Thesis (Ph. D.)--Universität Mannheim, 2004/2005. / Includes bibliographical references (p. [313]-344).

Thesis (Ph.D.)--Ohio University, November, 2004. / Title from PDF t.p. Includes bibliographical references (p. 202-211)

Thesis (Ph. D.)--University of Texas at Dallas, 2007. / Includes vita. Includes bibliographical references (leaves 117-122)

Coding theory has several applications in Genetics and Bioengineering. This thesis concentrates on a specific application from Computational Biology. This concerns the construction of new DNA codes which satisfy certain combinatorial constraints, using an alphabet of four symbols. The interest in these codes arises because it is possible to synthesise short single strands of DNA known as oligonucleotides. The codes can be useful in the design of these oligonucleotides. For example, the codes are used in DNA computing, as bar codes in molecular libraries and in microarray technologies. The computer algebra system Magma, which deals successfully with coding theory computation, is applied initially to the construction of DNA codes sat- isfying a GC-content constraint and a minimum Hamming distance constraint. The constraints are specified to avoid unwanted hybridizations and to ensure uniform melting temperatures. Additionally, another constraint, known as a reverse-complement constraint, is added to further prevent unwanted hybridiza- tions. This additional constraint is studied using involutions in a permutation group. Codes constructed in this thesis are derived from linear codes over GF(4) and Z4 and additive codes over GF(4). Previous approaches to the construction of these codes are extended in several ways. Longer codes are constructed, the examination of cyclic and extended cyclic codes is more comprehensive, and cosets of codes are considered. In addition, attention is paid to the mapping from field or ring elements to the DNA nucleotides; different mappings can give different lower bounds. Further improvements have been made after the tech- niques of shortening and puncturing are applied to the table of best codes, and also by searching for codes in the tables that have an all-ones vector in their dual. The use of a database of best known linear codes is also considered. In many cases codes are obtained which are larger than the best codes currently known. In the case of codes of length greater than twenty, linear DNA codes have not been constructed previously and so all codes obtained are the best known re- sults. Generator polynomials are given for the codes constructed. Coset leaders are also given in cases where cosets of linear codes are used. Thus it is possible for the reader to construct the codes without repeating the work presented in the thesis. Additionally, files of codewords are available online when the codes constructed are the best known codes and have fewer than 50000 codewords.

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On January 1, 2022, mandatory genetically engineered (GE) food disclosure labeling will be required nationwide in the United States. To date, the only mandatory GE labeling law implemented in the U.S. was Act 120 in Vermont. This thesis examines the consumer purchasing response to the implementation of Vermont Act 120 using store-level scanner data of food purchases. I measure the effects of Vermont Act 120 on the grocery store sales of non-GMO, organic, and GE- labeled products in Vermont. Using a difference-in-difference approach, I can compare stores in Vermont to control states before and after the law was passed, implemented, and repealed. I find that during the implementation period, sales of non-GMO and organic labeled products increased, and the sales of GE-labeled products decreased. The sales trend reverted after the law was repealed but not quite to the baseline levels for organic and GE-labeled products.

Wheat-derived products provide the basic nutrition for more than a billion of people in the world (about 40% of humankind). Humans consume more proteins from wheat than from any other source. However, the nutritional quality of wheat proteins is limited by the low content of lysine, one of the essential amino acids that we should incorporate through the diet. As part of this thesis work, we obtained transgenic wheat lines expressing the CI-2 gene from barley under the control of a promoter that is specific for endosperm. This gene has a high content of lysine, an essential amino acid in which wheat proteins are naturally deficient. These transgenic wheat lines have an improved nutritional quality because of the higher content of lysine of their proteins. Bread-making quality of wheat is determined by the number and type of high molecular weight (HMW) subunits of glutenins. The higher the number of HMW subunits of glutenins of a particular wheat variety, the better its bread-making quality. The HMW subunits of glutenins are very polymorphic (there are many different alleles or alternative forms of genes) and some types of subunits are associated with good bread-making quality while others confer a poor quality. The two HMW subunits of glutenins associated with the best bread-making quality in wheat are 1Dx5 and 1Ax1. HMW subunits of glutenins confer elasticity to the dough because of their particular spring shape.Dough with high elasticity are ideal to make bread. Using genetic engineering, we transformed (genetically modified) a commercially available variety of wheat to increase the number of HMW subunits of glutenins from 5 to 6 by introducing an extra HMW subunit known as 1Ax1, which caused an increase of 21% in the content of glutenin compared to the controls. In addition, we over-expressed 1Ax1 in a variety of wheat that already had this subunit by introducing extra gene copies of 1Ax1, which increased the content of 1Ax1 by 44% in this transgenic wheat variety compared to non-transgenic wheat control. Likewise, we over-expressed the HMW subunit of glutenin 1Dx5 causing an increase of 140% in the level of this subunit and a 20% increase in the total content of glutenin. Interestingly, the over-expression of the HMW subunits of glutenins 1Ax1 or 1Dx5 in some of the transgenic wheat lines induced the inactivation of few or all of the endogenous genes that codify for HMW subunits. This phenomenon is part of a mechanism that plants use to inactivate alien genes as a protection against viruses. As expected, these silenced transgenic wheat lines had very low levels of HMW subunit of glutenin and a very poor bread-making quality. However, these lines showed exceptional good quality for making other products such as cookies, crackers, and pizza.

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnology and Food Technology, Durban University of Technology, 2007 iv, 75 leaves / The development of transgenic plants resulted in the need to utilize the various molecular methods (e.g., ELISA, real - time PCR etc.) for the detection or analysis of the presence or absence of a specific trait in a particular plant (Bt in this study). The overall aim of this study was to optimize a half – seed extraction technique as part of a laboratory protocol for transgenic maize plants and to explore the possibility of using the following molecular techniques: horizontal isoelectric focusing, real - time PCR and ELISA, as methods for detection of the Bt trait for incorporation into the half – seed extraction protocol.