITS primers. In comparison with DNA detection we found that the limit of detection using baiting was 4 mcg mycelium g soil-1. Results below this limit were unreliable. The method suffered from the additional disadvantage that it took a long time in comparison to DNA detection. DNA detection methods do not distinguish between living and dead organisms in the soil. However it can be hypothesised that DNA is unlikely to persist for any significant length of time in soil. To test this, we added plasmid DNA to soil and tested the persistence of this DNA using a variety of methods such as precipitation of labelled DNA, southern blotting and PCR amplification. It was found that in general, in soils from different ecosystems, the bulk of the DNA was undetectable after 24 hours. The rate of DNA breakdown differed with the soil type. In some soils, the added DNA was not detected even after 2 hours, whereas in others it could be observed after 10 hours. The detection depended on the method. Southern blotting showed that although DNA could be observed at 10 hours, by 24 hours it was completely degraded. In contrast a PCR product could be obtained from the soil extracts up to 24 hours. In a separate experiment, plasmid DNA was detectable over a 24 hour incubation period in 5 soil samples from 5 different sites. The results suggest that DNA is degraded rapidly in soil and is unlikely to persist longer than 24 hours. The results in this thesis demonstrate that MALDI-TOF MS is a suitable alternative to agarose gel electrophoresis for analysis of PCR products. The technique is rapid, differentiates species from mixtures, is high-throughput and amenable to automation. Implementation will require further research to automate the primer extension assay to reduce the sensitivity to impurities in the DNA and to design parameters for sampling asymptomatic material.

The ability to monitor the presence of analytes is of great importance both in industrial applications and physiological systems. Since the crucial recognition events of chemistry, biology, and materials science occur in a much smaller world, it is very difficult to gather this kind of information. Therefore much effort has been devoted to the detection of chosen molecules selectively and signalling this presence. This thesis highlighted the uniqueness and utility of both fluorescent sensor and electrochemical sensor to investigate biologically important species. The determination of copper(II) ion is very crucial to both environment and human health. To utilise the fluorescent sensors for recognition has plenty of advantages, such as high sensitivity, “on-off” switch ability and submillisecond temporal resolution. Naphthalimide based probes has always been the key point of the chemosensors due to its excellent photophysical properties. Therefore, the aim of the project is to investigate boronic acid receptor linked to the naphthalimide fluorophore for copper(II) detection. And the utility of boronic acid as binding site is one of the rare examples of fluorescent chemosensors for Cu2+ detection. Neutral molecules such as glutathione (GSH) play a crucial role in maintaining appropriate redox homeostasis in biological systems. We creatively use the chromophore of dicyanomethylene-4H-pyran(DCM) for the design of probe, due to its emission located at the red or near infra-red (NIR) region, which is particularly suitable for application in biological samples. GSH, the most abundant cellular thiol, is of great importance in cellular defence against toxins and free radicals. Therefore we developed a colorimetric and NIR fluorescence turn-on thiol probe containing DCM as the fluorophore and DNBS as the fluorescence quencher and recognition moiety. The interaction of ferrocene-boronic acid with fructose is investigated in aqueous 0.1 M phosphate buffer at pH 7, 8, and 9. Two voltammetric methods, (i) based on a dual-plate generator-collector micro-trench electrode (steady state) and (ii) based on square-wave voltammetry (transient), are applied and compared in terms of mechanistic resolution. A combination of experimental data is employed to obtain new insights into the binding rates and the cumulative binding constants for both the reduced ferrocene-boronic acid (pH dependent and weakly binding) and for the oxidised ferrocene-boronic acid (pH independent and strongly binding). Finally, a redox-activated fluorescence switch based on a ferrocene - fluorophore - boronic ester conjugate was investigated. The development of multifunctional systems that can integrate individual basic logic gates into combinational circuits has drawn much attention to smart materials. A novel electrochemically and fluorescence active boronic ester sensor molecule has been developed containing ferrocence and naphthalimide as the redox and fluorophore units. The solid state electrochemical characterisation of the compound was investigated in aqueous media and it indicates a direct interaction with fluoride anions. The fluorescence can also be modulated through photoinduced electron transfer (PET) by a redox process. An OFF-ON fluorescence response occurs when the ferrocene is oxidised by Fe3+. While in the presence of F-, the fluorescence enhancement was offset. Therefore, the combinations of iron (Fe3+ ) ions, sodium L-ascorbate, and fluoride (F-) ions can be used to produce a molecular system displaying INHIBIT logic gate, due to indirect fluorescence quenching.

Aquatic invasive species are drivers of ecological change through directly competing with native counterparts, causing alterations in community structure and acting as vectors for the introduction of novel pathogens. A combination of human-mediated introductions and accidental releases from aquaculture facilities has enabled highly invasive species, including the American signal crayfish (Pacifastacus leniusculus), Chinese mitten crab (Eriocheir sinensis) and topmouth gudgeon (Pseudorasbora parva) to become established in Great Britain. I assessed the factors which could have facilitated their establishment success and dispersal, including genetic diversity. Novel tools such as environmental DNA and citizen science have been proven effective for detecting and monitoring aquatic invasive species. Yet, the motivation for participation and continued data collection in citizen science initiatives are not clear. I have determined that multiple introductions from different source populations are likely to have contributed to the invasion success of signal crayfish in Great Britain. Secondly, I have developed and employed a quantitative PCR environmental DNA multiplex which has enabled simultaneous detection of non-native pathogens (crayfish plague) alongside native and invasive crayfish species, providing information on the coexistence of native and invasive crayfish in absence of crayfish plague. Application of this assay in water and sediment samples has also highlighted the relative impacts of river barriers on mitten crab and signal crayfish dispersal and demonstrated that similar DNA results can be achieved by utilising both types of samples. I also developed a species-specific DNA assay for topmouth gudgeon which detected its presence despite lack of visual confirmation, emphasising the greater sensitivity of environmental DNA tools. Finally, I designed and launched a citizen science initiative in an attempt to assess distribution and pathogen status of signal crayfish, which highlighted the complexity of ensuring participation for successful invasive species initiatives.

This thesis reports work extending the scope of a recently developed gas sensing technique, multi-mode absorption spectroscopy (MUMAS). The ability of MUMAS to simultaneously detect multiple species from a mixture is demonstrated for the first time. The technique is subsequently extended to mid-infrared wavelengths, realising large gains in sensitivity. A solid-state, multi-mode laser has been developed to provide a high-performance comb source for use with MUMAS. This in-house constructed, diode-pumped, Er/Yb:glass laser operates on 10 longitudinal modes, separated by 18 GHz and centred close to 1565 nm. The extensive development and prototyping work leading to this final laser design is described. Multi-species detection with MUMAS is reported for the first time, thus demonstrating the ability of this technique to perform multi-gas sensing using a single laser and simple detection scheme. The previously described Er/Yb multi-mode laser was used to record MUMAS signals from a sample containing CO, C₂H₂, and N₂O. The components of the mixture were detected simultaneously by identifying multiple transitions in each of the species. Temperature- and pressure-dependent modelled spectral fits to the data were used to determine the partial pressures of each species in the mixture with an uncertainty better than +/-2%. Multi-mode radiation has been successfully generated at 3.3 μm using quasi phase matched difference frequency generation (QPM-DFG). A mid-infrared laser comb was produced by optically mixing the near-infrared, multi-mode comb produced by the previously developed Er/Yb:glass laser with the single-mode output of a Nd:YAG laser operating at 1064 nm. This multi-frequency laser source was characterised to verify performance, and subsequently used to perform proof-of-principle MUMAS measurements on the strong transitions found in this spectral region. Spectra were recorded of NH₃ and CH₄ both individually and as components of a mixture. A minimum detection level for this system was determined to be 4.3 μbar m^-1 for CH₄, a sensitivity increase of 300 over similar measurements performed in the near-IR.

The severe acute respiratory disease syndrome or SARS epidemic emerged in Hong Kong, China, in 2002 with a mortality rate of 15%. The etiological agent for SARS was identified to be a previously unrecognized coronavirus (SARS-CoV) which was found to be zoonotic in origin. A possible reservoir for the SARS-CoV was proposed to be the Chinese horseshoe bat species (Rhinolophus spp.) due to the detection of SARS-related bat coronaviruses (BtCoV) within these bat species. Since the SARS-CoV epidemic, new interest regarding the origin and pathogenicity of coronaviruses has been generated. As such, surveillance studies of BtCoV in numerous bat species have been performed in Asia, Europe, North and South America as well as 3 African countries. Recent BtCoV investigations in Kenya, Ghana and Nigeria identified BtCoV from both the Alpha- and Betacoronavirus genera and provided the first evidence for the presence of coronaviruses in African bats. Previously, the presence of antibodies against SARS-related CoV has been reported in two bat species native to South Africa. This study investigated the possible presence of BtCoV in a panel of bat specimens collected from sites in South Africa and Rwanda, and how they are related to previously detected BtCoVs from other parts of the world. Here we report the development of two PCR assays, the PanBtCoV/9 primer nested RT-PCR and PanBat/AB/6 primer hemi-nested RT-PCR assay, which were used in coronavirus detection from alimentary specimens collected from 15 bat genera. The combined assays amplified coronavirus RNA from 5 samples of the 201 analysed samples collected in South Africa (n=113) and Rwanda (n=88). Three alphacoronaviruses were detected in 3 different South African bat species, Miniopterus spp. (Miniopterus-Bat coronavirus/Irene/South Africa/2009), Neoromicia capensis (Neoromicia-Bat coronavirus/167/South Africa/2007), and Mops midas (Mops-Bat coronavirus/1364/South Africa/2011). From Rwanda, a single betacoronavirus, a SARSrCoV was detected within 2 Rhinolophus spp. individuals (Rh-BtCoV/441/Rwanda/08 and Rh- BtCoV/445/Rwanda/08). Phylogenetic analysis of these sequences was performed and showed that the South African Miniopterus alphacoronavirus and the Rwandan betacoronavirus cluster together with previously detected African BtCoV from the same host genera. The South African alphacoronavirus from Mops midas was closely related to an alphacoronavirus identified within another member of the Molossidae family, Chaerephon spp. from Kenya. Being the first BtCoV identified from the Neoromicia genus, no African BtCoV sequences were available for comparison and as such the virus clustered together with European BtCoV from the Nyctalus spp., another member of the Vespertilioninae subfamily. This study has detected the first BtCoV viral RNA from the native bat species of South Africa and Rwanda, providing confirmation to the presence of bat coronaviruses circulating in these countries. From these preliminary results further investigations into the prevalence and infection cycles of bat coronaviruses in specific bat populations can be performed in the future. The possibility of either these alpha- or betacoronaviruses spilling over and eventually adapting to and infecting other species, though unlikely, cannot be excluded since such rare events are hypothetically responsible for the establishment coronaviruses in humans, livestock, poultry and pets. Caution may still be merited when interacting with bats in roosts and caves.
Dissertation (MSc)--University of Pretoria, 2012.
National Research foundation (NRF)
Poliomyelitis Research Foundation (PRF)
Microbiology and Plant Pathology
MSc
Unrestricted

This thesis examined the hypotheses that the mucus lining of the gastrointestinal tract (GIT) of Australian marsupials is colonised with large populations of spiral and fusiform shaped bacteria, many of which belong to the genus Helicobacter and that these Helicobacter species are likely be unique. The presence of spiral and fusiform shaped bacteria in the GIT of 8 Australian marsupial species (32 animals in total) was examined using microscopy, culture and Helicobacter genus specific PCR. The marsupials studied included the brushtail possum, ringtail possum, koala, wombat, Eastern grey kangaroo, Tasmanian devil, Eastern quoll and long nosed bandicoot. The spiral and fusiform shaped isolates were characterised and identified using morphological appearance, Helicobacter genus specific PCR and 16S rRNA gene sequence comparisons. The spatial distribution of Helicobacter species in the GIT sections was examined microscopically in silver stained sections of the GIT and using Fluorescent in situ hybridisation (FISH) with a Helicobacter genus specific probe. Spiral and/or fusiform shaped bacteria were detected and/or isolated from all marsupials studied. The prevalence and bacterial load of these organisms was found to differ in each marsupial species. These bacteria were found to belong to 3 different genera (Helicobacter, Campylobacter and Desulfovibrio). Each marsupial species appeared to be colonised with one or more unique Helicobacter species. Comparison of the detection of Helicobacter species in different groups of marsupials (herbivores, omnivores and carnivores) suggests that diet as well as the function and structure of the GIT may have a significant impact on their colonisation. Phylogenetic analysis of the new possum Helicobacters showed that they shared a common ancestor. Comparison of Helicobacter species isolated from different species of marsupial and placental mammals, as well as birds, showed that differences in environmental location i.e. gastric vs lower bowel had a major impact on the position of the Helicobacters on the phylogenetic tree.

The Amazon represents more than half of the surviving tropical forest on Earth. However, despite its vast size and diversity, habitat loss is an increasing threat due to the growth of economic activities and infrastructure projects. Carnivores play an important role in reducing herbivore numbers through predation, thereby reducing the risk of over browsing and are particularly susceptible to habitat loss and fragmentation due to their large area requirements, low densities, and slow population growth. Altering herbivore communities via a change in carnivore density and habitat loss may change plant diversity by altering seed dispersal, and seed and seedling survival. The Madeira-Purus interfluvial plain in Brazil is a pristine and yet understudied part of the Amazon. I studied environmental factors affecting occupancy and detection of carnivores and herbivores in the Madeira-Purus interfluvial plain Amazonas state, Brazil. During 2010-12 remote cameras were used to investigate patterns of site occupancy and detection probabilities, as affected by habitat and anthropogenic influences, for several terrestrial mammal groups. Site occupancy and detection varied for all species groups across land protections types. Medium felids and peccaries showed a sharp decline in occupancy from unprotected lands to state-protected sites with the highest occupancy on the federally-protected site. Brocket deer increased in occupancy from unprotected to state-protected lands, and from state-protected to federally-protected lands. Large felid occupancy, however, was exactly the opposite, with the lowest occupancy at the federally-protected site. Species richness at camera sites was the most important covariate, positively influencing occupancy in all species groups. This helps inform wildlife management by providing suggestions to improve future occupancy studies and support for maintaining protected areas for the persistence of viable mammal populations. I found occupancy of many species groups (i.e. peccaries, medium felids and medium rodents) were lowest on state-protected land. Species richness was also lowest on state-protected land, implying a depletion of herbivore and carnivore species in that area, which may be due to local foraging and hunting of forest resources by humans. I recommend stricter laws and enforcement to limit the harvest of forest fruits and nuts and illegal hunting. Repaving local highways will likely increase human influence in these areas and increase pressure on forest resources.

The aim of this thesis is to investigate the use of hyperspectral reflectance signals for the discrimination of cogongrass (Imperata cylindrica) from other subtly different vegetation species. Receiver operating characteristics (ROC) curves are used to determine which spectral bands should be considered as candidate features. Multivariate statistical analysis is then applied to the candidate features to determine the optimum subset of spectral bands. Linear discriminant analysis (LDA) is used to compute the optimum linear combination of the selected subset to be used as a feature for classification. Similarly, for comparison purposes, ROC analysis, multivariate statistical analysis, and LDA are utilized to determine the most advantageous discrete wavelet coefficients for classification. The overall system was applied to hyperspectral signatures collected with a handheld spectroradiometer (ASD) and to simulated satellite signatures (Hyperion). A leave-one-out testing of a nearest mean classifier for the ASD data shows that cogongrass can be detected amongst various other grasses with an accuracy as high as 87.86% using just the pure spectral bands and with an accuracy of 92.77% using the Haar wavelet decomposition coefficients. Similarly, the Hyperion signatures resulted in classification accuracies of 92.20% using just the pure spectral bands and with an accuracy of 96.82% using the Haar wavelet decomposition coefficients. These results show that hyperspectral reflectance signals can be used to reliably detect cogongrass from subtly different vegetation.

Sperm cells need hexoses as a substrate for their function, for both the maintenance of membrane homeostasis and the movement of the tail. These cells have a peculiar metabolism that has not yet been fully understood, but it is clear that they obtain energy from hexoses through glycolisis and/or oxidative phosphorylation. Spermatozoa are in contact with different external environments, beginning from the testicular and epididymal fluid, passing to the seminal plasma and finally to the female genital tract fluids; in addition, with the spread of reproductive biotechnologies, sperm cells are diluted and stored in various media, containing different energetic substrates. To utilize these energetic sources, sperm cells, as other eukaryotic cells, have a well-constructed protein system, that is mainly represented by the GLUT family proteins. These transporters have a membrane-spanning α-helix structure and work as an enzymatic pump that permit a fast gradient dependent passage of sugar molecules through the lipidic bilayer of sperm membrane. Many GLUTs have been studied in man, bull and rat spermatozoa; the presence of some GLUTs has been also demonstrated in boar and dog spermatozoa. The aims of the present study were - to determine the presence of GLUTs 1, 2, 3, 4 and 5 in boar, horse, dog and donkey spermatozoa and to describe their localization; - to study eventual changes in GLUTs location after capacitation and acrosome reaction in boar, stallion and dog spermatozoa; - to determine possible changes in GLUTs localization after capacitation induced by insulin and IGF stimulation in boar spermatozoa; - to evaluate changes in GLUTs localization after flow-cytometric sex sorting in boar sperm cells. GLUTs 1, 2, 3 and 5 presence and localization have been demonstrated in boar, stallion, dog and donkey spermatozoa by western blotting and immunofluorescence analysis; a relocation in GLUTs after capacitation has been observed only in dog sperm cells, while no changes have been observed in the other species examined. As for boar, the stimulation of the capacitation with insulin and IGF didn’t cause any change in GLUTs localization, as well as for the flow cytometric sorting procedure. In conclusion, this study confirms the presence of GLUTs 1, 2 ,3 and 5 in boar, dog, stallion and donkey spermatozoa, while GLUT 4 seems to be absent, as a confirmation of other studies. Only in dog sperm cells capacitating conditions induce a change in GLUTs distribution, even if the physiological role of these changes should be deepened.
Gli spermatozoi di mammifero necessitano di zuccheri per espletare le loro funzioni, come il mantenimento dell’omeostasi membranale ed il movimento. Queste cellule hanno un metabolismo particolare, che non è ancora stato del tutto compreso, anche se è chiaro che ottengano energia da esosi tramite il processo glicolitico e la fosforilazione ossidativa. Gli spermatozoi sono a contatto con ambienti esterni molto diversi: dai fluidi testicolare ed epididimale, per passare al plasma seminale ed infine alle secrezioni dell’apparato genitale femminile. Inoltre, con la diffusione delle biotecnologie riproduttive, il liquido seminale è diluito e conservato in svariati media contenenti diversi substrati energetici. Per sfruttare queste fonti energetiche gli spermatozoi, come le altre cellule eucariotiche, hanno un sistema proteico di membrana ben definito, rappresentato principalmente dalla famiglia dei GLUT. Queste proteine hanno una struttura transmembranale ad alfa elica e funzionano come una pompa enzimatica che permette un trasporto passivo veloce e secondo gradiente di concentrazione delle molecole di zucchero attraverso lo strato lipidico. Alcuni GLUT sono stati studiati negli spermatozoi di uomo, ratto e toro e la presenza di alcuni altri è stata dimostrata in cane e maiale. Gli scopi di questo studio sono stati: • determinare la presenza dei GLUT 1, 2, 3, 4 e 5 in spermatozoi di maiale, cane , stallone e asino e descrivere la loro localizzazione; • studiare eventuali cambi di localizzazione dovuti alla capacitazione o alla reazione acrosomiale in spermatozoi di maiale, cane e stallone; • valutare cambiamenti nella disposizione dei GLUT negli spermatozoi di maiale in seguito a capacitazione stimolata con insulina ed IGF; • valutare possibili cambiamenti di localizzazione dei GLUT a seguito del processo di “sessaggio” mediante citofluorimetro sorter. La presenza e la localizzazione dei GLUT 1, 2, 3 e 5 sono state dimostrate negli spermatozoi di maiale, asino, cavallo e cane mediante le tecniche di western blotting ed immunofluorescenza indiretta; una rilocalizzazione delle proteine dopo capacitazione è stata osservata solo negli spermatozoi di cane e nessun cambiamento è stato registrato nelle altre specie. Per quanto riguarda il maiale, non si sono rilevate rilocalizzazioni dei GLUT a seguito della capacitazione con stimolazione con insulina ed IGF e nemmeno a seguito del processo di “sex sorting”. Concludendo, questo studio conferma la presenza dei GLUT 1, 2, 3 e 5 negli spermatozoi di maiale, cane stallone e asino, mentre il GLUT 4 sembra essere assente, a conferma di alcuni studi precedenti. Solo negli spermatozoi di cane le condizioni capacitanti inducono un cambiamento nella distribuzione dei GLUT, anche se il ruolo fisiologico di questi cambiamenti deve essere ancora approfondito.

The present PhD thesis entitled "Silica Hybrid Materials for detection of toxic species and clinical diagnosis" is focused on the design and synthesis of new hybrid materials, using different silica supports as inorganic scaffolds, with applications in recognition, sensing and diagnostic protocols. The first chapter of the PhD thesis is devoted to the definition and classification of hybrid materials, relying on concepts of Nanotechnology, Supramolecular and Materials Chemistry. State of art of this field of knowledge is described using numerous examples of applications for molecular recognition, especially about gated materials. In the second chapter, the general and specific objectives of the PhD thesis are presented. The third chapter shows the synthesis, characterization and sensing performances of hybrid silica nanoparticles for the chromogenic detection of formaldehyde. Commercially available silica nanoparticles are functionalized with thiol and polyamine moieties. These hybrid nanoparticles were used for the chromogenic recognition of formaldehyde using a blue squaraine indicator. In the absence of formaldehyde, suspensions of the functionalized nanoparticles are able to bleach the blue squaraine solutions due to a reaction between the grafted thiol moieties and the added dye. In the presence of formaldehyde, -SH moieties onto the surface reacts with this molecule with the subsequent inhibition of thiol-squaraine reaction. As a consequence suspension remains blue and formaldehyde is detected. These nanoparticles allows detection of formaldehyde in a selective and sensitive fashion in aqueous and in gas phase. The fourth chapter deals with the preparation of acetylcholinesterase capped mesoporous silica nanoparticle that are used for the selective and sensitive sensing of diisopropylfluorophosphate (DFP), a nerve agent mimic. Mesoporous silica nanoparticles are prepared and the pores loaded with rhodamine B dye. Then, the external surface of the loaded nanoparticles is functionalized with a pyridostigmine derivative (a reversible inhibitor of acetylcholinesterase enzyme). Finally the pores are capped upon acetylcholinesterase addition (by coordination with the grafted inhibitor). In the absence of DFP nanoparticles are tightly closed whereas in the presence of nerve agent simulant pore opening and dye release is observed (due to preferential coordination of DFP with the enzyme active sites and detachment from the nanoparticles surface). In an extension of the previous results, nanoparticles functionalized with a neostigmine derivative are prepared and characterized and its controlled release features studied in the presence of several acetylcholinesterase inhibitors. The selective recognition of Mycoplasma fermentans genomic DNA using capped mesoporous silica nanoparticles is presented in chapter fifth. Sensing nanodevices are based on mesoporous silica nanoparticles loaded with rhodamine B and with the external surface functionalized with isocyanatopropyl moieties. Then, a short DNA sequence was covalently attached to the surface of the nanoparticles through the formation of urea linkages. Finally, the pores were capped by adding a single stranded oligonucleotide which is a highly conserved sequence of the 16S ribosomal subunit of the mycoplasma species genome. Aqueous suspensions of the DNA-capped nanoparticles showed negligible dye release. However, only in the presence of Mycoplasma fermentans genomic DNA the pores are opened and a marked rhodamine B release is observed. Using these nanoparticles a limit of detection as low as 70 DNA copies uL-1 is achieved.
La presente tesis doctoral titulada "Silica Hybrid Materials for detection of toxic species and clinical diagnosis" está enfocada al diseño y síntesis de nuevos materiales hibridos usando diferentes soportes inorgánicos basados en sílice, con aplicaciones en protocolos de reconocimiento, sensado y diagnóstico. El primer capítulo de la tesis está dedicado a la definición y clasificación de los materiales híbridos, basándose en conceptos de Nanotecnología, Química Supramolecular y Química de Materiales. El estado del arte de este campo de conocimiento se describe usando numerosas aplicaciones para reconocimiento molecular, especialmente sobre materiales de tipo puerta molecular. En el segundo capítulo se presentan los objetivos generales y específicos de la presente tesis. El tercer capítulo presenta la síntesis, caracterización y capacidades sensoras de nanopartículas híbridas de sílice para la detección de formaldehído. Nanopartículas silíceas comerciales se funcionalizan con grupos tiol y poliamina. Estas nanopartículas híbridas han sido usadas para el reconocimiento cromogénico de formaldehído usando un indicador azul de escuaridina. En ausencia de formaldehído, suspensiones de nanopartículas son capaces de decolorar las disoluciones azules de escuaridina debido a una reacción entre los tioles insertados y el colorante añadido. En presencia de formaldehído, los grupos -SH de la superficie reaccionan con esta molécula con la consiguiente inhibición de la reacción tiol-escuaridina. Como consecuencia la suspensión permanece azul y el formaldehído es detectado. Estas nanopartículas permiten la detección de formaldehído de manera sensitiva y selectiva en disolución y fase gas. El cuarto capítulo trata de la preparación de nanopartículas mesoporosas de sílice tapadas con acetilcolinesterasa que son usadas para el sensado selectivo y sensitivo de diisopropilfluorofosfato (DFP), un simulante de gas nervioso. Nanopartículas mesoporosas de sílice se preparan y sus poros se cargan con rodamina B. Entonces, la superficie externa de las nanopartículas cargadas se funcionalizan con un derivado de piridostigmina (un inhibidor reversible de la enzima acetilcolinesterasa). Finalmente los poros se tapan con la adición de acetilcolinesterasa (por coordinación con el inhibidor insertado). En ausencia de DFP, las nanopartículas permanecen cerradas mientras que en la presencia del simulante de agente nervioso los poros se abren y se observa la liberación del colorante (debido a la preferencia de coordinación de los sitios activos de la enzima con el DFP y el desanclaje de la superficie de las nanopartículas). En una extensión de los resultados comentados, se preparan nanopartículas funcionalizadas con un derivado de neostigmina para caracterizarlas y estudiar sus procesos de liberación controlada en presencia de distintos inhibidores de acetilcolinesterasa. El reconocimiento selectivo de ADN genómico de Mycoplasma fermentans usando nanopartículas mesoporosas de sílice se presenta en el quinto capítulo. Nanodispositivos sensores basados en nanopartículas de sílice mesoporosa cargadas con rodamina B y con la superficie externa funcionalizada con grupos isocianatopropilo. Entonces, una secuencia corta de ADN se ancla covalentemente a la superficie de las nanopartículas a través de la formación de enlaces urea. Finalmente, los poros se tapan añadiendo un oligonucleótido de cadena simple el cuál está formado por una secuencia altamente conservada de la subunidad ribosomal 16S del genoma de esta especie concreta de micoplasma. Suspensiones acuosas de nanopartículas tapadas con oligonucleótido presentan una liberación insignificante de colorante. Sin embargo, sólo en presencia de ADN genómico de Mycoplasma fermentans los poros se abren y se observa una marcada liberación de rodamina B. Usando estas nanopartículas se llegó a un límite de detección tan bajo como 70 c
La present tesi doctoral titulada "Silica Hybrid Materials for detection of toxic species and clinical diagnosis" està enfocada al disseny i síntesi de nous materials híbrids utilitzant diferents suports inorgànics basat en sílice, amb aplicacions en protocols de reconeixement, sensat i diagnòstic. El primer capítol de la tesi està dedicat a la definició i classificació dels materials híbrids , basant-se en conceptes de Nanotecnologia, Química Supramolecular i Química dels Materials. L'estat del art d'aquest camp de coneixement es descriu utilitzant nombroses exemples de aplicacions per a reconeixement molecular, especialment sobre materials de tipus porta molecular. En el segon capítol es presenten els objectius generals i específics de la present tesi. El tercer capítol presenta la síntesi, caracterització i capacitats sensores de nanopartícules híbrides de sílice per a la detecció de formaldehid. Nanopartícules silícies comercials es funcionalitzen amb grups tiol i poliamina. Estes nanopartícules híbrides han sigut utilitzades per al reconeixement cromogènic de formaldehid utilitzant un indicador blau de escuaridina. En absència de formaldehid, suspensions de nanopartícules son capaces de decolorar les dissolucions blaves de escuaridina degut a una reacció entre els tiols inserits i el colorant afegit. En presència de formaldehid els grups -SH de la superfície reaccionen amb esta molècula amb la conseqüent inhibició de la reacció tiol-escuaridina. Com a conseqüència la suspensió roman blava i el formaldehid es detecta. Estes nanopartícules permeten la detecció de formaldehid de forma sensitiva i selectiva en dissolució i en fase gas. El quart capítol de la tesi tracta de la preparació de nanopartícules mesoporoses de sílice tapades amv acetilcolinesterasa que són utilitzades per al sensat selectiu i sensitiu de diisopropilfluorofosfat (DFP), un simulant de gas nerviós. Nanopartícules mesoporoses de sílice es preparen i els seus porus es carreguen amb rodamina B. Llavors, la superfície externa de les nanopartícules carregades es funcionalitzen amb un derivat de piridostigmina (un inhibidor reversible de l'enzim acetilcolinesteras). Finalment els porus es tapen amb la addició de acetilcolinesterasa (per coordinació del inhibidor inserit). En absència de DFO, les nanopartícules romanen tancades mentre que en la presència del simulant d'agent nerviós els porus s'obrin i s'observa l'alliberament del colorant (degut a la preferència de coordinació dels centres actius de l'enzim amb el DFP i el desancoratge de la superfície de les nanopartícules). En una extensió dels resultats comentats, es preparen nanopartícules funcionalitzades amb un derivat de neostigmina per a caracteritzar-les i estudiar els seus processos d'alliberació controlada en presència de diferents inhibidors d'acetilcolinesterasa. El reconeixement selectiu d'ADN genòmic de Mycoplasma fermentans utilitzant nanopartícules mesoporoses de sílice es presenta en el quint capítol. Nanodispositius sensors basats en nanopartícules mesoporoses de sílice carregades amb rodamina B i amb la superfície externa funcionalitzada amb grups propilisocianat. Llavors, una seqüència curta d'ADN s'ancora covalentment a través de la formació d'enllaços urea. Finalment, els porus es tapen afegint un oligonucleòtid de cadena simple, el qual està composat per una seqüència altament conservada de la subunitat ribosomal 16S del genoma d'aquesta espècie concreta de micoplasma. Suspensions aquoses de nanopartícules tapades amb oligonucleòtids presenten una alliberació negligible de colorant. No obstant, solament en presència d'ADN genòmic de Mycoplasma fermentans els porus s'obrin i s'observa una marcada lliberació de rodamina B. Utilitzant estes nanopartícules es va aplegar a un límit de detecció tan baix com 70 còpies d'ADN per uL.
Pascual Vidal, L. (2017). Hybrid silica materials for detection of toxic species and clinical diagnosis [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/80076
TESIS

The aims of the thesis were to investigate, by simulation, various aspects of the QTL mapping methods and apply the methods to scan the porcine genome for QTLs. The mapping of the porcine genome was achieved using a Meishan x Large White F₂ population. These breeds were chosen because they differed significantly for several traits of economic interest. Markers covered approximately 85% of the porcine genome and animals were measured for growth and fatness traits. Chromosomes 4, 7 and 14 had a genome wide significant effect on at least one trait. In all cases the single gene model was significantly better than the polygenic model. The effects on chromosome 4 for growth were in agreement with previous studies notably a similar study using wild boar from Sweden. Chromosome 7 had a large effect on fatness (over 6mm between breeds) and is of considerable interest because the Large White carries the alleles for high fat depth. Chromosome 14 was shown to have a significant effect on growth rate on test. Confidence intervals were produced by the non-parametric bootstrap and were found to be relatively large (in excess of 30cM) for the location on chromosomes 4 and 14. In contrast the confidence intervals on chromosome 7 were smaller and corresponded to the major histocompatilibity complex, a very gene rich region of the genome.

Thesis advisor: Gabor T. Marth
This thesis concerns itself with the development of methods for comparing genomes. Chapter 2 is a comparative genomics investigation of coding regions across multiple species. Regions of the genome coding for proteins show higher conservation than non-coding regions. Furthermore, we show that a portion of coding regions are conserved beyond the requirements of protein conservation, supporting functions such as microRNA binding and splicing enhancement, providing the non-coding functional impetus to conservation. In Chapter 3, we focus on the detection and characterization of a particular type of structural variation - mobile element insertions (MEIs). While there are many types of mobile elements in the human genome, three of these are active and cause most of the MEI variation observed in humans: ALU, L1 and SVA elements. We detect variation across 1000 Genomes Pilot populations caused by these elements, assemble ALU elements to single nucleotide resolution, and determine actively copying species of this element. We've developed a variety of algorithmic approaches to MEI detection, and present these. Chapter 4 outlines an approach to remedy reference bias via the incorporation of variation data into the reference. In particular, we construct a pan-genome reference, demonstrated concretely via resolving ALU regions, and develop new alignment software to align against this enriched reference structure
Thesis (PhD) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology

Polycyclic aromatic hydrocarbons are ubiquitous pollutants and of these, benzo[a]pyrene (B[a]P) is the most widely characterised. B[a]P exerts its effects by the covalent binding of its metabolites to DNA. It has been well documented that the developmental stages of young organisms are highly susceptible to the effects of such pollutants. Presented here is a study on the effect or developmental stage in Xenopus laevis on the metabolism and subsequent adduct induction and repair. DNA adducts were measured by ³²P - postlabelling. Larvae were exposed at various stages of development, to waterborne B[a]P for 24 hours and allowed to recover for up to 6 days. A dose response of total adducts was seen at all stages studied. An increase in different adduct types was also observed with increasing liver development. Repair was biphasic, with adducts persisting for at least 6 days post exposure. Adducts were identified by the use of isomeric standards. The trans (+) anti B[a]PDE-N²-guanine adduct was detected in all stages and this adduct was shown to be non-repairable at stage 50. Larvae at stage 38 were shown to be the most sensitive to the effects of B[a]P, exhibiting signs of cyclopia and teratogenic effects to the forearms, up to 5 days post exposure. Young Xenopus laevis frogs exposed to B[a]P for 24 hours, were analysed for adducts in the liver, heart, pancreas, lungs, kidneys, brain, testes and ovaries. Adducts were detected in all organs except testes and ovaries, the greatest damage being observed in the liver and lungs. Adduct levels in the brain were close to the limit of detection. B[a]P-DNA adducts were examined in Scophthalmus maximus (turbot) a benthic marine organism, as a comparative species to Xenopus. Adduct profiles were different to those observed in Xenopus.

In Africa, bats have been implicated in a number of emerging and re-emerging diseases, mostly associated with viral infections – such as caused by rabies-related lyssaviruses, paramyxoviruses and coronaviruses. Whereas most infectious agents reported in bats have been viruses, bacterial species have rarely been reported. The main objective of this study was to identify bacterial species that may circulate in southern African bats by using nucleic acid detection methods. Two bacterial species were targeted: Rickettsia and Bartonella. These were chosen because they are capable of infecting and causing diseases in a wide range of hosts including humans. We evaluated and optimized several polymerase chain reaction (PCR) assays to detect Rickettsia and Bartonella. These included PCRs targeting the citrate synthase gene (gltA) and 16S rRNA gene for Rickettsia and the citrate synthase (gltA) gene for Bartonella. A panel of 354 bat blood samples, collected from different sites in South Africa and Swaziland, were tested using these assays. Rickettsia and Bartonella DNA was detected in 6/354 and 13/354 bats, respectively, and characterized using DNA sequencing. All the Rickettsias were closely related to other Rickettsia species circulating in these areas and all the Bartonellas clustered together, but were distantly related to Bartonella species from the same geographical area. This study reports for the first time the detection of Rickettsia and Bartonella DNA in southern African bats. This finding contributes to the knowledge regarding Rickettsia and Bartonella diversity and host distribution. The epidemiology and transmission pathways of these bacteria in bat populations remains to be elucidated as is the public health importance of the circulation of these potential pathogens in bats. A likely source of infection is unknown, but since bats carry ectoparasites (flies, fleas, ticks and mites); surveillance for these pathogens in ectoparasites should be a first step in elucidating epidemiology and transmission pathways to other hosts including humans. Given the potential for human disease, the surveillance and characterization of these pathogens will be in the interest of good public health practices.
Dissertation (MSc)--University of Pretoria, 2012.
Microbiology and Plant Pathology
MSc
Unrestricted

Numerous pathogenic bacterial species have been found in many freshwater systems around the world. These pathogens affect the overall water quality of these systems and may cause diseases in both aquatic and terrestrial animals which may lead to loss of species diversity and abundance in their environments. This study sought to identify and document pathogenic bacterial species that may inhabit the streams that flow through Great Smoky Mountains National Park. Bacterial cells were collected by filtering water from four streams (Oconaluftee River, Kephart Prong, Little Pigeon River and Hickory King Branch Stream) through separate capsule filters. The cells were later backflushed from the filters and cultured on various selective and differential media. Ten isolates were selected based on phenotypic characteristics such as colony color and growth on specific media type, and sample origin. The nearly full 16S rDNA was sequenced for all ten isolates and analyzed to determine their identity.

Out of the ten isolates, four isolates were from the phylum Firmicutes while the other six were in the phylum Proteobacteria. Phylogenetic analysis of these isolates showed eight out of the ten isolates were related to known opportunistic pathogens. The other two were related to a ubiquitous Bacillus species that is considered to be a probiotic. Although none of the isolates had a 100% match to a known obligate or opportunistic pathogen, many isolates matched > 97% to opportunistically pathogenic species. Follow up molecular and metabolic tests need to be employed to determine the pathogenicity of each isolate.

Malaria represents one of the oldest documented diseases among humans and even today organisms in the genus Plasmodium kill more people than any other infectious disease, especially in tropical and subtropical areas. The four most common species which infect humans are Plasmodium falciparum, Plasmodium vivax, Plasmodium ovale and Plasmodium malaria. Of these four species, Plasmodium falciparum and Plasmodium vivax account for 95 percent of infections globally. Microscopy has been used since early days for the diagnosis of malaria because this method is simple, does not require highly equipped facilities, and in most cases enables differentiation among the species causing malaria in humans when performed by skilled microscopy readers. However, this method has been misleading in identifying parasite species, especially in the case of low level parasitemia, a mixed parasite infection, or modification by drug treatment as well as in placental malaria. Malaria rapid diagnostic tests (RDT) have played a major role in malaria management; particularly in providing blood based diagnosis in remote locations where microscopy based diagnosis is unavailable. These diagnostic tests are fast and easy to perform and do not require electricity or specific equipment. As part of strengthening malaria diagnostics in Malawi, the Ministry of Health and Population strongly recommends the use of malaria RDT’s at all levels of the health care delivery system. However, malaria microscopy remains a gold standard test for malaria. All patients (regardless of age) with suspected uncomplicated malaria should have a confirmed diagnosis with malaria RDT before anti-malaria treatment is administered. Based on field performance evaluations that assessed performance, quality control and production capacities of the manufacturing companies of malaria RDT’s, the Ministry of Health and Population recommended two brands of Histidine Rich Protein 2 (HRP-2), RDT’s for use in Malawi. These are SD Bioline malaria Ag Pf and the New Paracheck malaria Ag Pf. All these RDT’s are able to detect only P. falciparum. However, other species have been reported to exist in the country and there is a need to find proper RDT’s which will be able to detect all other species including P. falciparum. The main aim of this study was to evaluate Paramax-3 Pf/Pv/Pan RDT (Zephyr Biomedicals, India), if used in Malawi, could be able to detect and identify the different species of Plasmodium causing malaria in Malawi. The study recruited a total of 250 adult and infants at Bwaila Hospital in Lilongwe, Malawi. Study results showed that the overall sensitivity and specificity of the Paramax-3 RDT used in the study were 100 percent and 83 percent respectively. However, it was observed that the RDT test was not able to identify the P. ovale, and in some cases, the RDT test was positive for P. falciparum when the PCR identified the species as P. ovale. No P. vivax was detected both by RDT and PCR. This study was able to detect and identify the presence of P. malaria and P. ovale in Malawi apart from the P. falciparum. There were no significant differences between microscopy results compared to both the RDT and the PCR, with 94 percent and 98 percent sensitivities of R1 and R2 compared to RDT, as well as 94 percent and 96 percent sensitivities for R1 and R2 compared to PCR respectively. Both R1 and R2 had low specificities for example, R1 had 72 percent and R2 had 80 percent compared to RDT. Comparing R1 and R2 to PCR, the sensitivities were 64.9 percent and 67.2 percent respectively. However, the readers had difficulties differentiating the different species microscopically. The history of anti-malaria treatment had no significant effect on the outcome of the results in both the RDT and PCR.

Thesis (MSc (Med)(Microbiology))--University of Limpopo (Medunsa Campus), 2010.
Mycoplasma genitalium, a human mycoplasma species has been established as a cause of nongonococcal urethritis (NGU) in men, particularly in Chlamydia trachomatis-negative patients. It was also shown to play a role in cervicitis and pelvic inflammatory disease (PID) in women. Due to difficulty in culturing, and the lack of routine molecular diagnostic tests, many M. genitalium infections are undetected. The purpose of this study was to evaluate three nucleic acid amplification tests (NAATs) i.e. a recently developed Gen-Probe research only transcription mediated amplification (TMA) assay, a conventional polymerase chain reaction (PCR) assay and a real-time PCR (q-PCR) assay for the detection of M. genitalium in urine specimens of men with symptoms of urethritis. To evaluate the three assays, 300 urine specimens were collected between June 2007 and July 2008 from sexually active male patients presenting with discharge (N=94) and/or burning on micturition (N=206) to a private medical practitioner in Silverton, Pretoria. A specimen was considered positive by extension of the gold standard i.e. if any two of the three assays were positive. This was used to calculate the sensitivity and specificity of each method. TMA detected M. genitalium in 62 (21%), PCR in 43 (14%) and q-PCR in 48 (16%) of the 300 patients. The sensitivities of the assays were 100% (TMA), 92% (q-PCR) and 78% (PCR), with specificities of 90% (TMA), 95% (q-PCR) and 97% (PCR). The sensitivity of the TMA assay was higher than that of the q-PCR and PCR assays. The lower sensitivity obtained by the q-PCR assay might have been due to inhibition and limitations in the amount of the DNA template. However, the q-PCR assay was easy to perform as it combines amplification and detection thus eliminating further handling of PCR products. The PCR, although with a higher specificity, was the least desirable in terms of testing time and problems with subjectivity when reading agarose gels. v We concluded that the Gen-Probe TMA assay is a highly sensitive method for detection of M. genitalium in urine specimens of men. The use of Gen-Probe TMA and the q-PCR assay, will increase the detection of M. genitalium in clinical specimens at this catchment area.

For the first time in Lithuania the foliage spectral reflectance properties of common tree species were investigated using hyperspectral imaging. The methodological outline was formulated and the procedures of practical hyperspectral imaging application were developed to stimulate the progress of hyperspectral remote sensing in Lithuanian forestry. Information extracted from foliage hyperspectral reflectance data was used to accurately determine forest tree species and the provenances of Scots Pine trees. The satisfactory results of determination of Scots Pine crown defoliation and the concentration of some needles chemical constituents were achieved investigating the foliar hyperspectral reflectance, too. The first spectral libraries of common Lithuanian tree species foliar reflectance were built considering the growing season.
Suformuoti hiperspektrinio skenavimo naudojimo įvairioms miško medžių savybėms tirti metodiniai ir praktiniai pagrindai – sukurtos ir išbandytos mėginių paėmimo, jų paruošimo skenuoti, skenavimo atlikimo ir gautos informacijos apdorojimo metodikos, kurios aprobuotos vykdant mokslinius tyrimus. Nustatyti vegetacijos sezono momentai, kuriais skirtingų miško medžių rūšių atpažinimas nuotoliniu būdu pagal jų spektrinus atspindžius būtų tiksliausias, o tai sudaro prielaidas tobulinti kitas nuotoliniais. Pasiūlyti metodai paprastosios pušies spyglių kai kurių cheminių elementų koncentracijai nustatyti naudojant hiperspektrinį skenavimą. Sukurtos Lietuvos miškuose augančių pagrindinių medžių rūšių lapijos spektrinio atspindžio kreivių bibliotekos, naudotinos miškų inventorizacijoje, kalibruoti ir klasifikuoti orlaiviuose sumontuotais jutikliais išgautus Lietuvos medynų hiperspektrinius vaizdus.