<p> This work focuses on members of the Boletales. This order is comprised of a morphological and ecologically diverse set of species. While the vast majority of species are pileate-stipitate with pores and have a mutualistic nutritional strategy ectomycorrhal (ECM), there are resupinate and gilled species, and saprotrophs and mycoparasites as well. In the first chapter, we review the ecological niche occupied by <i>Boletinellus merulioides. </i> This species was originally considered to be ECM, the symbiont to <i> Fraxinus americana.</i> This hypothesis was rejected, and replaced by the possibility of a mutualism with an <i>F. americana</i> aphid pest, <i>Prociphilus fraxinifolii.</i> We present the first study that observed all three species, since the original publication, the first molecular data for each species, and isotopic fractionation results for <i> B. merulioides</i> and <i>P. fraxinifolii.</i> Additionally, we describe a new morphology for sclerotia of <i>B. merulioides.</i> In total, we are unable to reject the possibility of a facultative mutualism between <i>B. merulioides</i> and <i>P. fraxinifolii.</i></p><p> Chapters two through five review systematics in the <i>Boletineae. </i> Chapter two presents the most comprehensive phylogenetic review of the <i>Boletineae,</i> at the time publication, and remains one of the most inclusive <i>Boletineae phylogenies.</i> Three genes, nuclear large subunit, translation elongation factor 1-alpha, and DNA directed RNA polymerase II largest subunit, were used. This chapter is a summary of <i> Boletineae</i> taxonomy and morphological characteristics, with a clade by clade analysis. We present compelling evidence for the mycoparasitic nutritional mode of <i>Buchwaldoboletus lignicola.</i> Additionally, we found that <i>Chalciporus piperatus,</i> a close relative of <i> B. lignicola</i>, is likely to be a mycoparasite. We present strong evidence that the genus <i>Boletus</i> is limited to single clade that contains approximately 10% of the validly published <i>Boletus</i> species. </p><p> A subset of the taxa sampled in chapter two was used in the phylogenies presented in chapters three, four, and five. Each of these chapters reviews the phylogenetic placement of traditionally problematic species/genera; <i> Surotius eximius, Harrya chromapes</i> and allies, and the Boletaceae species with longitudinally striated spores. These groups have been in multiple. Our results show that <i>Sutorius</i> and <i>Harrya</i> species are distinct from other Boletacaea species and that the longitudinally striated species have been lumped together. By correcting taxonomic confusion and using a multigene data set we are able to resolve these problematic species, and provide a path for future systematics and evolutionary analysis.</p>

<p> Most plants harbor microbial symbionts, which often affect host performance and fitness. Endophytic <i>Epichlo&euml;</i> species are systemic fungal microbial symbionts of many cool-season pooid grasses. Benefits to the host from <i>Epichlo&euml;</i> infection include increased resistance to stressful environmental factors, such as drought and limited soil nutrients, due to morphological and physiological changes. The major benefit of <i> Epichloe</i> infection is enhanced protection against herbivory due to production of fungal alkaloids. The fungal alkaloids have varying activity against invertebrate or mammalian grazers. Although <i>Epichlo&euml; </i> endophytes are well-studied in agronomic grasses such as tall fescue and perennial ryegrass, little is known about the how the presence of different endophyte species and their frequencies and distribution are related to environmental factors in native grasses. Using two native grasses to eastern [<i>Poa alsodes</i> (Grove Bluegrass)] and western [<i>Achnatherum robustum </i> (Sleepygrass)] North America, I addressed the following questions: 1) how are endophyte species distributed among populations along a latitudinal gradient, 2) what fungal alkaloids are produced by different endophyte species, 3) how do fungal alkaloids affect insect herbivores, and 4) what are the effects of different endophytes on host plant growth? (Abstract shortened by ProQuest.) </p>

<p> During leaf senescence nutrients are mobilized towards newly developing vegetative and reproductive structures. The IAOx pathway that produces auxin and defense molecules [indole glucosinolates (IGs) and camalexin] is up-regulated during senescence. To investigate the role of the IAOx metabolites we isolated two independent cyp79B2/cyp79B3 double mutants, which are deficient in IGs and camalexin and had reduced auxin levels. Chlorophyll, protein, and gene expression data indicate that cyp79B2/cyp79B3 mutants display early leaf senescence. Furthermore, leaves accumulated higher levels of hydrogen peroxide and seed production was significantly reduced. Auxin signaling at hydathodes and vascular tissue decreased as leaves aged, even though endogenous auxin levels increased. Since CYP79B2/CYP79B3 play only a minor role in auxin synthesis, it is most likely that IGs and/or camalexin are playing a protective role during age-induced developmental leaf senescence. Identifying molecules that slow down the rate of senescence may allow for genetic manipulation to increase nutritional value and crop yield</p>

<p>Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.

<p> Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The <i>Suessiales</i> were found to be sister to the <i>Peridinales.</i> The <i>Prorocentrales </i> formed a monophyletic group with the Dinophysiales that was sister to the <i>Gonyaulacales.</i> The <i>Gymnodinales</i> was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.</p>

<p> Plants produce a variety of small molecules, including those essential for survival in all conditions (primary metabolites) or for more ecologically specific conditions (secondary metabolites). While primary metabolic pathways are broadly shared among plants, secondary metabolism is under constant selective pressure towards chemical innovation, given the continual fluctuation of the environment. Thus, plant secondary metabolism - whose constituents number in the hundreds of thousands - is lineage-specific, highly structurally diverse, and ultimately of high value to medicine, agriculture, and industry. Efforts to optimize the production of specific metabolites or to discover new compounds remain difficult primarily due to inadequate understandings of the metabolic genes involved and how these genes are regulated. This work first examines co-regulation, a major form of organization by which plant secondary metabolic genes are organized. In response to the bacterial crop pathogen <i>Pseudomonas syringae, Arabidopsis thaliana</i> and its relatives in the mustard family produce numerous secondary metabolites from the amino acid tryptophan, including the antimicrobial compound camalexin. However, hundreds of biosynthetic genes of unknown function are also simultaneously upregulated. Using metabolic profiling and co-expression analysis, I helped to identify the complete biosynthetic pathway to the indole-3-carbonylnitriles (ICNs), a previously unknown class of compounds. When the cytochrome P450 gene <i>CYP82C2</i> is mutated, biosynthesis of the compound 4-hydroxy-ICN (4OH-ICN) is abolished, and plant defense against <i>P. syringae</i> is impaired. Conversely, addition of 4OH-ICN to plants is sufficient to suppress bacterial growth. Next, this work examines the evolution of camalexin and 4OH-ICN metabolism. Cytochrome P450-directed secondary metabolism has been shown almost without exception to be evolutionarily derived from changes to enzymes with broad substrate specificity. By contrast, I observe through genetics, enzyme phylogenetic analysis, and transient expression assays that the ICN and camalexin biosynthetic pathways evolved from a common chemical substrate. In particular, changes to camalexin catalysis by the newly duplicated gene <i>CYP71A12</i> led to the formation of ICN metabolism in several mustard species, although both compounds are directly derived from indole cyanohydrin. Furthermore, 40H-ICN is an extremely recently evolved metabolite, derived from a flurry of genic, epigenetic and transposon-mediated rearrangements of a yet-more recent gene duplicate (<i>CYP82C2</i>). These regulatory changes to <i>CYP82C2</i> lead to its pathogen-inducibility solely in the species <i>A. thaliana</i>. I additionally identify WRKY33 and MYB51 as two sets of defense regulators that carefully fine-tune 40H-ICN metabolism by direct biosynthetic gene regulation. WRKY33 transcription factor, which is involved in the species-specific regulation of <i>CYP82C2</i>, is conserved throughout flowering plants, indicating that transcriptional recruitment is an important feature in the expansion of secondary metabolism. Finally, this work probes possible molecular functions of 40H-ICN and camalexin by exploring the molecular mechanisms underlying their secretion from roots and regulation of cell death processes. This study ultimately reveals that the proliferation of diverse chemical arsenals in plants is greatly aided by the regulatory capture of new and rapidly evolving genes by evolutionarily more stable transcription factors. Future emphases on transcriptional regulators of secondary metabolism may thus aid in the discovery of new secondary metabolic pathways on a more rapid scale.</p><p>

<p> The major barrier to curing HIV-1 infection is latency. HIV-1 latent cells are those in which the viral genome has been integrated into the host cell genome but the virus does not produce the primary infectious agents, viral RNA and proteins. Latency can occur when the virus directly infects long-lived memory CD4+ T cells or infects active CD4+ T cells that have the potential to become memory T cells. The virus persists inside those cells as long as they are alive. This dormancy provides a reservoir of HIV-1 virus in memory T cells, which can cause infection relapse whenever antiretroviral therapy (ART) is discontinued. The situation is further complicated by the fact that multiple reservoirs of HIV-1 virus can be established at early stages of infection. </p><p> The major reservoir lies in the CD4+ T cells present in blood, lymph nodes and the spleen. Unfortunately, ART fails to target hidden HIV-1 virus that persists in resting T-cells. Furthermore, life-long ART use increases the chances that mutant virus will develop which will be resistant to continued therapy. Therefore, various studies have explored mechanisms to eradicate the latent HIV-1 reservoir. One proposed strategy to target this reservoir is known as &ldquo;shock and kill&rdquo;. The proposed shock and kill strategy initially &ldquo;shocks&rdquo; the HIV-1 virus out of latency with latency reversing agents (LRAs). The reactivated virus can then be controlled by ART and cytotoxic CD8+ T cells (CTLs), which kill the infected cells. Despite the great findings regarding reactivating HIV-1 latency <i>in vitro</i> and <i>ex vivo</i>, tested LRAs proved unsuccessful in reactivating HIV-1 virus in clinical trials. </p><p> Different factors can contribute to establishment of HIV-1 latency and different reservoirs in different immune cells and tissues are established early after HIV-1 infection. Therefore, synergy between multiple LRAs should be sought and studied for successful reactivation of the latent viral pool. </p><p> Runt Related Transcription Factor 1 (RUNX1) is a key transcription factor that is important during T cell development and has been shown to recruit different transcription factors in a context dependent manner. It has been shown to be involved in repressing various genes and it also interacts with chromatin modifiers that can alter the landscape of the chromatin and modify its compaction. Our lab has shown that there is a putative RUNX1 binding site on HIV-1 long terminal repeats (LTR) and the transfection of RUNX1 can suppress HIV-1 transcription. In addition, our lab has shown that the benzodiazepine, RO5-3335, which pharmacologically inhibits RUNX1, synergizes with vorinostat (SAHA), an HDAC inhibitor to reactivate latent HIV-1. </p><p> Using DNA cloning, an HIV-1 virus with a mutated RUNX1 binding site was constructed. Then, replication, infectivity and fitness of the mutated virus were examined and compared to a control virus using ELISA, RT, PCR, and TA cloning techniques. We have found that this mutated virus replicates faster and has more fitness and infectivity than the control virus with an intact RUNX1 binding site. Our results show that inhibition of RUNX1 binding to HIV-1 3&rsquo; long terminal repeat (LTR) positively affects viral replication and infectivity. This suggests that RUNX1 host transcription factor suppresses HIV-1 replication through its transcriptional repressor function and it possibly contributes to establishment of latency. </p><p> We screened clinically prescribed benzodiazepines (BDZs) to identify reactivators for latent HIV-1 virus. Using flow cytometry, we have found most of these BDZs synergized with SAHA in reactivation of latent HIV-1. Unlike the other BDZs tested, alprazolam was able to reactivate HIV-1 even when not in combination with SAHA. The effect of alprazolam on RUNX1 responsive genes was further investigated using qPCR. Alprazolam was found to affect RUNX1 responsive genes similarly to RO5-3335, a known RUNX1 inhibitor. The effect of alprazolam on IFN&gamma; and TNF&alpha; that are produced from cytotoxic T cells (CTLs) was also examined. Alprazolam enhanced CTL function that was shown in the literature to be attenuated by SAHA. Thus, alprazolam successfully reverses HIV-1 latency and decreases the side effects of SAHA on CTL function when used in combination. </p><p>

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3342. Advisers: Steven M. Finkbeiner; Graeme Davis.

Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009. / Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3351. Adviser: Philip M. Best. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 70-04, Section: B, page: 2016. Adviser: Dean Sheppard.