Massive parallel sequencing (MPS) data analysis tasks are often computationally demanding and their execution time would take too long using standard computing machines. Thus there is a need for parallelization of this tasks and ability to execute them on a sufficiently powerful computing machines. In the first chapter we describe a newly created platform for resequencing analysis of MPS data - MOLDIMED and novel annotation tool, which is ready to deploy on HPC infrastructure. The second chapter describes MPS approaches in Diamond-Blackfan anaemia (DBA), which is predominantly underlined by mutations in genes encoding ribosomal proteins (RP); however, its etiology remains unexplained in approximately 25% of patients. We performed panel sequencing of all ribosomal genes in DBA patient without previously known molecular pathology. A novel heterozygous RPS7 mutation coding RPS7 p.V134F was found in one female patient and subsequently confirmed in two asymptomatic family members, in whom mild anemia were detected on further examination. Subsequently, we performed whole transcriptome analysis in all family members and patient with RPS7 mutation in comparison with healthy control group and with DBA patients with known mutation in RPS19. We observed dysregulation mainly in signal pathways of translation,...

Carbon nanotubes (CNTs) have attracted a significant attention in a wide variety of applications due to their excellent physical and chemical properties. Specifically, CNTs reinforced polymer nanocomposites have considerable potential for the realization of highly sensitive, flexible, stable and durable strain sensors. However, the performance of polymer/CNTs strain sensors is influenced by many factors. Especially, the homogeneity of the CNTs distribution within the polymer matrix and the adhesion of nanocomposite film to the polymer substrate play a decisive role. Additionally, the electrical and piezoresistive responses of polymer/CNTs nanocomposites, as well as their response under variable environmental conditions need to be considered. The main aim of this thesis is to develop polymer/CNTs nanocomposites for strain sensing applications. Thereby, the focus is on the development of suitable, cost-effective and simple preparation methods of polymer/CNTs-based strain sensitive nanocomposites and on the selection of suitable flexible substrate. However, during deposition, residual stress can be formed at the interface between the film and the substrate, which leads to thin film failures. Therefore, an analytical model is developed to predict the stress distribution in the film aiming to define the suitable processing conditions for low residual stress formations. Furthermore, specific surface treatments are proposed in order to enhance the adhesion between the substrate and the thin film, which are investigated by contact angle measurement (CAM), X-rays spectroscopy (XPS)and atomic force microscopy (AFM). Nanocomposites with up to 1 wt.% multi-walled carbon nanotubes (MWCNTs) were prepared using a simple direct mixing method. The process parameters, such as sonication time and curing time, have been determined based on several characterization techniques. Dispersions qualities were examined using morphological and topography characterizations including scanning electron microscopy (SEM) and AFM. Additionally, DC measurements were performed on the polymer/CNTs nanocomposites in order to optimize the process parameters depending on the electrical conductivity and piezoresistivity of the nanocomposite. The impact of surface treatment on the strain sensing behavior was evaluated. Furthermore, electrical and piezoresistive responses under humidity and temperature effects were investigated. Analytical investigations show that the residual stresses can be minimized by using low deposition temperatures and by increasing the film thickness. Comparison of surface treatment techniques demonstrates that oxygen plasma cleaning improves adhesion at the interface by enlarging the surface area and enhancing the surface wettability and the surface polarity due to the introduction of functional groups. Morphological characterizations show the good homogeneity of MWCNTs and depict the importance of optimization of sonication time for the uniform filler distribution. Furthermore, AFM analysis show that the surface roughness is reduced as sonication time is increased due to the debundling of CNTs agglomeration. However, excessive sonication time can lead to higher roughness caused by breaking of CNTs, which get thereby the tendency to re-agglomerate. A low percolation threshold was achieved at a CNTs concentration of 0.3 wt.% which is significantly lower than the CNT concentrations reported in literature and demonstrating the quality of dispersion process adopted. Higher sensitivity is achieved at this CNTs concentration with approximately linear piezoresistive behavior of around R 2 = 0.9904. The novel strain sensitive nanocomposites show good stability at ambient conditions and good durability under mechanical cyclic test. In addition, it is found that the sensing behavior depends greatly on the surface roughness. A high stability and linearity with good sensitivity were observed for the sensor having low surface roughness. The temperature and humidity dependency of the composite is affected by the environmental changes. Therefore, an encapsulation of the film is required to minimize moisture absorption in addition to get better sensor recovery under mechanical load comparing to non-encapsulated film. / Kohlenstoff-Nanoröhrchen (CNTs) genießen aufgrund ihrer hervorragenden physikalischen und chemischen Eigenschaften in einer Vielzahl von Anwendungen eine große Aufmerksamkeit. Insbesondere CNT-verstärkte polymere Nanokomposite haben ein erhebliches Potenzial für die Realisierung hochempfindlicher, flexibler, stabiler und langlebiger Dehnungssensoren. Die Eigenschaften von Polymer/CNT-Dehnungssensoren werden von vielen Faktoren beeinflusst. Insbesondere die Homogenität der CNT-Verteilung innerhalb der Polymermatrix und die Haftung des Nanokompositfilms auf dem Polymersubstrat spielen eine entscheidende Rolle. Darüber hinaus müssen die elektrischen und piezoresistiven Eigenschaften von Polymer/CNTs-Nanokompositen sowie deren Reaktion auf variable Umgebungsbedingungen berücksichtigt werden. Das Hauptziel dieser Arbeit ist die Entwicklung von Polymer/CNT-Nanokompositen für die Anwendung als Dehnungsmessstreifen. Der Fokus liegt auf der Entwicklung geeigneter, kostengünstiger und einfacher Präparationsmethoden von Polymer/CNT-basierten dehnungsempfindlichen Nanokompositen und deren Realisierung auf geeigneten flexiblen Substraten. Während der Abscheidung kann an der Grenzfläche zwischen Film und Substrat Eigenspannung entstehen, die zu Dünnschichtfehlern führt. Daher wird ein analytisches Modell zur Vorhersage der Spannungsverteilung im Film entwickelt, um die geeigneten Verarbeitungsbedingungen für geringe Eigenspannungsformationen zu definieren. Darüber hinaus werden spezifische Oberflächenbehandlungen vorgeschlagen, um die Haftung zwischen dem Substrat und dem Dünnfilm zu verbessern, die durch Kontaktwinkelmessung (CAM), Röntgenspektroskopie und Rasterkraftmikroskopie (AFM) untersucht werden. Nanokompositen mit bis zu 1 wt.% mehrwandigen Kohlenstoff-Nanoröhren (MWCNTs) wurden mit einem einfachen Direktmischverfahren hergestellt. Die Prozessparameter, wie Ultraschallzeit und Aushärtezeit, wurden auf der Grundlage verschiedener Charakterisierungstechniken bestimmt. Die Dispersionsqualitäten wurden mittels morphologischer und topographischer Charakterisierungen einschließlich Rasterelektronenmikroskopie (REM) und AFM untersucht. Zusätzlich wurden DC-Messungen an den Polymer/CNT-Nanokompositen durchgeführt, um die Prozessparameter in Abhängigkeit von der elektrischen Leitfähigkeit und der Piezoresistivität des Nanokomposits zu optimieren. Der Einfluss der Oberflächenbehandlung auf das Verhalten des Dehnungssensors wurde bewertet. Darüber hinaus wurden elektrische und piezoresistive Reaktionen unter Feuchtigkeits- und Temperatureinflüssen untersucht. Analytische Untersuchungen zeigen, dass die Eigenspannungen durch niedrige Depositionstemperaturen und eine Erhöhung der Schichtdicke minimiert werden können. Der Vergleich von Oberflächenbehandlungstechniken zeigt, dass die Sauerstoff-Plasma-Reinigung die Haftung an der Grenzfläche verbessert, in dem sie die Oberfläche vergrößert und die Benetzbarkeit der Oberfläche sowie die Oberflächenpolarität durch die Einführung von Funktionsgruppen verbessert. Morphologische Charakterisierungen zeigen die gute Homogenität vom Epoxid /MWCNTs Nanokompositen und die Bedeutung der Optimierung der Ultraschallzeit für die gleichmäßige Füllstoffverteilung. Darüber hinaus zeigt die AFM Analyse, dass die Oberflächenrauhigkeit durch die Entbündelung der CNT-Agglomerate für eine längere Ultraschallzeit reduziert wird. Eine übermäßige Ultraschallzeit kann jedoch zu einer höheren Rauigkeit durch Brüche von CNTs führen, die dadurch zu einer erhöhten Reagglomerationsneigung führen. Ein niedriger Perkolationsschwellenwert wurde bei einer CNT-Konzentration von 0.3 wt.% erreicht, welches deutlich niedriger als die in der Literatur berichteten CNT-Konzentrationen ist. Dies belegt die hohe Qualität des vorgeschlagenen Dispersionsprozesses. Eine höhere Empfindlichkeit wird bei dieser CNT-Konzentration mit einem annähernd linearen piezoresistiven Verhalten von etwa R 2 = 0.9904 erreicht. Die neuartigen spannungsempfindlichen Nanokompositen weisen eine gute Stabilität der Umgebungsbedingungen und eine gute Haltbarkeit im mechanischen Zyklustest auf. Darüber hinaus wird festgestellt, dass das Abtastverhalten stark von der Oberflächenrauheit abhängt. Eine hohe Stabilität und Linearität bei guter Empfindlichkeit wurde für den Sensor mit geringer Oberflächenrauigkeit beobachtet. Das Verhalten des Sensors wird durch Umweltveränderungen aufgrund von Temperatur und Luftfeuchtigkeit beeinflusst. Daher ist eine Verkapselung des Films erforderlich, um die Feuchtigkeitsaufnahme zu minimieren. Die realisierte Verkapselung hat zusätzliche Vorteile in Bezug auf die Sensor Rückgewinnung unter mechanischer Belastung im Vergleich zu nicht gekapseltem Film gezeigt.

Mosses are some of the first colonizers to disturbed sites, yet their roles in early plant community structuring are not well understood. The primary succession zones of volcanoes provide opportunities to conduct natural experiments into how mosses contribute to early plant community formation, as well as how the unique environments found in such zones affect plant traits, particularly those associated with stress tolerance. Though plant community changes have been well-documented since Mount St. Helens (MSH) volcano erupted in 1980, the volcano's moss assemblages, their influence on other plants, and their potential roles in chemical-mediated competition and biogeochemical cycling have garnered little attention. Using a natural stress gradient from primary to secondary succession zones on MSH, and in control and nutrient manipulated test plots, I sought to elucidate how populations of three dominant moss species, Polytrichum juniperinum, Ceratodon purpureus, and Racomitrium canescens, respond to abiotic stress, as well as to provide life history and interaction data on establishment stages of these stress tolerant taxa. I first analyzed possible tradeoffs in survival strategies of four moss communities in test plots along an abiotic stress gradient. In P. juniperinum, seta specific density (mg/mm) increased significantly in response to nitrogen (N) addition. Differences in both vegetative and sexual reproductive morphological measurements were dependent on site and did not correlate with abiotic stress. In C. purpureus, the percentage of total spores germinated increased with N addition. Site dependent responses in nutrient allocation to vegetative and reproductive structures may be a result of phenotypic plasticity alone or may be a result of local adaptation. In mosses adapted to environmental stress, the allocation of nitrogen must be balanced between growth and survival. Efficient nitrogen uptake confers a competitive advantage if allocated to the higher dispersal of quickly germinating spores. Second, my results show the moss R. canescens may be able to inhibit the germination rate of co-occurring moss spores when spores were germinated in moss gametophyte infusions. R. canescens may also inhibit the germination of the co-occurring vascular plant Lupinus lepidus when seeds are germinated within intact moss patches. By uncovering chemical-mediated interactions between mosses on the germination and initial growth of neighboring mosses and vascular plants we can gain a better understanding of the mechanisms stress tolerant plants may use to limit resource competition. Such advantages offer insight into how mosses effectively colonize and affect primary succession landscapes.

Vegetation status is a key indicator of the ecosystem condition in a particular area. The study objective was about the estimation of leaf nitrogen (N) as an indicator of vegetation water stress using vegetation indices especially the red edge based ones, and how leaf N concentration is influenced by various environmental factors. Leaf nitrogen was estimated using univariate and multivariate regression techniques of stepwise multiple linear regression (SMLR) and random forest. The effects of environmental parameters on leaf nitrogen distribution were tested through univariate regression and analysis of variance (ANOVA). Vegetation indices were evaluated derived from the analytical spectral device (ASD) data, resampled to RapidEye. The multivariate models were also developed to predict leaf N. The best model was chosen based on the lowest root mean square error (RMSE) and higher coefficient of determination (R2) values. Univariate results showed that red edge based vegetation index called MERRIS Terrestrial Chlorophyll Index (MTCI) yielded higher leaf N estimation accuracy as compared to other vegetation indices. Simple ratio (SR) based on the bands red and near-infrared was found to be the best vegetation index for leaf N estimation with exclusion of red edge band for stepwise multiple linear regression (SMLR) method. Simple ratio (SR3) was the best vegetation index when red edge was included for stepwise linear regression (SMLR) method. Random forest prediction model achieved the highest leaf N estimation accuracy, the best vegetation index was Red Green Index (RGI1) based on all bands with red green index when including the red edge band. When red edge band was excluded the best vegetation index for random forest was Difference Vegetation Index (DVI1). The results for univariate and multivariate results indicated that the inclusion of the red edge band provides opportunity to accurately estimate leaf N. Analysis of variance results showed that vegetation and soil types have a significant effect on leaf N distribution with p-values<0.05. Red edge based indices provides opportunity to assess vegetation health using remote sensing techniques. / Environmental Sciences / M. Sc. (Environmental Management)

Bambara groundnut (Vigna subterranea L. Verdc) is a drought tolerant African legume capable of producing reasonable yields where other crops may fail. However, it remains an underutilised crop, owing to limited research, cultivated using landraces, of which scant information is available describing their agronomy and genetic diversity. The aim of this study was to evaluate the response of bambara landraces from different geographical locations to water stress under controlled and field conditions. Seeds were sourced from subsistence farmers of Tugela Ferry and Deepdale in KwaZulu-Natal (South Africa) and Zimbabwe, and characterised into three seed coat colours: light-brown, brown and red. Seed quality was assessed using the standard germination test. Vigour indices of germination velocity index and mean germination time were determined. Seedling establishment was evaluated using seedling trays using a factorial experiment, with four factors: 1. provenance – (Tugela Ferry and Deepdale), 2. seed colour – (red, light-brown and brown), 3. water regimes – (30%, 60% and 100% field capacity), and 4. soil media – (clay, sand and clay + sand). Seedling leaf samples were used to evaluate proline accumulation as an indicator of stress tolerance. A field trial was used to evaluate productivity of bambara landraces under rainfed and irrigated conditions. A pot trial was conducted under controlled environment conditions with three factors: temperature (33/27°C and 21/15°C), water regimes (30% and 100% of crop water requirement) and bambara landrace selections. Results showed no significant differences in germination capacity between bambara landrace selections. Germination time differed significantly (P<0.001) between bambara landrace selections. The Jozini provenance was shown to perform best, followed by Zimbabwe, Tugela Ferry and Deepdale. Brown landrace selections had higher (P<0.001) germination compared with red and light-brown selections, respectively. Seedling establishment showed that emergence was higher (P<0.001) at 100% FC compared with 60% FC and 30% FC. Emergence was higher (P<0.001) in the Sand+Clay mixture compared with Clay and Sand media. Dark-coloured selections had higher (P<0.001) emergence compared with light-coloured selections. Results from the field trial showed that the red landrace selections emerged better (P<0.001) than the light-brown and brown landrace selections, respectively. Plant growth was lower under irrigated compared with rainfed conditions. Stomatal conductance was higher (P<0.001) under irrigated compared with rainfed conditions, whereas chlorophyll content index was higher (P<0.05) under rainfed compared with irrigated conditions. Results of the pot trial showed that emergence was significantly (P<0.001) affected by temperature. It was higher at 33/27°C compared with 21/15°C (P<0.001). Dark-coloured landraces had higher emergence compared with the light-brown landraces. Stomatal conductance was lower at 30% ET relative to 100% ETc. There were no significant differences between water regimes with respect to biomass, pod number per plant, pod mass per plant, seed number per pod, seed mass per plant and harvest index. It is concluded that seed colour is an important variable in the identity of bambara landraces. Provenance plays a significant role in seed performance and there is a significant interaction between provenance and seed coat colour. This study could be expanded to obtain more data for crop improvement through inclusion of many sites and seasons for better agronomic advice to farmers. / Thesis (M.Sc.Agric.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Local maize landraces have evolved over hundreds of years of natural and farmer selection under varying conditions. These landraces may have developed tolerance to abiotic stresses such as water deficits during this cycle of selection. However, despite its continued existence and importance, little is known on their agronomy and responses to water stress. If indeed landraces have developed tolerance to water stress, they may prove a key genetic resource for future crop improvement in light of increasing water scarcity. The primary objective of this study was to evaluate the responses of a local maize landrace to water stress at different stages of growth in comparison to two known commercial hybrids, SC701 and SR52. Seed from a local maize landrace was multiplied and characterised according to kernel colour. Two distinct colours were selected for the purposes of this study, white (Land A) and dark red (Land B). In a holistic approach, the thesis consisted of four separate studies whose overall objective was to evaluate the responses of the maize landraces to water stress at different growth stages, up to and including yield and its components. These comprised three controlled environment studies (25°C; 60% RH) and a field trial. For the controlled environment, two water regimes were used, 25% field capacity (FC) (stress treatment) and 75% FC (non-stress). The first study investigated the effect of water stress on early establishment performance. Seed quality was evaluated using the standard germination test together with electrolyte leakage. Catalase activity and accumulation of proline were examined as seedling physiological response to water stress. The second study was conducted as a pot trial to investigate the effect of water stress on growth, photosynthesis and yield. Photosynthesis was measured as chlorophyll fluorescence (CF). In addition, a field study over three planting dates was conducted at Ukulinga Research Farm in Pietermaritzburg, under dryland conditions, during the period from August 2008 to June 2009. The objective was to evaluate the effect of planting dates and changing soil water content on growth, yield and yield components. Three planting dates were used, representative of early (28 August 2008), optimum (21 October 2008) and late planting (9 January 2009). Lastly, a study on hydro-priming was conducted, necessitated by observations made primarily in the first study. The study was carried out under controlled environment conditions. The objective was to evaluate whether hydropriming can improve germination, vigour and emergence under water stress. Seeds were soaked in water for 0 hours (Un-primed or control), 12 hours (P12) and 24 hours (P24). Results from the first study showed that maize landraces were slower to germinate and emerge, and produced less vigorous seedlings compared to the hybrids. The study showed that hybrids were more superior under optimum (75% FC) conditions than under stress conditions (25% FC). Physiological showed that both hybrids and landraces expressed catalase under water stress, with landraces showing slightly better expression compared to the hybrids. Proline accumulation was observed in both hybrids and landraces as a response to water stress, with hybrids being more sensitive to water stress. In the pot trial, results showed that the vegetative stage of both hybrids and landraces was less sensitive to water stress than the reproductive stage. Results showed no differences between field capacities, with respect to emergence, mean emergence time, leaf number, CF, ear prolificacy and ear length. Photosynthesis, as measured by CF, was shown to be desiccation tolerant. Water stress had a negative effect on cob mass, lines per cob, grains per cob and total grain mass, and resulted in barrenness in the landraces. The hybrids had superior yield compared to the landraces. Results for the field trials showed that planting date had highly significant effects on emergence, plant height, leaf number and days to tasseling (DTT). Landraces emerged better than hybrids in all plantings; highest emergence was in the early and late plantings. Optimum and late planting resulted in maximum plant height and leaf number, respectively, compared to early planting. Hybrids were superior, growing taller and with more leaves than landraces in all plantings. DTT decreased with successive plantings. Planting date had an effect on ear prolificacy (EP), kernels/ear (KNE) and 100 grain mass. Planting date had no effect on ear length and mass, kernel rows/cob, grain mass and yield. With the exception of EP, hybrids out-yielded the landraces in all three planting dates. Hydro-priming landraces for 12 hours and 24 hours, respectively, improved germination velocity index, reduced mean germination time and improved emergence and mean emergence time of maize landraces under water stress. Performance of hybrid seeds remained superior to that of landraces even after seed treatment to improve germination and vigour. Landraces were slower to germinate and emerge and produced less vigorous seedlings in controlled conditions only. Both hybrids and landraces expressed catalase activity and also accumulated proline in response to water stress, although hybrids were more sensitive to stress in the establishment phase. Results confirmed literature, showing that, for both hybrids and landraces, the vegetative stage is less sensitive to stress than the reproductive stage. Hybrids produced superior yields compared to landraces in both controlled environment and field conditions. However, the pattern of seedling establishment observed in the initial controlled environment study for hybrids and landraces was reversed in the field study. Lastly, hydro-priming is of some benefit to maize establishment. / Thesis (M.Sc.)-University of KwaZulu-Natal, Pietermaritzburg, 2009.

This thesis is aimed to Design of Experiments methodology. Main purpose of this thesis is to create detailed materials for lessons of Design of Experiments in Quality Control courses. Thesis contains case studies which are applicable for education purposes. Design of Experiments has been applied for solder joints quality evaluation. Solder joints have been modeled in software ANSYS and finite element method has been applied for thermomechanical stress evaluation.

MSCAGR (Plant Production) / Department of Plant Production / Chickpea (Cicer arietinum L.) is an excellent utilizer of residual soil moisture in agricultural ecosystems. However, its seed quality and hence reproduction is constrained by water stress, seed size and storage conditions. This study was carried out at the University of KwaZulu- Natal (UKZN), Pietermaritzburg Campus. It was conducted to evaluate the performance of chickpea genotypes (Desi-K, Saina-K and ICCV-K) with different seed sizes on seedling emergence (i), seed ageing effect on seed quality and imbibition of genotypes produced under water stressed and non-stressed conditions (ii), and (iii) the effect of water stress during seed development on sugars and protein accumulation, germination and seed vigour. Pot experiments were conducted under glasshouse / tunnel conditions at the Controlled Environment Facilities (CEF). The experiment for objective 1 was laid out as a single factor in completely randomized design (CRD). Data on emergence rate, final hypocotyl and complete emergence was collected. The small seeded Desi-K showed higher and faster emergence compared to medium sized Saina-K and large seeded ICCV-K. In the experiment of the second objective, seeds of the three genotypes were first obtained by production under water stressed and non-stressed growing conditions. They were then aged for 0, 1, 3, 5, or 7 days at 41 ºC and 100% relative humidity to form a 2 x 3 x 5 (water levels x genotypes x ageing) factorial design. Data was collected on germination percentage (GP), mean germination time (MGT), electrical conductivity (EC), tetrazolium chloride test (TZ) and imbibition weight. Seed ageing caused progressive loss of seed viability and vigour in all genotypes, which resulted in lower GP, delayed MGT, reduced TZ staining, cell death and high solute leakage from the seeds produced under the two water regimes. However, the effect was more severe under water stressed conditions. In the experiment for objective 3, seeds of all three genotypes were larger when grown under non-stressed condition compared to those under water stressed condition. These larger seeds had higher seed viability and germination percentage but lower electrical conductivity and mean germination time. Stressed seeds had higher soluble sugars than non-stressed seeds. It was deduced that irrigation during seed development reduces the final sugars and protein content but increases the seed size and physiological quality parameters allied to production of chickpea. Therefore, water provision to chickpea crop is critical during seed development. / NRF

Indiana University-Purdue University Indianapolis (IUPUI) / Dehydrins are type II LEA proteins induced in many plants during drought, low temperature, and high salinity to confer stress tolerance. AtERD14 is an Arabidopsis thaliana dehydrin that functions in part of the cold stress pathway. AtERD14 has chaperone-like capabilities that allow it to bind and protect various proteins from dehydration stresses. In order to determine the necessary components for cold induction of AtERD14, AtERD14prom::GFP/GUS and AtERD14prom::AtERD14 in AtERD14 KO constructs were created and stably transformed into A. thaliana. Analysis of the constructs showed the AtERD14 promoter alone was insufficient to respond to cold, and it was necessary to attach the AtERD14 coding region to the promoter to induce a cold response in ERD14. On the other hand, the RD29aprom::GFP/GUS promoter did respond to cold stress, indicating that RD29a does not require its coding region to support an increased amount of reporter activity after cold stress. The protoplast transformation system, while capable of transient expression of introduced constructs in protoplasts, was difficult for use for cold-inducible expression.