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Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the species. Interspecific hybridization can greatly increase the amount of genetic variation available to plant breeders for improvement. Interspecific hybrids between sorghum and the 19 species in the tertiary gene pool have, until recently, not been successful. The Australian species, S. macrospermum, was recently successfully hybridized with sorghum by using germplasm homozygous for the iap allele, which eliminated reproductive isolation barriers. The objectives of this research were to evaluate the potential for use of S. macrospermum in an introgression breeding program, determine the map position of the Iap locus, and backcross the iap allele into elite Texas A&M germplasm. Interspecific hybrids between S. bicolor and S. macrospermum revealed moderate levels (2.6 II per PMC) of allosyndetic recombination, indicating that introgression through genetic recombination is possible. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ, Y and Z remain unknown. In backcrosses to S. bicolor using the female interspecific hybrid gamete and embryo rescue, BC1F1 plants were recovered. They had high chromosome numbers (2n = 35-70) and were male-sterile but three plants set backcross seed. Ninety-five percent of BC2F1 plants were 2n = 20 chromosomes and 75% of them contained S. macrospermum introgression. BC2F1 plants carried between 0-18.5% S. macrospermum introgression; in total 26% of the S. macrospermum genome was detected in the BC2 generation. Three types of introgression germplasm were created: alien addition lines; alien substitution lines; and introgression lines. Recombinant chromosomes, containing S. macrospermum introgression sites, were identified in multiple introgression lines. The Iap locus was genetically mapped to sorghum chromosome 2 (SBI-02), flanking AFLP markers were 2.1 and 2.7cM away, one AFLP marker shared the same map position (0.0cM). A genetic stock, Tx3361, was created which has iap iap genotype and improved agronomic qualities such as short plant height, white seed color, non-pigmented testa, no awns, reduced lodging, early maturity, and backcross segregation of male-sterility (ms3). This research shows that S. macrospermum is now available to plant breeders for sorghum improvement.

The unprecedented growth of computing power and communication bandwidth in the last few decades has driven an explosion in the size and complexity of application software. Specifically, it has spurred an almost universal adoption of modular and extensible software designs, from ordinary PC applications, to operating systems kernels, and even to embedded systems. In many cases, however, the ability to extend software systems has come hand in hand with the need to isolate them from untrusted or potentially faulty extensions. This dissertation will focus on the important problem of code isolation, where existing techniques vary in many and often interrelated dimensions such as granularity, code complexity, invocation latency, dynamism, isolation strategy, permissible extension functionality, and degree of integration with the operating system kernel. Specifically, the implementation of a particular technique imposes restrictions on the properties of extensions. Examples include proof-based techniques that are only applicable to simple extensions of small granularity, hardware-based isolation techniques that typically incur a measurable invocation latency due to hardware re-configuration overhead, and programming language techniques that impose implementation and compiler restrictions. The goal of this dissertation is to explore the design space of code isolation techniques, identify characteristics of individual approaches, and then argue for and design a hybrid approach that combines their advantages while avoiding their drawbacks. The contributions of this thesis will be threefold: (1) a taxonomy of metrics and properties relevant to software code isolation techniques, (2) the design and implementation of a novel hybrid architecture for safe kernel extension with pliable characteristics, and (3) an evaluation of the hybrid approach and comparison with homogeneous alternatives.

Sorghum has been improved by plant breeders for yield, biotic and abiotic stress resistance, as well as quality traits by using germplasm from within the species. Interspecific hybridization can greatly increase the amount of genetic variation available to plant breeders for improvement. Interspecific hybrids between sorghum and the 19 species in the tertiary gene pool have, until recently, not been successful. The Australian species, S. macrospermum, was recently successfully hybridized with sorghum by using germplasm homozygous for the iap allele, which eliminated reproductive isolation barriers. The objectives of this research were to evaluate the potential for use of S. macrospermum in an introgression breeding program, determine the map position of the Iap locus, and backcross the iap allele into elite Texas A&M germplasm. Interspecific hybrids between S. bicolor and S. macrospermum revealed moderate levels (2.6 II per PMC) of allosyndetic recombination, indicating that introgression through genetic recombination is possible. Genomic relationships were sufficient to assign S. macrospermum the genomic formula AAB1B1YYZZ, Y and Z remain unknown. In backcrosses to S. bicolor using the female interspecific hybrid gamete and embryo rescue, BC1F1 plants were recovered. They had high chromosome numbers (2n = 35-70) and were male-sterile but three plants set backcross seed. Ninety-five percent of BC2F1 plants were 2n = 20 chromosomes and 75% of them contained S. macrospermum introgression. BC2F1 plants carried between 0-18.5% S. macrospermum introgression; in total 26% of the S. macrospermum genome was detected in the BC2 generation. Three types of introgression germplasm were created: alien addition lines; alien substitution lines; and introgression lines. Recombinant chromosomes, containing S. macrospermum introgression sites, were identified in multiple introgression lines. The Iap locus was genetically mapped to sorghum chromosome 2 (SBI-02), flanking AFLP markers were 2.1 and 2.7cM away, one AFLP marker shared the same map position (0.0cM). A genetic stock, Tx3361, was created which has iap iap genotype and improved agronomic qualities such as short plant height, white seed color, non-pigmented testa, no awns, reduced lodging, early maturity, and backcross segregation of male-sterility (ms3). This research shows that S. macrospermum is now available to plant breeders for sorghum improvement.

Phosphofructokinase from Bacillus stearothermophilus (BsPFK) is a homotetrameric enzyme with an average of one active site and one allosteric site per subunit. BsPFK is inhibited by phosphoenolpyruvate (PEP) and how this inhibitory signal is propagated throughout the enzyme is the main question we address through this investigation. By possessing a total of eight binding sites, a potential for twenty-eight total pair-wise allosteric interactions result within BsPFK, ten of which are unique. Of these ten interactions, four are heterotropic interactions, or interactions between unlike binding sites, while the remaining six interactions are homotropic interactions, or interactions between like binding sites. Thus, to address the question of how BsPFK is inhibited by PEP, each of these ten interactions needs to be quantified and their roles in the inhibition process assessed. In order to quantify the roles of the 10 allosteric interactions, we created, purified and characterized several different hybrid enzymes by using site-directed mutagenesis to reduce the number of native active sites and native allosteric sites to permit the isolation of specific allosteric interaction(s). Through the creation and isolation of 1:3 hybrid enzymes, in which one native active site and one native allosteric site remain, each of the four heterotropic interactions were characterized. Moreover, through the creation and isolation of the 2:2 hybrid enzymes, in which two native active sites and two native allosteric sites remain, characterization of the remaining six homotropic interactions was performed. Utilizing a linked function approach to quantify the heterotropic and homotropic effects for each hybrid enzyme, we determined that 5 to 6 of the ten pair-wise allosteric interactions found in BsPFK are involved in the inhibition process depending upon pH. More importantly however, our data provides definitive results that the traditional two-state models used to describe an allosteric effect are not sufficient to describe the allosteric effect measured for BsPFK. Rather, our results show that the linked function approach is a more appropriate way to unambiguously measure the nature and magnitude of an allosteric effect. Moreover, this approach can also be used to explain the allosteric behavior of a dimeric enzyme.

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