Theses and Dissertations at Montana State University (MSU)
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Item The impact of Teosinte branched1 and reduced height mutations in durum wheat(Montana State University - Bozeman, College of Agriculture, 2021) Brown, McKenna Margaret; Chairperson, Graduate Committee: Michael J. GirouxIncreasing the yield of wheat requires identifying new genetic combinations of alleles by crossing or by creating variation in yield limiting genes. Wheat yield is impacted by tiller number and seeds per tiller, both of which are impacted by the Reduced height (Rht) and Teosinte branched1 (TB1) genes. In this study, durum plants varying for Rht and TB1 alleles created by EMS mutagenesis were studied to determine the impact of each allele upon agronomic and seed traits. Both projects aimed to increase durum yield, one through an increase in tiller number; the other through the development of a plant with height between current full-height and semi-dwarf varieties that can allocate more resources to seed production. The impact of TB1 null alleles were studied alone and together in greenhouse and field trials, along with an RNA sequencing study to determine the impact of TB1 mutation upon global gene expression in developing meristems. TB1 single and double null mutants produced more biomass and tillers per plant, and expression of genes in meristems varied. A screen of wheat varieties grown in Montana identified that several spring and durum wheat varieties contain different TB1 alleles, but none contained TB1 null alleles. Rht experiments included field trials, coleoptile length and gibberellic acid responsiveness assays, and an in-vitro test to determine the impact of each Rht mutation upon binding to Gibberellin Interacting Domain 1 (GID1) that directly influences plant height. It was found that the previously described Rht-B1b-E529K allele reduced both plant height and coleoptile length while two newly characterized Rht mutations had lesser impacts with trends towards intermediate-height plants. The results of this research demonstrate that Rht alleles that alter RHT binding to GID1 and TB1 null alleles may prove useful in increasing durum tillering and optimizing plant height for different growing conditions.Item Duplications and deletions in genomes: theory and applications(Montana State University - Bozeman, College of Engineering, 2022) Zou, Peng; Chairperson, Graduate Committee: Binhai ZhuIn computational biology, duplications and deletions in genome rearrangements are important to understand an evolutionary process. In cancer genomics research, intra-tumor genetic heterogeneity is one of the central problems. Gene duplications and deletions are observed occurring rapidly in cancer during tumour formation. Hence, they are recognized as critical mutations of cancer evolution. Understanding these mutations are important to understand the origins of cancer cell diversity which could help with cancer prognostics as well as drug resistance explanation. In this dissertation, first, we prove that the tandem duplication distance problem is NP-complete, even if |sigma| > or = 4, settling a 16-year old open problem. And we obtain some positive results by showing that if one of the input sequences, S, is exemplar, then one can decide if S can be transformed into T using at most k tandem duplications in time 2 O (k 2) + poly(n). Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest letter-duplicated subsequence (LLDS) is investigated. We investigate several variants of this problem. Due to fast mutations in cancer, genome rearrangements on copy number profiles are used more often than genome themselves. We explore the Minimum Copy Number Generation problem. We prove that it is NP-hard to even obtain a constant factor approximation. We also show that the corresponding parameterized version is W[1]-hard. These either improve the previous hardness result or solve an open problem. And we then give a polynomial algorithm for the Copy Number Profile Conforming problem. Finally, we investigate the pattern matching with 1-reversal distance problem. With the known results on Longest Common Extension queries, one can design an O(n+m) time algorithm for this problem. However, we find empirically that this algorithm is very slow for small m. We then design an algorithm based on the Karp-Rabin fingerprints which runs in an expected O(nm) time. The algorithms are implemented and tested on real bacterial sequence dataset. The empirical results shows that the shorter the pattern length is (i.e., when m < 200), the more substrings with 1-reversal distance the bacterial sequences have.Item Effects of a barley chromosome 6H grain protein QTL on agronomic traits, malt quality traits, and stomatal control under two irrigation and nitrogen fertilization regimes(Montana State University - Bozeman, College of Agriculture, 2018) Mangel, Dylan J. L.; Chairperson, Graduate Committee: Andreas FischerCereal grain protein concentration (GPC) is an important quality parameter, with high GPC desirable when grain is used for food or feed, while low (typically below 12- 13%) GPC is needed when barley grain is used for malting. A major QTL controlling grain protein has previously been identified on barley chromosome 6H. Based on the comparison with a co-linear region on wheat chromosome 6B, the functional status of a gene coding for a NAC transcription factor (HvNAM-1) is responsible for controlling whole-plant senescence, nutrient remobilization from leaves to developing grains, and grain protein concentration. In this context, the purpose of this study was the analysis of the influence of a low- vs. a high-grain protein allele at this locus on barley agronomic and malting quality parameters in different genetic backgrounds. Integration of the low-protein allele stably lowered GPC by 1.6-1.8%, in both years and across all combinations of genetic backgrounds and management practices. Lines with the low-protein allele matured 1.4 to 2.5 days later, dependent on management, and had stably lower malt protein and diastatic power. Effects on additional agronomic and malt quality parameters including yield, test weight, percentage of plump kernels, free amino nitrogen and alpha-amylase activity were subtler and depended on the genetic background tested. Our data also provide important information on the influence of soil N and water availability on malt quality characteristics. Overall, use of the chromosome 6H low-grain protein allele stably lowered grain and malt protein levels without important negative influences on any of the tested agronomic and malt quality parameters, indicating its usefulness in the development of new malting barley germplasm. The studied chromosome 6H GPC QTL also controls expression of a gene coding for a glycine-rich RNA-binding protein (HvGR-RBP1) that may improve drought tolerance. Stomatal conductance and canopy thermal imaging assays did not show consistent effects of the allelic state of the GPC QTL on stomatal control. However, our data showed important correlations between stomatal conductance, canopy temperature depression and agronomic parameters including yield, demonstrating the value of the performed assays for variety selection and breeding.Item The mutagenicity of inorganic ions in microbial systems(Montana State University - Bozeman, College of Letters & Science, 1977) Tindall, Kenneth RaymondItem NMR investigations of the role of intrinsic flexibility of the tryptophan repressor(Montana State University - Bozeman, College of Letters & Science, 2012) Goel, Anupam; Chairperson, Graduate Committee: Valerie CopieThe tryptophan repressor protein regulates intracellular concentration of Tryptophan in Escherichia coli by binding to DNA operators and is activated in the presence of high L-Trp concentration by formation of an L-Trp-bound holo-repressor. A Leu to Phe mutation at position 75 generates a temperature-sensitive mutant of TrpR, L75F-TrpR, whereas an Ala to Val mutation only two residue positions further on the protein sequence, at residue position 77, generates a super-repressor mutant of TrpR. Backbone amide dynamics studies on TrpR and the two variants using ¹⁵ N-NMR relaxation techniques at a magnetic field strength of 600 MHz (¹ H Larmor frequency) indicate that all three repressors exhibit comparable diffusion properties, implying that they exhibit very similar global shape, structure, and rotational diffusion properties in both apo- and holo- states, in solution. However, internal backbone amide dynamics of the three apo-repressors reveal small but significant differences in flexibility, which are found primarily for residues spanning the Helix-Turn-Helix DNA-binding domain. These results indicate that the fine-tuning of L-Trp binding interaction is modulated in different ways via small but significant changes in protein flexibility in the two TrpR variants in apo and L-Trp bound forms. Sulfolobus solfataricus, a model organism for Archaea, lives in extreme thermal and acidic environments such as the hot springs of Yellowstone National Park, and is host to diverse archaeal viruses including Sulfolobus spindle shaped virus-1 (SSV1) and Sulfolobus spindle shaped virus-Ragged Hills (SSV-RH). SSV viruses exhibit remarkable morphology and genetic diversity, but are poorly understood as many proteins encoded by their genomes have very little sequence homology to proteins of known functions. We have performed detailed backbone dynamics studies to better understand the mode of ligand recognition by E73, a 73-residue, homodimeric protein encoded within SSV-RH genome. Analysis of backbone dynamics measurements obtained for E73 provides evidence for fast time scale dynamics in the proposed nucleic-acid binding site and motion on the microsecond to millisecond time scale in the loop connecting helices alpha A and alpha B.