The structural and functional abnormalities of the tumor vasculature generate regions of elevated interstitial fluid pressure and aberrant flow shear stress within the tumor microenvironment. While research has shown that the hydrodynamics of the tumor vasculature reduce transport and uptake of therapeutic agents, the underlying mechanisms by which fluid forces regulate vascular organization are not well known. Understanding the reciprocal interaction between tumor and endothelial cells to mediate angiogenesis, and the role of flow shear stress on this process, may offer insight into the design of improved therapeutic strategies to control vascularized tumors. Instrumental to this is the development of physiologically relevant models that enable tumor-endothelial co-culture under dynamic conditions. By integrating tissue-engineering strategies with cancer biology, micro-scale fluid mechanics, and optical flow diagnostics, the goal of this research was to develop a 3D in vitro microfluidic culture model to investigate tumor-endothelial cross talk under physiologically relevant flow shear stress. This objective was motivated by early findings demonstrating a contact-independent, paracrine-mediated mechanism by which endothelial cells enhance tumor-expressed angiogenic factors during 2D, static co-culture. The 3D tumor vascular model consists of a central microchannel embedded within a type I collagen hydrogel, through which a range of normal (4 dyn/cm^2), low (1 dyn/cm^2) and high (10 dyn/cm^2) microvascular wall shear stresses (WSS) were introduced. Endothelial cells lining the microchannel lumen form a confluent endothelium across which soluble growth factors are exchanged with tumor cells in the gel. Microscopic particle image velocimetry ("-PIV) was integrated within the model to enable noninvasive optical measurement of velocity profiles and quantification of WSS, which were then correlated with angiogenic potential. Results demonstrate that endothelial permeability decreases as a function of increasing WSS, while co-culture with tumor cells increases permeability. This response is likely due to shear stress-mediated endothelial cell alignment and tumor-VEGF-induced permeability. In addition, high WSS (10 dyn/cm^2) significantly down-regulates tumor-expressed angiogenic factors, suggesting flow shear stress-mediates endothelial cross talk with surrounding tumor cells. Collectively, this research demonstrates the utility of the 3D in vitro microfluidic culture model as a versatile platform for elucidating the role of tumor-relevant hydrodynamic stress on cellular response. / Ph. D.

Electroporation is an efficient, low-toxic physical method which is used to deliver impermeant macromolecules such as genes and drugs into cells. Genetic modification of the cell is critical for many cell and gene therapy techniques. Common electroporation protocols can only handle small volumes of cell samples. Also, most of the conventional electroporation methods require expensive and sophisticated electro-pulsation equipment. In our lab, we have developed new electroporation methods conducted in microfluidic devices. In microfluidic-base electroporation, exogenous macromolecules can be delivered into cells continuously. Flow-through electroporation systems can overcome the issue of low sample volume limitation. In addition, in our method, electro-pulsation can be done by using a simple dc power supply, without the need for any extra equipment. Furthermore, our microfluidic chips are completely disposable and cheap to produce. We show that electroporation and electroporation-based gene delivery can be conducted employing tapered asymmetric curving channels. The size variation in the channel's cross-sectional area makes it possible to produce electric pulses of various parameters by using a dc power supply. We successfully delivered Enhanced Green Fluorescent Protein, EGFP, plasmid DNA into Chinese Hamster Ovary, CHO-K1, cells in our microfluidic chips. We show that the particles/cells undergo Dean flow in our asymmetric curving channels. We demonstrate that there are three main regimes for particle motion in our channels. At low flow rates (from 0 to ~75μl/min) cells do not focus and they randomly follow stream lines. However, as flow rate increases (~75 to 500μl/min), cells begin to focus into one line and they follow a single path throughout the micro-channel. When flow rate exceeds ~500μl/min, cells do not follow a single line and demonstrate more complex pattern. We show that the electric parameters affect the transfection efficiency and cell viability. Higher electric field intensity results in higher transfection efficiency. This is also true in the cases with longer electroporation duration time. In our experimental work, we executed flow-through electroporation for various duration times (t = 2 ms, 5 ms, and 7 ms), and at various electric field intensities (from 300 to 2200 V/cm) while we utilized different flow rates as well, i. e. 150 μl/min (focused flow) and 600 μl/min (complex flow). To explore the impact of individual electric pulse length and electric pulse number on electroporation results, we designed control channels with straight narrow sections. Cells experience different hydrodynamic forces in straight channels compared to curving channels. Flow pattern and cell focusing were also studied in control channels as well. Also, electroporation on CHO-K1 cells was successfully conducted in control channels. The hydrodynamic forces under the conditions we used do not appear to show substantial impact on transfection efficiency. / Master of Science

The inability to monitor the molecular trajectories of whole organs throughout the clinically relevant ischemic interval is a critical problem underlying the organ shortage crisis. Here, we report a novel technique for fabricating manufacturing conformal microfluidic devices for organ interface. 3D conformal printing was leveraged to engineer and fabricate novel organ-conforming microfluidic devices that endow the interface between microfluidic channels and the organ cortex. Large animal studies reveal microfluidic biopsy samples contain rich diagnostic information, including clinically relevant biomarkers of ischemic pathophysiology. Overall, these results suggest microfluidic biopsy via 3D printed organ-conforming microfluidic devices could shift the paradigm for whole organ preservation and assessment, thereby relieving the organ shortage crisis through increased availability and quality of donor organs. / Master of Science / Organ failure is one of the most common cause of morbidity and mortality in humans. Unfortunately, there are not enough donor organs to meet the present demand, often referred to as the organ shortage crisis. To compound the problem, there is lack of understanding of the biological processes occurring in organs during the transplantation interval. Here, we present a method to manufacture a biomedical device using a 3D printing technique to monitor, collect, and isolate diagnostically relevant biological species released during the transplantation interval. This information has the potential to lead to a better understanding of organ health, which ultimately could increase the availability and quality of donor organs.

The pervasive issue of bacterial infections underscores the critical need for advancedpathogen diagnosis techniques. Traditional methods often fall short in sensitivity and specificity, necessitating innovations that can enhance pathogen concentration and detection in clinical samples. This study introduces a novel approach utilizing microfluidic droplet technology to partition bulk samples, significantly improving the concentration of bacteria in minuscule volumes. This method inherently amplifies detection sensitivity, offering a substantial leap forward in diagnostic capabilities. To capture the dynamic process of bacterial partitioning and concentration, we have developed a real-time fluorescence imaging system. This system not only facilitates the monitoring of droplet encapsulation but also enables the quantification of bacterial presence, crucial for applications such as quantitative PCR (qPCR). The efficacy of this integrated dropletbased microfluidic device and fluorescence imaging system was rigorously tested using Escherichia coli (E. coli), a prevalent bacterium responsible for urinary tract infections (UTIs), demonstrating its potential in clinical diagnostics. Looking beyond the immediate scope of this study, the presented system holds promise for extensive future development aimed at addressing a wider array of pathogens. Additionally, its versatility positions it as a foundational tool for a range of generalized applications in the ii fields of microbiology, bioengineering, and diagnostic medicine, highlighting its capacity to significantly impact methods of pathogen detection and analysis.

Interleukin-1 (IL-1) is a multifunctional cytokine produced primarily by activated monocytes/macrophages and by a variety of other cell types. IL-1 plays an integral role in the immuno-inflammatory response of the body to a variety of stimuli including infection, trauma and other bodily injuries. Once IL-1 is released from the synthesizing cell, it acts as a hormone, initializing a variety of responses in different cells and tissues. These responses are believed to be crucial to survival and are termed acute-phase responses. NF-κB is a family of dimeric transcription factors that control the expression of hundreds of genes which regulate cellular stress responses, cell division, apoptosis, and inflammation. NF-κB dwells in the cytoplasm of the cell until activation in response to a wide range of extracellular stimuli including signaling molecules such as cytokines. NF-κB regulates transcription and gene expression through nucleocytoplasmic transport. Most previous studies on NF-κB activation have been performed using bulk assays to look at populations of cells. Determining cell variance at a single-cell level is crucial in understanding the full mechanisms of drug response. The goal of this study is to analyze the effects of variant concentrations of IL-1β on the activation of NF-κB in individual cells through use of a microfluidic gradient generator. The gradient generator was adopted from Jeon et al and used principles of diffusive mixing and splitting of flows in order create a solute concentration gradient. A soft lithography procedure was used. Briefly, the design was printed on a transparency using a high resolution printer. A master of the design is then created using an SU-8 photoresist and UV light to imprint the design on a silicon wafer. The master is then used to create a Polydimethylsiloxane (PDMS) mold of the design which can be irreversibly attached to a glass slide through oxidation in order to close off the microfluidic channels. FITC-conjugated β-Casein (a protein with similar molecular weight to IL-1β) was used in order to verify the gradient generated by the design. The concentration gradient was analyzed by measuring fluorescent intensity of images taken under a UV light microscope and found to agree with microfluidic simulations run on COMSOL. A procedure for culturing cells in a microfluidic device was then adapted from Jeon that is explained in detail in Chapter 3. Two main trends were revealed; firstly, as IL-1β concentration decreased, the percent of cells activated also decreased. Secondly, as IL-1β concentration decreased, the activation time of the responding cells increased. Cells were observed to act in a single-cell manner; in which multiple cells subjected to the same concentration would not all respond in the same fashion. No major activation threshold was observed but two minor thresholds were; the first at 0.02 ng/mL IL-1β where activation levels drop from 20% to around 5%. The second around 1 ng/mL, in which all greater concentrations show nearly complete activation of all cells exposed. Of the cells that activated, the activation times were recorded and analyzed as well. In general, a decrease in IL-1β concentration caused cells to take longer to activate. Concentrations greater than 5 ng/mL responded on average in 30 minutes with a significant amount of variation. Between 5 ng/mL and 0.1 ng/mL, activation time increased as IL-1β concentration decreased in a linear fashion when concentration was plotted on a base-10 log scale. Below 0.1 ng/mL, the trend disappears and an average activation time of around 95 minutes is observed that no longer depended on concentration. This is interesting because fewer and fewer cells are activating in this concentration range but activation time follows no trend and remains partially stochastic with times ranging from 80 to 105 minutes. The previous results were all observed with a continuous flow and stimulation of the cells. Experiments were also run by only exposing the cells to the IL-1β for 10 minutes and then replacing the flow with a buffer. These studies yielded interesting results; the fraction of activated cells reported the same trends and values as those that were continuously stimulated. The activation times, however, were delayed between 10 and 20 minutes but otherwise followed the same trend as the continuous stimulation. These results suggest that a brief exposure to an external stimulant is all it takes for the cascade of intercellular events to take place and cause NF-κB translocation. / Master of Science

In recent years, space exploration has been driving studies that enable sustained human presence in space. In such studies, fluidics relating to biology have become important. Fluids in biological systems span from large-scale flows relevant to circulatory, digestion, and pulmonary systems, but also involve many micro-scale porous flows. Hence, space exploration is driving a novel need to characterize fluidics in microscales in microgravity conditions. In this work, we study the porous flow network within bones that stimulates cellular growth and has the potential to relate to osteoporosis (including driving osteoporosis in astronauts). To study this effect, computational fluid dynamics (CFD) simulations are performed on a microfluidic device with a hexagon structure and compared to experimental results in both normal gravity (1g) and microgravity (0g) via Blue Origin's New Shepard Vehicle (NS-23 attempt and NS-24 launch). CFD results have been created to predict the transport character of nutrients in the bones. These insights have the potential to lead to preventative measures for osteoporosis in astronauts.

The advancement of cancer immunotherapy, especially in the manipulation of NK cells, holds promise for targeted cancer treatment. NK cell effectiveness is currently assessed using cell populations in cytotoxicity assays, but these lack the details to observe individual cellular behaviours in real time. Droplet-based microfluidics is emerging as a solution to address these limitations by allowing the encapsulation of cells at specific ratios in controlled microenvironments. This advancement enhances the accuracy of immunotherapeutic assessments by providing a more detailed understanding of cellular interactions. In our study, we employed droplet microfluidics to encapsulate and analyze the interactions between NK cells and K562 cancer cells at predetermined effector-to-target (E:T) ratios. Each droplet served as an isolated microreactor, where individual NK cell interactions with cancer cells could be monitored in real-time. The results of our study revealed that droplet-based microfluidics provide detailed insights into the differential cytotoxic capacities of primary (Pri), suppressed (Supp), expanded (Exp), and post-expansion suppressed (PES) NK cells. Notably, expanded NK cells exhibited not only higher cytotoxic activity at a faster rate but also greater serial killing capabilities across different donors and varying E:T ratios, indicating their potential for effective immunotherapy. Additionally, suppressed NK cells showed reduced cytotoxic abilities, emphasizing the importance of overcoming the suppressive factors within the tumour microenvironment. These findings are pivotal for the field of immunotherapy and hold promising implications for the selection and optimization of NK cell-based treatments tailored to individual patient needs. / Thesis / Master of Applied Science (MASc)

Optical manipulation covers a wide range of techniques to guide and trap cells using only the forces exerted by light. Another optical tool is photoporation, the technique of injecting membrane-impermeable molecules using light, which has become an important alternative to other injection techniques. Together they provided sterile tools for manipulation and molecule delivery at the single-cell level. In this thesis, the properties of low Reynolds fluid flows are exploited to guide cells though a femtosecond Bessel beam. This design allows for high-throughput optical injection of cells without the need to individually target cells. A method of 'off-chip' hydrodynamic focusing was evaluated and was found to confine 95.6% of the sample within a region which would receive a femtosecond dose compared to 20% without any hydrodynamic focusing. The system was tested using two cell lines to optically inject the membrane-impermeable dye, propidium iodide. This resulted in an increase of throughput by an order of magnitude compared to the previous microfluidic design (to up to 10 cells per second). Next optical trapping and photoporation were combined to create a multimodal workstation. The system provides 3D beam control using spatial light modulators integrated into a custom user interface. The efficiency of optical injection of adherent cells and trapping capabilities were tested. The development of the system provides the groundwork for exploration of the parameters required for photoporation of non-adherent cells. Finally optical trapping is combined with temporally focused multiphoton illumination for scanless imaging. The axial resolution of the system was measured using different microscope objectives before imaging cells stained with calcein. Both single and a pair of recently trypsinised cells were optically trapped and imaged. The position of the trapped cells was manipulated using a spatial light modulator in order to obtain a z-stack of images without adjusting the objective position.

A new microrheology set-up is described, which allows us to quantitatively measure the transient rheological properties and microstructure of a variety of solvent-responsive complex fluids. The device was constructed by integrating particle tracking microrheology and microfluidics and offers unique experimental capabilities for performing solvent-response measurements on soft fragile materials without applying external shear forces. Transient analysis methods to quantitatively obtain rheological properties were also constructed, and guidelines for the trade-off between statistical validity and temporal resolution were developed to accurately capture physical transitions. With the new device and methodology, we successfully quantified the transient rheological and microstructural responses during gel formation and break-up, and viscosity changes of solvent-responsive complex fluids. The analysis method was expanded for heterogeneous samples, incorporating methods to quantify the microrheology of samples with broad distributions of individual particle dynamics. Transient microrheology measurements of fragile, heterogeneous, self-assembled block copolypeptide hydrogels revealed that solvent exchange via convective mixing and dialysis can lead to significantly different gel properties and that commonly applied sample preparation protocols for the characterization of soft biomaterials could lead to erroneous conclusions about microstructural dynamics. Systematic investigations by varying key parameters, like molecular structure, gel concentration, salt concentration, and tracer particle size for microrheology, revealed that subtle variations in molecular architecture can cause major structural and microrheological changes in response dynamics. Moreover, the results showed that the method can be applied for studying gel formation and breakup kinetics. The research in this thesis facilitates the design of solvent-responsive soft materials with appropriate microstructural dynamics for in vivo applications like tissue engineering and drug delivery, and can also be applied to study the effect of solvents on self-assembly mechanisms in other responsive soft materials, such as polymer solutions and colloidal dispersions.

Due to the large extent to which important biological mechanisms are conserved evolutionarily, the study of a simple soil nematode, C. elegans, has provided the template for significant advances in biology. Use of this model organism has accelerated in recent years as developments of advanced reagents such as synapse localized fluorescent markers have provided powerful tools to study the complex process of synapse formation and remodeling. Even as much routine biology work, such as sequencing, has become faster and easier, imaging protocols have remained essentially unchanged over the past forty years of research. This, coupled with the ability to visualize small, complex features as a result of new fluorescent reagents, has resulted in genetic screens in C. elegans becoming increasingly labor intensive and slow because microscopy mainly relies on manual mounting of animals and phenotyping is usually visually done by experts. Genetic screens have become the rate limiting factor for much of modern C. elegans research. Furthermore, phenotyping of fluorescent expression has remained a primarily qualitative process which has prevented statistical analysis of subtle features. To address these issues, a comprehensive system to allow autonomous screening for novel mutants was created. This was done by developing novel microfluidic devices to enable high-throughput screening, systems-level components to allow automated operation, and a computer vision framework for identification and quantitative phenotyping of synaptic patterns. The microfluidic platform allows for imaging and sorting of thousands of animals at high-magnification within hours. The computer vision framework employs a two-stage feature extraction to incorporate local and regional features and allows for synapse identification in near real-time with an extremely low error rate. Using this system thousands of mutagenized animals were screened to indentify numerous novel mutants expressing altered synaptic placement and development. Fully automated screening and analysis of subtle fluorescent phenotypes will allow large scale RNAi and drug screens. Combining microfluidics and computer vision approaches will have a significant impact on the biological community by removing a significant bottleneck and allowing large-scale screens that would have previously been too labor intensive to attempt.