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3D printing has gained substantial interest as an adaptable and low-cost technology for rapid prototyping and production of research tools owing to its fast design-to-object workflow (Fig. 1), ease of operation, and ability to fabricate relatively complex and intricate structures directly from computer-aided design (CAD) representations. Due to the advantages 3D printing offers over other more time-consuming and labor-intensive fabrication methods like photolithography, 3D printing has been especially helpful in the development and production of flow cells and other fluidic devices. 3D printing allows for complex channel geometries, and the complete structure, including ports for connecting commercially available tubing, may be prepared from a single CAD file. As a result of these conveniences, 3D-printed fluidic devices have recently emerged as effective candidates for research in sensing applications. In these studies, we demonstrate electrochemical immunoassays for the biomarker protein S100B, which has been related to conditions like skin cancer and brain injuries, based on 3D-printed flow-cells with modularly integrated electrodes. The fluidic devices in these studies are prepared from photocurable resin and feature channel dimensions of ~400 µm. The device design includes ports for interfacing the channel with commercial fittings and tubing for fluid delivery as well as an access point for the antibody-modified electrode. Sensing is accomplished through a sandwich-type electrochemical immunoassay strategy, leading to sensitive detection of S100B.

In this dissertation, microfluidic systems that integrate antibody-based sample preparation methods with electrophoretic separation are developed to analyze multiple biomarkers in a point-of-care setting. To form an affinity column, both monolith materials and wall-coated channels were explored. I successfully demonstrated that monolith columns can be prepared in microfluidic devices via photopolymerization. The selectivity of monolith columns was improved by immobilizing antibodies on the surface. These affinity columns can selectively enrich target analytes and reduce the signal of contaminant proteins up to 25,000 fold after immunoaffinity extraction. These results clearly demonstrate that microchip affinity monoliths can selectively concentrate and purify target analytes through specific antibody-antigen interactions. These monolith columns operated well for simple systems such as buffered solution, but suffered from clogging with real biological samples such as human serum. Therefore, I developed new affinity columns using a wall coating protocol. To form the affinity columns, a thin film of a reactive polymer was UV polymerized in a microchannel. Antibodies were attached by reaction between the polymer epoxy groups and antibody amine groups. All steps, including loading, washing, and elution for affinity extraction, as well as capillary electrophoresis analysis, were achieved simply via applying voltages to reservoirs on the microdevice. By adding reservoirs containing alpha-fetoprotein (AFP) standard into the same device, a quantitative method, either standard addition or calibration curve, can also be performed on-chip. These polymer microdevices have been applied in determining AFP levels in spiked serum samples, and the results are comparable with the values measured using a commercial enzyme linked immunosorbent assay kit. These microchips have also been adapted for detection of multiple biomarkers by immobilizing different antibodies on the affinity column. Four kinds of antibodies were attached to microchip columns, and the amounts of immobilized antibodies were characterized. The fluorescence signals of all four protein antigens were in the same range after rinsing, indicating that the derivatization reaction had little bias toward any of the four antibodies. With spiked human blood serum samples, four proteins in the ng/mL range were simultaneously quantified using both calibration curves and standard addition. In general, the calibration curve and standard addition results were close to the known spiked concentrations. These results indicate that my integrated microdevices can selectively retain and analyze targeted compounds in clinical samples. Moreover, my platform is generalizable and applicable for the simultaneous quantification of multiple biomarkers in complex matrices.

Biomarkers present a non-invasive means of detecting cancer because they can be obtained from body fluids. They can also be used for prognosis and assessing response to treatment. To limit interferences it is essential to pretreat biological samples before analysis. Sample preparation methods include extraction of analyte from an unsuitable matrix, purification, concentration or dilution and labeling. The many advantages offered by microfluidics include portability, speed, automation and integration. Because of the difficulties encountered in integrating this step in microfluidic devices most sample preparation methods are often carried out off-chip. In the fabrication of micro-total analysis systems it is important that all steps be integrated in a single platform. To fabricate polymeric microdevices, I prepared templates from silicon wafers by the process of photolithography. The design on the template was transferred to a polymer piece by hot embossing, and a complete device was formed by bonding the imprinted piece with a cover plate. I prepared affinity columns in these devices and used them for protein extraction. The affinity monolith was prepared from reactive monomers to facilitate immobilization of antibodies. Extraction and concentration of biomarkers on this column showed specificity to the target molecule. This shows that biomarkers could be extracted, purified and concentrated with the use of microfluidic affinity columns.I prepared negatively charged ion-permeable membranes in poly(methyl methacrylate) microchips by in situ polymerization just beyond the injection intersection. Cancer marker proteins were electrophoretically concentrated at the intersection by exclusion from this membrane on the basis of both size and charge, prior to microchip capillary electrophoresis. I optimized separation conditions to achieve baseline separation of the proteins. Band broadening and peak tailing were limited by controlling the preconcentration time. Under my optimized conditions a 40-fold enrichment of bovine serum albumin was achieved with 4 min of preconcentration while >10-fold enrichment was obtained for cancer biomarker proteins with just 1 min of preconcentration. I have also demonstrated that the processes of sample enrichment, on-chip fluorescence labeling and purification could be automated in a single voltage-driven platform. This required the preparation of a reversed-phase monolithic column, polymerized from butyl methacrylate monomers, in cyclic olefin copolymer microdevices. Samples enriched through solid phase extraction were labeled on the column, and much of the unreacted dye was rinsed off before elution. The retention and elution characteristics of fluorophores, amino acids and proteins on these columns were investigated. A linear relationship between eluted peak areas and protein concentration demonstrated that this technique could be used to quantify on-chip labeled samples. This approach could also be used to simultaneously concentrate, label and separate multiple proteins.

Rapid determination of the concentrations of molecules related to diseases can provide timely information for treatment options. However, most biomarker quantitation methods require costly and complex equipment. On the other hand, point-of-care systems have less complex instrumentation needs than laboratory-based equipment, but often provide less information; for example, biomarker presence or absence instead of concentration. A complete analysis setup addressing key limitations of both laboratory-based and portable systems is highly desirable. I developed microfluidic devices with visual inspection readout of a target’s concentration from microliter volumes of solution flowed into a microchannel. Microchannels are formed within polydimethylsiloxane (PDMS), and the surfaces are coated with receptors. Capillary flow of target solution in the channel crosslinks the top and bottom surfaces, which constricts the channel and stops flow. The flow distance of the target solution in the channel before flow stops indicates the target’s concentration, enabling simple visual inspection readout without complex detection instrumentation. Because of its easy readout and portability, my system has great potential for use in point-of-care diagnostics. I initially demonstrated a proof-of-concept assay using biotin-streptavidin. Solution capillary flow distances scaled linearly with the negative logarithm of streptavidin concentration over a 100,000-fold range. I measured streptavidin concentrations as low as 1 ng/mL using these microsystems, demonstrating low detection limits. I also characterized the mechanism wherein time-dependent channel constriction in the first few millimeters leads to concentration-dependent flow distances. I demonstrated the visual detection and quantification capability of my system to determine an antigen target, thymidine kinase 1 (TK1). I developed surface modification methods for carrying out flow assays and verified receptor attachment on channel surfaces using fluorescence imaging. I obtained a 1 ng/mL TK1 detection limit in flow assays. I also demonstrated nucleic acid quantitation in my flow devices. I detected specific DNA targets in buffer and synthetic urine at 10 pg/mL levels. A dynamic range of 106 was obtained with single-base mismatch specificity. DNA analogues of two miRNA biomarkers were measured near clinically significant levels, showing great promise for future medical application. The promising results demonstrate that this diagnostic tool offers a simple route to analyte quantitation in microliter volumes, with excellent potential for point-of-care application.

Inexpensive label-free detection of biomarker panels in serum could revolutionize earlycancer diagnosis and treatment. Such detection capabilities may be possible with dynamicnanochannels in conjunction with electrical impedance measurement. In Dr. Greg Nordin's lab I designed, fabricated and tested several iterations of these sensors with polydimethyl-siloxane microfluidics. The final design yielded a dynamic nanochannel array sensor thatshowed a 140% impedance change when exposed to 14µM bovine serum albumin in phos-phate buffered saline. For the geometry and noise limits of the tested device, simulationsindicated that a minimum detectable concentration of 20pM with specifically bound strep-tavidin should be possible. However, the polydimethylsiloxane approach is also shown to beproblematic in meeting the trade-offs required for a practical device. Consequently, alter-native materials and designs are suggested to reduce the minimum detectable concentrationto the high femtomolar range, which would be attractive for detection of many medicalbiomarkers.

Ideally, a nutritional biomarker serves as an objective measure of the intake of a particular food or nutrient, may provide a reflection of health and disease processes, and can aid in the development of personalized nutritional recommendations. However, few food biomarkers have been validated and most have yet to be critically appraised in the literature. With the increased use of metabolomics in population-based studies, it is important to identify the sources of variability in nutritional biomarkers that may be attributed to intrinsic physiologic characteristics and extrinsic factors so that exposure-outcome associations can be examined more accurately. Additionally, circulating metabolites are associated with obesity-related changes in gut microbiome but there has been limited integration of metabolomics with microbiome in childhood obesity, and even less is known in non-white populations. This dissertation presents a series of studies that provide direct support for utility of nutritional biomarkers in population-based studies. The first study, presented in Chapter 2, contributes to the growing literature on food-based biomarkers by generating a comprehensive list of metabolites associated with a comprehensive list of all individual foods and food groups, and rated the evidence based on interstudy repeatability and study design. Chapter 3 identifies sources of variability in serum metabolite concentrations in White Europeans and South Asian pregnant women, thereby guiding appropriate statistical modeling when utilizing metabolomics in nutritional epidemiological studies. Chapter 4 provides results from a multi-omics integration analysis of serum metabolites and amplicon sequence variants of 16S ribosomal RNA genes to identify biomarkers that discriminate children with and without obesity. Collectively, the results showed that a specific food/food group may give rise to many metabolites, however in several cases, a single metabolite can be a good indicator of food intake. Dietary factors explained the highest proportion of variability in exogenous food-based biomarkers relative to non-dietary factors, whereas the contribution of non-dietary factors was either similar or lower for metabolites that can either be produced endogenously, biotransformed by gut microbiota, and/or derived from more than one food source. Most of the circulating metabolites differed by ethnicity (South Asian and White Europeans). Biomarkers with good evidence can be considered direct surrogates for food intake, however, they can be influenced by several non-dietary factors, which require appropriate consideration during the statistical analyses of the data. Finally, the results showed notable differences in serum metabolome and specific gut bacterial species, and between specific metabolites and bacterial species related to childhood obesity. Obesity related metabolic pathways such as glutamate and carnitine metabolism may provide insight into the metabolic processes related to early onset of obesity in childhood. / Dissertation / Doctor of Philosophy (Medical Science)

Thesis / Doctor of Philosophy (PhD)

In modern-day psycholinguistics, there is a rising interest in looking at bilingualism from a holistic perspective. Yet, only a few are the methods employed as efficient and comprehensive of all the variables and factors that affect language acquisition and the motivation for someone to seek to acquire another language. Historically, research has also recognized the extreme value of bilingualism at a neurological level (we know that it offers protection against neurodegeneration and increased grey matter presence in some brain regions, aiding in cognitive performance overall). However, we ignore the full extent of the mechanisms that aid this complex process and the trajectory the speaker takes from initial exposure to another language to becoming competent. Vocal biomarkers are a currently emerging topic in behavioral research due to their potential uses in the early detection of psychopathology and neurodegeneration, potentially by just recording a person's voice and relying on an app to analyze and provide a report. We created a comprehensive battery to measure bilingualism, including surveys and a vocal assessment, considering specific vocal patterns (jitteriness, sustentation, and others). Participants took a modified version of a golden reference test for bilingualism research, the Bilingual Language Profile, to which we added a technology usage question and a cultural influences section. We then collected voice samples from them, completing three tasks.

Most of existing techniques cannot be used to detect molecular biomarkers (i.e., protein and DNA) contained in complex body fluids due to issues such as enzyme inhibition or signal interference. This thesis describes a nanoparticle-based thermal detection method for the highly sensitive detections of multiple DNA biomarkers or proteins contained in different type of fluids such as buffer solution, cell lysate and milk by using solid-liquid phase change nanoparticles as thermal barcodes. Besides, this method has also been applied for thrombin detection by using RNA aptamer-functionalized phase change nanoparticles as thermal probes. Furthermore, using nanostructured Si surface that have higher specific area can enhance the detection sensitivity by four times compared to use flat aluminum surfaces. The detection is based on the principle that the temperature of solid will not rise above its melting temperature unless all solid is molten, thus nanoparticles will have sharp melting peak during a linear thermal scan process. A one-to-one correspondence can be created between one type of nanoparticles and one type of biomarker, and multiple biomarkers can be detected simultaneously using different type nanoparticles. The melting temperature and the heat flow reflect the type and the concentration of biomarker, respectively. The melting temperatures of nanoparticles are designed to be over 100°C to avoid interference from species contained in fluids. The use of thermal nanoparticles allows detection of multiple low concentration DNAs or proteins in a complex fluid such as cell lysate regardless of the color, salt concentration, and conductivity of the sample.