The conserved metabolites, oleic acid (18:1), a major monounsaturated fatty acid (FA), and glycerol-3-phosphate (G3P) are obligatory precursors of glycerolipid biosynthesis in plants. In Arabidopsis, the SSI2-encoded SACPD is the major isoform that contributes to 18:1 biosynthesis. Signaling induced upon reduction in oleic acid (18:1) levels not only upregulates salicylic acid (SA)-mediated responses but also inhibits jasmonic acid (JA)- inducible defenses. I examined the transcription profile of ssi2 plants and identified two transcription factors, WRKY50 and WRKY51. Although the ssi2 wrky50 and ssi2 wrky51 plants were constitutively upregulated in SA-derived signaling, they were restored in JAdependent defense signaling. Not only did these plants show JA-inducible PDF1.2 expression, but they were also restored for basal resistance to the necrotrophic pathogen, Botrytis cinerea. Overall, my results show that the WRKY50 and WRKY51 proteins mediate both SA- and low 18:1-dependent repression of JA signaling in Arabidopsis plants. My studies also show that cellular G3P levels are important for plant defense to necrotrophic pathogens. I showed that G3P levels are induced in Arabidopsis in response to the necrotrophic fungal pathogen B. cinerea. G3P-dependant induction of basal defense is not via the activities of other defense-related hormones such as SA, JA or the phytoalexin camalexin. Arabidopsis mutants unable to accumulate G3P (gly1, gli1) showed enhanced susceptibility to B. cinerea. Previous studies in our lab identified acyl-carrier protein 4 (ACP4), a component of FA and lipid biosynthesis, as an important regulator of plant systemic immunity. ACP4 mutant plants were defective in systemic acquired resistance (SAR) because they contained a defective cuticle. I further investigated the role of the plant cuticle in SAR by studying the involvement of long-chain acyl-CoA synthetases (LACS), a gene family involved in long-chain FA and cuticle biosynthesis, in SAR. In all, eight lacs mutants (lacs1, lacs2, lacs3, lacs4, lacs6, lacs7, lacs8, lacs9) were isolated and characterized. Six mutants were compromised in SAR. Together, my studies show that the various LACS isoforms contribute differentially to both cuticle formation and systemic immunity in Arabidopsis.

Identification of allelic variation through quantitative trait loci (QTL) mapping offers possibilities for the improvement of quantitatively inherited traits. This requires a genetic map along with the phenotypic characterization of a mapping population. A doubled haploid (DH) Polo X Topas population consisting of 194 lines and a recombinant inbred line population of 92 lines was developed. Individual genetic maps derived from each population were integrated into a consensus map. The DH-based genetic map was used for QTL mapping. The DH-based map was comprised of 620 loci that were assembled into 19 linkage groups that were anchored to the B. napus chromosomes. The DH-based map covered 2244.1 cM genomic distance with an average marker interval of 3.7 cM. The DH population was phenotyped in four environments with each line replicated twice in a randomized complete block design. Days to flowering was recorded and oil content and fatty acid composition were determined using Near Infrared spectroscopy (NIR) and Gas Chromatography, respectively. Fourteen QTL were identified for oil content, 33 QTL for palmitic acid content, 18 QTL for stearic acid content, 21 QTL for oleic acid content, 20 QTL for linoleic acid content, 23 QTL for linolenic acid content, 16 QTL for arachidic acid content and 14 QTL for flowering time. Oil content QTL were identified on five linkage groups, A3, A10, C1, C5, and C6. An oil content QTL, qOIL-A10c appeared in all four environments, whereas qOIL-A10a appeared in only one environment but explained 26.99% variation. The oil content in the population ranged from 35% to 55.5% with the parents having values of 42% to 46%. Two genomic regions on C3, with map positions at 147.83 cM and 154.55 cM harbored QTL (rQTL) for all the fatty acids studied. The additive effects of the rQTL reveal a correlation pattern which is supported by the phenotypic correlation observed between the fatty acids. This suggests rQTL have role in the fatty acid composition and possibly determine total seed oil content. The rQTL and flanking markers of the identified QTL offer utility in further development of B. napus. / October 2015

Rhamnolipids are surface-active molecules produced by Pseudomonas aeruginosa as congener mixtures. They are considered “green” alternatives to synthetic surfactants used in many applications. Optimizing yield and controlling congener distribution are necessary steps for successful commercialization. Studies have noted that vegetable oils, composed of a mixture of fatty acids, increase rhamnolipid yield. The physiological explanation for this is not yet understood. Furthermore the exact effects of various fatty acid components in the oils on rhamnolipid production have not been reported. The first part of the dissertation was to investigate rhamnolipid biosynthesis when fatty acid substrates are present. A combination of stable isotope tracing and gene expression assays were used to identify rhamnolipid lipid precursors and potential lipid metabolic pathways used in rhamnolipid synthesis. Result suggests that an octanoyl-CoA intermediate of β-oxidation is diverted from β-oxidation to de novo fatty acid synthesis via a “bypass route”, and is incorporated into either a 2-carbon or a 4 carbon β-ketoacyl- ACP, which can then be recognized by the RhlA enzyme for the biosynthesis of rhamnolipid lipid moiety. The second part of the dissertation focuses on studying how fatty acid substrates of different chain length (C₁₂ to C₂₂) and saturation (C(18:1) and C(18:2)) affect rhamnolipid yield, carbon conversion rate, and congener distribution. Results showed that stearic acid significantly increased rhamnolipid yield. A positive linear correlation between the mass percent of stearic acid used and the carbon conversion rate was observed. For all treatments, the RhaC₁₀C₁₀ was the most abundant and RhaC₁₀C(12:1) was the least abundant of the major congeners produced. However, the relative amounts of RhaC₁₀C₈ and RhaC₁₀C₁₂ congeners were dependent on several factors. In general, fatty acid substrates with relatively short chain length (C₁₂ and C₁₄), the unsaturated fatty acid C(18:2), and longer cultivation times resulted in a higher RhaC₁₀C₈/ RhaC₁₀C₁₂ ratio. The studies presented here demonstrate that the medium composition, in particular the organic substrate component, can affect rhamnolipid biosynthesis, yield, and congener distribution. Furthermore, this work presents evidence that C₁₈ fatty acids as co-substrates increase rhamnolipid yield by draining rhamnolipid intermediates directly from the β-oxidation pathway.

Microalgae has shown to be an ideal choice for biofuel industry. Algae has high oil productivity, a short growth cycle and survives in a wide variety of water sources including high salinity and waste water. For this project, four different species of marine microalgae were screened based on oil content. They were Dunaliella tertiolecta (CCMP364), Nannochloropsis gaditana (CCMP527), Tetraselmis sp (CCMP 908) and Nannochloropsis salina (CCMP1776). Experimental results showed that CCMP 527 and 1776 strains had higher lipid content and better fatty acids profile than the other two. Further investigations were carried on CCMP 527 in order to maximize biomass productivity and lipid content. Nutrients, salinity, pH, temperature, light intensity and aging of the culture can all affect both lipid content and fatty acid profile and were investigated. Nutrient stress is the easiest way to manipulate lipid composition and increase lipid content. Hence, various carbon and nitrogen sources were investigated to determine the range and amount of substrates that may be feasible for cultivation. For supplying lipid for biodiesel production, the optimum culture conditions for strain Nannochloropsis gaditana are using CO₂ enriched air bubbling, f/2-Si medium, pH control, and nitrate as the nitrogen source. Use of other fertilizers is feasible as well, however, the nitrogen source greatly affects lipid productivity, but trace amounts of organics in ground water do not.A model which predicts cell growth, nitrogen concentration, and lipid yield in batch systems is developed that is applicable for low nitrogen conditions. Plus, a sensitivity analysis of three major parameters was done to validate how variations in these key parameters affect simulation results. The fatty acid profile as a function of time was shown not to vary from mid-exponential to stationary phase. The model describes reactor behavior well, therefore it can be applied to the genus of Nannochloropsis to predict biomass yield and lipid accumulation, and be a useful tool to optimize and compare bioreactor systems for the biofuel industry. In addition, effects of nitrate and urea under repletion condition on microalgae growth, lipid yield and fatty acids profile for microalgae Nannochloropsis gaditana were investigated. Replacing nitrate by urea didn't show positive influence on lipid content and yield compared to normal medium. The major fatty acids for these two mediums were palmitic acid (C16:0) and palmitioleic acid (C16:1). Nannochloropsis gaditana still shows to be ideal candidate for biodiesel production using urea or nitrate enriched agriculture wastewater.

One of the cellular responses to temperature fluctuations in plants is the adjustment in the degree of membrane unsaturation. Glycerolipids are major constituents of cellular membranes. In higher plants, glycerolipids are synthesized via two major metabolic pathways compartmentalized in the ER and chloroplast. Adaptive responses in membrane lipids include alterations in fatty acid desaturation, proportional changes in membrane lipids as well as molecular composition of each lipid species. In this study, I systematically explored the significance of glycerolipid pathway balance in temperature induced lipid composition changes in three plant species that have distinctive modes of lipid pathway interactions through a combination of biochemical and molecular approaches including lipidomics and RNA-seq analysis. In Arabidopsis thaliana, a 16:3 plant, low temperature induces an augmented prokaryotic pathway, whereas high temperature enhances the eukaryotic pathway. Atriplex lentiformis reduces its overall lipid desaturation at high temperature and switches lipid phenotype from 16:3 to 18:3 through drastically increasing the contribution of the eukaryotic pathway as well as suppression of the prokaryotic pathway. In sync with the metabolic changes, coordinated expression of glycerolipid pathway genes, as revealed by RNA-seq also occurs. In Triticum aestivum, an 18:3 plant, low temperature leads to a reduced glycerolipid flux from ER to chloroplast. Evidence of differential trafficking of diacylglycerol (DAG) moieties from ER to chloroplast was uncovered in three plant species as another layer of metabolic adaptation under different temperatures. Taken together, this study has established a biochemical basis that highlights the predominance and prevalence of lipid pathway interactions in temperature induced lipid compositional changes.

The rehabilitation of degraded soils, such as those associated with post-mining sites, requires knowledge of the soil ecosystem and its physical, chemical, and biological composition in order for rehabilitation efforts to fulfil the long-term goal of reconstructing a stable ecosystem for rehabilitated mine soil. This study addresses the need for appropriate assessment criteria to determine the progress of rehabilitation and subsequently the success of management practices. Significant contributions made by this investigation included the establishment of minimum and maximum values for microbial community measurements from two case studies of rehabilitated coal discard sites. Furthermore, it was shown that there was no relationship between changes in microbial community function and structure and the rehabilitation age of the sites. Following this, the considerable impact of management practices on microbial communities was illustrated. The first part of the study investigated the temporal changes in microbial community function and structure in a chronosequence of rehabilitated coal discard sites aged 1 to 11 years. The most important observation made during the investigation of the microbial communities in the different aged soil covers of the rehabilitated coal discard sites, was that there was no relationship between rehabilitation age and microbial activity or abundance of certain microbial groups. What was responsible for a clear differentiation between sites and a shift in microbial community attributes was the management practices applied. A comparison of two chronosequences of rehabilitated coal discard sites was achieved by an application of the 'space-for-time' hypothesis. Sites of different ages and at separate locations ('space') were identified to obtain a chronosequence of ages ('time'). The two chronosequences included sites aged 1 to 11 years (chronosequence A) and 6 to 17 years (chronosequence B), respectively. Sites in the same chronosequence were managed identically, while there was a distinct difference in management practices applied to each chronosequence. The long-term effect of the different management regimes on the soil microbial community function and structure was investigated. Again, there was no relationship between rehabilitation age and microbial community measurements. Fluctuations of selected microbial properties occurred in both chronosequences and similar temporal trends existed over the rehabilitation periods. However, the less intensively managed chronosequence (8) seemed more stable (less fluctuation occurred) over the rehabilitation period than the more intensively managed chronosequence (A). It was therefore concluded that the microbial communities in the less managed sites maintained their functional and structural integrity within bounds in the absence of management inputs or disturbance. While there was similarity in the trends over time for individual microbial community measurements, the seemingly more stable conditions in chronosequence 6 are important in terms of the goal of rehabilitation. / Thesis (Ph.D. (Environmental Science)--North-West University, Potchefstroom Campus, 2007

Polyunsaturated fatty acids are major structural components of plant chloroplast and endoplasmic reticulum membranes. Two fatty acid desaturases (designated FAD2 and FAD3) desaturate 75% of the fatty acids in the endoplasmic reticulum. The w -6 fatty acid desaturase (FAD2) may be responsible for cold acclimation response, since polyunsaturated phospholipids are important in helping maintain plant viability at lowered temperatures. To study regulation of FAD2 gene expression in cotton, a FAD2 gene was isolated from two genomic libraries using an Arabidopsis FAD2 hybridization probe and a cotton FAD2 5¢ -flanking region gene-specific probe, respectively. A cotton FAD2 gene was found to be in two overlapping genomic clones by physical mapping and DNA sequencing. The cloned DNA fragments are identical in size to cotton FAD2 genomic DNA fragments shown by genomic blot hybridization. The cotton FAD2 coding region has 1,155 bp with no introns and would encode a putative polypeptide of 384 amino acids. The cotton FAD2 enzyme has a high identity of 75% with other plant FAD2 enzymes. The enzyme has three histidine-rich motifs that are conserved in all plant membrane desaturases. These histidine boxes may be the iron-binding domains for reduction of oxygen during desaturation. To confirm that this FAD2 enzyme is functional, a plasmid construct containing the cotton FAD2 coding region was transformed into Saccharomyces cerevisiae. The transformed yeast cells were able to catalyze the conversion of oleic acid (C18:1) into linoleic acid (C18:2). The FAD2 gene contains an intron of 2,967 bp in its 5¢ -flanking region, 11 bp upstream from the initiation codon. The intron could be essential for transcriptional regulation of FAD2 gene expression. Several putative promoter elements occur in the 5¢ -flanking region of this gene. A potential TATA basal promoter element occurs at 41 bp upstream from the cap site. Two presumptive helix-loop-helix (bHLH) motifs that may be seed-specific promoter elements are located at 109 bp and 135 bp upstream from the potential cap site.

The field of lipidomics encompasses the study of pathways, networks, and functionality of cellular lipids in biological systems. The lipid subclass, primary fatty acid amides, are crucial to nervous system signaling, receptor function, and numerous other physiological roles. Chapter 1 details these bioactive properties of several well-studied primary fatty acid amides as well as their biosynthesis, degradation, and most common analysis techniques. As these bioactive lipids are endogenously present in trace and ultra-trace abundancies, the field of microfluidics presents an attractive alternative analysis system to incorporate minimization of sample and reagent usage, analysis cost reduction, highly sensitive detection pairing, and decreased analysis time, all while limiting sample handling. Chapter 2 provides a microfluidics-based review of common device fabrication techniques, droplet microfluidics, and detection systems. Current primary fatty acid amide analysis techniques have detection limits on the periphery of endogenous concentrations, presenting the need for a more sensitive detection system, such as fluorescence. Chapter 3 serves as the foundation in developing methodology to analyze these amides and their conjugate fluorescently-tagged primary amines. Chapter 4 focuses on the development of a microfluidic platform capable of efficient on-chip fluorescent tagging reactions and the coupling of a highly sensitive laser induced fluorescence detection system capable of detection limits several orders of magnitude lower than currently employed mass spectrometry techniques. In addition, the appendix details the method development for the quantitative analysis of the anti-inflammatory and anti-cancer drug, celecoxib, uptake into novel drug delivery vehicles. / Bayer School of Natural and Environmental Sciences; / Chemistry and Biochemistry / PhD / Dissertation;

No description available.

Dairy farmers in the Northeastern Unites States are paid based on the amount of fat and protein in their cows' milk, and improving fat and protein production is linked with improved financial sustainability for dairy farms. However, not all farmers are motivated to make changes to increase milk fat and protein production. Previous research has identified a positive correlation between a group of fatty acids, known as the de novo fatty acids, and the fat and protein content of bulk tank milk from commercial dairy farms. Therefore, the first objective of this research was to explore the relationship of farm management, the cow's diet, and lactation performance with de novo fatty acid content on Northeastern US dairy farms. Results from the first objective were communicated with dairy farmers; therefore, the second objective was to understand how to communicate with farmers to influence their behavior. We hypothesized that farms with high de novo fatty acids in bulk tank milk would manage and feed their cows to optimize rumen fermentation conditions. The first (Chapter 2) and second (Chapter 3) studies were methodologically very similar. Farms were categorized as either high de novo (HDN) or low de novo (LDN) based on the concentration of de novo fatty acids in their bulk tank milk for the 6 months prior to the farm visit. Farms were then visited once in March or April, 2014 (Chapter 2) or between February and April, 2015 (Chapter 3) to assess management practices and collect samples of the cows' diet. There were no differences in days in milk in Chapter 2 or Chapter 3. Yield of milk, fat, and true protein per cow were higher for HDN versus LDN farms in Chapter 2. In both chapters, HDN farms had higher milk fat and true protein content and higher de novo fatty acid yield per day. The HDN farms had lower freestall stocking density in Chapter 2 and provided more feedbunk space per cow in Chapter 3. Additionally, tiestall feeding frequency was higher for HDN than LDN farms. No differences were detected for dietary chemical composition, except ether extract was lower for HDN than LDN farms in both chapters. Chapter 4 explored how to communicate the results of Chapter 2 and Chapter 3 through eleven qualitative, semi-structured interviews and insight from the 83 farm visits. Farmers identified the cooperative, expert consultants (nutritionist, veterinarian, and agronomists), financial advisers, print publications, and other farmers as principal sources of information. However, barriers to the transfer of information included family dynamics, lack of access to high speed internet, and difficulties evaluating divergent recommendations from experts. Several farmers expressed an incorrect perception of their farms' fat and protein production compared with cooperative averages which reduced their motivation to incorporate management changes. Recommendations to overcome these barriers include integrating management team meetings and facilitating informal discussion groups between farmers. This research is correlational in nature, and future research is needed to verify a causal relationship between de novo fatty acids and milk fat and protein content. However, the results of this research can be used to help farmers increase their cows' milk fat and protein content, improve the transfer of knowledge to dairy farmers, and ultimately support the financial sustainability of dairy farms in the Northeastern US.