Plants are fed upon by a range of insect foragers, including herbivores and pollinators. Because herbivores damage plant parts and pollinators transfer pollen among plants, plants generally benefit by avoiding herbivores and attracting pollinators. Through interactions with their host plants, herbivores and pollinators can influence the expression and evolution of plant traits. While there is a substantial body of research on plant-herbivore and plant-pollinator interactions, and increasing appreciation for the joint effects of herbivores and pollinators on plants, there are still aspects of plant-pollinator-herbivore interactions that warrant attention, including the persistence of effects beyond the year in which the interaction occurred, the effects of variability in herbivory and pollination on the evolution of plant traits, and the effects of herbivores and pollinators on asexual reproduction in plants. Ecological interactions between foragers (pollinators and herbivores) and host plants make possible a network of feedbacks in which foragers both influence and respond to plant traits. These feedbacks can link the plant traits to which foragers respond, and thus may help explain observed variation in plant traits. Interactions among plants, herbivores, and pollinators have been well documented, but addressing interactions among all three across years in a single system is rare. Across year effects are particularly important because single-year studies might misinterpret plant responses to their environment. In chapter two I describe two experiments using the perennial plant Chamerion angustifolium that address plant-forager interactions. In one I manipulated herbivory and pollen receipt to quantify forager effects on plant traits and in another I manipulated plant size and flowering phenotype to quantify forager response. I found pathways of interaction between plants and insects both within and across years, suggesting the potential for feedback between foragers and plant traits. Results suggest that while pollinators prefer plants with more flowers, and pollen receipt results in smaller plants, herbivores cause size overcompensation and flower reduction. Together these effects of both herbivores and pollinators may help maintain intermediate values of size and flowering traits. Environmental conditions can have a profound influence on plant fitness, and can vary substantially in time. When environmental variability is unpredictable, that is, when plants have no cues as to upcoming environmental conditions, they should evolve a bet-hedging strategy to deal with environmental variability. In chapter three, I constructed a simulation model to address the evolution of the timing and pattern of resource allocation (allocation schedules) in annual and perennial plants under stochastic variability in herbivory and pollination. Both herbivory and pollination can be highly variable in space and time, but we don't fully understand how this variability influences the evolution of plant traits. I found that annual plants flower later in the growing season and perennial plants have early and prolonged flowering under high environmental variability. I found that across-year variability selected for late flowering in annuals and for early and prolonged flowering in perennials, suggesting that populations of annuals and perennials should evolve different types of allocation schedules under variable herbivory and pollination. The biotic environment plays an important role in whether a species will be able to invade a new habitat. Herbivores and pollinators may influence the spread of plant species by influencing allocation to reproduction. Many plants reproduce both sexually and asexually, and the mode of reproduction a plant expresses can influence colonization of and establishment in new habitats. In chapter four, , I describe a series of studies using Eichhornia crassipes (water hyacinth) to examine the effects of pollination and simulated (manual) larval and adult herbivore damage on plant growth, sexual and asexual reproduction, and herbivore resistance. Herbivores and pollinators are known to influence a wide variety of plant traits, but despite the importance of mode of reproduction for plant population dynamics, we know little about how clonal plants respond reproductively to herbivory or pollination. I conducted surveys of natural populations to assess differences in allocation pattern, herbivore damage, and herbivore resistance, and used a common garden experiment to determine if differences in allocation pattern or resistance are due to environment or among-population genotypic differences. I found that the damage mimicking larval feeding generally shifted plant responses toward asexual reproduction, while adult-type damage and pollination had no effect, demonstrating that plant foragers and forager identity can have important, but as yet incompletely understood, effects on asexual plant reproduction. Although there is a large body of research on plant-herbivore and plant-pollinator interactions, there remain complexities in these interactions that warrant further research. Results from my dissertation demonstrate that (1) multi-year studies on perennial plants are necessary to understand the effects of foragers on perennial plants, (2) forager variability might have important effects on the evolution of plant traits, and (3) foragers can have important effects on plant asexual reproduction. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2012. / June 7, 2012. / clonal plants, herbivory, perennial, plant-insect interactions, pollination, variable environments / Includes bibliographical references. / Nora Underwood, Professor Co-Directing Dissertation; Brian Inouye, Professor Co-Directing Dissertation; Paul Ruscher, University Representative; Thomas E. Miller, Committee Member; Alice Winn, Committee Member.

Plant cytogenetics has continued to flourish and make essential contributions to genomics projects by delineating marker order, defining contig gaps, and revealing genome rearrangements. Here we review the field of plant cytogenetics from its conception through the eras of molecular biology and genomics (Chapter 1). Significant advances in chromosome preparation, such as extended fiber-FISH, have greatly increased the axial resolution limits, while imaging and signal amplification technologies have improved our ability to detect small gene-sized probes. These advances are described, together with selected examples that illustrate the power of plant cytogenetics in guiding genome projects. The integration of genetic and physical maps of maize is progressing rapidly, but the cytogenetic maps lag behind, with the exception of the pachytene fluorescence in situ hybridization (FISH) maps of maize chromosome 9. We sought to produce integrated FISH maps of other maize chromosomes using the landmark Core Bin Marker loci. Because these 1 Kb restriction fragment length polymorphism (RFLP) probes are below the FISH detection limit, we used BACs from sorghum, a small-genome relative of maize, as surrogate clones for FISH mapping. We sequenced 151 maize RFLP probes and compared in silico BAC selection methods to that of library filter hybridization and found the latter to be the best. BAC library screening, clone verification, and single-clone selection criteria are presented in Chapter 2. The use of homologous sorghum BACs as representative FISH probes for the creation of cytogenetic FISH maps for six maize chromosomes as well as in the mapping of duplicate maize regions are presented in Chapters 3 and 4, respectively. Finally, in Chapter 5 we compare our pachytene cytogenetic maps as well as the high-density chromosome 9 FISH map to the maize genomic map (Schnable et al., 2009), the UMC98 genetic linkage map (Davis et al., 1999), and to recombination nodule-based predictions of meiotic cytological coordinates (Anderson et al., 2004; Lawrence et al., 2006). / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Fall Semester, 2011. / October 14, 2011. / BAC, cytogenetics, FISH, maize, mapping, pachytene / Includes bibliographical references. / Hank W. Bass, Professor Directing Dissertation; Cathy W. Levenson, University Representative; Austin R. Mast, Committee Member; Lloyd M. Epstein, Committee Member; James M. Fadool, Committee Member.

Computational analysis of cDNA sequences from multiple organisms suggests that a large portion of transcribed DNA does not code for a functional protein. As studies begin to delve into the possible functions of these noncoding transcripts, the results are revealing an ever more complex genome, where what was once dubbed "junk" is now seemingly necessary. The characterization of several long noncoding (lnc)RNAs in human and mouse has involved the analysis of raw genomic sequence data with a set of rules to computationally predict functional noncoding transcripts; other approaches involve expression datasets from microarray or RNAseq technology to achieve the same end. As these studies increase, the number of functions, classes and names, of noncoding transcripts increase as well. Many examples of lncRNAs appear to have an epigenetic role in humans, including HOTAIR and XIST. While epigenetic gene regulation is clearly an essential mechanism in plants, relatively little is known about the presence or function of lncRNAs in plants. To explore the connection between lncRNA and epigenetic regulation of gene expression in plants, a computational pipeline using the programming language Python that will identify, classify, and localize potential lncRNAs has been developed and applied to maize full length cDNA sequences. This analysis revealed that a large portion of transcribed sequences in maize are not predicted to be coding. In addition, over half of the predicted noncoding transcripts contain small RNA sequences. Also, approximately half of the predicted noncoding transcripts are associated with a gene model. Of these, roughly 20 percent are antisense to their host gene loci. Sequence analysis identified a GA rich motif that is similar to two known motifs in previously charatercterized lncRNAs, roX2 and HOTAIR. Overall these results suggest that lncRNAs may be a component of genome regulation in maize. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Spring Semester, 2012. / March 29, 2012. / long non-coding RNA, maize, non-coding, RNA, Zea mays / Includes bibliographical references. / Karen McGinnis, Professor Directing Thesis; Hank Bass, Committee Member; Brian Chadwick, Committee Member.

The Notch signaling pathway is a means of cell-to-cell communication during vertebrate and invertebrate development that regulates aspects of cell cycle exit, cell type specification and differentiation. In the nervous system, Notch is necessary for proper development of neurons and glia. Many studies demonstrate that active Notch in the retina suppresses neuronal differentiation and promotes the M'ller glia fate. However, the role of Notch retinal progenitor cell proliferation differs among varying animal models and in is unclear in zebrafish. The current study investigated this role in the developing zebrafish retina using the mibta52b mutant, which exhibits a loss of canonical Notch signaling, and heat-shock transgenic lines allowing temporal control of pathway activity. The data presented here confirm a role for Notch in promoting the M'ller glia fate, but reveal that Notch signaling is not necessary for all cells to maintain proliferation, nor for the specification of early cell types. I demonstrate that Notch has differing effects on subsets of retinal progenitors. Canonical Notch signaling is not required by all cells to maintain proliferation, nor for specification of early neuronal cell types. NICD expression specifies progenitors for the M'ller glia fate at the expense of other cell types. However, these effects are not seen across all mitotic progenitors. This may be due to the inherent heterogeneity of gene expression present in progenitor cells, including cell cycle genes and transcription factors, giving them different competency to respond to Notch activity. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Fall Semester, 2009. / August 5, 2009. / Includes bibliographical references. / James M. Fadool, Professor Directing Thesis; Richard Hyson, Committee Member; Hong-Guo Yu, Committee Member.

Biologists have long been interested in the diversity of organisms on earth. With their joint presentation to the Linnean Society of London in 1858, Darwin and Wallace proposed natural selection as a clear mechanism to explain the diversity of life. In the 155 years since this seminal presentation, evolutionary biologists have explored the patterns and processes of diversification in a vast number of taxonomic groups, including proposing additional mechanisms and confirming the dominant presence of natural selection in the role of diversification. The last few decades have seen rigorous debates on the study of these patterns and processes (e.g. adaptive radiation, species concepts) and advances in theory, data acquisition, and analytical methods to address a number of questions associated with diversification. Yet, much of the attention has been on model systems, resulting in deficiencies in our knowledge of how widespread certain phenomena are (e.g. adaptive radiation) or how general certain modes of speciation may be. In the present study, I explore various patterns and processes responsible for the diversification of salamanders in the Spelerpinae (Caudata: Plethodontidae). I examine the role of adaptive radiation in the subfamily, using a completely sampled phylogeny based on multiple loci, by testing a number of predictions based on general theory of the process. I also test a number of hypotheses to explain the diversification patterns observed in a range-wide phylogeographic analysis of the Eurycea quadridigitata species complex. Finally, I use a multilocus nuclear phylogeny and a relatively new species delimitation method to test whether genetic lineages are linked to breeding habitats represent distinct species. Using the species delimitation results, I look for congruence in a number of morphologic traits. I find that adaptive radiation is not a good model for the diversification of the Spelerpinae. In addition, I show strong molecular evidence that habitat isolation has likely lead to ecological speciation in at least three lineages of the complex, with moderate support from the morphology. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2013. / July 1, 2013. / adaptation, Eurycea, phylogenetics, Plethodontidae, radiation, speciation / Includes bibliographical references. / Scott J. Steppan, Professor Directing Dissertation; William C. Parker, University Representative; Joseph Travis, Committee Member; Austin R. Mast, Committee Member; Peter Beerli, Committee Member; D. Bruce Means, Committee Member.

The Drosophila somatic follicle cells are excellent for the study of cell-cycle regulation and cell differentiation. During oogenesis, the follicle cells go through three variations of cell cycle programs, the mitotic cycle, the endocycle and gene amplification. Notch signaling activation is required for the switch from the mitotic cycle to the endocycle (the M/E switch) and its downregulation is necessary for the switch from the endocycle to gene amplification (the E/A switch) in these cells. Recently, we have found that Broad, a zinc-finger transcription factor, is directly up-regulated by Notch signaling during the M/E switch in the follicle cells (Jia and Deng, unpublished data). During late oogenesis, Broad is also regulated by EGFR and Dpp pathways for chorionic appendage formation. To explore how these different signaling pathways regulate follicle cell differentiation and cell cycle switches, we performed an in vivo RNAi screen to examine the effect of induced knockdown of gene expression on Br expression during oogenesis. So far, 350 different RNAi lines have been screened and about 20 of them showed defects in either early or late Br expression in follicle cells. Knockdown of Me31B, a putative RNA helicase belonging to the DEAD-box family and component of ribonucleoprotein complex (RNP), resulted in disruption of the Br early expression pattern during the endocycle stages. In our studies with Drosophila have revealed that Hindsight and Cut, in follicle cells, Cut and Wg, in wing disc, are also regulated by me31B, suggesting a potential role of me31B in Notch signaling. In addition, here we report that me31B shows genetic interaction with Notch and acts upstream of the Notch signaling. Besides, experimental results also show that knockdown of me31B causes upregulation of Dl in follicle cells and cis-inhibition accordingly. Therefore, based on these findings I hypothesized that me31B potentially regulates Notch signaling by targeting Dl in follicle cells through miRNA pathway. / A Thesis submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science. / Summer Semester, 2013. / June 24, 2013. / DROSOPHILA OOGENESIS, ME31B, miRNA PATHWAY, NOTCH SIGNALING / Includes bibliographical references. / Wu-Min Deng, Professor Directing Thesis; George W. Bates, Committee Member; James M. Fadool, Committee Member; Timothy Megraw, Committee Member.

Humans are largely dependent upon cone-mediated vision. However, death or dysfunction of rods, the predominant photoreceptor subtype, results in secondary loss of cones, remodeling of retinal circuitry, and blindness. The changes in circuitry may contribute to the vision deficit and undermine attempts at restoring sight. I exploit zebrafish larvae as a genetic model to specifically characterize changes associated with photoreceptor degenerations in a cone-dominated retina. Photoreceptors form chemical synapses with two types of second-order neurons, bipolar cells, and horizontal cells. Using cell-specific reporter gene expression and immunolabeling for postsynaptic glutamate receptors, I demonstrate that significant remodeling is observed following cone degeneration in the pde6cw59 larval retina but not rod degeneration in the Xops:mCFPq13 line. In adults, rods and cones are present in approximately equal numbers. In Xops:mCFP q13 retinas, increased numbers of horizontal cell processes are observed increasing each cone pedicle. Surprisingly in pde6cw59 mutants, glutamate receptor expression and synaptic structures in the outer plexiform layer are also preserved, and visual responses are gained in these once-blind fish. I propose that the abundance of rods in the adult protects the retina from cone degeneration-induced remodeling. I test this hypothesis by genetically manipulating the number of rods in larvae. I show that an increased number and uniform distribution of rods in lor/tbx2bp25bbtl or six7 morpholino-injected larvae protect from pde6cw59-induced secondary changes. Ultrastructural evidence shows that the additional rods recruit postsynaptic processes and successfully form invaginating ribbon synapses in the outer plexiform layer. Combined, these results suggest that in photoreceptor degeneration, compensatory mechanisms lead to synapse formation between second order neurons and the available photoreceptors. Furthermore, the observation that in zebrafish a small number of surviving photoreceptors afford protection from degeneration-induced changes provides a model for systematic analysis of factors that slow or even prevent the secondary deteriorations associated with neural degenerative disease. This plasticity provides an avenue for maintaining proper retinal morphology and connectivity in the context of photoreceptor degenerations, which may be essential to facilitate attempts at restoring vision through retinal prostheses or stem cell therapies. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2013. / June 18, 2013. / Degeneration, Plasticity, Protection, Retina, Synapse, Zebrafish / Includes bibliographical references. / James M. Fadool, Professor Directing Dissertation; Myra M. Hurt, University Representative; Lisa Lyons, Committee Member; Cathy W. Levenson, Committee Member; Thomas C. S. Keller, III, Committee Member.

Symbioses are pervasive in life and confer novel adaptive capabilities that enable ecological expansion into unexplored niches. Evolutionary transitions in symbiosis (terminations, origins, host shifts, or changes in relationship outcomes) can therefore have dramatic effects on the fitness, life history, and distribution of organisms. Because symbiotic interactions require coordination among traits that control recognition, colonization, and maintenance of symbiosis, transitions in symbiosis should generally be rare and conserved across evolutionary time. Cnidarians in the order Zoanthidea (class Anthozoa) are symbionts of taxa representing at least five invertebrate phyla and occur in most major benthic habitats from the intertidal to the deep sea. The Zoanthidea exhibit a startling array of evolutionary transitions in symbioses, and host associations and relationship outcomes appear to be highly homoplasious. To better understand these transitions and the effects of symbioses on Zoanthidea, I use a multifaceted approach that combines molecular phylogenetics and morphology with manipulative field experiments and surveys to clarify species delimitations, diversity and specificity of host associations, context-dependent relationship outcomes, and the evolution of symbioses. The results of this research indicate that our current understanding of symbiosis evolution in Zoanthidea is confounded by incomplete data on associations and relationships, and systematics that do not reflect evolutionary relationships; the data presented here indicate that host associations are largely conserved across evolutionary time. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2010. / May 4, 2010. / Includes bibliographical references. / Janie L. Wulff, Professor Directing Dissertation; David Thistle, University Representative; Don R. Levitan, Committee Member; Thomas E. Miller, Committee Member; Scott J. Steppan, Committee Member.

Maintaining genome integrity and epigenetic programming is essential to avoid disease and retain the identity and proper function of the multitude of specialized differentiated cell types in the body. Much progress has been made in the past 10 years toward identifying and understanding the range of proteins and complexes involved in these processes. Many of these are chromatin-remodeling complexes, including those that contain the Williams syndrome transcription factor (WSTF). This protein is particularly interesting for two reasons. First, it functions in many central nuclear processes, such as DNA replication, transcription, and DNA repair. Second, WSTF is haploinsufficient in Williams-Beuren syndrome (WBS) patients. This is because the WSTF gene, BAZ1B, is deleted, along with approximately 27 other genes, from one copy of chromosome 7 in affected individuals. Prior research has implicated WSTF in contributing to several of the phenotypes exhibited in WBS, yet many aspects concerning the function of WSTF remain unclear. A more detailed understanding of WSTF function is necessary to appreciate how this versatile protein contributes to general nuclear processes, and how perturbation of these roles contribute to the symptoms displayed in WBS patients. This study examines the function of WSTF in several ways. First, this research identifies and characterizes the relationship between WSTF and heterochromatin, with a particular focus on facultative heterochromatin of the human inactive X chromosome (Xi). Next, it describes the generation of human cell lines that either lack or are happloinsufficient for WSTF through the generation of heterozygous and homozygous mutant BAZ1B alleles. Using these invaluable model cell lines, this research explores the impact of WSTF reduction or loss on several processes, including heterochromatin maintenance, the DNA damage response, and vitamin D induced gene expression. This work reveals that WSTF is necessary to maintain appropriate expression of a substantial number of genes, and describes a novel nuclear phenotype in BAZ1B knockout cells, characterized by the spontaneous formation and subsequent resolution of extensive regions of heterochromatin throughout the nucleus. This research contributes to and extends current understanding of WSTF function, and provides BAZ1B knockout cells to further investigate WSTF mechanism, as well as providing BAZ1B heterozygous knockouts that will serve as a model to examine how WSTF haploinsufficiency contribute to WBS in the absence of the effects of the other 27 genes that are typically deleted in the disorder. Analyses found in this dissertation link WSTF function to maintenance of chromatin and transcriptional states. Through the examination of BAZ1B knockout cells, this work also underscores that the current understanding of WSTF is not as clear as anticipated, given that processes expected to be disrupted in the absence of WSTF were unaffected. This dissertation concludes with a discussion of these findings as well as future implications. / A Dissertation submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2013. / June 28, 2013. / chromatin maintenance, epigenetics, gene targeting, heterochromatin, Williams-Beuren syndrome, WSTF / Includes bibliographical references. / Brian P. Chadwick, Professor Directing Dissertation; Myra M. Hurt, University Representative; Jonathan H. Dennis, Committee Member; Karen M. McGinnis, Committee Member; Hengli Tang, Committee Member.

Depression, anxiety, and impairments in learning and memory are all associated with traumatic brain injury (TBI). While zinc deficiency has been correlated with depression, supplemental zinc appears to have antidepressant effects in both humans and rodent models. We hypothesized that zinc supplementation normalizes gene expression, enhances TBI-induced hippocampal neurogenesis, and prevents injury-related behaviors in a rat model of TBI. Adult male rats were fed a marginal zinc deficient (5 ppm), zinc-adequate (30 ppm), or zinc supplemented (180 ppm) diet for 4 wk followed by a moderately-severe TBI to the frontal cortex produced by controlled cortical impact. This injury induces depression- and anxiety-like behaviors as well as impairments in the Morris water maze (MWM) test. While moderate zinc deficiency did not worsen outcomes following TBI, supplemental zinc resulted in significant reductions in post-injury adrenal gland weights and clear trends toward reduced anxiety. Furthermore, zinc supplemented diets significantly reduced anhedonia, a depression-like behavior, and significantly improved MWM performance after TBI. A second study was performed to examine the possible efficacy of providing supplemental zinc as a treatment after injury. While zinc treatment performance in the MWM test, it was not as effective in treating depression and did not reduce adrenal weight. To elucidate the neurobiological mechanisms responsible for the improvements in behavioral resiliency, we took both a cellular and molecular approach. First, we tested the hypothesis that zinc supplementation increases hippocampal stem cell proliferation and survival. TBI doubled the number of proliferating cells in the dentate gyrus 24 h post-injury, and supplemental zinc increased this number by an additional 2-fold. The long term fate of these proliferating cells was determined 1 wk after TBI. While the number proliferating cells decreased at the same rate in zinc supplemented and in zinc adequate fed rats, the total number of stem cells was almost 60% higher in supplemented animals 1 wk after TBI. Secondly, we employed a large scale genomic analysis of differential gene expression in the hippocampus. TBI altered the expression of over 170 mRNAs, approximately 70 of which were normalized in rats supplemented with zinc. This included genes involved in endogenous repair processes such as neurotransmission, proliferation, survival, differentiation, synaptic plasticity, and protein biosynthesis. The data suggest that chronic zinc supplementation may be a novel and effective strategy for improving the cellular, molecular, and behavioral outcomes associated with TBI. / A Dissertation submitted to the Department of Biomedical Sciences in partial fulfillment of the requirements for the degree of Doctor of Philosophy. / Summer Semester, 2013. / June 5, 2013. / depression, stem cells, traumatic brain injury, zinc / Includes bibliographical references. / Cathy W. Levenson, Professor Directing Dissertation; Richard Hyson, University Representative; J. Michael Overton, Committee Member; Mohamed Kabbaj, Committee Member.