Chapter One reviews examples of adaptive transgenerational plasticity in plants, the potential mechanistic bases of these inherited effects, and their ecological and evolutionary implications. Chapter Two demonstrates that adaptive transgenerational effects of drought stress persist over two generations in the annual plant *Polygonum persicaria*. These inherited effects enhanced the growth and survival of grandoffspring grown under severe drought stress. Chapter Three shows, through experimental demethylation, that DNA methylation mediates the inherited effects of drought stress in *P. persicaria*. Furthermore, these methylation-mediated effects of parental drought were genotype-specific. A central conclusion of this study is that genotype, epigenotype, and parental soil-moisture environment interact to adaptively influence functional traits in *P. persicaria*. Chapter Four examines the relationship between DNA methylation and adaptive within-generation plasticity. Drought stress, low-nutrient stress, and shade each induced DNA methylation changes, as measured by methylation-sensitive AFLP. However, stress-induced methylation changes were not detected in response to each stress in each genetic line. Because genetic lines expressed similar degrees of adaptive plasticity, there was not a consistent association between stress-induced changes in phenotypes and methylation patterns. While this subject requires further study, these results suggest that genotypespecific DNA methylation changes may contribute to the expression of adaptive plasticity. Such genotypic differences underscore the importance of incorporating genetic variation into ecological epigenetics studies.

Together, these studies indicate that interactions between genotype, epigenotype, and environmental signals – including those in previous generations – are a meaningful source of phenotypic variation. Further investigating these interactions represents a promising new direction in evolutionary biology.

]]>Chapter 1 concerns product constructions within the continuous-logic framework of Ben Yaacov, Berenstein, Henson, and Usvyatsov. Continuous-logic analogues are presented for the direct product, direct sum, countably direct sum, almost everywhere direct product, cardinal sum, ordinal sum, and ordinal product analyzed in the work of Feferman and Vaught. We show that these constructions possess a number of preservation properties analogous to those enjoyed by their classical counterparts in ordinary first-order logic. For example, each of the above constructions preserves elementary equivalence in the following sense. Given a nonempty index set *I* and collections of metric structures *M _{i}* and

We also analyze several preservation properties of the classical direct product, direct sum, countably direct sum, almost everywhere direct product, and cardinal sum which follow (in ordinary model theory) from the Feferman-Vaught Theorem. Although the techniques of Feferman and Vaught do not carry over directly to the continuous-logic context, appropriate analogues of these results are established using other methods. For example, we show that given a collection of metric structures Mi indexed by the natural numbers: if a sentence *Θ* is true in ∏^{k}_{i=0}*M _{i}* for every

In Chapter 2, the focus is on Scott's topological model for intuitionistic analysis and the truth conditions for certain kinds of formula within this context. Attention is I Ii restricted to a certain class of real-algebraic predicates which behave, in Scott's model, much as they do when classically interpreted. Given predicates *M* and *N* belonging to this class, we extend prior work of Scowcroft to obtain decision procedures for sentences of the form ∀*x̄*(*M*(*x̄*)→¬¬∃*ȳN*(*x̄*,*ȳ*) and ∀*x̄*(*M*(*x̄*)→∃*y¬¬N*(*x̄*,*y*)). Sentences of the first form are shown to hold in Scott's model just in case they are true classically. Given a sentence of the second form, we obtain (effectively) a new sentence in the same language whose classical truth is equivalent to the truth of the original statement in Scott's model.

We developed an enhanced hydroxyl radical footprinting protocol that allows determination of structures of ligand-quadrplex complexes at nucleotide resolution. The protocol revealed that NSC-176319, a quinolinium derivative, binds specifically to the two TT loops of the thrombin binding aptamer, TBA. NMR was used to demonstrate that NSC-176319 disrupts the base pairing of T4 and T13, validating the footprinting results. We applied this protocol further to other biologically relevant quadruplexes and found ten drug like molecules that exhibit binding to the loop and tetrad regions of these quadruplexes. CD spectroscopy was used to study the effects of these ligands on structure and thermal stability quadruplexes.

While investigating the interactions of ligands with quadruplex at various temperatures, we discovered the presence of two slow conformational transitions in TBA. One of these transitions consists of the TT loop residues T4 and T13. The enthalpic contribution to the free energy barrier for this transition is twice as high as the entropic contribution. The presence of NSC-176319 and higher potassium decreases the rate of this transition. The other transition consists at least the G1 and G14 residues that are in the quartets. The enthalpic contribution to the free energy barrier for this transition is similar to the entropic contribution. The rate for this transition is not affected by the concentration of potassium in the range of 10 to 40 mM.

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