Morphogenesis, or the development of tissues, structures, and organs, is at the heart of embryonic development. Morphogenesis is a complex, multi-tissue process that requires coordinated cellular communication, migration, and differentiation; due to this complexity, the mechanisms that underlie morphogenesis remain poorly understood. The sea urchin embryo is morphologically and genetically more simple than most other developmental model organisms, and is optically transparent, making it a highly tractable system in which to study morphogenetic processes. The sea urchin larval endoskeleton is a biomineral that is secreted by primary mesenchyme cells (PMCs). The PMCs ingress into the embryo and remain individual, mesenchymal cells that migrate into a stereotypic three-dimensional (3-D) pattern within the blastocoel, prefiguring the form of the ensuing skeleton, which they subsequently secrete. PMC positioning is directed by cues originating in the overlying ectoderm; however, the molecular identity of those cues has remained unknown. The work described in this dissertation combines systems-level approaches with in vivo 3-D spatial analysis to identify novel skeletal patterning genes and to define their functional roles in skeletal patterning. A transcriptomics-based screen identified numerous novel candidate skeletal patterning cues. Of those cues, two were further pursued for detailed functional studies. First, the sulfate transporter SLC26a2/7 (SLC) was found to promote ventral accumulation of sulfated proteoglycans that is both necessary and sufficient to attract PMCs to the ventral territory for ventral skeleton formation. Second, the enzyme 5-lipoxygenase (LOX) was found to be required for ventral and rotational skeletal patterning, and its product, 5(S)-HETE was found to be a chemoattractant for PMCs, thereby identifying a novel role for lipoxygenase enzymes in embryonic patterning and morphogenesis. Recent work from other groups has demonstrated that PMCs diversify their gene expression profiles during skeletal patterning, implying that PMC diversification is involved in skeletal patterning, likely as a response to locally distinct spatial cues. The studies herein identify Tbx2/3 and Pks2 as important PMC subset-specific genes whose spatial expression is modulated by SLC and LOX, respectively. Together, these results provide new mechanistic insights that define our molecular understanding of the regulation of sea urchin ventral skeletal patterning.

My PhD work focuses on developing new methods to create the macroscopic patterns in a simple, robust, and versatile way. For macroscopic pattern formation, we first use flow coating as an assembly technique, uniquely balancing two driving forces: (i) evaporative deposition of nonvolatile solutes at a three-phase contact line and (ii) precision movement of a confined meniscus layer. This balance leads to the formation of line-based patterns that range in height and width from nanometers to microns, with lengths greater than centimeters. Moreover, we couple this deposition methodology with functional ligand chemistry on the nanoparticle surface, which allows us to create complex nanoparticle structures. By lifting crosslinked nanoparticle ribbons and ropes, exceptionally intriguing structures emanate from this process. The nanoparticle ribbons and ropes demonstrate a leap forward in nanomaterials fabrication, since the nanoscale properties are embedded within a macroscale object that can be manipulated with conventional methods and engineered into advanced technologies Using mechanical instability, we fabricate a simple, robust stimuli-responsive surface with periodic structures over a large area based upon osmotically-driven surface wrinkling. Although surface wrinkling has received considerable attention in the scientific literature, only a handful of papers have shown the ability to harness perhaps the greatest potential attribute of surface wrinkles: their active reversible nature. The ability to precisely control surface topographic morphologies in accordance with established scaling relationships opens a wide array of advanced materials applications, which do not rely upon cost-limiting fabrication techniques. Specifically, the surfaces respond to solvent exposure by developing well-defined topographic structures over laterally extensive areas due to osmotically-driven differential strains between a surface layer and underlying soft substrate. The observed wrinkling occurs spontaneously, forming hierarchical morphologies with controlled dimensions, and vanishes upon removal of the solvent driving force. The combined responsiveness and reversibility of wrinkling allow for the realization of functional devices, such as smart windows, smart microlens arrays, reversible channels in microfluidic devices. Moreover, by using thermal and osmotic approaches, we study the influence of geometry and material properties on surface instability such as cracking and wrinkling in a trilayer system consisting of a thin film on a soft foundation supported by a rigid substrate.

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Additive manufacturing in the form of 3D printing is a revolutionary technology that has developed within the last two decades. Its ability to print an object with accurate features down to the micro scale have made its use in medical devices and research feasible. A range of life-saving technologies can now go from the laboratory and into field with the application of 3D-printing. This technology can be applied to medical diagnosis of patients in at-risk populations. Living biosensors are limited by being Genetically Modified Organisms (GMOs) from being employed for medical diagnosis. However, by containing them within a 3D-printed enclosure, these technologies can serve as a vehicle to translate life-saving diagnosis technologies from the laboratory and into the field where the lower cost would allow more people to benefit from inexpensive diagnosis. Also, the GMO biosensors would be contained with a press-fit, ensuring that the living biosensors are unable to escape into the environment without user input. In addition, 3D-printing can also be applied to reduce the cost of lab-based technologies. Cell patterning technology is a target of interest for applying more cost-effective technologies, as elucidation of the variables defining cell patterning and motility may help explain the mechanics of cancer and other diseases. Through the use of a 3D-printed stamp, bacterial cells can be patterning without the use of a clean room, thus lowering the entry-barrier for researchers to explore cell patterning. With the commercialization of 3D-printing an opportunity has arisen to transition life-saving technologies into more cost-effective versions of existing technologies. This would not only allow more research into existing fields, but also to ensure that potentially life-saving technologies reach the people that need them. / Ph. D.

Anodization is a kind of method that can produce oxide layer in a large area and on flexible shaped metals. In some specific conditions, anodic oxide layers exhibit interesting nanopore/nanotube structures. In this work, focused ion beam patterning method is introduced to general anodization, aiming to make highly ordered anodic porous alumina and titania nanotubes. Focused ion beam guided porous anodic alumina is carried out by pre-designing hexagonal and square guiding patterns with different interpore distances on well electropolished Al foil before anodization. After anodization, the guiding interpore distance is found to affect the new pores' locations and shapes. Two important elements, electrical field and mechanical stress, are discussed for the development of the guiding pores and the generation of new pores. Based on the proposed pore growth mechanism, novel patterns, non-spherical pores, and large patterns across the grain boundaries are successfully produced. The research on focused ion beam guided anodic titania nanotubes begins with surface polishing. The influence of four polishing conditions, as-received, chemically polished, mechanically polished, and electropolished samples, are investigated. A polished smooth sample provides a desired surface for focused ion beam guided anodization. Hexagonal guiding patterns with different interpore distances are created on Ti surface. Ordered nanotube arrays are produced, and the structure of the anodized guiding pattern is identified. / Master of Science