In cell biology and chemistry, total internal reflection microscopy (TIRFM) has proven to be a useful technique that allows the probing of cellular processes with high-signal-to-noise ratio imaging. However, samples on solid substrates limit the accessibility to probe processes on extracellular membrane surface closest to the microscope objective. Colloidal crystals provide a porous alternative to the traditional solid substrates. Thin crystals exhibit optical properties similar to that of a fused silica coverslip allowing for TIRFM in the same manner as with a typical coverslip as demonstrated by the observance of Chinese hamster ovary cells with fluorescently labeled receptors on both types of substrates. Accessibility of the cell membrane closest to the substrate and the ability to probe fluorophore orientation information was observed by the binding of TIPP-cy5 to the human delta opioid receptor.

The ever-increasing number of devices capable of, not only connecting to existing communication networks, but also, independently creating new ones is defining a new communication network, in which the Internet is only one of the substrate networks pro- viding connectivity between diverse devices. This is a network with many interconnected mobile devices connecting to infrastructure networks and creating their own dynamic substrate networks. We present a novel routing scheme for diverse collections of substrate networks with a mix of mobile and static nodes. A key element of the routing scheme is to utilize the exiting routing paths in substrate networks, and set up routing paths between substrate networks. We use sets of nodes as landmarks and define locators that describe node position in the network relative to landmarks. This allows our routing scheme to scale to a large number of nodes, as only information about landmarks needs to be propagated throughout the network.

The ever-increasing number of devices capable of, not only connecting to existing communication networks, but also, independently creating new ones is defining a new communication network, in which the Internet is only one of the substrate networks pro- viding connectivity between diverse devices. This is a network with many interconnected mobile devices connecting to infrastructure networks and creating their own dynamic substrate networks. We present a novel routing scheme for diverse collections of substrate networks with a mix of mobile and static nodes. A key element of the routing scheme is to utilize the exiting routing paths in substrate networks, and set up routing paths between substrate networks. We use sets of nodes as landmarks and define locators that describe node position in the network relative to landmarks. This allows our routing scheme to scale to a large number of nodes, as only information about landmarks needs to be propagated throughout the network.

Biochemical and mechanical properties of the extracellular matrix (ECM) are known to independently influence cell function. Given the complexity of cellular responses, I hypothesized that the integration of multiple matrix factors as opposed to their individual contribution is key to understanding and controlling cell function. The objective of this thesis was to systematically investigate matrix biochemical and mechanical regulation of multipotent stromal cell (MSC) osteogenesis. First, I demonstrated that substrate stiffness-dependent MSC spreading, proliferation and osteogenic response were differentially regulated by matrix protein type (collagen I vs. fibronectin) and concentration. Second, I developed and characterized a matrix microarray platform that enabled the efficient screening of multiple matrix-derived cues (substrate stiffness, ECM type and density). I implemented the matrix microarray platform together with parametric regression models to elucidate novel matrix interactions in directing mouse MSC osteogenic and adipogenic differentiation. Third, I extended the screening study to examine matrix-dependent human MSC osteogenesis. Non-parametric regression models were used to provide a nuanced description of the multi-factorial matrix regulation in MSC osteogenesis. The response surfaces revealed a biphasic relationship between osteogenesis and substrate stiffness, with the exact location and magnitude of the optimum contingent on matrix composition. Guided by the screening results and perturbation to key cytoskeletal regulators, I identified a novel pathway involving Cdc42 in matrix mechanical and biochemical regulation of MSC osteogenesis. Surprisingly, Cdc42 mediated stiffness-dependent MSC osteogenesis independent of ROCK, suggestive of a contractility-independent mechanism in matrix rigidity signal transduction. In summary, the integration of cell-based arrays and statistical modeling has enabled the systematic investigation of complex cell-matrix interactions. This generalizable approach is readily adaptable to other cellular contexts, complementing hypothesis-driven strategies to facilitate non-intuitive mechanistic discovery. Moreover, the improved understanding of matrix-dependent MSC function also has practical relevance to the development of biomaterials for tissue engineering applications.

This thesis investigates the integration of planar antennas, such as Dielectric Resonator Antennas (DRAs) to the planar waveguide structure, specifically the Substrate Integrated Waveguide (SIW) for high radiation efficiency millimeter-wave (mm-wave) applications. The SIW is a low cost and low loss technology, since it almost keeps the guided wave inside the structure. Therefore, it is an excellent candidate feeding scheme compared to traditional planar (multi-conductor) structures, such as the Microstrip Line (MSL) and Co-planar Waveguide (CPW) for many planar antennas. It enhances the antenna???s overall radiation efficiency by minimizing the conduction loss, which dominates at the mm-wave frequency band. For this thesis, two different SIW-integrated DRA configurations operating at mm-wave frequency band are presented. The rectangular DRA is excited in its fundamental mode TE??11 for radiation through a narrow slot cut on the SIW broad wall. However, the coupling slot itself is excited by the SIW TE10 fundamental mode. In addition, the design guidelines, and a parametric study is also conducted on the proposed antenna parameters to investigate their impact on the antenna???s overall performance including the reflection coefficient and radiation pattern (gain). The results are provided within this thesis. The antenna is made of low cost and low loss materials that are available commercially. It is fabricated by using a novel and simple technique, which is compatible with the Printed Circuit Board (PCB) technology. The board is treated as multi-layers composed of the SIW-layer, and DRA element(s) layer, respectively. The fabricated antenna prototypes are tested to demonstrate their validity for real microwave/mm-wave applications. Their reflection coefficients and radiation patterns are measured, and the antenna shows a boresight gain of 5.51 dB and a radiation efficiency of more than 90 % over the operating frequency band of 33-40 GHz. Antenna arrays based on the SIW integrated DRA are investigated for high gain/radiation efficiency applications. Different array configurations such as, linear (series-fed and corporate-fed) and two-dimensional (2D) arrays are presented. The series-fed DRA array is characterized by a single SIW line loaded by DRA-slot pairs, whereas the SIW-power splitter is used to form the corporate-fed DRA array, when loaded by DRA-slot pairs. While the SIW hybrid-feeding scheme (series-feed combined with corporate-feed) is used to form 2D DRA arrays. In this design, the SIW-power splitter is used to split the power equally and in-phase among the sets (rows) of SIW series fed-DRA elements (columns). A simple and generic Transmission Line (T.L.) circuit model is proposed to simplify and expedite the antenna array design process. It is used to calculate the antenna reflection coefficient and radiation pattern (gain). The T.L. model does not take the mutual coupling between the DRA elements into account, since our study shows that its less than -20 dB over the operating bandwidth. However, it is useful and faster than full-wave solvers, such as HFSS, which consumes time and memory due to the huge generated mesh. The developed T.L. circuit model is used to design the antenna array and study the impact of its main designed parameters on the antenna performance. The developed antenna array T.L. model leads to a general design methodology (guidelines). It also allows for optimum array designs for a given set of performance requirements and to have more physical insight into the SIW technology based antenna systems for mm-wave bands. The designed antenna array samples are fabricated and tested within the operating frequency band 33-40 GHz. The series-fed antenna array shows a measured boresight gain of 11.70 dB, and high radiation efficiency, which is more than 90 % over an operating frequency band of 4%. Furthermore, the measured results are compared to these calculated by the proposed T.L. circuit model and full-wave solver. A good agreement between the measured and the HFSS results are observed, especially near the frequency at which the reflection coefficient is minimum. However, some deviation is noticed between the proposed circuit model and the measured results. This deviation is attributed to the discrete nature of the SIW structure that affects the Short Circuit (SC) performance (magnitude and phase), the T.L. lengths, and the mutual coupling between any two adjacent antenna elements. All these issues are handled efficiently and are taken into account by the full-wave solver. Therefore, the measured reflection coefficient agrees with that of the HFSS, except for a very small deviation, caused by the fabrication tolerances and measurement errors. However, the proposed T.L. circuit model is still valid and can easily predict and estimate the resonance behavior and the impedance bandwidth of the proposed antenna arrays in a very short time compared with the full-wave solver.

In the lower millimetre-wave frequency range, Substrate Integrated Waveguide (SIW) circuits have emerged as a reasonable compromise between rectangular waveguide and standard microstrip technologies. They are formed by a top- and bottom-metalized substrate and two arrays of plated or riveted holes (via holes) to replace the vertical metallic walls in conventional rectangular waveguide. Although many passive components known from traditional waveguide technology have been fabricated in SIW, one of the main challenges is to integrate active components with typical coaxial-type interfaces within the SIW environment. Therefore, the work presented in this dissertation focuses on new broadband transitions from SIW to other planar transmission-line technologies such as microstrip coplanar waveguide, coplanar strip line, slot line and coupled microstrips. Several of the new transitions are prototyped and experimentally verified. Two of these transitions are then used to integrate a low noise amplifier within SIW input and output ports. The measurements of fabricated SIW amplifier prototypes show very promising performance and clearly demonstrate successful integrations of active components within SIW. Finally, one of the new SIW-to-coplanar-waveguide transitions is employed as an interface to an SIW-based antenna, thus demonstrating the principle of connectivity of SIW to all currently used planar circuit technologies. / Graduate

Biochemical and mechanical properties of the extracellular matrix (ECM) are known to independently influence cell function. Given the complexity of cellular responses, I hypothesized that the integration of multiple matrix factors as opposed to their individual contribution is key to understanding and controlling cell function. The objective of this thesis was to systematically investigate matrix biochemical and mechanical regulation of multipotent stromal cell (MSC) osteogenesis. First, I demonstrated that substrate stiffness-dependent MSC spreading, proliferation and osteogenic response were differentially regulated by matrix protein type (collagen I vs. fibronectin) and concentration. Second, I developed and characterized a matrix microarray platform that enabled the efficient screening of multiple matrix-derived cues (substrate stiffness, ECM type and density). I implemented the matrix microarray platform together with parametric regression models to elucidate novel matrix interactions in directing mouse MSC osteogenic and adipogenic differentiation. Third, I extended the screening study to examine matrix-dependent human MSC osteogenesis. Non-parametric regression models were used to provide a nuanced description of the multi-factorial matrix regulation in MSC osteogenesis. The response surfaces revealed a biphasic relationship between osteogenesis and substrate stiffness, with the exact location and magnitude of the optimum contingent on matrix composition. Guided by the screening results and perturbation to key cytoskeletal regulators, I identified a novel pathway involving Cdc42 in matrix mechanical and biochemical regulation of MSC osteogenesis. Surprisingly, Cdc42 mediated stiffness-dependent MSC osteogenesis independent of ROCK, suggestive of a contractility-independent mechanism in matrix rigidity signal transduction. In summary, the integration of cell-based arrays and statistical modeling has enabled the systematic investigation of complex cell-matrix interactions. This generalizable approach is readily adaptable to other cellular contexts, complementing hypothesis-driven strategies to facilitate non-intuitive mechanistic discovery. Moreover, the improved understanding of matrix-dependent MSC function also has practical relevance to the development of biomaterials for tissue engineering applications.

Mammalian cells can initiate intracellular signalling pathways that activate pro-survival changes to maintain their integrity following their exposure to a range of extracellular stresses. One group of changes preserves cellular integrity through the regulation of cytoskeletal organization. Despite the recognised importance of maintaining microtubule (MT) networks, the specific mechanisms regulating cytoskeleton organisation in response to stress remain relatively poorly explored. Among the numerous proteins that regulate MT organisation, stathmin (STMN) is a key MT destabilising protein that regulates MT disassembly through its ability to bind tubulin dimers. The actions of STMN can be regulated by a number of growth factor-activated and cell cycle regulatory protein kinases. In preliminary work, our studies suggest the potential regulation of STMN by c-Jun N-terminal Kinase (JNK) in cells exposed to stress. Specifically, we observed changes in STMN phosphorylation which were coordinated with JNK activation. / This project has explored the contribution of stress-activated c-Jun N-terminal Kinase (JNK) to STMN phosphorylation observed during osmotic stress. More detailed in vitro biochemical analysis has revealed that JNK directly phosphorylates STMN. In addition, we have compared STMN phosphorylation by different MAPK family member. In particular, our results illustrated that JNK predominantly phosphorylate STMN on serine residue 38 (S38) whereas ERK most likely targeted STMN S25. By examining specifically the phosphorylation of the four regulatory serine residues in vitro, we proposed a model of hierarchical phosphorylation among STMN serine residues. Specifically, our results demonstrated that phosphorylation of S38 was a pre-requisite for S25 phosphorylation by JNK in vitro. Furthermore, our results also demonstrated the impacts of JNK binding domain (JBD) and tubulin on STMN phosphorylation in vitro. Overall, this project identified STMN as a novel JNK substrate. The results have broadened our understanding on the JNK-mediated STMN phosphorylation as the first step to provide deeper insights into the different functions of JNK in the mammalian stress response.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

Thesis (M.S.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 80-81). Also available on the World Wide Web.