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A fundamental question in biology is: How is variation generated? At a basic level, the vast amount of variation and biodiversity is generated through a combination of genetic and environmental processes. Traditionally these processes were treated independently, but recently fields such as evolutionary development have worked to unify our understanding of these mechanisms and to investigate how these processes interact with each other to generate variation. Developmental plasticity provides a fantastic framework for studying how genetic and environmental (GxE) interactions shape and maintain natural variation. Butterflies and their wing color patterns have long been model systems for plasticity. This dissertation seeks to address the gxe mechanisms responsible for generating color variation in the Dogface butterfly, Zerene. Zerene is comprised of only two species Z. cesonia, the Southern Dogface, and Z. eurydice, the California Dogface, that differ in their color patterns. Z. cesonia also exhibits a seasonal plastic color pattern, where Z. eurydice does not. These features make the Zerene system an excellent model for disentangling the gxe processes contributing to variation both within and between species. Using an integrative approach these studies address the role of 1.) larval host plant divergence 2.) seasonal fluctuations and 3.) hybridization on the development of wing coloration variation. The findings of these studies contribute not only to our understanding of how butterflies generate their colors, but also to the wider knowledge base on how genetics and the environment influence the generation and maintenance of biological variation.

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DNA arrays, capable of detecting specific DNA sequences from a sample have become widely used. They rely on DNA heterogeneous hybridization, which is the binding between a single strand of DNA immobilized on a surface (probe) and its complementary strand present in the bulk (target). In order to improve the hybridization time in DNA arrays, it is crucial to understand the kinetics of DNA hybridization. The study of the Damkohler number that compares the DNA supply by diffusion to the DNA consumption by reaction (hybridization) shows that in many cases we can expect DNA hybridization to be a diffusion limited process. This is verified by a finite element study, where a whole microfluidic chamber (bulk and reacting surface) is simulated. In these cases, the formation of a depletion zone above the sensing zone is observed. The reaction rate is much lower than in the ideal case where the reaction would be reaction rate limited. A better DNA transport could be a solution to overcome the diffusion barrier. Therefore, the influence of convection on DNA hybridization was studied. Finite element simulation shows that even a small DNA velocity (10 ƒ�m/s) can greatly enhance the overall reaction rate and help preventing the formation of a depletion zone. These observations are valid when one kind of probe reacts with one kind of target. In reality, non specific hybridization can happen between a probe and a non complementary target. We show that in some cases, non specific hybridization can slow down the kinetics and reduce the fraction of specifically hybridized probes at equilibrium. The fraction of non specific hybrids can reach a maximum before decreasing and reaching equilibrium, suggesting that a longer hybridization time would lead to a better specificity. The addition of convective transport does not affect the equilibrium, but allows to reach it faster and with a better ratio between specific and non specific hybrids during the process. Therefore, convective transport of DNA appears to be beneficial. Another possibility is to act on the DNA itself to focus it near the sensing zone. Our study of the different electrokinetic forces leads us to derive the expression of the dielectrophoretic force in a field resulting from the combination of a DC field and an AC field. This could be a novel way to act on polarizable particles like DNA.

A new format for microfluidic based DNA biosensors is presented in which the biorecognition element (single stranded DNA probes) is immobilized as a continuous density gradient of probes along the length of a microfluidic channel instead of a standard array format commonly used in microarray technologies or DNA based biosensors. The development of continuous density gradients of immobilized probe was achieved by electrokinetically subjecting probes that were terminated with an appropriate functional group for a surface coupling reaction to increasing convective velocity along the length of the microfluidic channel. This gradient format was able to discriminate between a fully complementary target and one containing 3 BPM based on the spatial pattern of hybridization for picomole quantities of DNA targets. Temperature mediated destabilization of DNA hybrids demonstrated that the density of immobilized probes plays an important role in the thermodynamic stability of DNA hybrids. In addition, it was found that efficiency, selectivity and melt temperature of DNA hybrids for surface based hybridization is dependent on the density of the probe molecules.

A new format for microfluidic based DNA biosensors is presented in which the biorecognition element (single stranded DNA probes) is immobilized as a continuous density gradient of probes along the length of a microfluidic channel instead of a standard array format commonly used in microarray technologies or DNA based biosensors. The development of continuous density gradients of immobilized probe was achieved by electrokinetically subjecting probes that were terminated with an appropriate functional group for a surface coupling reaction to increasing convective velocity along the length of the microfluidic channel. This gradient format was able to discriminate between a fully complementary target and one containing 3 BPM based on the spatial pattern of hybridization for picomole quantities of DNA targets. Temperature mediated destabilization of DNA hybrids demonstrated that the density of immobilized probes plays an important role in the thermodynamic stability of DNA hybrids. In addition, it was found that efficiency, selectivity and melt temperature of DNA hybrids for surface based hybridization is dependent on the density of the probe molecules.