Myogenesis is the process of skeletal muscle tissue formation where committed muscle progenitor cells differentiate into skeletal muscle fibres. Depending on the instructive cues the muscle progenitor cells receive they will differentiate into specific fibre types with different properties. The skeletal muscle fibres can be broadly classified as fast-twitch fibres or slow-twitch fibres, based on their contractile speed. However, subgroups of fast- and slow-twitch fibres with different metabolic properties, endurance and different isoforms of sarcomeric components have also been identified, adding complexity to the process of muscle tissue patterning. The skeletal muscle tissue has the capacity to regenerate throughout life. Upon muscle tissue damage muscle satellite cells are recruited to the area of injury where they proliferate and either form new fibres similar to those damaged, or fuse with existing fibres. This thesis aims to investigate the process of muscle progenitor cell proliferation and differentiation, as well as the fast-twitch fibre formation and muscle tissue patterning in the zebrafish embryo. I present results identifying the previously uncharacterised gene myl1, encoding an alkali-like myosin light chain, which is specifically expressed in fast-twitch muscle progenitors before fibre formation. Furthermore, I introduce data showing that the transcription factor six1 is expressed in Pax7+ muscle progenitor cells, which has been reported to contribute to part of the fast-twitch muscle tissue as well as to a pool of quiescent muscle satellite cells. With support from the presented data, I hypothesise that six1 keeps the Pax7+ muscle progenitor cells in a proliferative state and consequently prevents them from differentiating into muscle fibres. In addition, I demonstrate that the zebrafish fast-twitch muscle fibres can be divided into different subgroups that express unique forms of fast myosin heavy chain genes along the anterior-posterior (head-tail) axis, and that this subspecification depends on a balance between RA and Wnt signalling. Collectively I propose a previously unknown role for Six1 in zebrafish Pax7+ muscle progenitor cell proliferation and differentiation. Furthermore, I present novel data suggesting that distinct regions of the zebrafish body musculature are composed of different fast-twitch fibre types, and that this regionalisation is conserved in adult zebrafish.

The bony fin rays of the zebrafish caudal fin are a convenient system for studying bone morphogenesis and patterning. Joints and bifurcations in fin rays follow predictable spatial patterns, though the mechanisms underlying these patterns are not well understood. We developed simulation models to explore ray pattern formation mechanisms in growing fins. In all models, the fin ray growth rates are based on quantitative experimental data. The different models simulate ray joint formation and bifurcation formation using different hypothetical mechanisms. In the most plausible model, ray joint and bifurcation formation result from the accumulation of two substances, arbitrarily named J and B. Model parameters were optimized to find the best fit between model output and quantitative experimental data on fin ray patterns. The model will be tested in the future by evaluating how well it can predict fin ray patterns in different fin shapes, mutant zebrafish fins, and other fish species.

Cell behavior is influenced to a large extent by the surrounding microenvironment. Therefore, in the body, the cellular microenvironment is highly controlled with cells growing within well-defined tissue architectures. However, traditional culture techniques allow only for the random placement of cells onto culture dishes and biomaterials. Cell micropatterning strategies aim to control the spatial localization of cells on their underlying material and in relation to other cells. Developing such strategies provides us with tools necessary to eventually fabricate the highly-controlled microenvironments found in multicellular organisms. Employing natural extracellular matrix (ECM) materials in patterning techniques can increase biocompatibility. In the future, with such technologies, we can hope to conduct novel studies in cell biology or optimize cell behavior and function towards the development of new cell-based devices and tissue engineering constructs. Herein, a novel cell patterning platform was developed on a hydrogel base of crosslinked hyaluronic acid (HA). Hydrogels are often employed in tissue engineering due to their ability to mimic the physicochemical properties of natural tissues. HA is a polymer present in all connective tissues. Cell-adhesive regions on the hydrogel were created using the RGDS peptide sequence, found within the cell-adhesive ECM protein, fibronectin. The peptide was bound to a 2-nitrobenzyl “caging group” via a photolabile bond to render the peptide light-responsive. Finally, this “caged” peptide was covalently bound to the hydrogel to form a novel HA hydrogel with a cell non-adhesive surface which could be activated with near-UV light to become adhesive. In this way, we successfully formed chemically patterned cell-adhesive regions on a HA hydrogel using light as a stimulus to form controlled cell patterns. While the majority of cell patterning strategies to date are limited to patterning one cell population and cannot be changed with time, our strategy was novel in using small, adhesive, caged peptides combined with multiple, aligned light exposure steps to allow for dynamic chemical cell patterning on a hydrogel. Multiple cell populations, even held apart from one another, were successfully patterned on the same hydrogel. Furthermore, cell patterns were deliberately modified with time to direct cell growth and/or migration on the hydrogel base.

Thermochemical Nanolithography (TCNL) is a scanning probe microscope (SPM) based lithographic technique modified with a semi-conducting cantilever. This cantilever is capable of locally heating a surface and with a well-engineered substrate, this spatially confined heating induces chemical or physical transformation. While previous works focused primarily on proof of principle and binary studies, there is limited research on controlling and understanding the underlying mechanisms governing the technique. In this thesis, a chemical kinetics model is employed to explain the driving mechanisms and to control the technique. The first part focuses on studying surface reactions. By coupling a thermally activated organic polymer with fluorescence microscopy, the chemical kinetics model is not only verified but also applied to control the surface reactions. The work is then expanded to include 3D effects, and some preliminary results are introduced. Finally, applications are discussed.

<p>Sea urchin larvae possess a beautiful, intricately patterned, calcium-carbonate skeleton. Formation of this complex structure results from two independent processes within the developing embryo: specification of the mesenchymal cells that produce the skeletal rods, and patterning inputs from the ectoderm, which secretes signals directing the growth and shape of the skeleton. To understand patterning of the skeleton therefore, the specification events behind these two processes must be understood separately, and then connected in order to understand how ectoderm signaling directs skeletal growth. While the former processes of mesenchyme specification and mineralization are under study elsewhere, the means by which ectodermal cues directing skeletal growth are activated and localized is not known. Using molecular genetics, including gene knock downs and mis-expression, as well as microsurgical manipulations of early cleavage embryos, I show how a previously undescribed territory within the ectoderm, the border ectoderm (BE) is specified with short range signaling inputs. Then, experiments show that the BE provides signals that initiate, and contribute to the propagation of skeletogenesis. From this dataset, and from biological experiments I outline a model for how the BE patterns and contributes to the directed growth of the skeleton. I also discuss challenges to this model that need to be addressed in future research. In principle, the mechanism proposed herein depends on the integration of information from both the primary and secondary embryonic axes. It requires both short-range signaling by Wnt5 from the endoderm to establish the BE fate, and TGFß signaling from the oral and aboral ectoderm which subdivides the BE into four territories. These findings demonstrate that the short-range signaling cascade that subdivides the embryo into first mesoderm and then endoderm also specifies ectodermal fates. Ultimately, this research paves the way for understanding how the larval skeleton is patterned during embryogenesis and may provide a paradigm for understanding other, more complex, developmental problems.</p> / Dissertation

Expanding the optical lithography to 32-nm node and beyond is impossible using existing single exposure systems. As such, double patterning lithography (DPL) is the most promising option to generate the required lithography resolution, where the target layout is printed with two separate imaging processes. Among different DPL techniques litho-etch-litho-etch (LELE) and self-aligned double patterning (SADP) methods are the most popular ones, which apply two complete exposure lithography steps and an exposure lithography followed by a chemical imaging process, respectively. To realize double patterning lithography, patterns located within a sub-resolution distance should be assigned to either of the imaging sub-processes, so-called layout decomposition. To achieve the optimal design yield, layout decomposition problem should be solved with respect to characteristics and limitations of the applied DPL method. For example, although patterns can be split between the two sub-masks in the LELE method to generate conflict free masks, this pattern split is not favorable due to its sensitivity to lithography imperfections such as the overlay error. On the other hand, pattern split is forbidden in SADP method because it results in non-resolvable gap failures in the final image. In addition to the functional yield, layout decomposition affects parametric yield of the designs printed by double patterning. To deal with both functional and parametric challenges of DPL in dense and large layouts, EDA solutions for DPL are addressed in this thesis. To this end, we proposed a statistical method to determine the interconnect width and space for the LELE method under the effect of random overlay error. In addition to yield maximization and achieving near-optimal trade-off between different parametric requirements, the proposed method provides valuable insight about the trend of parametric and functional yields in future technology nodes. Next, we focused on self-aligned double patterning and proposed layout design and decomposition methods to provide SADP-compatible layouts and litho-friendly decomposed layouts. Precisely, a grid-based ILP formulation of SADP decomposition was proposed to avoid decomposition conflicts and improve overall printability of layout patterns. To overcome the limited applicability of this ILP-based method to fully-decomposable layouts, a partitioning-based method is also proposed which is faster than the grid-based ILP decomposition method too. Moreover, an A∗-based SADP-aware detailed routing method was proposed which performs detailed routing and layout decomposition simultaneously to avoid litho-limited layout configurations. The proposed router preserves the uniformity of pattern density between the two sub-masks of the SADP process. We finally extended our decomposition method for double patterning to triple patterning and formulated SATP decomposition by integer linear programming. In addition to conventional minimum width and spacing constraints, the proposed decomposition method minimizes the mandrel-trim co-defined edges and maximizes the layout features printed by structural spacers to achieve the minimum pattern distortion. This thesis is one of the very early researches that investigates the concept of litho-friendliness in SADP-aware layout design and decomposition. Provided by experimental results, the proposed methods advance prior state-of-the-art algorithms in various aspects. Precisely, the suggested SADP decomposition methods improve total length of sensitive trim edges, total EPE and overall printability of attempted designs. Additionally, our SADP-detailed routing method provides SADP-decomposable layouts in which trim patterns are highly robust to lithography imperfections. The experimental results for SATP decomposition show that total length of overlay-sensitive layout patterns, total EPE and overall printability of the attempted designs are also improved considerably by the proposed decomposition method. Additionally, the methods in this PhD thesis reveal several insights for the upcoming technology nodes which can be considered for improving the manufacturability of these nodes.

The purpose of this study, based on the third year of a three-year research study, was to examine Grade 6 students’ previously developed abilities to integrate their understanding of geometric growing patterns with graphic representations as a means of further developing their conception of linear relationships. In addition, I included an investigation to determine whether the students’ understanding of linear relationships of positive values could be extended to support their understanding of negative numbers. The theoretical approach to the microgenetic analyses I conducted is based on Noss & Hoyles’ notion of situated abstractions, which can be defined as the development of successive approximation of formal mathematical knowledge in individuals. I also looked to Roschelle’s work on collaborative conceptual change, which allowed me to examine and document successive mathematical abstractions at a whole-class level. I documented in detail the development of ten grade 6 students’ understanding of linear relationships as they engaged in seven experimental lessons. The results show that these learners were all able to grasp the connections among multiple representations of linear relationships. The students were also able to use their grasp of pattern sequences, graphs and tables of value to work out how to operate with negative numbers, both as the multiplier and as the additive constant. As a contribution to research methodology, the use of two analytical frameworks provides a model of how frameworks can be used to make sense of data and in particular to pinpoint the interplay between individual and collective actions and understanding.

Delivery of a desired ‘active’ compound (for example, starch (as an energy substrate)) to the gastrointestinal (GI) tract is most easily achieved by oral administration. Unfortunately, the efficacy of most actives is greatly reduced due to the aggressive nature of digestive enzymes and processes which occur in this environment. A commonly applied strategy to prevent deactivation of the active prior to absorption at the target site is to encapsulate the active in another ‘sacrificial’ or non-degradable polymer matrix. Traditionally, the active and matrix is processed into a microparticle format for easy oral delivery (dispersed in a liquid or paste). However, established encapsulation methods which rely on bulk-phase processing to produce these microparticles (e.g. emulsification) are far from ideal as they lack control over the final microparticle size, size distribution, composition and shape. The lack of control in the physical properties of the resultant microparticles in turn results in an inherent lack of control over the kinetics of release of the active at the target site. In contrast, recent advances in microfluidic device fabrication and methodology development have firmly proven that these new generation devices can produce monodisperse droplets and microparticles in a continuous, controllable and predictable manner. Their potential as a processing tool for the production of highly tailored microparticles for targeted delivery, however, remains to be fully explored. Both the physical and chemical (physicochemical) properties of microparticles made from a single polymer system may be altered by the deposition of one or more additional polymer layers onto the microparticle surface (for example, alternating layers of oppositely charged polyelectrolytes to produce core-shell like particles), and this method has proven to be favorable with regards to retarding the release of active compounds. However, this addition of alternate layers of oppositely charged polyelectrolytes (so called Layer-by-Layer (LbL) deposition or assembly) does increase the number of processing steps the particles must undergo prior to storage or delivery. Further, the overall effectiveness of this additional processing is still highly dependent on the properties of the original (core) microparticles. In this thesis, a microfluidic technique was developed to encapsulate starch granules in alginate-based microparticles. Using this continuous technique, the size of the microparticles produced were shown to be monodisperse and reproducible. The developed microfluidic device included a drop formation section, followed by a gelation region and a transfer section, where the particles made on-chip are transferred from the carrier oil phase to an aqueous phase prior to collection. The microparticles collected from this microfluidic device were found to be stable for several weeks and in stark contrast to particles produced via a standard bulk emulsification routes, no aggregation was observed over this time frame. The release profile of glucose (as a result of starch hydrolysation) from microparticles produced using both a standard bulk emulsification method and the developed microfluidic-based method were compared. It was found that the monodisperse particles produced using the microfluidic method showed significantly more retardation to release compared to the glucose release profile from bulk-processed particles. This retardation effect was more pronounced when a thin layer of an oppositely charged polyelectrolyte (chitosan) was adsorbed onto the negatively charged surface (alginate is an anionic polyelectrolyte) of the microfluidic-processed microparticle. The microfluidic device developed within this thesis and the resulting tailored microparticles thus show significant potential with regards to offering a new generation of microparticle delivery systems with highly deterministic delivery over extended lifetimes.

Delivery of a desired ‘active’ compound (for example, starch (as an energy substrate)) to the gastrointestinal (GI) tract is most easily achieved by oral administration. Unfortunately, the efficacy of most actives is greatly reduced due to the aggressive nature of digestive enzymes and processes which occur in this environment. A commonly applied strategy to prevent deactivation of the active prior to absorption at the target site is to encapsulate the active in another ‘sacrificial’ or non-degradable polymer matrix. Traditionally, the active and matrix is processed into a microparticle format for easy oral delivery (dispersed in a liquid or paste). However, established encapsulation methods which rely on bulk-phase processing to produce these microparticles (e.g. emulsification) are far from ideal as they lack control over the final microparticle size, size distribution, composition and shape. The lack of control in the physical properties of the resultant microparticles in turn results in an inherent lack of control over the kinetics of release of the active at the target site. In contrast, recent advances in microfluidic device fabrication and methodology development have firmly proven that these new generation devices can produce monodisperse droplets and microparticles in a continuous, controllable and predictable manner. Their potential as a processing tool for the production of highly tailored microparticles for targeted delivery, however, remains to be fully explored. Both the physical and chemical (physicochemical) properties of microparticles made from a single polymer system may be altered by the deposition of one or more additional polymer layers onto the microparticle surface (for example, alternating layers of oppositely charged polyelectrolytes to produce core-shell like particles), and this method has proven to be favorable with regards to retarding the release of active compounds. However, this addition of alternate layers of oppositely charged polyelectrolytes (so called Layer-by-Layer (LbL) deposition or assembly) does increase the number of processing steps the particles must undergo prior to storage or delivery. Further, the overall effectiveness of this additional processing is still highly dependent on the properties of the original (core) microparticles. In this thesis, a microfluidic technique was developed to encapsulate starch granules in alginate-based microparticles. Using this continuous technique, the size of the microparticles produced were shown to be monodisperse and reproducible. The developed microfluidic device included a drop formation section, followed by a gelation region and a transfer section, where the particles made on-chip are transferred from the carrier oil phase to an aqueous phase prior to collection. The microparticles collected from this microfluidic device were found to be stable for several weeks and in stark contrast to particles produced via a standard bulk emulsification routes, no aggregation was observed over this time frame. The release profile of glucose (as a result of starch hydrolysation) from microparticles produced using both a standard bulk emulsification method and the developed microfluidic-based method were compared. It was found that the monodisperse particles produced using the microfluidic method showed significantly more retardation to release compared to the glucose release profile from bulk-processed particles. This retardation effect was more pronounced when a thin layer of an oppositely charged polyelectrolyte (chitosan) was adsorbed onto the negatively charged surface (alginate is an anionic polyelectrolyte) of the microfluidic-processed microparticle. The microfluidic device developed within this thesis and the resulting tailored microparticles thus show significant potential with regards to offering a new generation of microparticle delivery systems with highly deterministic delivery over extended lifetimes.

Delivery of a desired ‘active’ compound (for example, starch (as an energy substrate)) to the gastrointestinal (GI) tract is most easily achieved by oral administration. Unfortunately, the efficacy of most actives is greatly reduced due to the aggressive nature of digestive enzymes and processes which occur in this environment. A commonly applied strategy to prevent deactivation of the active prior to absorption at the target site is to encapsulate the active in another ‘sacrificial’ or non-degradable polymer matrix. Traditionally, the active and matrix is processed into a microparticle format for easy oral delivery (dispersed in a liquid or paste). However, established encapsulation methods which rely on bulk-phase processing to produce these microparticles (e.g. emulsification) are far from ideal as they lack control over the final microparticle size, size distribution, composition and shape. The lack of control in the physical properties of the resultant microparticles in turn results in an inherent lack of control over the kinetics of release of the active at the target site. In contrast, recent advances in microfluidic device fabrication and methodology development have firmly proven that these new generation devices can produce monodisperse droplets and microparticles in a continuous, controllable and predictable manner. Their potential as a processing tool for the production of highly tailored microparticles for targeted delivery, however, remains to be fully explored. Both the physical and chemical (physicochemical) properties of microparticles made from a single polymer system may be altered by the deposition of one or more additional polymer layers onto the microparticle surface (for example, alternating layers of oppositely charged polyelectrolytes to produce core-shell like particles), and this method has proven to be favorable with regards to retarding the release of active compounds. However, this addition of alternate layers of oppositely charged polyelectrolytes (so called Layer-by-Layer (LbL) deposition or assembly) does increase the number of processing steps the particles must undergo prior to storage or delivery. Further, the overall effectiveness of this additional processing is still highly dependent on the properties of the original (core) microparticles. In this thesis, a microfluidic technique was developed to encapsulate starch granules in alginate-based microparticles. Using this continuous technique, the size of the microparticles produced were shown to be monodisperse and reproducible. The developed microfluidic device included a drop formation section, followed by a gelation region and a transfer section, where the particles made on-chip are transferred from the carrier oil phase to an aqueous phase prior to collection. The microparticles collected from this microfluidic device were found to be stable for several weeks and in stark contrast to particles produced via a standard bulk emulsification routes, no aggregation was observed over this time frame. The release profile of glucose (as a result of starch hydrolysation) from microparticles produced using both a standard bulk emulsification method and the developed microfluidic-based method were compared. It was found that the monodisperse particles produced using the microfluidic method showed significantly more retardation to release compared to the glucose release profile from bulk-processed particles. This retardation effect was more pronounced when a thin layer of an oppositely charged polyelectrolyte (chitosan) was adsorbed onto the negatively charged surface (alginate is an anionic polyelectrolyte) of the microfluidic-processed microparticle. The microfluidic device developed within this thesis and the resulting tailored microparticles thus show significant potential with regards to offering a new generation of microparticle delivery systems with highly deterministic delivery over extended lifetimes.