Fluorescence-based assays have gained an ever-increasing popularity in life sciences. One of these rapidly emerging techniques is Protein Induced Fluorescence Enhancement (PIFE). Traditional explanations of PIFE focused exclusively on the role of the protein and largely neglected the role of the mediator DNA. In the same time, the existing models of PIFE were denying its exactly opposite effect. In the first part of the current dissertation we focus on a better understanding of PIFE, stimulated by the direct observation of its opposite effect, Induced Fluorescence Enhancement Quenching (PIFQ). This study offered us the leverage for obtaining on-demand fluorescence modulation in cyanine dyes. The following two chapters harvest this control over fluorescence modulation to generate two biotechnology applications: a sensitive potassium sensor with embedded fluorescent transducer, and a simple protocol for the fluorescent detection of His-tagged proteins. In the last part, a variety of fluorescence tools including Förster resonance energy transfer, fluorescence enhancement, and fluorescence quenching are employed for a much more complex task; to demystify the behavior of the human Maturation of Okazaki Fragments (MOF) machinery. First, we reconstituted the human MOF reaction and showed that it behaves considerably different than its well-established yeast homolog. Subsequently, our toolbox of fluorescence-based assays was used to pinpoint the kinetics and dynamics that lead to this unexpected MOF behavior.

A biosensor is an analytical device integrating a biological element and a physicochemical transducer that convert a biological response into a measurable signal. The advantages of biosensors include low cost, small size, quick, sensitivity and selectivity greater than the conventional instruments. Biosensors have a wide range of applications ranging from clinical diagnostics through to environmental monitoring, agriculture industry, et al. The different types of biosensors are classified based on the sensor device as well as the biological material. Biosensors can be broadly classified into (piezoelectric, etc.), electrochemical biosensors (potentiometric, amperometric, etc.), and optical types of biosensors (fiber optics, etc.). Here, we introduce a novel microfluidics-integrated biosensor platform system that can be flexibly adapted to form individual biosensors for different applications. In this dissertation, we present five examples of different emerging areas with this biosensor system including anti-cancer drug screening, glucose monitoring, heavy metal elements measurement, obesity healthcare, and waterborne pathogen DNA detection. These micro-biosensors have great potential to be further developed to emerging portable sensing devices especially for the uses in the developing and undeveloped world. At the last chapter, Raman spectroscopy applied to assess gestational status and the potential for pregnancy complications is presented and discussed. This technique could significantly benefit animal reproduction.

No description available.

Magnetic biosensors detect biological targets through sensing the stray field of magnetic beads which label the targets. Commonly, magnetic biosensors employ the “sandwich” method to immobilize biological targets, i.e., the targets are sandwiched between a bio-functionalized sensor surface and bio-functionalized magnetic beads. This method has been used very successfully in different application, but its execution requires a rather elaborate procedure including several washing and incubation steps. This dissertation investigates a new magnetic biosensor concept, which enables a simple and effective detection of biological targets. The biosensor takes advantage of the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. First, the detection of super-paramagnetic beads via magnetic tunnel junction (MTJ) sensors is implemented. Frequency modulation is used to enhance the signal-to-noise ratio, enabling the detection of a single magnetic bead. Second, the concept of the magnetic biosensor is investigated theoretically. The biosensor consists of an MTJ sensor, which detects the stray field of magnetic beads inside of a trap on top of the MTJ. A microwire between the trap and the MTJ is used to attract magnetic beads to the trapping well by applying a current to it. The MTJ sensor’s output depends on the number of beads inside the trap. If biological targets are in the sample solution, the beads will form bead compounds consisting of beads linked to the biological targets. Since bead compounds are larger than bare beads, the number of beads inside the trapping well will depend on the presence of biological targets. Hence, the output of the MTJ sensor will depend on the biological targets. The dependences of sensor signals on the sizes of the MTJ sensor, magnetic beads and biological targets are studied to find the optimum constellations for the detection of specific biological targets. The optimization is demonstrated for the detection of E. coli, and similar optimization processes can be performed for the detection of other biological targets. Third, we demonstrate the new magnetic biosensor concept using a mechanical trap capable of detecting nucleic acids via the size difference between bare magnetic beads and bead compounds. The bead compounds are formed through linking nonmagnetic beads of 1 µm in diameter and magnetic beads of 2.8 µm in diameter by the target nucleic acids. The purpose of the nonmagnetic beads is to increase the size of the compounds, since the nucleic acid is very small compared to the magnetic beads. Alternatively, smaller magnetic beads could be used but their detection would be more challenging. Finally, an enhanced version of the magnetic biosensor concept is developed using an electromagnetic trap for the detection of E. coli. The trap is formed by a current-carrying microwire that attracts magnetic beads into a virtual sensing space. As in the case of the mechanical trap, the sensor signal depends on the number of beads inside of the sensing space. The distance which magnetic beads can be detected from by the MTJ sensor defines the sensing space. The results showed that the output signal depends on the concentration of E. coli in the sample solution and that individual E. coli bacterium inside the sensing space could be detected using super-paramagnetic beads that are 2.8 µm in diameter. In summary, this dissertation investigates a new magnetic biosensor concept, which detects biological targets via the size difference between bare magnetic beads and compounds of magnetic beads and biological targets. The new method is extremely simple and enables the detection of biological targets in two simple steps and within a short time. The concept is demonstrated for the detection of nucleic acid and E. coli.

No description available.

Biosensors monitor physiological activities for diagnosis and treatment of disease. Molecularly imprinted polymers (MIPs) are a viable synthetic approach for molecular recognition in biosensing. For biosensing purposes, the most important properties in MIP optimization are sensitivity and selectivity towards a desired analyte. This study aims to optimize MIP sensitivity and selectivity by varying the amount and type of cross-linker used in the synthesis of cortisol and melatonin. The four cross-linkers tested were trimethylpropane trimethacrylate (TRIM), ethyleneglycodimethacrylate (EGDMA), divinylbenzene (DVB), and pentaerythritol triacrylate (PETRA). Based on literature, the following ratios were used for the template molecule to functional monomer to cross-linker in MIP synthesis: for EGDMA cross-linked polymers, 1:6:30; for TRIM and PETRA cross-linked polymers, 1:8:8, 1:6:3, and 1:8:35; for DVB cross-linked polymers, 1:6:30, 1:4:16, and 4:1:60. The polymers were ground and washed, then suspended in a polyvinyl matrix which was spin-coated onto an organic electrochemical transducer (OECT). The device performance was evaluated using electrochemical impedance spectroscopy. For each device, the impedance was measured in electrolyte solutions containing target molecules in concentrations ranging from 1 pM to 100 uM. The impedance was plotted against the analyte concentration to give the sensing slope, which is a measurement for the binding affinity of the polymer. For a device to be considered sensitive, its sensing slope should be greater than its non-imprinted counterpart by a factor above the error margin (+/- 1.79). Of the devices tested, CM1835T (highly cross-linked with TRIM) showed sensitivity towards cortisol, but lacks selectivity towards cortisol over its structural analog, estradiol. Of the melatonin selective polymers, MM163T (low cross-linking with TRIM), MM1630D, and MM4160D (both highly cross-linked with DVB) all showed promising results in sensitivity to melatonin. Overall, the results indicate that high degrees of cross-linking in MIPs improve sensitivity for large, rigid, non-aromatic molecules such as cortisol; however there is no correlation between selectivity and the degree of cross-linking. Meanwhile, divinylbenzene as a cross-linker improves sensitivity and selectivity towards aromatic analytes such as melatonin and estradiol. This study could be improved upon by further characterization of imprinted and non-imprinted polymers, investigation of molecular dynamics, and optimization of devices.

Nanofabrication techniques produce materials with enhanced physicochemical properties through a combination of nanoscale roughness and the use of chemically diverse polymers which enable advanced applications in separation science (air/water purification), tissue engineering, and biosensing. Since the late 1990’s, electrospinning has been extensively studied and utilized to produce nano- to microfiber meshes with 3D porosity on the gram scale. By combining a high surface area to volume ratio and tunable surface chemistry, electrospinning is a facile platform for generating non-woven polymeric fibers for many biomedical and industrial applications. This thesis describes three applications of electrospun nano- and microfiber meshes spun from both commercially available and novel polymer systems for: 1) oil and water separation after an accidental oil spill; 2) ultraviolet light controlled protein and cell patterning throughout 3-dimensional nanofiber meshes; and 3) novel diagnostic platform by combining electrospun nanofiber meshes with solid state nanopores for enhanced single molecule nucleic acid and protein detection. Each application embodies the philosophy that electrospun materials have the potential to solve a wide variety of problems by simply tuning the physicochemical properties and mesh morphologies towards the design requirements for a specific problem. For example, to solve the problem of recovering crude oil after an oil spill while generating a minimal waste burden, a hydrophobic and biodegradable microfiber mesh was designed to repeatedly separate oil and water and naturally biodegrade after use. In order to solve the problem of spatiotemporal placement of cells within a 3-dimensional tissue engineering construct, an ultraviolet light activated mesh was designed to transition from hydrophobic (water impermeable) to hydrophilic (water permeable) upon exposure to ultraviolet light facilitating protein and cell patterning. Finally to address two problems with single molecule solid state nanopore biosensors, namely rapid nucleic acid translocation rates and limited protein identification capabilities, a new biosensor platform was developed based on two novel polymeric systems which were synthesized and electrospun into high surface area nanofiber mesh coatings. / 2018-02-17T00:00:00Z

Indiana University-Purdue University Indianapolis (IUPUI) / Type 1 diabetes (T1D) is a multifactorial disease involving genetic and environmental factors. One of the factors implicated in disease pathogenesis is early life viral infection. A typical immune response to viral infection includes production of type 1 interferons (IFN), such as IFN-α, which can induce stress in the pancreatic β-cells. Reactive oxygen species (ROS) accumulation occurs after exposure to other inflammatory cytokines, causing oxidative stress that may be linked to T1D pathogenesis. Therefore, we hypothesized that IFN-α may also elicit β-cell ROS accumulation. Our in vivo and in vitro experiments with human islets showed rapid and heterogenous ROS accumulation with IFN-α. Although T1D is characterized by autoimmune destruction of β-cells, some cells survive this persistent attack. We hypothesized that survival/ death of β-cells could be attributed to the ability to effectively mitigate ROS accumulation. One mechanism to mitigate ROS is autophagy, which degrades and recycles cellular components to promote cellular homeostasis. We observed an impairment in autophagy in β-cells of donors with T1D as well as in islets of diabetic non-obese diabetic (NOD) mouse model of autoimmune diabetes. Autophagic flux was also impaired in diabetic NOD mouse islets, further confirming impairment of autophagy. Interestingly, we observed an induction of autophagy after acute treatment with IFN-α both in vitro and in vivo, suggesting compensatory upregulation of autophagy to restore homeostasis. Similarly, we observed an increase in autophagosomes and telolysosomes in β-cells of normoglycemic autoantibody positive organ donors compared to nondiabetic organ donors. Together, these data implicate a defect in the final degradation step of autophagy involving lysosomes. Therefore, we analyzed the activity and expression of lysosomal cysteine protease Cathepsin H (CTSH, a T1D susceptibility locus), and found both to be increased in islets of pre-diabetic NOD mice. Together, these data support compensatory hyperactivation of lysosomal enzymes prior to overt diabetes, potentially to rid the cell of ROS and degradation-resistant oxidized proteins and lipids. We also observed that C57Bl/6J mice lacking a key autophagy enzyme, ATG7, in their β-cells, spontaneously developed hyperglycemia. Collectively, these data highlight the importance of -phagic degradation process in the pathogenesis of T1D. / 2022-12-28

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第17895号 / 農博第2018号 / 新制||農||1017(附属図書館) / 学位論文||H25||N4791(農学部図書室) / 30715 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 加納 健司, 教授 三芳 秀人, 教授 小川 順 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21799号 / 工博第4616号 / 新制||工||1719(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 浜地 格, 教授 跡見 晴幸, 教授 秋吉 一成 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM