Typical bacterial analysis involves culturing and visualizing colonies on an array of agar plates. The growth patterns and colors among the array are used to identify the bacteria. For fast growing bacteria such as Escherichia coli, analysis will take one to two days. However, slow growing bacteria such as mycobacteria can take weeks to identify. In addition, there are some species of bacteria that are viable but nonculturable. This lengthy analysis time is unacceptable for life-threatening infections and emergency situations. It is clear that to decrease the analysis of the bacteria, the culturing and growth steps must be avoided. The goal of this research is to design, build, and test a device that could decrease the analysis time of bacteria. Device design accommodates for the varied growth and environmental conditions of expected samples for bacterial analysis. Clinical samples containing bacteria come in a wide variety of forms including urine, saliva, sputum, blood, etc. Each medium will have associated debris and other contaminants that must be isolated from bacteria before identification. This process can be challenging as bacteria and debris can range in size from a fraction of a micrometer to tens of micrometers. In addition, a device must be equipped to accurately identify bacteria regardless of growth conditions. Thus, to decrease the analysis time of bacteria, a device must be capable of isolation, concentration, and identification at a micron level. In this dissertation, a device was designed, built, and tested that incorporates dielectrophoresis for cell sorting and Raman spectroscopy for identification. Using the device, bacteria (1 μm in length) were successfully isolated away from 5 μm polystyrene spheres and Raman spectra of the trapped bacteria were collected. The simultaneous isolation and identification of bacteria from a mixed sample indicates the capability for the cDEP-Raman device to decrease the analysis time of bacteria from clinical samples.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第19724号 / 工博第4179号 / 新制||工||1644(附属図書館) / 32760 / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 平尾 一之, 教授 三浦 清貴, 教授 田中 勝久 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第21433号 / 人博第871号 / 2018||人博||871(吉田南総合図書館) / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 内本 喜晴, 教授 吉田 寿雄, 准教授 戸﨑 充男 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DFAM

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Self-assembly of organothiols (OTs) and thiolated biomolecules onto gold nanoparticle (AuNP) surfaces remains one of the most intense areas of nanoscience research and understanding molecular interfacial phenomena is crucial. Investigation of OT adsorption onto AuNPs, including OT structure and orientation on nanoparticle surfaces, is of fundamental importance in understanding the structure and function relationship of functionalized nanoparticles. Despite the great importance of the interfacial interaction of AuNPs, the exact mechanism of OT interactions with AuNPs has remained unclear and quantitative investigation of OT adsorption has been very limited. The research reported here focused on developing a fundamental and quantitative understanding of OT interactions with AuNPs in water. In studies of OT interactions with AuNPs in water, we found that the OTs form an adsorbed monolayer on AuNPs by releasing the sulfur-bound hydrogen as a proton and acidifying the ligand binding solution. The pH measurements suggest that there is a substantial fraction (up to 45%) of the protons derived from the surface adsorbed OTs retained close to the gold surface, presumably as the counter-ion to the negatively- charged, thiolate-covered AuNPs. Charge-transfer between the surfacesorbed thiolate and the AuNPs is demonstrated by the quenching of the OT UV-vis absorption when the OTs are adsorbed onto the AuNPs. Using a combination of surface enhanced Raman spectroscopy (SERS), density function calculations, and normal Raman spectroscopy, the pH dependence of mercaptobenzimadazole (MBI) adsorption onto AuNPs was systematically studied. By using the ratiometric SERS ligand quantification technique, MBI adsorption isotherms were constructed at three different pHs (1.4, 7.9, and 12.5). The Langmuir isotherms indicate that MBI thione has a higher saturation packing density (~­631 pmol/cm2) than MBI thiolate (~­568 pmol/cm2), but its binding constant (2.14 x 106 M-1) is about five times smaller than the latter (10.12 x 106 M-1). The work described in this dissertation provides a series of new insights into AuNP-OT interaction, and structure and properties of OTs on AuNPs.

Malondialdehyde (MDA) is the commonly accepted biomarker of lipid peroxidation. We reported the surface-enhanced Raman (SERS) detection of MDA using Thiobarbituric acid (TBA) as a molecular probe. The lowest concentration of HPLC purified TBA-MDA adduct that can be determined with reasonable signal to noise ratio is 0.45 nM. The specificity of the SERS technique has been demonstrated by comparing the SERS spectrum of TBA-MDA adduct with other TBA-aldehyde adducts. As a small organosulfur compound, TBA exhibits tremendous structural complexity. Discussed in this thesis is the drastic pH and concentration dependence of TBA SERS spectral features. To understand the origins of the TBA SERS spectral variations, UV-Vis spectra of TBA were also acquired under same experimental conditions of SERS. Density function calculations (DFT) were performed for different TBA tautomers with different charge states to facilitate the SERS spectral interpretation, allowing us to speculate the type of tautomers dominating the nanoparticle surfaces.

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Polydopamine (PDA) surfaces have attracted much attention, both for their innate capability as a versatile biomaterial and their standalone antibacterial and adhesive properties. However, the mechanics of PDA deposition as well as the attributes of PDA-coated surfaces remain relatively underexplored despite their adaptability and ease of deposition. Two polydopamine surfaces from literature, smooth and rough PDA (sPDA and rPDA), were compared to a novel surface, inverted PDA (iPDA), to further explore their mechanochemical and bioactive properties. The iPDA surface displayed, by design, a smoother topography when compared to sPDA, with smaller aggregate structures covering 2.7% of the overall surface. However, the chemical signature obtained via Raman spectroscopy of these aggregates shared remarkable similarities at the 1370 cm-1 peak with the rougher rPDA surface, leading to the conclusion that gas exchange at the solution surface may play a critical role in determining PDA subunit composition despite dissimilar deposition methods. Atomic force microscopy (AFM) analysis concluded that the iPDA surface was ~17% more adhesive than other PDA types, while also displaying relatively large hysteresis and a small Young’s modulus. Human osteoblastic MG-63 cells cultured on all three surfaces revealed that a smoother surface topography correlated to more pronounced anisotropic spread independent of cell size, while a serum-independent component was also noted. This work provides a clearer insight into the nature of polydopamine surfaces by the creation of a viable new deposition method, providing an analysis of its mechanochemical and bioactive properties as well as a deeper understanding of the PDA coating process.