Master of Agribusiness / Department of Agricultural Economics / Vincent R. Amanor-Boadu / Livestock production is a crucial industry in North Carolina. Broilers, turkeys, and hogs all have tremendous amounts of production numbers that are steadily growing particularly on the broiler side. This thesis seeks to explore the trends in three basis indicators and explore their effects on corn prices in North Carolina. Given the significant role corn plays in livestock production in the state and the deficit situation it finds itself in with respect to corn, these analyses may illuminate some challenges that may adversely affect the long term competitiveness of the poultry industry in the state. Already, hog and turkey production seems to be migrating out of the state possibly due to feed costs. The importance of this study is to help identify innovative solutions to arrest the increasing adverse effects of feed costs on North Carolina’s livestock industry. Using statistical analyses and data on corn prices and three basis indicators, CSX-90, Norfolk-Southern 75, and Truck Only, we show that while corn prices, on average, have declined slightly over the past several years, the transportation costs associated with moving corn into North Carolina have increased for all three options evaluated. The average growth rate in CSX 90 was approximately 7.4% per annum compared to 7.7% for NS-75 and 12.4% for truck only. Thus, while average annual trucking costs were lower than the rail transportation by between 82% and 92%, it was growing at more than 50% the growth rate in rail prices. Interestingly, we observe that the difference between the paired basis were all statistically significant at the 1% level. For this example the difference between the monthly average CSX 90 and trucking only was about $0.29, with a t-statistic of 17.34 and a p-value of 0.00. Similarly, the difference between the monthly average CSX-90 and NS-75 was $-.04, with a t-statistic of 3.35 and a p-value of 0.00. The foregoing reveal the advantage of sourcing corn via trucking given its lower basis. However, the higher variability in trucking compared to rail and the rapid growth rate in trucking suggests that an innovative strategic approach be adopted to overcome its potential long-term effect on corn prices. We show that a careful assessment of what the livestock industry in North Carolina is currently doing and what it needs to do could shed light on how to deal with this situation. Fixed assets like feed mills, production facilities, and slaughter facilities determine the type of access to outside rail or access to local markets. These assets are unlikely to change and therefore it is important to build an efficient supply chain to decrease marginal costs.

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M.Com. (Financial Management) / This paper investigates the use of weather derivatives in the maize production industry of South Africa. The history, users and mechanics of weather derivatives and maize production are presented in the study. This study examines, by using experiential design, the potential revenue for a control and a test group of farmers using monthly, actual maize production and weather observations for the period 2000 - 2010. This study suggests, with reference to the results, an option strategy that ultimately results in the hedging of maize output risk for the farms investigated. Limitations of the study are basis risk, liquidity, the difficulties in pricing of the weather derivative and finally the reticence of agricultural business to explore these hedging instruments in practise. In conclusion the study presents suggestions for further research into the wider application of weather derivatives into other industries, the exploration of the effects of weather on changes in crop yield and the effects of a hybrid maize crop and its possible resilience to weather changes. This study also demonstrates the weather effects on maize output and suggests a hedging solution to yield.

赤黴素有多種生物學功能，包括促進莖的伸長、種子萌發以及花的發育。玉米赤黴素缺陷型突變體dwarf1 (d1) 表現出植株矮壯和雌雄兩性花，即原為雌花部位發育出雙性花。但是該突變的分子基礎尚不清楚。通過分析多個d1等位基因突變體的分子組成特征，我們證明d1突變體是由能催化赤黴素中間代謝物轉變為活性赤黴素的赤黴素3-氧化酶（ZmGA3ox2） 突變引起的。重組D1 蛋白能於體外催化至少4個反應，包括GA20 轉變為GA3，GA5轉變為GA3，GA20轉變為GA1 以及GA9轉變為GA4等。煙草細胞中D1-GFP 的瞬時表達和細胞組分蛋白質印染分析等兩個獨立的方法，揭示了D1 蛋白是雙定位於細胞核和細胞質中。此結果暗示活性赤黴素能夠在此兩種細胞器中合成。這個雙定位的結果與赤黴素受體GID1蛋白的定位壹致。在早期的玉米雌花發育的過程中，D1 蛋白特異且大量地表達在雌花中的雄花原基細胞，揭示了赤黴素發揮其抑制雄花原基發育的功能需要在該組織大量合成。 / DELLA 蛋白是赤黴素信號傳導的壹個阻遏物。玉米包含僅壹個DELLA蛋白命為DWARF8（D8）。發生在D8 蛋白N端的突變產生了赤黴素非敏感型突變體dwarf8 （d8）。d8突變體與d1突變體有很多共同特征，包括侏儒植株，深綠色的葉片以及雌雄兩性花。這些特點都表明玉米對赤黴素的響應是被DELLA蛋白所抑制的。DELLA蛋白是通過蛋白互作的方式來限制其互作蛋白功能，以達到抑制赤黴素下遊信號傳導的目的。多樣的赤黴素響應必然需要多樣的DELLA互作蛋白。基於赤黴素在調控玉米性別決定過程當中的獨特功能，我們提出假設：玉米當中存在未知的D8互作蛋白。通過酵母雙雜交方法篩選玉米雌花的cDNA文庫，找到14個在酵母系統與D8互作的蛋白。ZmSPX1是這些蛋白中的壹個但不清楚功能。通過雙分子熒光互補實驗和蛋白質體外結合實驗，D8和ZmSPX1之間的互作被進壹步確定。基于此，我们找到数个候选的D8互作蛋白以及证明了ZmSPX1是D8真正的互作蛋白；这些工作都为进一步研究ZmSPX1蛋白在调控性别分化、细胞分裂和分化等赤霉素响应中的作用提供了基础。 / Gibberellins (GA) have multiple biological functions including promoting stem elongation, seed germination and flower development. The GA deficient dwarf1 (d1) mutant in maize displays plant dwarfism and andromonoecy, i.e. forming anthers in the female flower. However, the molecular basis is not clear. Through molecular characterization of multiple d1 alleles, I prove that the d1 is caused by mutations in the GA 3-oxidase (ZmGA3ox2) that converts the inactive GA intermediates to bioactive GAs. The recombinant D1 protein catalyzes at least four reactions in vitro, converting GA20 to GA3, GA5 to GA3, GA20 to GA1 and GA9 to GA4. Subcellular localization analysis by two independent approaches which are in vivo D1-GFP analysis and western blot analysis of organelle fractions revealed that the D1 protein is dual-localized in the nucleus and the cytosol. ZmGA20ox was also localized in both the cytosol and the nucleus by the in vivo GFP fusion analysis. Interestingly, the dual-localization of D1 and ZmGA20ox coincides with the localization of the GA receptor GID1. In early phase of maize female flower development, the D1 protein was found specifically and highly expressed in the stamen primordia within the female florets. These results indicate that bioactive GAs can be synthesized in both the cytosol and the nucleus, and that the suppression of stamen in female florets is mediated by locally synthesized GAs. This finding provides new insights to the understanding of GA biosynthesis and signal transduction in plants. / DELLA proteins are repressors of GA signal transduction. DWARF8 (D8) is a DELLA protein in maize, Mutations in the N-terminal of D8 resulted in dominant GA insensitive dwarf8 (d8) phenotype. d8 displayed similar phenotypes as the d1mutants; i.e. plant dwarfism, dark green leaves and andromonoecy, indicating that D8 is a master repressor mediating these GA functions. DELLA proteins suppressed the downstream signal transduction of GA by restricting their interacting protein functions through protein-protein interaction. Diverse GA responses require numerous DELLA interacting proteins. Based on the unique function of GA in regulating sex determination in maize, I hypothesize that D8 mediates the GA responses by interacting with yet unknown proteins in maize. Through yeast two hybrid screening of the maize ear cDNA library, I identified 14 proteins that showed genuine interaction in yeast system. Among these, a SPX domain containing protein named as ZmSPX1 was present. SPX domain containing proteins in yeast are implicated in cell cycle regulation; however, their functions in plants are unknown. GFP fusion analysis indicated that ZmSPX1 co-localizes with D8 in the nucleus and their interaction was confirmed by bimolecular fluorescence complementation (BiFC) and in vitro pull-down assay. To this point, I have identified several candidates for D8 interacting proteins and provided strong evidence that ZmSPX1 is a bona fide D8 interacting protein which set a foundation for further analysis of its function in mediating GA responses including sex determination, cell division and elongation. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Chen, Yi. / Thesis (Ph.D.) Chinese University of Hong Kong, 2015. / Includes bibliographical references (leaves 60-67). / Abstracts also in Chinese. / Chen, Yi.

种子发育是开花植物生命周期中的一个关键阶段。理解控制这一过程的机理既是植物生物学的重要基础研究课题，也是农业应用上的重要任务。因为种子是我们的主食，而种子质量和大小正是主要由那些控制种子发育过程的基因控制着。玉米作为一种典型的单子叶植物，是很好的研究单子叶植物种子发育的模式植物。 / 在开花植物中，RNA编辑是发生在线粒体和质体中的一种转录后机制，主要将特定的胞嘧啶转换为尿嘧啶。这一过程很多时候将改变基因组的遗传信息。这是一种非常重要的转录后调节机制，许多案例表明它对编码蛋白的功能十分关键。例如，RNA编辑能修复一个保守的氨基酸密码，创造一个起始或终止密码子，或移除一个终止密码子而编码出一个更大的功能蛋白。因此，RNA编辑不能正常进行可能损害或完全失去编码蛋白的功能，对植物的生长和发育造成严重后果。 / 本研究中，我们报道了玉米种子突变体emp5(empty pericarp 5)的分子特征研究。Emp5基因的无效突变导致玉米种子胚和胚乳发育在早期发育阶段停止。Emp5基因编码一个定位在线粒体的PPR-DYW蛋白。对emp5突变体线粒体转录组的分析表明，EMP5蛋白功能失效阻碍了rpl16-458（野生型中100%被编辑）这一位点的C-to-U RNA编辑，降低了nad9, cox3和rps12这三个转录本中总共9个位点的C-to-U RNA编辑水平。令人意外的是，同时也增加了atp6, nad1, cob 和 rpl16 4个转录本中共5个位点的RNA编辑水平。EMP5蛋白缺失E+和DYW结构域仍然保留了底物的特异性和RNA编辑功能，只是编辑效率有所降低。这表明EMP5蛋白的E+和DYW结构域对其编辑功能不关键，但对编辑效率是必需的。对EMP5在水稻中的同源蛋白的分析表明，OsEMP5在水稻线粒体rpl16-458位点的编辑功能是保守的。OsEMP5的基因沉默表达导致水稻植株生长缓慢及种子缺陷。这些结果表明Emp5基因编码的这一PPR-DYW蛋白对多个线粒体转录本的RNA编辑是必需的。尤其是rpl16-458这一位点的编辑对线粒体的功能十分重要，因而对玉米种子发育非常关键。 / Seed development is a critical stage in the life cycle of flowering plants. Understanding the mechanism governing this process is both a fundamental question in plant biology and also an important task in agriculture application as seeds are staple food and seed quality and size are controlled by the genes governing seed development process. Maize as a typical monocot plant, is also an excellent model system for monocot seed development research. / In flowering plants, RNA editing is a post-transcriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the genetic information encoded by these genes. It is important for posttranscriptional regulation and in some cases critical to the functions of the encoded proteins. For example, editing can restore a conserved amino acid codon, create an initiation or stop codon, or remove a stop codon that leads to a functional larger protein. Therefore, deficiency in editing may result in a compromised or complete loss of function for the encoded proteins, leading to a severe consequence in plant growth and development. / In this study, we report the molecular characterization of the empty pericarp 5 (emp5) mutant in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion targeted DYW-subgroup PPR protein. Analysis of the mitochondrial transcripts reveals that loss of the EMP5 function abolishes the C-to-U editing of rpl16-458 (100% edited in the wildtype), decreases the editing at nine sites in nad9, cox3 and rps12, and surprisingly increases the editing at five sites of atp6, nad1, cob and rpl16. EMP5 lacking the E+ and DYW domain still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function, but necessary for efficiency. Analysis of the ortholog in rice indicates that OsEMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. Knock-down expression of OsEmp5 results in slow growth seedlings and defective seeds. These results demonstrate that EMP5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and hence to seed development in maize. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Detailed summary in vernacular field only. / Liu, Yujun. / Thesis (Ph.D.)--Chinese University of Hong Kong, 2013. / Includes bibliographical references (leaves 78-86). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstracts also in Chinese. / Thesis/Assessment Committee --- p.i / Statement --- p.ii / Acknowledgements --- p.iii / Abstract --- p.iv / 摘要 --- p.vi / Table of Contents --- p.viii / List of Tables --- p.xii / List of Figures --- p.xiii / List of Abbreviations --- p.xv / Chapter Chapter 1. --- General Introduction --- p.1 / Chapter Chapter 2. --- Literature Review --- p.6 / Chapter 2.1. --- Seed development in flowering plants --- p.7 / Chapter 2.1.1 --- Seed morphogenesis of flowering plants --- p.7 / Chapter 2.1.2 --- Molecular mechanisms of seed development --- p.8 / Chapter 2.2 --- PPR protein family --- p.11 / Chapter 2.2.1 --- Definition of PPR protein --- p.11 / Chapter 2.2.2 --- Subgroups of PPR protein --- p.12 / Chapter 2.2.3 --- PPR protein distribution and evolution --- p.13 / Chapter 2.2.4 --- Functions of PPR proteins in plants --- p.14 / Chapter 2.3 --- PPR proteins involving in seed development --- p.15 / Chapter 2.4 --- PPR proteins studied in maize --- p.17 / Chapter 2.5 --- RNA processing in plant mitochondria --- p.19 / Chapter 2.5.1 --- RNA splicing --- p.20 / Chapter 2.5.2 --- 5’ and 3’ processing of plant mitochondrial transcrips --- p.23 / Chapter 2.5.3 --- RNA stabilization --- p.24 / Chapter 2.6 --- RNA editing --- p.25 / Chapter 2.7 --- Status of C to U RNA editing mechanism --- p.28 / Chapter Chapter 3. --- Materials and methods --- p.31 / Chapter 3.1 --- Plant Materials --- p.32 / Chapter 3.2 --- Light Microscopy of Cytological Sections --- p.32 / Chapter 3.3 --- Immunohistochemistry Analysis Materials --- p.32 / Chapter 3.4 --- Isolation of genomic DNA Materials --- p.33 / Chapter 3.5 --- Southern Analysis Materials --- p.34 / Chapter 3.6 --- Inverse PCR cloning Materials --- p.35 / Chapter 3.7 --- RNA Extraction and RT-PCR Materials --- p.35 / Chapter 3.8 --- Subcellular Localization of EMP5 Protein Materials --- p.36 / Chapter 3.9 --- Analysis of Mitochondrial RNA Editing Materials --- p.37 / Chapter 3.10 --- Rice Transformation Materials --- p.37 / Chapter 3.10.1 --- OsEmp5 RNAi vector construction Materials --- p.37 / Chapter 3.10.2 --- Callus induction from mature rice seeds Materials --- p.38 / Chapter 3.10.3 --- Callus subculture Materials --- p.38 / Chapter 3.10.4 --- Preparation of Agrobacterium tumefaciens Materials --- p.38 / Chapter 3.10.5 --- Co-cultivation Materials --- p.39 / Chapter 3.10.6 --- Callus washing and selection Materials --- p.39 / Chapter 3.10.7 --- Regeneration Materials --- p.40 / Chapter 3.10.8 --- Screening of transgenic plants Materials --- p.40 / Chapter Chapter 4. --- Results --- p.42 / Chapter 4.1 --- Phenotypic and Genetic Characterization of emp5-1 --- p.43 / Chapter 4.2 --- Cloning of Emp5 --- p.45 / Chapter 4.3 --- Emp5 Encodes a Mitochondrion-Targeted PPR-DYW Subclass Protein --- p.48 / Chapter 4.4 --- Expression of Emp5 --- p.51 / Chapter 4.5 --- EMP5 is Required for Mitochondrial RNA Editing --- p.52 / Chapter 4.6 --- Molecular Characterization of emp5-4 Allele --- p.54 / Chapter 4.7 --- Functional Analysis of the Rice OsEmp5 Gene --- p.58 / Chapter Chapter 5. --- Discussion --- p.62 / Chapter 5.1 --- Abortion of emp5-1 Mutant Seed Development is Caused by Defective Mitochondrial RNA Editing --- p.63 / Chapter 5.2 --- Increased Editing in the emp5 Mutant --- p.65 / Chapter 5.3 --- Substrate Specifying Sequence of EMP5 Are Not Conserved --- p.66 / Chapter 5.4 --- The E+ and DYW Motif of EMP5 Is not Essential for This Protein Function --- p.67 / Chapter Chapter 6. --- Conclusion --- p.75 / References --- p.78

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