Food grade soybean production is a high value alternative to conventional soybean use. The production of natto, a fermented soyfood, requires soybean cultivars that consistently express specific quality traits over a range of growing environments. Therefore, it is necessary to evaluate genetic and environmental influence for natto quality traits to ensure consistent performance. A multi location experiment was conducted in 2006 and 2007 to address the influence of soybean cropping system (double crop vs. full season) and environmental factors on traits associated with natto quality. Two statistical models were used to analyze the effects of planting system and environment on agronomic traits such as yield, maturity, and seed size and natto quality traits such as water absorption, water loss after steaming, seed coat deficiency, and rate of water absorption. Genotype variation was significant for all traits, but genetic differences for water loss after steaming were minimal. Planting system significantly influenced all natto quality traits. Seed coat deficiency and rate of water absorption displayed the most differential response and double crop plantings produced superior characteristics. Genotype à environment interactions were significant for all traits, but they did not confound selecting superior natto cultivars. Significant environment and year effects indicate environmental sensitivity, but genotype rankings rarely changed. The results indicate that genotype was the most important factor controlling the natto quality traits tested. These results suggest breeding for superior natto cultivars is possible but environmental influence must be accounted for and multi environment testing is necessary for genotype natto quality evaluation. / Master of Science

Yes / Mycobacterium kansasii is an opportunistic pathogen and one of the most commonly encountered species in individuals with lung disease. We here report the complete genome sequence of 12 clinical isolates of M. kansasii from patients with pulmonary disease in Brazil. / CNPq (scholarships 207422/2014-1, 500769/2014-1, 311554/2013-0; grants 407624/2012-0, 459100/2014-9).

The aim of this work was to analyse sugarcane RB (Republic of Brazil) clones as part of the series 93 of PMGCA-CECA/UFAL, to identify the best clones and evaluate the representativity of the areas where the essays were performed and so to subsidiary the recommendations of clones of the referred series which are in releasing process for commercial cultivation. The study was based on three competition essays using 23 sugarcane RB clones of the 93 series, and three varieties patterns (RB72454, RB83102 and SP79-1011). The essays were installed in 1998 in the following sugarcane mills: Caeté (UCA), in the city of São Miguel dos Campos-AL; Coruripe (UCO), in the city of Coruripe-AL; and Santo Antônio (USA), in the city of São Luis do Quitunde-AL. The selected environment were constituted of the combination of the number of cuts and places forming nine environments. The experimental design used was randomized block with four repetitions, being each formed by 104 replications (26 genotypes x 4 repetitions) each one of them composed of five furrows of 6 m in length, spaced as pattern used by the sugarcane mills. The evaluated caracters were PC (Pol of the cane), TCH (tons of cane for hectare) in three successive cuting (plant cane, first ratoon, and second ratoon). The initial statistic procedures were constituted of analysis of variance for each environment, followed by an analysis of evaluation of the significance of the interaction genotype x environment and the possibility to put together the environments where the genotypes did met show difference of performance. It was also estimated the parameters of stability and adaptability, according to methodology proposed by Eberhart and Russel (1966). Based on the obtained results, it was concluded that the best sugarcane RB clones of the 93 series were: RB931011, RB931530, RB931565, RB931566 and RB931611; and among the best clones, RB931011 and RB931566 had good environment adaptability, and those clones with ample adaptability were RB931530, RB931565 and RB931611. The best clones shown low stability in relation to their results. / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Este trabalho teve como objetivo a análise da série 93 de clones RB de cana-de-açúcar, do PMGCA-CECA/UFAL, com o intuito de identificar os melhores clones, e avaliar a representatividade dos locais onde foram realizados os ensaios, subsidiando as recomendações de cultivos de clones dessa série que estão em processo de liberação para o cultivo comercial. O estudo foi desenvolvido com base nos resultados de três ensaios de competição de 23 clones RB (República do Brasil) de cana-de-açúcar da série 93, e três variedades padrões (RB72454, RB83102 e SP79-1011), instalados no ano de 1998, nas usinas: Caeté (UCA), no município de São Miguel dos Campos-AL; Coruripe (UCO), em Coruripe-AL; e Santo Antônio (USA), em São Luis do Quitunde-AL. Os ambientes avaliados foram constituídos da combinação do número de cortes e locais, constituindo-se de nove ambientes. O delineamento utilizado foi em blocos ao acaso com quatro repetições, sendo cada experimento constituído de 104 parcelas (26 genótipos x 4 repetições), cada uma delas composta de cinco sulcos de seis metros de comprimento, espaçados conforme padrão adotado na usina. Os caracteres avaliados foram PC (Pol da cana), TCH (toneladas de cana por hectare) e TPH (toneladas de pol por hectare), em três cortes sucessivos (cana-planta, cana-soca e cana-ressoca). Os procedimentos estatísticos iniciais constituíram-se de análise da variância para cada ambiente, seguida de uma análise conjunta entre os ambientes, para avaliar a significância da interação genótipo x ambiente e a possibilidade de se agruparem os ambientes onde os genótipos não apresentem diferenças de comportamento (estratificação de ambientes). Em seguida, utilizando-se os dados médios da análise conjunta, foram estimados os parâmetros de estabilidade e adaptabilidade, segundo a metodologia proposta por Eberhart & Russell (1966). Com base nos resultados obtidos, pode-se concluir que os melhores clones da série 93 de cana-de-açúcar RB foram: RB931011, RB931530, RB931565, RB931566 e RB931611; dentre os melhores clones dessa série, aqueles com adaptabilidade para ambientes favoráveis são: RB931011 e RB931566; e aqueles com adaptabilidade ampla ou geral, são: RB931530, RB931565 e RB931611; os melhores clones dessa série apresentaram baixa estabilidade de seus resultados; a estratificação de ambientes evidencia as diferenças existentes entre estes, destacando a representatividade dos locais de experimentação utilizados pelo PMGCACECA/ UFAL.

L'évolution climatique a été marquée ces dernières décennies par des changements importants, notamment une augmentation de température et une variation de la pluviométrie. Une des conséquences du changement climatique est son impact actuel et futur sur l'agriculture et la sécurité alimentaire. En région sahélienne, la sécurité alimentaire repose essentiellement sur quelques céréales, parmi lesquelles le mil occupe une place fondamentale. Un des traits qui permettent l'adaptation au climat de cette espèce est la date de floraison, dont la variation permet d'accomplir le cycle de vie de la plante dans des saisons pluvieuses plus ou moins courtes. Les bases génétiques de ce caractère adaptatif sont encore peu connues. Nous avons développé une méthodologie de cartographie d'association phénotype-génotype, afin d'identifier des gènes impliqués dans la variation de ce caractère. Cette étude a permis d'identifier deux gènes candidats, PHYC et MADS11, associés à la date de floraison et à la variation morphologique chez le mil. Nous avons validé ces associations par des analyses QTLs. Pour PHYC, nous avons aussi étudié le pattern de déséquilibre de liaison sur une zone d'environ 80 kb autour du gène, et développé une approche de Markov Chain Monte Carlo (MCMC) pour comparer les gènes identifiés dans la région. Cette analyse suggère que les polymorphismes à l'intérieur de PHYC sont les meilleurs candidats expliquant l'effet phénotypique observée dans cette région du génome. La seconde partie de ce projet a été consacrée à l'examen méthodologique de la cartographie d'association pour l'étude des interactions entre le génotype et l'environnement. Les résultats de cette thèse ont été discutés notamment dans la perspective de gestion de l'impact du changement climatique sur le mil, céréale majeure des zones semi-arides / In last decades, climate changes led to temperature increase and rainfall variation across the globe. One of the key consequences of these changes is their impact on agriculture and food security. In sahelian countries, food security relies on a few cereal crops, among which pearl millet plays a crucial role for population food supply. Sahel region is facing the impact of rainfall variability and drought since the 1970s. Flowering time variation is one of the main adaptations that allow pearl millet cultivation in drier and shorter rainy seasons. The genetic bases of this complex trait are still understudied. We developed an association mapping framework for the analysis of genotype-phenotype relationship in pearl millet. We successfully identified two genes associated with flowering time variation in pearl millet (PHYC and MADS11). We confirmed these associations using QTL studies. For PHYC, we also examined the pattern of linkage disequilibri um on a chromosomal region extending to 80 kb around the gene, and we developed a Markov Chain Monte Carlo approach (MCMC) to compare six genes identified in this region. Our results suggest that, among the polymorphisms observed in this region, polymorphisms in PHYC are the best candidate for a direct causative role. The second part of this project addressed methodological examination of association mapping framework to deal with genotype by environment interactions. The results of this work were discussed with regard to the challenge of pearl millet crop adaptation to climate change.

Hepatitis C virus is a pathogen causing severe hepatic diseases. Though HCV genotype 6a circulated prevalently in Hong Kong, its sequence information is greatly in deficient. The molecular characteristics and epidemiology of HCV 6a were thus extensively investigated in this thesis. The distribution of HCV genotypes in Hong Kong was analyzed from 1055 samples by the Ohno's method. HCV 6a accounted for 23.6% HCV infections in the general population and 58.5% in the injecting drug-users. It is prevalent in Hong Kong, associated with younger age, injecting drug-user status and the male gender. Fourteen independent HCV 6a isolates were sequenced for their full-genomes. They share a sequence homology of 94.5% between each other. HCV 6a had undergone high frequency of recombination. Four (28.5%) of 14 isolates were found having recombination with other strains in different genomic regions. Evolutionary pressure on HCV 6a genomes was analyzed by evaluating dS/dN ratio. NS4A, NS4B and NS3 showed higher dS/dN ratios (16.94-29.30) indicating a purification effect, whilst NS2, E2 and p7 showed lower dS/dN ratios (2.35-7.33) indicating a positive selection effect. This pattern of evolutionary pressure distribution alongside genomic regions was similar to the observations in HCV 1b. However HCV 6a eISDR experienced less extent of positive selection than HCV 1b eISDR (dS/dN = 12.82 vs 4.96) did. Evolutionary history of HCV 6a was inferred by Bayesian coalescent analysis. Twenty-six heterochronic, 513-bp HCV 6a partial-NS5A sequences and 63 HCV 1b sequences were analyzed. The time of exponential growth of HCV 6a in Hong Kong was postulated as during 1986 to 1994, overlaps with the time 1987 to 1997 when the second Vietnamese Boat People influx event occurred. Rooted phylogenetic analysis showed that Vietnamese HCV 6a strains were ancestors of the Hong Kong strains. Hence, a hypothesis was raised that HCV 6a outbreak in Hong Kong may be related to the Vietnamese Boat People influx event. The sequence variations within the eISDR of HCV 6a and HCV 1b were explored for correlation with the outcome of IFN-alpha/ribavirin combination treatment. Twenty-five HCV 6a patients and 37 HCV 1b patients were recruited. Three amino acid variations I2160V, V2256I, and I2292V were significantly correlated with the treatment outcome (P < 0.05) for HCV 6a. Three variations R2260H, V2268I and S2278T (P = 0.023-0.076) were weakly correlated with the outcome for HCV 1b. None of correlated variations located within the previously defined ISDR. These pieces of information can be helpful for predicting the outcome before the commencement of treatment. / Zhou Xiaoming. / "May 2006." / Adviser: Paul K. S. Chan. / Source: Dissertation Abstracts International, Volume: 69-01, Section: B, page: 0207. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2006. / Includes bibliographical references (p. 178-186). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. [Ann Arbor, MI] : ProQuest Information and Learning, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts in English and Chinese. / School code: 1307.

Contrary to the predictions of numerous theoretical models, variation in partner quality continues to persist in mutualisms, including in the symbiosis between legumes and rhizobia. One potential explanation for the maintenance of this genetic diversity is genotype × genotype interactions, however it is unknown which genetic regions might underlie these interactions. To investigate this question, I performed a quantitative trait loci mapping experiment with two different rhizobium strains to locate potential regions of the genome influencing genotype × genotype interactions between the legume Medicago truncatula and its symbiont Sinorhizobium meliloti. I found no evidence for genotype × genotype or QTL × rhizobium interactions, however some of the QTLs colocalized with genes involved in the symbiosis signaling pathway, suggesting variation in these genes could potentially affect plant performance and fitness traits. These findings have important implications for the evolutionary interactions between legumes and rhizobia, and the genetic architecture of Medicago truncatula.

Contrary to the predictions of numerous theoretical models, variation in partner quality continues to persist in mutualisms, including in the symbiosis between legumes and rhizobia. One potential explanation for the maintenance of this genetic diversity is genotype × genotype interactions, however it is unknown which genetic regions might underlie these interactions. To investigate this question, I performed a quantitative trait loci mapping experiment with two different rhizobium strains to locate potential regions of the genome influencing genotype × genotype interactions between the legume Medicago truncatula and its symbiont Sinorhizobium meliloti. I found no evidence for genotype × genotype or QTL × rhizobium interactions, however some of the QTLs colocalized with genes involved in the symbiosis signaling pathway, suggesting variation in these genes could potentially affect plant performance and fitness traits. These findings have important implications for the evolutionary interactions between legumes and rhizobia, and the genetic architecture of Medicago truncatula.

Cryptosporidium is a protozoan parasite infecting the intestines of its hosts, leading to acute diarrheal disease. Out of 26 recognized species, 14 are known to infect humans. Of most importance, from a human perspective are Cryptosporidium parvum and Cryptosporidium hominis, of which the former is known to have zoonotic potential. Globally, cryptosporidiosis affect people with lowered immune status particularly hard; among children under five it is the most important parasitic cause of gastroenteritis. In the region of KwaZulu-Natal, on the east coast of South Africa, Cryptosporidium is considered endemic. Drinking water is frequently collected from river systems and as Cryptosporidium spp. can be transmitted via contaminated water, this may be one source of infection. Research on the species distribution is important for outbreak investigations and prevention efforts. In water and wastewater such speciation is commonly performed using immunomagnetic separation, an antibody dependent method. There is however a suspicion that these antibodies have less affinity to some species and hence contorts the detected species distribution. An alternative approach is therefore of interest.   In the present study, Cryptosporidium diversity in wastewater collected from four different wastewater treatment plants in KwaZulu-Natal, is evaluated with an optimized antibody-free workflow and a single cell platform. It was shown that the workflow is suitable for complex samples, such as wastewater. Furthermore, diversity was assessed with amplicon sequencing, revealing four different species and genotypes. Further modifications of the methods used could benefit the field of Cryptosporidium research, along with improving global health and preventing disease outbreaks.

Master of Science / Department of Grain Science and Industry / Jon M. Faubion / Rebecca Miller / Water absorption tolerance is an important parameter in commercial bread production. Hard winter wheat (HWW) flours have shown different water absorption tolerance behaviors in routine wheat quality analysis. Flours with high water absorption tolerance allow broader variation in water addition without affecting optimum dough conditions. Although studies have demonstrated that genotype and environmental factors affect optimum water absorption, mixing time and dough strength, there is no research defining or quantifying water absorption tolerance behavior or explaining reasons and factors affecting such behavior and its correlation with end product quality. Using the mixograph®, this study identified high and low absorption tolerance behaviors in five HRW varieties (Jagger, Jagalene, Fuller, 2137 and Overley) grown in six locations (Finney, Labette, Republic, Thomas, Riley and Sumner Counties) in Kansas, during crop year 2009. Milling, wheat and flour quality tests, Solvent Retention Capacity (SRC), damaged starch, protein composition and identification, flour and starch particle size distribution and bread baking tests were conducted and analyzed. Jagger grown at Finney County possessed the largest water absorption tolerance range while the smallest range was observed for Fuller grown at Riley and Sumner Counties. A positive high correlation was observed between water absorption tolerance and the following parameters: protein content, kernel hardness, extractable polymeric proteins, unextractable polymeric proteins, gliadins and flour particle size (41-300 μm). SDS PAGE and proteomic analyses determined that γ-gliadins were present in a significantly higher concentration in the high tolerance sample suggesting that these proteins play a primary role in water absorption tolerance behavior. The five wheat varieties grown at locations with high and low water absorption tolerance were blended together by location and test baked at three different absorption levels. Loaf volume varied between flours but did not vary between different water levels. It is unclear if this was an effect of the differing protein contents of the blends, water tolerance or both. However, a negative effect on crumb grain characteristics was observed when lower water levels were used.

HCV infects 170 million persons worldwide and is a serious global health problem. Genotype-3a is the dominant genotype in newly diagnosed infections within the UK and has a high response rate to interferon therapy, with up to 70% patients achieving a sustained virological response (SVR). The reason(s) for this are unknown; therefore the aim was to assess host and viral factors that determine treatment outcome of subtype-3a infection. Full-length subtype-3a viral sequence analysis identified 2 novel regions of hypervariability within E2 - HVR495 and HVR575, that are subject to positive selection pressure. A 5 amino-acid insertion found only in subtype-3a and a putative glycosylation site were contained within HVR575. These data suggest that HVR495 and HVR575 may serve as major antigenic sites in subtype-3a HCV infection. Successful treatment of chronic subtype-3a infection was not associated with pre-treatment quasispecies diversity and complexity, PePHD, HVR495 or HVR575 sequence. Different patterns of quasispecies variation were observed in patients that failed treatment. Subtype-3a specific CD8+ T-cell responses in chronic infection target non-structural proteins, in contrast to pre-dominant genotype-1 core-specific CD4+ T-cell responses. SVR was associated with a decline in subtype-3a specific and non-specific T-cell responses, and also total lymphocyte counts, which all recovered after treatment. These data do not support the theory that clearance of subtype-3a is associated with an enhancement of antiviral T-cell responses. Overlapping peptides detected a greater number of subtype-3a T-cell responses compared with peptides representing putative predicted CD8 epitopes. Therefore subtype-3a HCV is distinct from genotype-1 in terms of genome sequence, effect of treatment on quasispecies and subtype-3a specific T-cell responses, further emphasising the importance in understanding this distinct subtype.