Doctor of Philosophy / Genetics Interdepartmental Program / Christopher Toomajian / Secondary metabolites (SMs), low molecular weight molecules that are not essential for normal organism growth and development, may confer a selective advantage in some environments. Fungal SMs are structurally and functionally diverse and include mycotoxins, plant regulators and pigments, and the genes that work together in SM biosynthetic pathways are physically clustered in the genome. Fusarium, a genus of filamentous fungi, is noted for SM production, especially mycotoxins, which may contribute to plant pathogenesis. Fusarium species exhibit differences in their SM profiles, and comparative genomics studies have found corresponding differences in the SM gene clusters in some Fusarium species. The investigation of differences in the genomes and SM gene clusters between closely related species, such as F. proliferatum and F. fujikuroi, may help explain their phenotypic divergence, including differences in SM profiles. In addition, the study of intra-species SM variation may indicate how SM loci affect a pathogen’s fitness traits. My research includes three main projects that address different aspects of Fusarium SM variability. To carry out my projects, I established a feasible Genotyping-by-Sequencing (GBS) protocol for Fusarium. One project explored the genetic bases underlying phenotypic divergence related to SM profiles and pathogenicity between F. proliferatum and F. fujikuroi using a quantitative genetics approach. Specifically, I 1) constructed the first high density genetic map based on progeny from an interspecific cross between these two species; and 2) detected a novel regulatory locus for gibberellic acid production and identified a region affecting onion virulence that includes the fumonisin gene cluster. The second project characterized the F. proliferatum parent genome from the previous cross and its SM gene clusters using a comparative genomics approach. Specifically, I 1) assembled the F. proliferatum genome into 12 chromosomes with a combined length of ~43 Mb; 2) annotated this assembly and characterized its 50 SM gene clusters; and 3) detected over 100 F. proliferatum specific genes that might play roles in this species’ host specificity and plant pathogenicity. The third project used a population genomics approach to explore how different F. graminearum chemotypes, or isolates classified based on the accumulation of alternate trichothecene toxin types, may differ for fitness traits and whether trichothecene genes are directly responsible for these differences. Specifically, I 1) genotyped over 300 F. graminearum strains from New York and the upper Midwest in the U.S. and from South America using our GBS protocol; 2) detected two major subpopulations that were correlated, though imperfectly, to the predicted 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes in the U.S.; 3) identified a rapid linkage disequilibrium decay over a few tens of kb followed by a slower decay to background levels over a distance of 200 kb to 400 kb in selected subpopulations in the U.S.; and 4) found that neither chemotype has a clear fitness advantage in a small set of isolates from New York, but that isolates belonging to one genetic subpopulation may on average have a fitness advantage over isolates from the other subpopulation.

Doctor of Philosophy / Genetics Interdepartmental Program / Christopher Toomajian / Secondary metabolites (SMs), low molecular weight molecules that are not essential for normal organism growth and development, may confer a selective advantage in some environments. Fungal SMs are structurally and functionally diverse and include mycotoxins, plant regulators and pigments, and the genes that work together in SM biosynthetic pathways are physically clustered in the genome. Fusarium, a genus of filamentous fungi, is noted for SM production, especially mycotoxins, which may contribute to plant pathogenesis. Fusarium species exhibit differences in their SM profiles, and comparative genomics studies have found corresponding differences in the SM gene clusters in some Fusarium species. The investigation of differences in the genomes and SM gene clusters between closely related species, such as F. proliferatum and F. fujikuroi, may help explain their phenotypic divergence, including differences in SM profiles. In addition, the study of intra-species SM variation may indicate how SM loci affect a pathogen’s fitness traits. My research includes three main projects that address different aspects of Fusarium SM variability. To carry out my projects, I established a feasible Genotyping-by-Sequencing (GBS) protocol for Fusarium. One project explored the genetic bases underlying phenotypic divergence related to SM profiles and pathogenicity between F. proliferatum and F. fujikuroi using a quantitative genetics approach. Specifically, I 1) constructed the first high density genetic map based on progeny from an interspecific cross between these two species; and 2) detected a novel regulatory locus for gibberellic acid production and identified a region affecting onion virulence that includes the fumonisin gene cluster. The second project characterized the F. proliferatum parent genome from the previous cross and its SM gene clusters using a comparative genomics approach. Specifically, I 1) assembled the F. proliferatum genome into 12 chromosomes with a combined length of ~43 Mb; 2) annotated this assembly and characterized its 50 SM gene clusters; and 3) detected over 100 F. proliferatum specific genes that might play roles in this species’ host specificity and plant pathogenicity. The third project used a population genomics approach to explore how different F. graminearum chemotypes, or isolates classified based on the accumulation of alternate trichothecene toxin types, may differ for fitness traits and whether trichothecene genes are directly responsible for these differences. Specifically, I 1) genotyped over 300 F. graminearum strains from New York and the upper Midwest in the U.S. and from South America using our GBS protocol; 2) detected two major subpopulations that were correlated, though imperfectly, to the predicted 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes in the U.S.; 3) identified a rapid linkage disequilibrium decay over a few tens of kb followed by a slower decay to background levels over a distance of 200 kb to 400 kb in selected subpopulations in the U.S.; and 4) found that neither chemotype has a clear fitness advantage in a small set of isolates from New York, but that isolates belonging to one genetic subpopulation may on average have a fitness advantage over isolates from the other subpopulation.

BACKGROUND:Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric.RESULTS:In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.CONCLUSION:A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.

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Nitrofurans have been widely used either in waterbath or feed additives for the prevention and treatment of aquatic products. The European Union was able to assign a maximum residue limit and prohibited nitrofurans used to animals in 1995, because of the potential carcinogenic effects of their residues on human health. This study is focusing on the analytical method of four kinds of commonly used nitrofurans and corresponding residual metabolites by LC-MS/MS. The detection limits of furazolidone, furaltadone, nitrofurazone and nitrofurntoin were 6.11, 3.63, 4.52 and 6.20 £gg kg-1,respectively. The detection limits of AOZ, AMOZ, SC and AH were 0.23, 0.30, 0.36, 0.53 £gg kg-1, respectively. The lightness is the main factor to cause the decomposition of nitrofurans. It is not significant for temperature to depredate nitrofurans. The adsorbtion of metabolites by the plastic tube was in the extraction procedure. Equipments in glass are suggested to be used for the sample pretreatment and plastic meterials are averted to be exercised. About the comparation of determination of AOZ by ELISA and LC-MS/MS. The result demonstrated that the ELISA method might overestimate the residual AOZ content at low concentrations. The detection limit and recovery of the known addition were 0.05 £gg kg-1 and 108% for the LC-MS/MS method and 0.31 £gg kg-1 and 305% for the ELISA method, respectively. The amounts of residual nitrofurans and metabolites in muscle, liver, gill and skin tissue of tilapia which were treated in different conditions were compared. The depletion data of bathing treatment group obtained showed similar be haviors of furazolidone, furaltadone, nitrofurazone, nitrofurantoin in tilapia which the residual time was less than 24 hr. The amounts of residual nitrofurans appeared the highest concentration in gill and the lowest concentration in muscle. Bonded residues of metabolites can be detected for at least 4 weeks after administration in muscle, skin, liver and gill. The concentrations of residual bonded metabolites were higher than non-bonded metabolites in gill and muscle besides liver during depletion periods. After bathing medication, there were more residual nitrofurans and corresponding metabolites in sea water tilapia than fresh water group, because sea water fish survives in high osmotic condition to reduce their urination. Nitrofurans and metabolites were deconstructed by enzyme in gills, livers, intestines and muscles. Then tissues of fish accumulated nitrofurans and metabolites soon after medication. The maturity of fish is one of facters to effect different residual concentration during depletion periods. Liver is the main tissue to deconstruct nitrofurans and metabolites for the bathing medication and intestine is the major tissue to decompose antibiotics for the feeding medicaton. In this research, we built a completed way to determine nitrofurans and corresponding metatbolites. Comparation of fish in different conditions and different medicative ways were in this investigation. These results could be helpful for aquacultures and government institutions.

This thesis is divided into two parts and covers biosynthetic studies on two secondary metabolites, tropic acid in Part I and piliformic acid, in Part II.(S)-Tropic acid is the acid moiety of the alkaloids hyoscyamine and scopolamine, which are produced by a number of plants of the Solanacae family. An intriguing rearrangement of the L-phenylalanine side chain gives rise to the isopropanoid (S)-tropic acid skeleton. The detailed nature of the rearrangement has however remained elusive despite continued interest over the years. In chapter two the identification of intermediates between L-phenylalanine and (S)-tropic acid is discussed, which has placed (R)-D-phenyllactic acid as an immediate precursor. The stereochemical features of the rearrangement are described in chapter 3 and finally in chapter 4 a mechanism for the rearrangement is proposed. This is based on information obtained from the incorporation of various isotopically labelled precursors to tropic acid into two of the minor alkaloids, 3a-2'-hydroxyacetoxytropane and 3a- phenylacetoxytropane. This work was carried out in collaboration with Dr Richard Robins at the AFRC Institute of Food Research in Norwich. Piliformic acid is elaborated by the slow growing fungus Poronia piliformis. The incorporation of a number of isotopically labelled substrates into piliformic acid has revealed a mixed biosynthetic origin, comprising C(_8) and C(_3) fragments. These have been shown to be of acetogenic and citric acid cycle origins respectively. The C(_8) fragment has been further demonstrated to be a degradation product of a longer chain fatty acid. The mode of coupling of the two fragments has been investigated and suggests the intermediacy of a novel a-carboxyoctanoate. A pathway for the assembly of piliformic acid, involving a 1,3-hydrogen shift, is proposed, consistent with the above findings. These results are the subject of chapter 6.

INTRODUCTION: Major depressive disorder (MDD) is characterized by ongoing feelings of guilt, sadness, and memory and cognition impairment. It is a multidimensional illness that affects many functionally integrated pathways of the brain. Understanding the underlying brain dysfunction that gives rise to this complex illness has been challenging, and by extension the search for appropriate treatments. MDD patients who are considered treatment resistant make up the primary population that receives electroconvulsive therapy (ECT). Remarkably, ECT shows a 75% remission rate in this patient population and is considered the “gold standard” treatment for major depression. Although the exact mechanism of its function is unknown, it is well accepted that the induced grand-mal seizure confers its therapeutic effect. The seizure likely has broad effect that somehow corrects the underlying dysfunction in brain circuitry. Here, we specifically examined studies of functional connectivity and metabolite changes. METHODS: Through literature search, we examined six studies in functional connectivity and four studies in magnetic resonance spectroscopy (MRS). RESULTS: Functional Connectivity: Studies have found that after bilateral ECT treatments, patients with major depression showed reduction of functional connectivity (FC) from the left dorsolateral prefrontal cortex (DLPFC) to other cortical and limbic structures. Correlated activity between the superior frontal gyri, middle frontal gyri and angular gyri were significantly increased after ECT. Hyperdeactivation of the orbitofrontal cortex to negative emotional stimuli in patients was decreased, and it was associated with improvement in depressive symptoms. Regional activity in the subgenual anterior cingulate cortex (sgACC) and functional connectivity between the sgACC and left hippocampus in treatment naïve patients after ECT were increased and correlated to reduction of depressive symptoms. Reduced connectivity between the amygdale and sgACC and increased connectivity between the amygdale and DLPFC was found by sequential assessments over a course of ECT treatments. Lastly, ECT increased the functional connectivity between DLPFC and the default mode network. MRS: Studies found decreased levels of glutamate or glx (glutamate/glutamine/ GABA) in patients in the anterior cingulate cortex and dorsolateral prefrontal cortex (DLPFC) compared to healthy controls. Additionally, it was found that glx levels increased after ECT treatments and that this increase was only in those who responded to treatment. Lastly, GABA level increased after ECT treatment in the occipital cortex. Discussion: Results from functional connectivity and brain metabolite studies in patients with major depression point to induced neuroplasticity as part of ECT’s therapeutic mechanism. Remodeling connectivity and mediating metabolite changes both will require modifications at the synaptic level. The wide spread changes seen in several different brain regions that have been implicated in depression further suggests that ECT’s effects are both highly specific and broad. CONCLUSION: Electroconvulsive therapy has consistently demonstrated impressive efficacy among the most severely depressed patients and is known to produce widely distributed effects in the brain. However, this also makes assessing its therapeutic mechanism challenging. Magnetic resonance imaging studies assessing functional connectivity and brain metabolite levels have demonstrated that ECT likely produces neuroplastic changes to remodel aberrant connectivity and dysfunctional excitatory and inhibitory neurotransmission in cortical and limbic areas. Although these findings should be interpreted with caution, this field of research has provided an unprecedented opportunity to examine the living brain in great detail. Further studies with larger sample sizes and improved technical specifications will likely yield greater results.

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