Relevant Degree Programs
Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - May 2019)
Integrated sensing and biosensing microfluidic systems often require sealing between polydimethylsiloxane (PDMS), glass, and gold interfaces. Studying substances that can self-organize onto glass and gold surfaces may achieve these goals and pave the way for new technological advances. Work presented in this thesis focuses on characterizing the adsorption of N-[(3-trimethoxysilyl)propyl]ethylene-diamine triacetic acid (or TMS-EDTA) on Au and applying this knowledge to construct leak-free PDMS-based electrochemical cells. First, surface analysis of TMS-EDTA-modified Au surfaces was conducted using various techniques. Water contact angle measurements and X-ray photoelectron spectroscopy confirm that the carboxylated silane can chemically modify Au surfaces. Atomic force microscopy studies indicate that a uniform surface coverage with monolayer thickness is formed. Infrared spectroscopy studies indicate that there is little evidence of siloxane cross-linking. Surface plasmon resonance results suggest that the carboxylates on TMS-EDTA-modified Au are available for streptavidin immobilization. Second, electrochemistry was used to determine the Gibbs free energies of adsorption of TMS-EDTA on Au under aqueous conditions. Electrochemical differential capacitance measurements reveal that the potential-dependent free energies of adsorption are ∼ - 20 to - 30 kJ/mol (for potentials between - 0.5 and 0.2 V) in the complex electrolyte solution used. Furthermore, at highly negative potentials ( ∼ - 1.1 V), TMS-EDTA adsorbs minimally onto the Au surface. Third, PDMS surfaces were functionalized to present primary amino groups, and glass or gold slides were functionalized to present carboxyl groups. Strong bonding was achieved by bringing the two surfaces in contact and reacting at room temperature. Shear tests reveal that the novel carboxyl-amine bonding strategy achieved a comparable bond strength as the conventional methods. Subsequently, TMS-EDTA was applied to construct leak-free PDMS-based electrochemical cells. Pressure leak tests were conducted to provide a more realistic measure of the bond strengths under aqueous conditions. A method to electrochemically remove the adsorbed TMS-EDTA layer off of the Au electrode, while maintaining the sealed cell chamber, was also developed. The characterization studies and fabrication strategy presented have led to the development of leak-free PDMS-based electrochemical devices that are suitable for sensing and biosensing applications.
The observation of biomolecular structure is critical for the fundamental understanding of biological function. In this work, Fiber-optic UV Resonance Raman Spectroscopy (FO-UVRRS) was employed to study a number of structure-function relationships.A suite of metal-containing dioxygenase enzymes were studied in order to determine the substrate protonation state in the enzyme-substrate complex. Two enzymes with a high degree of sequence identity were studied, where one naturally incorporates a Fe²⁺ metal and the other uses Mn²⁺. Both enzymes react with the same substrate to form an equivalent muconic semialdehyde product. The enzymes are capable of incorporating the non-native metal into the enzymes with no effect on the kinetic properties. The Raman results show that the nature of the metal has no effect on the substrate protonation state. The degradation of 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) by BphD in the biphenyl catabolic pathway was studied using FO-UVRRS. Previous reports suggest that enol-keto tautomerization was a critical step in the mechanism of the carbon-carbon bond hydrolase. Hydrolytically impaired variants of BphD were used to study the binding mode of HOPDA. The results show that HOPDA binds to these variants in a strained-enolate geometry and does not undergo an enol-keto tautomerization upon enzyme binding. A fundamental FO-UVRRS study of locked nucleic acid (LNA) olgiomers was performed. LNA bases contain a C4’ to O2’ methylene bridge within the furanose ring of the nucleotide. The research results show that incorporation of a LNA induces a conformational change in the glycosyl bond between the backbone and the base. The results also show that incorporation of an LNA base induces changes in the secondary structure of the nucleic acid.In another study, chemical contamination of synthetic DNA oligomers was observed using FO-UVRRS. The data showed that commercially-available oligomers purified using standard desalting conditions are contaminated with residual benzamide. The results show that a previously assigned –NH₂ scissors vibration in the Raman study of oligomers overlaps with a prominent benzamide vibrational band, calling into question these previous assignments. The results also demonstrate that the extent of benzamide contamination varies from sample-to-sample and between different commercial sources.
In research, the usefulness of the analytical results is crucially dependent upon the quality of the measurements. However, data measured by instruments is always corrupted. The desired information—-the "signal"-—may be distorted by a variety of effects, especially noise. In spectroscopy, there are two additional significant causes of signal corruption—-instrumental blurring and baseline distortion.Consequently, signal processing is required to extract the desired signal from the undesired components. Thus, there is an on-going need for signal enhancement algorithms which collectively can 1) perform high quality signal-to-noise-ratio (SNR) enhancement, especially in very noisy environments, 2) remove instrumental blurring, and 3) correct baseline distortions. Also, there is a growing need for automated versions of these algorithms. Furthermore, the spectral analysis technique, Two-Dimensional Correlation Spectroscopy (2DCoS), needs similar solutions to these same problems.This dissertation presents the design of four new signal enhancement algorithms, plus the application of two others, to address these measurement problems and issues. Firstly, methods for one-dimensional (1D) data are introduced—-beginning with an existing algorithm, the Two-Point Maximum Entropy Method (TPMEM). This regularization-based method is very effective in low-SNR signal enhancement and deconvolution. TPMEM is re-examined to clarify its strengths and weaknesses, and to provide ways to compensate for its limitations. Next, a new regularization method, based on the chi-squared statistic, is introduced and demonstrated in its ability for noise reduction and deconvolution. Then, two new 1D automated algorithms are introduced and demonstrated: a noise filter and a baseline correction scheme.Secondly, a new two-dimensional (2D) regularization method (Matrix-MEM or MxMEM), derived from TPMEM, is introduced and applied to SNR enhancement of images. Lastly, MxMEM and 2D wavelets are applied to 2DCoS noise reduction.The main research contributions of this work are 1) the design of three new high performance signal enhancement algorithms for 1D data which collectively address noise, instrumental blurring, baseline correction, and automation, 2) the design of a new high performance SNR enhancement method for 2D data, and 3) the novel application of 2D methods to 2DCoS.
Master's Student Supervision (2010 - 2018)
Raman microspectroscopy is a non-destructive, label-free technique that offers information-rich molecular analysis of living cells. This work is the first reported Raman spectroscopic study of human induced pluripotent cells (hiPSCs), a very promising new source of non-embryonic pluripotent stem cells for drug screening, toxicity assessment, regenerative therapies, and clinical research. The Raman signatures of hiPSCs and human embryonic stem cells (hESCs) were found to be highly similar, and both distinguishable from differentiated hESCs in terms of relative Raman peak intensities and variances. Principal component analysis (PCA) of the Raman spectra demonstrated a clear distinction between hiPSCs and differentiated hESCs. Additionally, the effects of culture confluencies and cell line differences on Raman spectra of hiPS cells was investigated. It was confirmed that the spectral similarity between hiPSCs and hESCs, along with the dissimilarity between hiPSCs and differentiated hESCs were qualitatively consistent over various cell culture confluencies, and between the two available hiPS cell lines. Therefore, the results suggested that the overall cellular composition of hiPSC was more similar to that of the hESC that these cells were designed to resemble than the somatics cell from which they were derived. It is suggested that the observed spectral differences between hiPSC and hESC may be due to factors relating to reprogramming (rather than cell density difference or cell line artifacts). Attempts were also made to investigate how Raman features of hiPS cells change during their differentiation. The pluripotent and differentiated iPSCs exhibited significantly different Raman spectral profiles; these differences were qualitatively similar to, but less marked, than differences between pluripotent and differentiated hESC. Overall, this work contributed important new data and practical insights into the utility of Raman microspectroscopy for characterization, identification, and discrimination of iPSCs and hESCs.