Prophylactic and therapeutic antibiotic treatments have the potential to increase excretion of antibiotic resistance genes (ARGs) by dairy cattle through selection pressure on the gut microbiome. The objective of these studies was to evaluate the effect of cephapirin benzathine administered prophylactically at the end of lactation and pirlimycin hydrochloride administered therapeutically during a clinical mastitis infection on the abundance and relative abundance of ARGs in dairy cow feces. For prophylactic treatment using cephapirin benzathine, nineteen end-of-lactation cows were used. Treatment cows (n = 9) received cephapirin benzathine as an intramammary infusion prior to dry-off, and control cows (n =10) received no antibiotics. All cows received an internal non-antibiotic teat sealant. Fecal grab samples were collected for each cow on d -2 (baseline, used as covariate), d 1, 3, 5, 7, and once per week until d 49. Fecal samples were collected in sterile containers, then freeze-dried and subject to DNA extraction. The abundance of ampC, blaCMY-2, ermB, sul1, tetO, tetW, integrase-specific gene int1, and 16S rRNA were quantified using quantitative polymerase chain reaction (qPCR). The genes ampC and blaCMY-2 encode resistance to ß-lactam antibiotics, ermB to macrolides, sul1 to sulfonamides, tetO and tetW to tetracyclines, and int1 a class-1 integrase gene that facilitates horizontal transfer of ARGs across bacteria. The 16S rRNA gene was used as a representation of bacterial population. Absolute abundance was defined as number of ARG copies per gram of freeze-dried feces, while relative abundance was defined as ARG copy numbers per copy of 16S rRNA gene, which is indicative of the proportion of bacteria carrying ARGs. Non-normal data were logarithmically transformed and were statistically analyzed using PROC GLIMMIX in SAS 9.2. Abundance and relative abundance of sul1 and blaCMY-2 were below the limit of quantification in most samples and therefore not suitable for statistical comparisons. The int1 gene was not detectable in any sample. There were significant interactions between treatment and day for the abundance and relative abundance of ampC, tetO, and tetW. The abundance and relative abundance of ampC increased with time in control cows while remaining constant in antibiotic treated cows through the dry period. Antibiotics may act to stabilize the gut microbiome in response to diet and housing changes. There was a significant main effect of treatment for ermB with a significantly greater proportion of bacteria carrying ermB in control cows when compared to antibiotic treated cows. The tetracycline resistance genes tetO and tetW behaved similarly with a significant treatment by day interaction for the abundance and relative abundance of both genes. The relative abundance of both tetO and tetW were greater in control cows when compared to antibiotic treated cows on days 3, 5, 7, and 14. The abundance of both tetO and tetW resistance genes increased in antibiotic treated cows from day 1 to 49. There was also a significant increase in tetW relative abundance when comparing day 1 to 49. Administering long-acting antibiotics as intramammary dry treatment changed fecal bacteria composition during the dry period perhaps by stabilizing GI bacteria through dietary and housing changes. However, the use of prophylactic dry cow treatment does not uniformly or predictably lead to changes in fecal ARGs. In a second study, after clinical mastitis detection and identification, 6 lactating dairy cows received therapeutic mastitis treatment (pirlimycin hydrochloride as an intramammary infusion). Fecal grab samples were collected from each cow on d 0, 3, 9, and 12. Collection and analytical methods were as previously described. Abundance and relative abundance of sul1 and blaCMY-2 were again below the limit of quantification and therefore not suitable for statistical comparison. The int1 gene was not detected in any sample. The abundance of 16S rRNA genes decreased with day and relative abundance ermB, tetO, and tetW increased with day. There was no significant effect of day on the relative abundance of ampC or the abundance of ampC, ermB, tetO, and tetW in feces of cows with clinical mastitis. Administering fast-acting antibiotics as therapeutic intramammary mastitis treatment to dairy cows increased the relative abundance (gene copies per 16S rRNA) of selected ARGs but not the total abundance of ARGs in feces. The use of antibiotics for prevention and treatment of bacterial infections does not uniformly or predictably increase ARGs. / Master of Science

Switchgrass (Panicum virgatum) is a native warm-season grass where weed control during establishment is a limiting factor for stand. Objectives of this research are to develop a herbicide resistant cultivar and to test a variety of seed safeners to improve first year growth. Phenotypic recurrent selection (PRS) was used to select ‘Alamo’ switchgrass seedlings that showed resistance to imazapic herbicide at 245 g a.i./ha. Initial screenings of 364, 650 seedlings resulted in 63 survivors, a selection intensity of 0.0172%. Subsequent testing of the next generation of seedlings indicated that multiple generations of selection were needed in order to transfer greater resistance to the offspring. Seed safener testing consisted of three trials. Field data taken included emergence counts, weed control ratings, and end of season harvest. Results showed fluxofenin (a.i. in Concep III) as being only safener providing protection against metolachlor (83.7% a.i.).

Salt-affected soil is a prominent challenge in agriculture. Nowadays, more than 800 million hectares of land (about 6% of the world’s total land area) are induced with high salt concentrations, and thus, are unsuitable for growing typically salt-sensitive crop plants. The ongoing salinization of arable land exacerbates this limitation. To address this issue, the development of salinity-tolerant crop plants has gained considerable interest, with a protein identified by Prof. Mark Tester's group, named "SALTY2," offering promising potential. SALTY2 is overexpressed in response to NaCl treatment on Salicornia plants conferring salinity tolerance, and following the function of the SALTY2 protein from Salicornia and analogous proteins in Arabidopsis, yeast and in vitro, a universal mechanism in evolution is suggested. During my thesis, we analyzed the biophysical properties of SALTY2, and based on spectroscopic methods we confirmed it is an intrinsic disordered protein (IDP), which is consistent with previous studies claiming that IDPs play a vital role in stress response pathways. We have identified and characterized the loss-of-function "RG/RGG" to "KG/KGG" type mutation and a deltaSTM1 N-terminal mutation, and investigated the interaction of SALTY2 and other cellular components, including short fragment RNA, and 80S ribosome. Together with state-of-the-art high-resolution NMR and Cryo-EM methods we validated the direct interaction of SALTY2 with plant ribosomes, and 25nts random RNA, and determined the 3D structure of ribosome with the potential binding site of the SALTY2 protein. Combining biophysical, structural and functional analyses of the wild-type and loss-of-function mutants of SALTY2, we proposed a potential mechanism by which the IDP protein SALTY2 confers salinity tolerance in plants. These findings offer a deeper understanding of the molecular basis of salinity tolerance in plants via IDPs and contribute to the ongoing efforts to develop salinity-tolerant crop plants.

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