Orientador: Douglas Silva Domingues / Resumo: O café é uma das commodities agrícolas tropicais mais comercializadas no mundo. Coffea arabica é a principal espécie utilizada para a produção comercial de café. A espécie é originária da Etiópia. Ela é única espécie alotetraploide do gênero (2n = 4x = 44) e se reproduz predominantemente por autofecundação. As cultivares comerciais de C. arabica possuem baixa diversidade genética, o que indica a necessidade de introgressão de alelos de germoplasma para o melhoramento dessas cultivares. Acessos do centro de origem da espécie possuem maior diversidade que as cultivares comerciais e podem ser utilizados para a identificação de novos alelos. O conteúdo de macronutrientes em grãos do cafeeiro tem impacto direto na qualidade do produto. No entanto, a base molecular da composição mineral de grãos de cafeeiro ainda é pouco conhecida. Com isso, o objetivo desse trabalho foi identificar marcadores SNP possivelmente associados com a composição de macronutrientes em grãos de C. arabica. Para alcance deste objetivo, foram comparados três métodos de imputação de genótipos, bem como foi realizado o mapeamento associativo em estudo de associação genômica ampla (GWAS). Foi utilizado um painel de 110 genótipos de C. arabica, composto por genótipos elite do programa de melhoramento do Instituto Agronômico do Paraná (3), cultivares comerciais (11) e acessos selvagens (96). Foram realizadas análises da composição de cinco macronutrientes (N, P, K, Ca e Mg) em grãos de cafeeiro coletados de 70 e 1... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Coffee is one of the most traded tropical commodities in the world. Coffea arabica is the main species used for commercial production. The species is originally from Ethiopia. In the Coffea genus, C. arabica is the only allotetraploid species (2n = 4x = 44) and it reproduces predominantly by self-fertilization. The commercial cultivars of C. arabica have a narrow genetic base that indicates the need for the introgression of new alleles from germplasm into coffee breeding programs. Wild accessions of C. arabica, from Ethiopia, have higher genetic diversity and can be used to identify new alleles. The macronutrient composition of the coffee grains has a direct impact on grain quality. However, the molecular basis for the mineral composition in coffee grains still poorly understood. Thus, the aim of this work was to perform mapping association analyses using the genome-wide association study (GWAS) technique to identify single nucleotide polymorphisms (SNPs) associated with macronutrient content in coffee grains from C. arabica. We also tested three imputation methods (haplotype missing allele imputation - Beagle, K-nearest neighbors, and Random Forest) in the genotypic data, and mapped it to two C. arabica reference genomes from the cultivar Caturra red and the spontaneous dihaploid Et39. We used a panel of 110 C. arabica genotypes, including elite landraces from the IAPAR coffee breeding program (3), commercial cultivars (11) and wild accessions (96). Analysis of the compositi... (Complete abstract click electronic access below) / Doutor

MSCAGR (Plant Production) / Department of Plant Production / Chickpea (Cicer arietinum L.) is an important grain legume in the world, ranking second after soybean (Glycine max L.). It accounts for a substantial proportion of human dietary nitrogen intake and plays a crucial role in food security in developing countries. Chickpea can grow in areas with low rainfall and poor soils, and thus may be an important food security crop for smallholder resource-poor farmers in the semi-arid tropics such as the dry environments of the Limpopo and Mpumalanga Provinces of South Africa. Preliminary studies showed the huge potential of chickpea production in these environments. However, no suitable genotypes have been identified and recommended for different agro-ecological zones of Limpopo and Mpumalanga Provinces. Therefore, the objective of this study was to evaluate the performance, and hence, identify the genotypes that are adapted/suitable to the contrasting agro-ecological conditions of Limpopo and Mpumalanga Provinces for production. Field experiments were conducted in the winter cropping seasons of 2016 and 2017 at Thohoyandou (University of Venda experimental station), Syferkuil (University of Limpopo experimental station) and Nelspruit (University of Mpumalanga experimental station). Ten desi chickpea genotypes were sown in a completely randomized block design replicated three times on 10 May 2016 and 10 April 2017 (Thohoyandou), 13 May 2016 and 11 April 2017 (Syferkuil) and 03 May 2016 and 24 May 2017 (Nelspruit). Plant growth characteristics were assessed by determining plant height, crop phenology, number of primary and secondary branches, and canopy cover. Yield and yield components were assessed at harvest after physiological maturity. Carbon dioxide exchange rates (CER) was determined at different growth stages using the InfraRed Gas Analyzer (IRGA). Chlorophyll content (CC) and intercepted radiation were determined weekly using the chlorophyll content meter (CCM-200 PLUS, Opti-Science, Tyngsboro, Massachusetts), and the AccuPAR, LP-80 ceptometer (Deacon Devices Ltd., Pullman, USA), respectively. Genotypes did not vary in CC at Thohoyandou in all seasons, but CC increased with stages of growth. Genotypes varied in the proportion of intercepted radiation (IR) at all measurement dates in Thohoyandou during the 2016 and 2017 growing seasons. The proportion of IR increased with growth stage, reached a peak and declined with plant age. Genotype affected photosynthesis and intercellular CO2 concentration (Ci) but did not have any significant effect on stomatal conductance (gs), transpiration (T) and Leaf Vapour Pressure Deficit (VPDL) during the 2016 season in Thohoyandou. In contrast, genotype did not affect photosynthesis, Ci, gs, T and VPDL in the 2017 season in Thohoyandou. There was no variation among genotypes on number of primary and secondary branches in Thohoyandou in both seasons. Genotypes showed no variation in plant height in the 2016 season in Thohoyandou agro-ecological condition. However, genotypes showed significant variation in plant height at 14, 70 and 84 days after emergence (DAE) in the 2017 cropping season. Moreover, genotypes showed significant variations in days to 50% flowering in Thohoyandou during the 2016 season, but showed no variations in days to 50% emergence and 75% physiological maturity. Genotypes showed no variations in days to 50% emergence, 50% flowering, 50% podding and 75% physiological maturity in the 2017 season in all locations. Genotypes showed significant variation in grain yield in Syferkuil agro-ecological condition, but showed no significant variations on all the other studied traits, while genotypes varied in 100 seed weight (SW) in Thohoyandou, but did not show any variations on the other studied traits during the 2016 season. Moreover, genotypes did not vary for all studied traits in Nelspruit during the 2016 season. The 2016 genotype and environment (G X E) interaction results showed no significant variations. However, results showed G X E interactions during the 2017 growing season suggesting that genotypes responded to environmental variation in a different way. Syferkuil had the greatest grain yield (2811 kg ha-1 and 3122 kg ha-1) in both the 2016 and 2017 growing seasons respectively, as compared to Thohoyandou and Nelspruit. These preliminary findings show that the studied genotypes responded differently in contrasting agro-ecological regions of Limpopo and Mpumalanga Provinces and that Syferkuil might be the best environment for chickpea production in this region due to its cooler temperatures. Of the genotypes evaluated the most promising genotypes are ICCV8101, ICCV3203 and ICCV4110 in these regions in terms of grain yield. / NRF

White Band disease has devastated the staghorn coral Acropora cervicornis in recent decades, and it continues to impinge upon restoration efforts. The etiological agent(s) remain unknown as Koch’s postulates have yet to be satisfied, but disease may originate when opportunistic pathogens in the surface mucus layer exploit a stressed host. Using 16s rRNA sequencing, differences in the taxonomic diversity and relative abundances of bacteria within the mucus of A. cervicornis were documented between colonies of the same genotype, genotypes (n=8) categorized as having either high or low WBD susceptibility, and during a transplantation event. A. cervicornis colonies suspended from midwater PVC trees via monofilament were sampled for mucus, after which half of the sampled colonies were relocated to the unconsolidated sediments below. Temporal changes in the microbiome of the pelagic and benthic corals were then monitored by sampling the same apical tip over time. Incidentally, all benthic colonies for this experiment became afflicted with WBD; thereby differences in healthy vs. diseased colonies and the effects of disease progression on the microbiome were documented. Water was sampled concurrently with all mucus experiments to resolve the degree of commonality in bacterial species between the two environments, and sediments were sampled in the transplant experiment to determine if sediments may act as a pathogen reservoir. In addition, sediment samples were collected to assess site and temporal differences in the benthic microbiome along a nearshore to offshore transect off Key Largo, Florida. Irrespective of the inclusion of water operational taxonomic units (OTUs), no differences between colonies of the same genotype were observed with regards to the bacterial communities sampled from mucus in either alpha diversity metrics [species richness, Shannon, Inverse Simpson] or phylogenetic relatedness as determined by weighted unique fraction (UniFrac) were detected between colonies. However, differences were observed in the Bray-Curtis dissimiliarity matrices based on relative abundance and presence/absence of either [with and without water OTU] scenarios. Bacterial communities associated with different coral genotypes differed in species richness and Inverse Simpson in both water scenarios, as did weighted UniFrac and Bray-Curtis relative abundance and presence/absence transformed dissimilarity matrices. Alpha diversity of mucus bacteria was similar between corals of different disease-susceptibilities when water OTUs were either included or excluded, except for the Inverse Simpson index upon removal of water OTUs. Removal of aqueous bacteria also revealed significant differences between disease-susceptibility groups in Bray-Curtis relative abundance and presence/absence dissimiliarity values that was not detected with the incorporation of water OTUs. Regardless of the presence of water OTUs, weighted UniFrac was similar between corals of different disease susceptibilities. Most notably, dispersion increased in the microbiome of coral genotypes with high disease susceptibility in all cases except for the relative abundance transformed Bray-Curtis dissimilarity matrix when water OTUs were incorporated. This finding is in accordance with the Anna Karenina Principle, which states that loss of microbial regulation leads to an unpredictable microbiome in diseased individuals. In the sediment experiment, location was the only factor influencing microbiome composition. These findings may be due to the short duration of the experiment and differences between the carbonate content of the sediments and hydrological regimes between sites.

No description available.

Edamame is becoming more popular in the U.S. due to its high nutritional value and potential health benefits. However, more than 70% of edamame is imported from outside of the U.S. Therefore, developing elite edamame genotypes is critically desirable to increase the domestic production of edamame in the U.S. Genotype, planting location, and harvest time play essential roles in the chemical composition of edamame, which further decide edamame's nutritional value and sensory characteristics. Therefore, the first goal of this study is to comprehensively evaluate the chemical composition of edamame genotypes grown in different locations. Ten selected edamame genotypes were grown in three locations in the U.S. - Whitethorne, Virginia (VA), Little Rock, Arkansas (AR) and Painter, VA. Sugars, alanine, protein, oil, neutral detergent fiber (NDF), starch, ash, and moisture contents, were comprehensively analyzed. The results showed that location had significant effects on all chemical components of edamame with p < 0.05. Compared to Painter and Little Rock, genotypes planted in Whitethorne had higher averaged free sucrose, fructose, glucose, raffinose, stachyose, and starch contents and total sweetness. The highest crude protein and oil contents were found on edamame planted in Painter, while Little Rock produced edamame with the highest free alanine, ash, and moisture contents. Genotype significantly affected chemical compositions except for NDF and raffinose. Therefore, planting location and edamame genotype should be considered when producing elite edamame for the U.S. market. Chemical composition changes with the development of edamame; therefore, harvest time is essential for harvesting high-quality edamame. The second objective of this study is to quantify the changes in both physical and chemical properties of edamame over bean development and apply a combined spectroscopy and machine learning (ML) technique to help determine the optimal harvest time. Physical and chemical properties were analyzed for edamame harvested at R5 (beginning seed), R6 (full seed), and R7 (beginning maturity) growth stages, and the spectral reflectance (360 – 740 nm) of edamame pods was measured using a handheld spectrophotometer. The samples harvested at different stages were labeled as 'early,' 'ready,' and 'late.' At R6, pod/bean weight and pod thickness reached the peak and then stayed stable, while sugar, alanine, starch, and glycine also peaked at R6 but declined afterward. The spectra-based ML method had high accuracy (0.95) when classifying 'early' and 'late' edamame, and the accuracy was 0.87 for classifying 'early' and 'ready' edamame. These results indicated that this spectra-based ML method could determine the optimal harvest time of edamame. Food waste and loss not only lead to economic loss but also significant greenhouse gas emissions. With edamame food/snack production increasing, edamame shells, the low-value byproduct from this processing, will potentially threaten the environment. Similar to other food processing byproducts, edamame shell is rich in dietary fiber (DF). However, the high concentration of insoluble dietary fiber (IDF) limits its application as a food additive. Therefore, extraction/modification processes are needed to convert IDF to soluble dietary fiber (SDF) and improve the properties of edamame shell-derived DF. Ball milling is one of the most efficient techniques to break down biomaterials into sub-micro-level particles. Citric acid, as a natural and safe food additive, can help break down cell walls and improve the dissolution of SDF by ionizing the hydrogen ions with carboxyl groups. Therefore, the third objective of this study is to develop a process that combines ball milling and citric acid treatments to produce SDF from edamame shells. We investigated different treatment parameters, including different citric acid concentrations, treatment temperatures and time, and the application of ball milling. To determine if the combined treatment can potentially improve the properties of the produced SDFs, we characterized the physicochemical, morphological, structural, rheological, thermal, and functional properties of SDFs produced at different conditions. The results showed that the highest SDF yield (19.5%) was found when the edamame shells were pretreated by a ball mill. In addition, the combined citric acid and ball milling treatment altered several properties of the produced SDFs, including particle size, morphology, and crystallinity. Moreover, ball milling treatment led to a higher exothermic temperature peak of SDF indicating better thermal stability. All produced SDFs significantly elevated the production of short-chain fatty acids during in vitro fermentation (compared to the control fermentation) which indicated their potential benefits of promoting gut health. Overall, we demonstrated that ball-milling-assisted citric acid processing can be an effective green technique to produce SDF from edamame shells. The SDF produced from edamame shells can be regarded as a promising and novel ingredient with great potential to be used in foods. / Doctor of Philosophy / Edamame is becoming increasingly popular among consumers in the U.S. because it is nutritious and good for health. However, more than 70% of edamame in the U.S. market is imported from other countries. Therefore, having more edamame genotypes that adapt to the growing environment in the U.S. will help increase the domestic production of edamame. Genotype and planting location are essential in deciding edamame's nutritional value and taste. Therefore, the first objective of this study is to comprehensively understand the nutritional value of different edamame genotypes grown in three planting locations. The results showed that both location and genotype affected the nutritional values of edamame, indicating that planting location and edamame genotype should be considered when developing better edamame for the U.S. market. Nutritional value and sweetness change with the growth of edamame beans. Therefore, harvest time is crucial for harvesting edamame with better nutrition and taste. This study's second objective is to observe edamame's nutritional factors and sweetness over bean development and develop a method using a handheld colorimeter to help determine the optimal harvest time. The results showed that the edamame harvested at the full seed stage (called R6) is the sweetest compared to the other two stages. In addition, the handheld colorimeter combined with the machine learning technique showed high accuracy in separating 'early' and 'late' harvested edamame and 'early' and 'ready' harvested samples. These results indicated that the combination of colorimeter and machine learning could help determine the optimal harvest time of edamame. Food waste and loss not only lead to economic loss but also significant greenhouse gas emissions. Edamame shells, the low-value byproduct from edamame snack/food processing, will potentially threaten the environment if edamame consumption keeps increasing. Like other food waste, edamame shell is rich in dietary fiber (DF). Therefore, it is vital to find a way to recover the DF in edamame for other applications. Ball milling is a green technology that can efficiently break down big particles. Citric acid is a natural and safe food additive and can help break down insoluble cell walls. Therefore, this study aims to produce soluble dietary fiber (SDF) from edamame shells using ball milling and citric acid. We proved that ball-milling assisted acid processing can be an environmentally friendly method to produce edamame shell SDF which can potentially be used as a suitable food ingredient.

Master of Science / Department of Agronomy / Robert M. Aiken / Mary B. Kirkham / Transpiration efficiency (TE) is defined as total biomass produced per unit of water transpired. Improvement of TE means maximizing crop production per unit of water used. The objectives of the study were to examine, at the leaf level and the whole plant level, the variation in TE for sorghum [Sorghum bicolor (L.) Moench] accessions, previously screened for TE and to test physiological mechanisms that may account for differences in TE. Three field studies and two mini-lysimeter studies (one done in pots under greenhouse conditions and one done in pots in the field) were conducted with eight accessions. Instantaneous measurements of assimilation (A), stomatal conductance (gs), and transpiration by gas exchange provided measures of the transpiration efficiency at the leaf level. Growth observations and soil water balance in field plots quantified components of whole-plant TE. Growth and development measurements showed significant difference, explaining the existence of photoperiod sensitivity among the sorghum genotypes. Assimilation (A), stomatal conductance (gs), and maximum quantum efficiency of photosystem II (Fv/Fm) were consistently greater for accession PI533946 (from India) and greater for accession PI295121 (from Australia) in both field and the field-pot studies (p<0.05). Internal carbon dioxide (Ci), an indicator of intrinsic transpiration efficiency, differed among lines under field conditions (p<0.05). Leaf relative water content (RWC), measured in the greenhouse, and did not differ among the eight accessions. No consistent differences in biomass and water use were detected among lines under field conditions. In conclusion, developing reliable selection indices for TE will require a greater understanding of whole-plant physiological processes to utilize the differences in TE observed at the leaf level.

Rotavirus infection causes acute gastroenteritis in children younger than five years of age, and commonly occurring human rotavirus strains include G1 - G4 and G9 associated with P[4], P[6] and P[8]. In this study, of 6050 stool samples collected from a Private Pathology Practice in Pretoria, March 2010 - August 2011, 664 tested positive using Coris test-strips. Of these samples, 752 were retested using EIA and, results showed: Coris sensitivity was 93,7% and specificity 99,8%; the winter epidemic peaked in July of both years; more males and children under 30 months of age were particularly vulnerable to infections. Rotavirus-positive samples from Trichardt, Rustenburg and Middelburg were analysed by PAGE and RT-PCR showing circulating strains as mainly G8P[4] (60%) with short electropherotypes, G12P[8] (66%) with long electropherotypes, and G1P[8] at low incidence in the 2010/2011 seasons. These results suggest additional research to monitor the impacts of recently introduced rotavirus vaccines on changing strain profiles in South African communities / Life & Consumer Sciences / M.Sc. (Life Sciences)

Thesis (PhD)--University of Stellenbosch, 2011. / ENGLISH ABSTRACT: The tuberculosis (TB) incidence has increased in Southern Africa and the situation is worsened by the emergence of drug-resistant Mycobacterium tuberculosis strains. Molecular biological techniques have been used to understand the disease dynamics of TB. In a series of studies we describe the use of these techniques to understand the disease dynamics of TB in Southern Africa. Using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) to characterize M. tuberculosis strains from TB patients in Zimbabwe, we identified a genotype causing a disproportionate number of TB cases. The genotype belonged to the Latin American Mediterranean (LAM) lineage and we named it the Southern Africa1 (SAF1) family and later renamed it SAF1/RDRio, also reflecting its predominance in South America. To establish if this family of strains was predominant elsewhere in Southern Africa, genotypes were compared to those from Western Cape, South Africa and Zambia. The SAF1/RDRio strains were highly prevalent in Zambia but were only a minor fraction of the strains in South Africa. The geographical distribution of SAF1/RDRio strains was determined in Gweru, Zimbabwe, and was found to be spread in high incidence areas. From these two studies it was hypothesized that certain host and bacterial factors were associated with disease due to SAF1/RDRio. Subsequently potential risk factors and clinical outcomes of disease due to SAF1/RDRio strains were explored. An association was found with smoking and cavitary pulmonary disease suggesting that SAF1/RDRio caused a more severe and highly transmissible formof TB Using IS6110-RFLP, principal genetic grouping, spoligotyping, IS6110 insertion-site mapping and variable-number tandem repeats (VNTR) typing, low IS6110 copy clade (LCC) identified in Zimbabwe were characterized and compared to the strains from Cape Town, South Africa and other regions. The LCC strains from Cape Town, South Africa, were found to have close evolutionary relationship with strains from Zimbabwe and other regions and were widely distributed suggesting they play an important role in the global TB epidemic. Observations from these studies and those from other studies led to the hypothesis that specific genotypes of M. tuberculosis predominate in regions of Southern Africa. To gain an insight on the population structure of M. tuberculosis strains in Southern Africa, spoligotyping and/or IS6110-RFLP data from eight countries were compared. This is the first study to describe the M. tuberculosis population structure in Southern Africa. Distinct genotypes were associated with specific geographic regions. These findings have important implications for TB diagnostics, anti-TB drug and vaccine development. The population structure of multidrug-resistant (MDR), pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) M. tuberculosis isolates from provinces in South Africa was also determined. This is again the first study to describe the population structure of drug-resistant M. tuberculosis in South Africa. The results also showed geographic localization of genotypes and an association with resistance class. However, decreasing strain diversity was observed as the isolates evolved from MDR-TB to XDR-TB suggesting selection for the specific genotypes. These findings highlight the importance of identifying genetic markers in drug-resistant strains, to enhance early detection of those at risk of developing XDR-TB. / AFIKAANSE OPSOMMING: Die voorkoms van tuberkulose (TB) in Suider Afrika word vererger deur stamme van Mycobacterium tuberculosis wat weerstandig is teen die beskikbare anti-tuberkulose middels. Molekulêre tegnieke word gebruik om in hierdie reeks studies die dinamika van TB in Suider Afrika te ondersoek Deur spoligotipering en IS6110 restriksie fragment lengte polimorfisme (RFLP) tegnieke te gebruik om M. tuberculosis stamme van pasiente in Zimbabwe te beskryf, het ons ‘n genotipe gevind wat ‘n buitengewone aantal TB gevalle veroorsaak het. Hierdie genotipe is deel van die internasionaal beskryfde Latyns Amerikaase en Meditereense (LAM) stam familie. Ons het dit die Suider Afrikaanse Familie1 (SAF1) genoem, maar later hernoem na SAF1/RDRio, omdat dieselfde genotipe in ook volop is in Suid Amerika. Om vas te stel of hierdie familie ook oorheesend is in die res van Suider Afrika, is dit vergelyk met beskikbare databasisse van die Wes-Kaap, Suid-Afrika en Zambië. Alhoewel SAF1/RDRio in die Wes-Kaap gevind is, dra dit slegs tot ‘n mindere mate by tot die plaaslike TB epidemie. Aan die anderkant kom SAF1/RDRio baie algemeen in Zambië voor. ‘n Verdere studie wys ook dat die SAF1/RDRio familie eweredig en wyd verspreid voorkom in hoë insidensie gebiede in Gweru, Zimbabwe. Vanuit die bevindings van hierdie 2 studies, kan ons aflei dat sekere gasheer- en bakteriële eienskappe geassosieer is met SAF1/RDRio-TB-infeksie. Hierna is potensiële risiko faktore en kliniese uitkomste van siekte as gevolg van infeksie met SAF1/RDRio ondersoek. ‘n Assosiasie met rook en kaviterende pulmonale infeksie is gevind,wat daarop dui dat SAF1/RDRio erger vorm van TB veroorsaak en hoogs oordraagbaar is. Deur gebruik te maak van IS6110- (RFLP), hoof groep groepering, spoligotipering, IS6110 invoegings kaartering en veranderlike getal tandem herhaling (VNTR) tipering kon lae IS6110 invoeginsgetal (LCC) stamme van Kaapstad, Zimbabwe en ander gebiede vergelyk word. Al die LCC stamme in die studie is evolusionêr naby verwant aan mekaar en is wyd verspreid, wat dui op hulle belangrike rol in die wêreldwye TB epidemie. Waarnemings in hierdie asook ander studies het tot die hipotese gely dat spesifieke genotipes van M. tuberculosis dominant is in verskillende gebiede van Suider Afrika. Om meer insig tot die populasie samestelling van M. tuberculosis stamme in Suider Afrika in te win is spoligotipes en RFLP-data van 8 lande vergelyk. Hierdie is die eerste studie om die populasie samestelling van M. tuberculosis in Suider Afrika te beskryf en is belangrike fir toekomstige ontwikkeling van nuwe TB diagnose tegnieke, anti-TB middels en TB entstowwe. Die populasie samestelling van multiweerstandige (MDR), pre-ekstreme weerstandige (pre-XDR) en ekstreme weerstandige (XDR) M. tuberculosis van verskillende provinsies in Suid-Afrika is ook bepaal. Hierdie studie is ook die eerste wat die populasie samestelling van weerstandige M. tuberculosis in Suid-Afrika beskryf. Die resultate wys geografiese lokalisering van genotipes en ‘n assosiasie met weerstandigheidsklas. ‘n Afname in stam diversiteit soos die isolate van MDR-TB tot XDR-TB ontwikkel, dui op seleksie van spesifieke genotipes. Hierdie bevinding lê die klem op die belangrikheid van die identifisering van genetiese merkers in weerstandige stamme om die risiko vir die ontwikkeling van XDR-TB te verminder deur vroë deteksie.

Background Cardiovascular diseases, including myocardial infarction and stroke, are the main reason of death in Sweden and Western Europe. High iron stores are believed to produce oxygen radicals, which is the presumed putative mechanism behind lipid peroxidation, atherosclerosis and subsequent cardiovascular disease. Iron levels are associated with the hemochromatosis associated HFE single nucleotide polymorphisms C282Y and H63D. Bilirubin is an antioxidant present in relatively high levels in the human body. Several previous studies have found an association between high bilirubin levels and a lower risk for cardiovascular disease. Bilirubin levels are highly influenced by the common promoter polymorphism TA-insertion UGT1A1*28, the main reason for benign hyperbilirubinemia in Caucasians. There is a lack of prospective studies on both the association of iron and bilirubin levels, and the risk for myocardial infarction and ischemic stroke. Material and methods Iron, transferrin iron saturation, TIBC, ferritin and bilirubin were analyzed and HFE C282Y, HFE H63D and UGT1A1*28 were determined in myocardial infarction and stroke cases, and their double matched referents within the Northern Sweden Health and Disease Study Cohort. Results There were no associations between iron levels in the upper normal range and risk for myocardial infarction or stroke. No associations were seen for HFE-genotypes, except for a near fivefold increase in risk for myocardial infarction in HFE H63D homozygous women. Plasma bilirubin was lower in cases vs. referents both in the myocardial infarction and the stroke cohort. Despite a strong gene-dosage effect on bilirubin levels in both cases and referents, the UGT1A1*28 polymorphism did not influence the risk for myocardial infarction or stroke. Conclusion High iron stores are not associated with increased risk for neither myocardial infarction, nor stroke. There was no association between UGT1A1*28 and the risk for myocardial infarction or stroke. Consequently data suggests that other factors, which also may lower bilirubin, are responsible for the elevated risk observed in conjunction with lower bilirubin levels.

Doctor of Philosophy / Department of Plant Pathology / Megan Kennelly / Large patch, caused by the fungus Rhizoctonia solani anastomosis group (AG) 2-2 LP, is the most common and severe disease of zoysiagrass (Zoysia spp). Despite the importance of this disease, few studies have examined pathogen biology, cultivar susceptibility, cultural controls, and chemical controls. The objectives of this dissertation were: (1) Characterize large patch isolates based on anastomosis pairing, in-vitro mycelial growth rates, nuclear counts, virulence, PCR, and amplified fragment length polymorphism (AFLP); (2) Determine the effects of cultivation (aerification, verticutting, and sand topdressing) on disease severity; (3) Evaluate different fall and spring applications of the fungicides flutolanil, azoxystrobin, and triticonazole; (4) Evaluate the susceptibility of fifteen new zoysiagrass germplasm lines from parental crosses including Z. japonica, Z. matrella, and Z. pacifica. All the R. solani isolates from large patch-infected zoysiagrass from Kansas belonged to AG 2-2 LP. Variations were observed among the isolates in their average number of nuclei per cell, mycelial growth rates and virulence. There was also variation in the amplified fragment length polymorphism (AFLP) DNA fingerprints, suggesting possible underlying genetic differences of biological significance among members of AG 2-2 LP. Cultivation did not affect soil moisture or temperature. Cultivation also did not reduce patch sizes, nor influence turf recovery rate from large patch. From 2009 to 2011, spring and fall N fertility was consistently associated with lower percentages of diseased turf in both cultivated and non-cultivated plots at Manhattan and Haysville. In general, two fall applications of fungicide did not reduce disease compared to one fall application. Fungicides applied in the fall when thatch temperatures ranged from 17.8oC to 23.2oC reduced disease compared to untreated controls. Early spring applications reduced disease compared to later spring applications. In germplasm screening studies, all progeny had similar disease levels compared to Meyer in the growth chamber, but only 6 consistently had disease levels as low as Meyer in the field. Growth chamber results did not correlate to field results.