A technology for biomolecular processing and localization of gene expression at the single cell level is essential to understanding cellular heterogeneity. Traditional methods of tissue analysis cannot identify the stochastic variation that makes individual cells unique because these differences are masked by bulk measurements. In this dissertation, two technologies are described for different aspects of single cell analysis. The first part is a sample preparation method for biomolecular processing from single cell using advanced microfluidic devices with permeable polymer barriers; the second one is digital quantification and localization of biomolecules at the single cell level. Microfluidic devices provide a powerful tool for cells and biomolecular processing due to their ability to compartmentalize reactions at physiologically relevant concentrations in a highly parallelizable manner. However, the serial biochemical reaction required for efficient and low-loss single-cell analysis cannot be performed in a single fluidic chamber. In the first part of the dissertation a novel microfluidic architecture is described that uses semipermeable polymer barriers to enables the capture and transportation of DNA and cells, solution exchange, and serial biochemical reactions to be carried out in a single microfluidic chamber. Meanwhile, advancements in single-cell sequencing techniques have allowed the full gene expression of single cell to be profiled. However, the native spatial context of the cell is lost because of the process of cell lysis. In the second part of the dissertation, a highly multiplexed method to selectively detect and localize hundreds of targeted genes in-situ is presented. This method retains local information of targeted genes by processing enzymatic reactions in-situ without destroying cells. It also utilizes the multiplexing capability and high specificity of padlock probes to detect targets of interest at a high signal-to-noise ratio by selectively amplifying biomolecules of interest

MicroRNAs play central roles in controlling gene expression in human cells. Sequencing data show that many miRNAs are produced at different levels and as multiple isoforms that can vary in length at their 5' or 3' ends, but the biogenesis and functional significance of these RNAs are largely unknown. We show here that the human trans-activation response (TAR) RNA binding protein (TRBP), a known molecular partner of the miRNA processing enzyme Dicer, changes the rates of pre-miRNA cleavage in an RNA-structure-specific manner. Furthermore, TRBP can trigger the generation of iso-miRNAs (isomiRs) that are longer than the canonical sequence by one nucleotide. We show that this change in miRNA processing site can alter guide strand selection, resulting in preferential silencing of a different mRNA target. These results implicate TRBP as a key regulator of miRNA processing and targeting in humans.

PDZ domains are abundant protein interaction modules that often recognize short amino acid motifs at the C-termini of target proteins. They regulate multiple biological processes such as transport, ion channel signaling, and other signal transduction systems. This review discusses the structural characterization of PDZ domains and the use of recently emerging technologies such as proteomic arrays and peptide libraries to study the binding properties of PDZ-mediated interactions. Regulatory mechanisms responsible for PDZ-mediated interactions, such as phosphorylation in the PDZ ligands or PDZ domains, are also discussed. A better understanding of PDZ protein-protein interaction networks and regulatory mechanisms will improve our knowledge of many cellular and biological processes.

The intracellular signaling molecule Dishevelled (Dvl) mediates canonical and non-canonical Wnt signaling via its PDZ domain. Different pathways diverge at this point by a mechanism that remains unclear. Here we show that the peptide-binding pocket of the Dvl PDZ domain can be occupied by Dvl's own highly conserved C-terminus, inducing a closed conformation. In Xenopus, Wnt-regulated convergent extension (CE) is readily affected by Dvl mutants unable to form the closed conformation than by wild-type Dvl. We also demonstrate that while Dvl cooperates with other Wnt pathway elements to activate canonical Wnt signaling, the open conformation of Dvl more effectively activates Jun N-terminal kinase (JNK). These results suggest that together with other players in the Wnt signaling pathway, the conformational change of Dvl regulates Wnt stimulated JNK activity in the non-canonical Wnt signaling.

We demonstrate an electrically tunable ultracompact plasmonic modulator with large modulation strength (>10 dB) and a small footprint (~1 μm in length) via plasmon-induced transparency (PIT) configuration. The modulator based on a metal-oxide-semiconductor (MOS) slot waveguide structure consists of two stubs embedded on the same side of a bus waveguide forming a coupled system. Heavily n-doped indium tin oxide (ITO) is used as the semiconductor in the MOS waveguide. A large modulation strength is realized due to the formation of the epsilon-near-zero (ENZ) layer at the ITO-oxide interface at the wavelength of the modulated signal. Numerical simulation results reveal that such a significant modulation can be achieved with a small applied voltage of ~3V. This result shows promise in developing nanoscale modulators for next generation compact photonic/plasmonic integrated circuits.

Genomic structural alteration is common in pediatric cancers, and analysis of data generated by the Pediatric Cancer Genome Project reveals such tumor-related alterations in many Wnt signaling-associated genes. Most pediatric cancers are thought to arise within developing tissues that undergo substantial expansion during early organ formation, growth and maturation, and Wnt signaling plays an important role in this development. We examined three pediatric tumors-medullobastoma, early T-cell precursor acute lymphoblastic leukemia, and retinoblastoma-that show multiple genomic structural variations within Wnt signaling pathways. We mathematically modeled this pathway to investigate the effects of cancer-related structural variations on Wnt signaling. Surprisingly, we found that an outcome measure of canonical Wnt signaling was consistently similar in matched cancer cells and normal cells, even in the context of different cancers, different mutations, and different Wnt-related genes. Our results suggest that the cancer cells maintain a normal level of Wnt signaling by developing multiple mutations.

We report a novel optical waveguide design of a hollow step index fiber modified with a thin layer of indium tin oxide (ITO). We show an excitation of highly confined waveguide mode in the proposed fiber near the wavelength where permittivity of ITO approaches zero. Due to the high field confinement within thin ITO shell inside the fiber, the epsilon-near-zero (ENZ) mode can be characterized by a peak in modal loss of the hybrid waveguide. Our results show that such in-fiber excitation of ENZ mode is due to the coupling of the guided core mode to the thin-film ENZ mode. We also show that the phase matching wavelength, where the coupling takes place, varies depending on the refractive index of the constituents inside the central bore of the fiber. These ENZ nanostructured optical fibers have many potential applications, for example, in ENZ nonlinear and magneto-optics, as in-fiber wavelength-dependent filters, and as subwavelength fluid channel for optical and bio-photonic sensing.

Ultraviolet (UV) irradiation is an effective bacterial inactivation technique with broad applications in environmental disinfection. However, biomedical applications are limited due to the low selectivity, undesired inactivation of beneficial bacteria and damage of healthy tissue. New approaches are needed for the protection of biological cells from UV radiation for the development of controlled treatment and improved biosensors. Aluminum plasmonics offers attractive opportunities for the control of light-matter interactions in the UV range, which have not yet been explored in microbiology. Here, we investigate the effects of aluminum nanoparticles (Al NPs) prepared by sonication of aluminum foil on the UVC inactivation of E. coli bacteria and demonstrate a new radiation protection mechanism via plasmonic nanoshielding. We observe direct interaction of the bacterial cells with Al NPs and elucidate the nanoshielding mechanism via UV plasmonic resonance and nanotailing effects. Concentration and wavelength dependence studies reveal the role and range of control parameters for regulating the radiation dosage to achieve effective UVC protection. Our results provide a step towards developing improved radiation-based bacterial treatments.

During RNA interference and related gene regulatory pathways, the endonuclease Dicer cleaves precursor RNA molecules to produce microRNAs (miRNAs) and short interfering RNAs (siRNAs). Human cells encode a single Dicer enzyme that can associate with two different double-stranded RNA (dsRNA)-binding proteins, protein activator of PKR (PACT) and trans-activation response RNA-binding protein (TRBP). However, the functional redundancy or differentiation of PACT and TRBP in miRNA and siRNA biogenesis is not well understood. Using a reconstituted system, we show here that PACT and TRBP have distinct effects on Dicer-mediated dsRNA processing. In particular, we found that PACT in complex with Dicer inhibits the processing of pre-siRNA substrates when compared with Dicer and a Dicer-TRBP complex. In addition, PACT and TRBP show non-redundant effects on the production of different-sized miRNAs (isomiRs), which in turn alter target-binding specificities. Experiments using chimeric versions of PACT and TRBP suggest that the two N-terminal RNA-binding domains of each protein confer the observed differences in dsRNA substrate recognition and processing behavior of Dicer-dsRNA-binding protein complexes. These results support the conclusion that in humans, Dicer-associated dsRNA-binding proteins are important regulatory factors that contribute both substrate and cleavage specificity during miRNA and siRNA production.