Thesis (M.S.)--University of Missouri-Columbia, 2005. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file viewed on (December 18, 2006). Includes bibliographical references.

Proefschrift Universiteit Maastricht. / Met bibliogr., lit. opg.

MSCAGR (Plant Production) / Department of Plant Production / Soil infertility, water scarcity, and availability of high yielding and drought tolerant crop genotypes remain major constraints for agricultural production in semi-arid regions. These constraints are major threats to sustainable crop production and food security. Management practices in such areas should always be geared towards improving productivity at a low cost while sustaining soil fertility. Preliminary studies showed the huge potential of chickpea in the dry environments of the North Eastern South Africa. However, lack of nodulation in chickpea has been reported in these regions probably due to low soil pH, insufficient rhizobial populations or total lack of infective native rhizobia. Therefore this study assessed the effect of biochar and rhizobium inoculation on soil pH, nodulation, growth, yield and chlorophyll content of chickpea in Mpumalanga (Nelspruit) and Limpopo (Thohoyandou) Provinces, South Africa. Two field experiments were planted during winter 2015 and 2016. Treatments consisted of three levels of biochar (0, 10 and 20 t ha-1), two Rhizobium inoculation levels (with and without Rhizobium inoculation) and three chickpea genotypes (ACC #4, ACC #5, and ACC #6) in a factorial combination arranged in randomized complete block design replicated three times. Crop phenology (days to 50% emergence, flowering, podding, and physiological maturity), crop growth (plant height, canopy cover, number of primary and secondary branches), nodulation (number of nodules per plant and nodule dry weight), yield and yield components (number of pods per plant, number of seeds per pod and 100 seed weight [100-SW]), and chlorophyll content were determined at various crop growth stages. Identification and isolation of native rhizobia from soils was done using standard protocols. Data obtained were subjected to analyses of variance using the general linear model of Genstat software version 17. Significant differences between the treatments means were compared using the standard error of difference (SED) of the means at 5% level. Correlation analyses were performed to assess the relationship between parameters. Molecular data was subjected to BLASTn in National Centre for Biotechnology Information (NCBI) searches for identification of isolated strains Application of biochar at 10 and 20 t ha-1 increased soil pH by 0.7 pH units in Thohoyandou (clay soil) in 2015 and 2016, respectively. Soil pH increased by 0.77 pH units at 10 t ha-1 and 1.2 pH units at 20 t ha-1 in Nelspruit (loamy sand) in 2015 and 2016, respectively. Similarly, rhizobium inoculation increased soil pH by 0.2 (Thohoyandou) and 0.5 (Nelspruit) pH units in 2015 and 2016, respectively. There was a 100% increase in nodulation in inoculated compared to uninoculated treatments. There was no effect of biochar and rhizobium inoculation on number of days to 50% flowering, podding, v physiological maturity and on plant height. However, plant height varied with genotypes. Biochar application increased above ground biomass by 17% (10 t ha-1) and 12% (20 t ha-1), and 100 seed weight by 9% (10 t ha-1) and 7% (20 t ha-1) in Thohoyandou in 2015. Rhizobium inoculation increased yield and yield components in Thohoyandou in both seasons; biomass was greater by (31 and 23%), grain yield (26 and 24%), number of pods per plant (18 and 31%), and 100-SW (10 and 13%) in 2015 and 2016, respectively. Similarly, rhizobium inoculation increased biomass (53.4%), grain yield (81%), number of pods per plant (54%) and number of seeds per pod (89%) in Nelspruit in 2015. Genotype did not affect yield and yield components in Nelspruit. In contrast, genotype affected above ground biomass, grain yield, harvest index, number of pods per plant, and number of seeds per pod in 2015 in Thohoyandou with ACC #6 producing greater yield compared to ACC #4 and 5. The analysis for native rhizobia showed that agricultural fields in Nelspruit and Thohoyandou lack effective strains of rhizobium. The identified strains according to 16s gene region were Klebsiella variicola, Burkholderia cenocepacia, Bacillus subtilis and Ochrobactrum spp. The effects of biochar and rhizobium inoculation were more pronounced in Thohoyandou compared to Nelspruit. Therefore biochar and rhizobium inoculation may improve chickpea productivity in Limpopo and Mpumalanga Provinces through improved soil pH, nodulation, growth, yield and yield components. / NRF

Vegetable soybean, also known as edamame, has become increasingly popular in the United States due to its excellent nutrition and health benefits. This rising demand has sparked the interest of local farmers in growing edamame. However, a significant problem in edamame production is the poor seedling emergence. This dissertation focuses on three key objectives: 1) exploring the physiological traits linked to the low emergence of edamame seeds; 2) enhancing edamame seedling emergence by identifying genotypes with high vigor and resistance to soil-borne diseases; and 3) determining the optimal temperature for edamame seedling emergence. The study includes newly developed edamame breeding lines from the soybean breeding programs at Virginia Tech and the University of Arkansas, and major edamame cultivars commonly used in the Mid-Atlantic region. The results have identified several genotypes that exhibit high seeding vigor, aging tolerance, and consistently achieve a plant stand of over 80% in both laboratory and field conditions. It is also clarified that edamame's larger seed size leads to lower germination rates and slower emergence, although this is not correlated to total emergence. Moreover, environmental factors, pathogens and temperature, impact emergence. The study highlights that current edamame genotypes are commonly affected by soilborne pathogens, including Rhizoctonia solani, Athelia rolfsii, and Pythium irregulare, leading to seed rot and seedling damping off. However, the research has successfully identified partially resistant varieties characterized by significantly low disease indexes (p<0.05). Furthermore, the optimal temperature range for edamame seedling emergence (25-32°C) was found to be lower than that of other types of soybeans such as grain-type soybeans (29-36°C). This research provides a scientific foundation to improve edamame production practices. / Doctor of Philosophy / Vegetable soybean, also known as edamame, commonly consumed as a healthy snack, is steadily gaining popularity in the United States. However, there are significant challenges in achieving successful edamame plant growth from seeds. This research focuses on three primary objectives: first, understanding the underlying factors contributing to poor seedling emergence in edamame; second, identifying edamame genotypes with exceptional vigor and resistance to soil-borne diseases; and third, determining the ideal temperature conditions for optimal edamame seedling development. To accomplish these goals, a comprehensive study was conducted, encompassing various edamame varieties, including those developed by Virginia Tech and the University of Arkansas. The research identified some edamame genotypes that exhibited exceptional seed vigor, aging tolerance, and consistently achieved plant stands of over 80% under both laboratory and field conditions. Additionally, we also learned that bigger edamame seeds take longer time to grow, but the seed size does not affect the total emergence. Furthermore, we found that some diseases in the soil can hurt edamame seedlings, but we identified a few genotypes that are more resistant to these diseases. Lastly, in terms of temperature, we found that edamame seedlings grow the best between 25-32°C, which is slightly lower than other types of soybeans. Overall, this research helps farmers grow better edamame and brings more delicious and healthy food to our tables.

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Understanding the relationship between gene expression and phenotype is important in many areas of biology and medicine. Current methods for measuring gene expression such as microarrays however are invasive, require biopsy, and expensive. These factors limit experiments to low rate temporal sampling of gene expression and prevent longitudinal studies within a single subject, reducing their statistical power. Thus methods for non-invasive measurements of gene expression are an important and current topic of research. An interesting approach (Segal et al, Nature Biotechnology 25 (6) 2007) to indirect measurements of gene expression has recently been reported that uses existing imaging techniques and machine learning to estimate a function mapping image features to gene expression patterns, providing an image-derived surrogate for gene expression. However, the design of machine learning methods for this purpose is hampered by the cost of training and validation. My thesis shows that populations of artificial organisms simulating genetic variation can be used for designing machine learning approaches to decoding gene expression patterns from images. If analysis of these images proves successful, then this can be applied to real biomedical images reducing the limitations of invasive imaging. The results showed that the box counting dimension was a suitable feature extraction method yielding a classification rate of at least 90% for mutation rates up to 40%. Also, the box-counting dimension was robust in dealing with distorted images. The performance of the classifiers using the fractal dimension as features, actually, seemed more vulnerable to the mutation rate as opposed to the applied distortion level. / Master of Science

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Mycobacterium tuberculosis (M. tuberculosis) is the causative agent of tuberculosis (TB), a disease that affects millions of people world-wide. The species M. tuberculosis consists of a large number of different strains that can be grouped into at least 40 different known strain families. Many of the strains present with different pathogenic characteristics and host adaptations. The F11 LAM strains and Beijing strains currently have a nearly equal representation in the population of Cape Town, making up a total of 45% of all strains in this setting. The Latin-American Mediterranean (LAM) family of M. tuberculosis is proved to be the cause of a large percentage of TB cases worldwide and it is the predominant strain in high-prevalence regions such as the Western Cape and KwaZulu-Natal regions of South Africa, Zambia, Zimbabwe, and South America. This project aimed to investigate the evolution and biological characteristics of the members of the principle genetic group (PGG) 2 Latin-American Mediterranean (LAM) genotype of M. tuberculosis using a combination of whole genomic and proteomic analyses, coupled to mycobacterial molecular epidemiological techniques. The evolution of M. tuberculosis strain families from the Western Cape Province of South Africa proved to be consistent with previous evolutionary scenarios for M. tuberculosis isolated from other parts of the world. This genome-wide SNP-based phylogeny for the evolution of M. tuberculosis offers novel insight into the unique global representation of the M. tuberculosis isolates from the Western Cape, South Africa. The evolutionary scenario presented confirms six LAM sub-lineages, namely IS6110 RFLP families F9, F11, F13, F14, F15, and F26. A subset of sub-lineage defining SNPs was determined for each of the six LAM sub-lineages. The genomic changes in the LAM genotype strains observed through the SNP analysis presented here mostly occur in the genes involved in the cell wall, cell processes, intermediary metabolism and respiration. The same phenomenon was observed when the non-redundant SNPs of the non-LAM isolates were functionally annotated. The functional classification of the regulated proteins in the representative of the LAM RDRio lineage of M. tuberculosis suggests that proteins involved in the lipid metabolism, intermediary metabolism and respiration may be the key to the pathogenic effectiveness of the RDRio LAM lineage. A combination of the LAM SNP analysis and the LAM RDRio/non-RDRio comparison showed that the overall genomic- and proteomic features involved in the cell wall and cell processes of the LAM genotype differ to a large extent from what is seen in the reference strain, M. tuberculosis H37Rv. This genome wide phylogenetic study is the first of its kind in a South African context, and not only presents a robust phylogeny of the M. tuberculosis strain families, and specifically the LAM lineage, but also gives the first ever insight into the protein differences which distinguishes RDRio and non-RDRio M. tuberculosis strains from each other. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis (M. tuberculosis) is die mikrobiese agent wat tuberkulose (TB), 'n siekte wat miljoene mense wêreldwyd affekteer, veroorsaak. Die spesie M. tuberculosis bestaan uit 'n groot aantal verskillende stamme wat in ten minste 40 verskillende bekende stam-families gegroepeer word. Baie van die stamme toon verskillende patogeniese eienskappe en gasheer aanpassings. Die F11 LAM stam en Beijing stam het tans 'n byna gelyke verteenwoordiging in die bevolking van Kaapstad, wat 'n totaal opmaak van 45% van stamme wat in hierdie gebied gevind word. Die Latyns-Amerikaanse Meditereense (LAM) familie van M. tuberculosis is bewys om die oorsaak van 'n groot persentasie van TB-gevalle wêreldwyd te wees, en dit is die oorheersende stam in hoë voorkoms streke soos die Wes-Kaap en KwaZulu-Natal streke van Suid-Afrika, Zambië, Zimbabwe en Suid-Amerika. Hierdie projek het ten doel gehad om die evolusie en biologiese eienskappe van die lede van die basiese genetiese groep (BGG) 2 Latyns-Amerikaanse Meditereense (LAM) genotipe van M. tuberculosis te ondersoek deur gebruik te maak van 'n kombinasie van heel genoom en proteoom analise, gekoppel aan mikobakteriële molekulêre epidemiologiese tegnieke. Die evolusie van M. tuberculosis stam families van die Wes-Kaap Provinsie van Suid-Afrika blyk om in ooreenstemming te wees met vorige evolusionêre scenario's vir M. tuberculosis wat in ander dele van die wêreld geïsoleer is. Die genoom-wye enkelnukleotied polimorfisme-gebaseerde filogenetiese hipotese vir die evolusie van M. tuberculosis bied nuwe insig in die unieke wêreldwye verteenwoordiging van die M. tuberculosis isolate van die Wes-Kaap, Suid-Afrika. Die evolusionêre scenario wat hier aangetoon word bevestig ses LAM sub-lyne, naamlik IS6110 RFLP families F9, F11, F13, F14, F15, en F26. 'n Versameling sub-lyn definiërende enkelnukleotied polimorfismes was bepaal vir elk van die ses LAM sub-afstammelinge. Die genomiese veranderinge wat waargeneem is in die LAM-genotipe isolate deur die enkelnukleotied polimorfisme analise wat hier aangebied word, is meestal in die gene wat betrokke is in die selwand, selprosesse, intermediêre metabolisme en respirasie. Dieselfde verskynsel is waargeneem wanneer die nie-oorbodige enkelnukleotied polimorfismes van die nie-LAM isolate funksioneel geannoteer is. Die funksionele klassifikasie van die gereguleerde proteïene in die verteenwoordiger van die LAM RDRio-lyn van M. tuberculosis dui daarop dat die proteïene wat betrokke is in die lipiedmetabolisme, intermediêre metabolisme en respirasie die sleutel tot die patogene doeltreffendheid van die RDRio-LAM-lyn kan wees. 'n Kombinasie van die LAM enkelnukleotied polimorfisme analise en die LAM-RDRio/nie-RDRio vergelyking het getoon dat die totale genomiese- en proteomiese kenmerke wat verwant is aan selwand en selprosesse van die LAM genotipe tot ʼn groot mate verskil van wat gesien word in die verwysing stam, M. tuberculosis H37Rv. Hierdie genoom-wye filogenetiese studie is die eerste van sy soort in 'n Suid-Afrikaanse konteks, en bied nie net ‗n robuuste filogenie van die M. tuberculosis stam families, en spesifiek die LAM genotipe van M. tuberculosis nie, maar gee ook die eerste keer ooit insig in die proteïen verskille wat RDRio en nie-RDRio M. tuberculosis stamme van mekaar onderskei.

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