Optical fibers have been mostly used in fiber optic communications, imaging optics, sensing technology, etc. Fiber optic sensors have gained increasing attention for scientific and structural health monitoring (SHM) applications. In this study, fiber loop ringdown (FLRD) sensors were fabricated for scientific, SHM, and sensor networking applications. FLRD biosensors were fabricated for both bulk refractive index (RI)- and surface RI-based DNA sensing and one type of bacteria sensing. Furthermore, the effect of glucose oxidase (GOD) immobilization at the sensor head on sensor performance was evaluated for both glucose and synthetic urine solutions with glucose concentration between 0.1% and 10%. Detection sensitivities of the glucose sensors were achieved as low as 0.05%. For chemical sensing, heavy water, ranging from 97% to 10%, and several elemental solutions were monitored by using the FLRD chemical sensors. Bulk indexbased FLRD sensing showed that trace elements can be detected in deionized water. For physical sensing, water and cracking sensors were fabricated and embedded into concrete. A partially-etched single-mode fiber (SMF) was embedded into a concrete bar for water monitoring while a bare SMF without any treatment was directly embedded into another concrete bar for monitoring cracks. Furthermore, detection sensitivities of water and crack sensors were investigated as 10 ml water and 0.5 mm surface crack width, respectively Additionally fiber loop ringdowniber Bragg grating temperature sensors were developed in the laboratory; two sensor units for water, crack, and temperature sensing were deployed into a concrete cube in a US Department of Energy test bed (Miami, FL). Multi-sensor applications in a real concrete structure were accomplished by testing the six FLRD sensors. As a final stage, a sensor network was assembled by multiplexing two or three FLRD sensors in series and parallel. Additionally, two FLRD sensors were combined in series and parallel by using a 2×1 micro-electromechanical system optical switch to control sensors individually. For both configurations, contributions of each sensor to two or three coupled signals were simulated theoretically. Results show that numerous FLRD sensors can be connected in different configurations, and a sensor network can be built up for multiunction sensing applications.

Non-coding RNAs are involved in the regulation of most major cellular process in Escherichia coli. With current technologies, many of these molecules have been identified; however, the full scope of their regulatory interactions is still unknown. None of the techniques currently in use employ the regulatory effect of the RNAs, which is the major unifying attribute of these molecules, for their identification. This thesis presents projects involving the design of a dual-reporter plasmid and screening method in the discovery and characterization of RNA regulatory interactions The first project details the engineering of the dual reporter plasmid. This vector utilizes one fluorescent protein to detect regulatory events and a second to normalize for off-target effects. The second project utilizes this tool in the discovery and characterization of novel regulatory responses. This is accomplished by screening a library of intergenic regions for regulatory responses against a collection of metabolite. Interesting interactions involving nitrogen abundance, iron and uracil are identified and further examined. Finally, this thesis examines how this technology can be further expanded for the study of RNA regulatory functions. The use of the screening method for the detection of regulatory events caused by alternative minimal media composition and the potential for the dual reporter plasmid to aid in the study of riboswitches are investigated. / Thesis / Doctor of Science (PhD)

In zahlreichen lebenswichtigen Bereichen haben sich Biosensoren als unverzichtbare Messgeräte erwiesen. Der Nachweis von spezifischen Molekülen im Körper für eine frühzeitige Krankheitserkennung erfordert empfindliche und zugleich zuverlässige Messmethoden. Ein rasantes Fortschreiten im Bereich der Nanotechnologie führt dabei zur Entwicklung von Materialien mit neuen Eigenschaften, und damit verbunden, auch zu innovativen Anwendungsmöglichkeiten im Bereich der Biosensorik. Das Zusammenspiel von Nanotechnologie und Sensortechnik gewährleistet die Konstruktion von Sensoren mit empfindlicheren Nachweisgrenzen und kürzeren Reaktionszeiten. Die Option zur Integration und Miniaturisierung stellen daher einen erfolgreichen Einsatz in direkter Patientennähe in Aussicht, sodass Nanobiosensoren die Brücke zwischen Laborddiagnostik und Standardanwendungen schließen können. Die folgende Arbeit widmet sich der Anwendung von nanostrukturierten Biosensoren für einen empfindlichen und markierungsfreien Nachweis von Zielmolekülen. Ein Hauptaugenmerk liegt dabei auf der kontinuierlichen Messung von Biomarkern mit kompakten Auslesesystemen, die eine direkte Signalmeldung und somit eine Detektion in Echtzeit ermöglichen. Dies erfordert zunächst die sorgfältige Funktionalisierung von Sensoroberflächen mit geeigneten DNA-basierten Rezeptoren. Infolgedessen werden beispielhaft verschiedene Sensorsysteme, Analyten und Charakterisierungsmethoden vorgestellt sowie universelle Strategien für die erfolgreiche Konfiguration von Nanobiosensorplattformen präsentiert. Das erste Anwendungsbeispiel widmet sich einem plasmonischen Biosensor, bei dem vertikal ausgerichtete Gold-Nanoantennen Signale mittels sog. lokalisierter Oberflächenplasmonenresonanz (LSPR) erzeugen. Mit dem Sensor konnte erfolgreich die Immobilisierung, das nachträgliche Blocken sowie die anschließende Hybridisierung von DNA nachgewiesen werden. Mithilfe des LSPR-Sensors wurden gleichzeitig grundlegende Hybridisierungsmechanismen auf nanostrukturierten und planaren Oberflächen verglichen und damit verbunden die einzigartigen optischen Eigenschaften metallischer Nanostrukturen betont. In einem zweiten Anwendungsbeispiel misst ein elektrischer Biosensor kontinuierlich die Konzentration des Stressmarkers Cortisol im menschlichen Speichel. Der direkte, markierungsfreie Nachweis von Cortisol mit Silizium-Nanodraht basierten Feldeffekttransistoren (SiNW FET) wurde anhand zugrunde liegender Ladungsverteilungen innerhalb des entstandenen Rezeptor-Analyte-Komplexes bewertet, sodass ein Nachweis des Analyten innerhalb der sog. Debye-Länge ermöglicht wird. Die erfolgreiche Strategie zur Oberflächenfunktionalisierung im Zusammenspiel mit dem Einsatz von SiNW FETs auf einem tragbaren Messgerät wurde anhand des Cortisolnachweises im Speichel belegt. Ein übereinstimmender Vergleich der gemessenen Corisolkonzentrationen mit Werten, die mit einer kommerziellen Alternative ermittelt wurden, verdeutlichen das Potential der entwickelten Plattform. Zusammenfassend veranschaulichen beide vorgestellten Nanobiosensor-Plattformen die vielseitige und vorteilhafte Leistungsfähigkeit der Systeme für einen kontinuierlichen Nachweis von Biomarkern in Echtzeit und vorzugsweise in Patientennähe.:Kurzfassung I Abstract III Abbreviations and symbols V Content VII 1 Introduction 1 1.1 Scope of the thesis 4 1.2 References 6 2 Fundamentals 9 2.1 Biosensors 9 2.2 Influence of nanotechnology on sensor development 10 2.3 Biorecognition elements 12 2.3.1 Biorecognition element: DNA 13 2.3.2 Aptamers 14 2.3.3 Immobilization of receptors 15 2.4 Transducer systems 17 2.4.1 Optical biosensors - surface plasmon resonance 17 2.4.2 Electric Biosensors – Field-effect transistors (FETs) 21 2.5 Metal oxide semiconductor field-effect transistor - MOSFET 21 2.6 Summary 26 2.7 References 27 3 Materials and methods 33 3.1 Plasmonic biosensors based on vertically aligned gold nanoantennas 33 3.1.1 Materials 33 3.1.2 Manufacturing of nanoantenna arrays 34 3.1.3 Surface modification and characterization 35 3.1.4 Measurement setup for detection of analytes 38 3.2 SiNW FET-based real-time monitoring of cortisol 40 3.2.1 Materials 40 3.2.2 Manufacturing of silicon nanowire field effect transistors (SiNW FETs) 42 3.2.3 Integration of SiNW FETs into a portable platform 42 3.2.4 Biomodification and characterization of electronic biosensors SiNW FETs 42 3.2.5 Electric characterization of FETs 47 3.3 References 50 4 Plasmonic DNA biosensor based on vertical arrays of gold nanoantennas 51 4.1 Introduction - Optical biosensors operating by means of LSPR 53 4.2 Biosensing with vertically aligned gold nanoantennas 56 4.2.1 Sensor fabrication, characterization, and integration 56 4.2.2 Integration of microfluidics 58 4.2.3 Immobilization of probe DNA and backfilling 58 4.2.4 Hybridization of complementary DNA strands 62 4.2.5 Surface coverage and hybridization efficiency of DNA 69 4.2.6 Refractive index sensing 72 4.2.7 Backfilling and blocking 73 4.3 Summary 75 4.4 References 77 5 Label-free detection of salivary cortisol with SiNW FETs 83 5.1 Introduction 85 5.2 Design, integration, and performance of SiNW FETs into a portable platform 89 5.2.1 Structure and electrical characteristics of honeycomb SiNW FETs 89 5.2.2 Integration of SiNW FET into a portable measuring unit 91 5.2.3 Performance of SiNW FET arrays 93 5.3 Detection of biomolecules with SiNW FETs 102 5.3.1 General considerations for biodetection with FETs 102 5.3.2 Sensing aptamers with FETs 103 5.3.3 Biodetection of the analyte cortisol with SiNW FETs 104 5.3.4 Detection of cortisol with SiNW FETs 112 5.4 Summary 119 5.5 References 121 6 Summary and outlook 131 6.1 Summary 131 6.2 Perspectives – toward multiplexed biosensing applications 134 6.3 References 137 Appendix i A.1 Protocols i A.1.1 Functionalization of gold antennas with thiolated DNA i A.1.2 Functionalization of SiO2 with TESPSA and amino-modified receptors i A.1.3 Functionalization with APTES and carboxyl-modified receptors ii A.1.4 Preparation of microfluidic channels via soft lithography ii A.2 Predicted secondary structures iv A.2.1 Secondary structures of 100base pair target without probe-strands iv A.2.2 Secondary structures of 100base pair target with 25 base pair probe-strand x Versicherung xvii Acknowledgments xix List of publications xxi Peer-reviewed publications xxi Publications in preparation xxi Selected international conferences xxii Curriculum Vitae xxiii / Biosensors have proven to be indispensable in numerous vital areas. For example, detecting the presence and concentration of specific biomarkers requires sensitive and reliable measurement methods. Rapid developments in the field of nanotechnology lead to nanomaterials with new properties and associated innovative applications. Thus, nanotechnology has a far-reaching impact on biosensors' development, e.g., delivery of biosensing devices with greater sensitivity, shorter response times, and precise but cost-effective sensor platforms. In addition, nanobiosensors hold high potential for integration and miniaturization and can operate directly at the point of care - serving as a bridge between diagnostics and routine tests. This work focuses on applying nanostructured biosensors for the sensitive and label-free detection of analytes. A distinct aim is the continuous monitoring of biomarkers with compact read-out systems to provide direct, valuable feedback in real-time. The first step in achieving this goal is the adequate functionalization of nanostructured sensor surfaces with suitable receptors to detect analytes of interest. Due to their thermal and chemical stability with the possibility for customizable functionalization, DNA-based receptors are selected. Thereupon, universal strategies for confining nanobiosensor platforms are presented using different sensor systems, analytes, and characterization methods. As a first application, a plasmonic biosensor based on vertically aligned gold nanoantennas tracked the immobilization, blocking, and subsequent hybridization of DNA by means of localized surface plasmon resonance (LSPR). At the same time, the LSPR sensor was used to evaluate fundamental hybridization mechanisms on nanostructured and planar surfaces, emphasizing the unique optical properties of metallic nanostructures. In a second application, an electric sensor based on silicon nanowire field-effect transistors (SiNW FET) monitored the level of the stress marker cortisol in human saliva. Based on evaluating the underlying charge distributions within the resulting receptor-analyte complex of molecules, the detection of cortisol within the Debye length is facilitated. Thus, direct, label-free detection of cortisol in human saliva using SiNW FET was successfully applied to the developed platform and compared to cortisol levels obtained using a commercial alternative. In summary, both presented platforms indicate a highly versatile and beneficial performance of nanobiosensors for continuous detection of biomarkers in real-time and preferably point-of-care (POC).:Kurzfassung I Abstract III Abbreviations and symbols V Content VII 1 Introduction 1 1.1 Scope of the thesis 4 1.2 References 6 2 Fundamentals 9 2.1 Biosensors 9 2.2 Influence of nanotechnology on sensor development 10 2.3 Biorecognition elements 12 2.3.1 Biorecognition element: DNA 13 2.3.2 Aptamers 14 2.3.3 Immobilization of receptors 15 2.4 Transducer systems 17 2.4.1 Optical biosensors - surface plasmon resonance 17 2.4.2 Electric Biosensors – Field-effect transistors (FETs) 21 2.5 Metal oxide semiconductor field-effect transistor - MOSFET 21 2.6 Summary 26 2.7 References 27 3 Materials and methods 33 3.1 Plasmonic biosensors based on vertically aligned gold nanoantennas 33 3.1.1 Materials 33 3.1.2 Manufacturing of nanoantenna arrays 34 3.1.3 Surface modification and characterization 35 3.1.4 Measurement setup for detection of analytes 38 3.2 SiNW FET-based real-time monitoring of cortisol 40 3.2.1 Materials 40 3.2.2 Manufacturing of silicon nanowire field effect transistors (SiNW FETs) 42 3.2.3 Integration of SiNW FETs into a portable platform 42 3.2.4 Biomodification and characterization of electronic biosensors SiNW FETs 42 3.2.5 Electric characterization of FETs 47 3.3 References 50 4 Plasmonic DNA biosensor based on vertical arrays of gold nanoantennas 51 4.1 Introduction - Optical biosensors operating by means of LSPR 53 4.2 Biosensing with vertically aligned gold nanoantennas 56 4.2.1 Sensor fabrication, characterization, and integration 56 4.2.2 Integration of microfluidics 58 4.2.3 Immobilization of probe DNA and backfilling 58 4.2.4 Hybridization of complementary DNA strands 62 4.2.5 Surface coverage and hybridization efficiency of DNA 69 4.2.6 Refractive index sensing 72 4.2.7 Backfilling and blocking 73 4.3 Summary 75 4.4 References 77 5 Label-free detection of salivary cortisol with SiNW FETs 83 5.1 Introduction 85 5.2 Design, integration, and performance of SiNW FETs into a portable platform 89 5.2.1 Structure and electrical characteristics of honeycomb SiNW FETs 89 5.2.2 Integration of SiNW FET into a portable measuring unit 91 5.2.3 Performance of SiNW FET arrays 93 5.3 Detection of biomolecules with SiNW FETs 102 5.3.1 General considerations for biodetection with FETs 102 5.3.2 Sensing aptamers with FETs 103 5.3.3 Biodetection of the analyte cortisol with SiNW FETs 104 5.3.4 Detection of cortisol with SiNW FETs 112 5.4 Summary 119 5.5 References 121 6 Summary and outlook 131 6.1 Summary 131 6.2 Perspectives – toward multiplexed biosensing applications 134 6.3 References 137 Appendix i A.1 Protocols i A.1.1 Functionalization of gold antennas with thiolated DNA i A.1.2 Functionalization of SiO2 with TESPSA and amino-modified receptors i A.1.3 Functionalization with APTES and carboxyl-modified receptors ii A.1.4 Preparation of microfluidic channels via soft lithography ii A.2 Predicted secondary structures iv A.2.1 Secondary structures of 100base pair target without probe-strands iv A.2.2 Secondary structures of 100base pair target with 25 base pair probe-strand x Versicherung xvii Acknowledgments xix List of publications xxi Peer-reviewed publications xxi Publications in preparation xxi Selected international conferences xxii Curriculum Vitae xxiii

No description available.

No description available.

Rapid and high-sensitivity detections of biological analytes are critically important to ensure timely diagnosis of disease and effective monitoring of public health. Although various new biosensing platforms have been established as alternatives to conventional laboratory methods, most of these biosensing platforms suffer from insufficient sensitivities that severely limit their wide applications. To improve the detection sensitivities of these biosensors, surface modifications based on poly(amidoamine) (PAMAM) dendrimers and rolling circle amplification (RCA) have been proven to be effective methods. In this thesis, surface modification strategies based on PAMAM dendrimers and RCA have been applied on three biosensing platforms, including enzyme-linked immunosorbent assay (ELISA), localized surface plasmon resonance (LSPR) sensor chip, and affinity membrane, to improve their detection sensitivities. For the ELISA platform, glass-bottom and poly(styrene) 96-well plates are surface modified by dendrimer-aptamer conjugates to improve detection performances of human platelet-derived growth factor-BB using ELISA. The results show that the ELISA performed using the modified 96-well plates presents a much broader linear detection range and a significantly lower limit of detection (LOD) than conventional ELISA plates. For the LSPR platform, the dendrimer and aptamer modification strategy is employed to surface modify LSPR sensor chips for sensitive detection of the SARS-CoV-2 virus, and an RCA-AuNPs complex is developed to amplify the detection signals. The results show that the modified chip can sensitively detect the SARS-CoV-2 virus with a LOD of 148 vp/mL, suggesting that the modified LSPR chip and signal amplification method can be used for early diagnosis of Covid-19. For the affinity membrane platform, nylon membranes with dendrimer and dual-RCA surface modifications are developed to detect Escherichia coli O157:H7 in food samples. The surface-modified membranes significantly reduce the detection time of the target bacteria to two hours instead of several days using traditional bacterial detection methods. In addition, the new membranes achieve higher sample throughputs (around 4-5 mL/s) with a lower LOD (10 cells/ 250 mL) in processing real-world food samples compared to other similar detection platforms. The excellent properties of our surface modification approaches may provide further advantages when employed in other platforms, such as target separation and enrichment, antifouling and antibacterial, and drug delivery applications.

京都大学 / 新制・課程博士 / 博士(エネルギー科学) / 甲第23998号 / エネ博第434号 / 新制||エネ||82(附属図書館) / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 森井 孝, 教授 片平 正人, 教授 佐川 尚 / 学位規則第4条第1項該当 / Doctor of Energy Science / Kyoto University / DFAM

Naturally occurring biological nanoparticles (BNPs) and synthetic nanoparticles have a significant role in a wide range of biomedical applications. For instance, direct detection of BNPs, such as viruses, can provide new methods of viral diagnostics while synthetic particles can be used as labels to indirectly detect biomarkers for drug discovery. Therefore, developing advanced tools for nanoparticle detection has gained popularity in biotechnological research. One of the most exciting recent developments in BNP detection has been single particle (or digital) counting of individual particles which offers unprecedented sensitivity levels. However, standard optical techniques face a significant challenge for nanoparticle detection, due the weak optical contrast of sub-wavelength particles. Interferometric microscopy, overcomes the limitations imposed by particle size which allows for visualizing unresolved (diffraction-limited) optical signatures of sub-wavelength particles. Single-particle interferometric reflectance imaging sensor (SP-IRIS), is a widefield microscopy platform, developed by our group over the last years. SP-IRIS uses interferometric enhancement and a layered substrate to increase the optical contrast for the target particles of interest. While this microscopy technique has shown remarkable sensitivity levels for numerous applications including detection of viral particles and nucleic acids, it has remained a specialty tool due to the utilization of z-scan measurements for extracting the optical signature of particles. The z-scan measurements that consist of multiple frames acquired at different focal positions impose two major drawbacks. The first is the requirement of repeatable and high resolution scanning optics and the second is the time and computational processing power required to analyze the image stacks. In this thesis we describe a novel imaging method termed `pixel-diversity‘ IRIS (PD-IRIS), which aims to provide a more practical detection method for nanoparticles by eliminating the need for acquiring z-stacks. PD-IRIS is built upon SP-IRIS, however it introduces a paradigm shift for encoding the necessary optical signature of target particles. PD-IRIS compresses the relevant optical information within a single image frame rather than an image stack. This is achieved by using camera sensors that simultaneously record multiple spectral or polarization channels. Therefore, a single image can record distinct spectral responses of target particles with respect to different excitation wavelengths (multi-spectral PD-IRIS) or the distinct scattering characteristics with respect to polarization (polarization PD-IRIS). This dissertation presents a rigorous study for both PD-IRIS modes and demonstrates the practical applications of nanoparticle detection with proof-of-concept measurements. / 2024-01-16T00:00:00Z

No description available.

Cerium oxide has been used extensively for various applications over the past two decades. The use of cerium oxide nanoparticles is beneficial in present applications and can open avenues for future applications. The present study utilizes the microemulsion technique to synthesize uniformly distributed cerium oxide nanoparticles. The same technique was also used to synthesize cerium oxide nanoparticles doped with trivalent elements (La and Nd). The fundamental study of cerium oxide nanoparticles identified variations in properties as a function of particle size and also due to doping with trivalent elements (La and Nd). It was found that the lattice parameter of cerium oxide nanoparticles increases with decrease in particle size. Also Raman allowed mode shift to lower energies and the peak at 464 cm-1 becomes broader and asymmetric. The size dependent changes in cerium oxide were correlated to increase in oxygen vacancy concentration in the cerium oxide lattice. The doping of cerium oxide nanoparticles with trivalent elements introduces more oxygen vacancies and expands the cerium oxide lattice further (in addition to the lattice expansion due to the size effect). The lattice expansion is greater for La-doped cerium oxide nanoparticles compared to Nd-doping due to the larger ionic radius of La compared to Nd, the lattice expansion is directly proportional to the dopant concentration. The synthesized cerium oxide nanoparticles were used to develop an electrochemical biosensor of hydrogen peroxide (H2O2). The sensor was useful to detect H2O2 concentrations as low as 1µM in water. Also the preliminary testing of the sensor on tomato stem and leaf extracts indicated that the sensor can be used in practical applications such as plant physiological studies etc. The nanomolar concentrations of cerium oxide nanoparticles were also found to be useful in decreasing ROS (reactive oxygen species) mediated cellular damages in various in vitro cell cultures. Cerium oxide nanoparticles reduced the cellular damages to the normal breast epithelial cell line (CRL 8798) induced by X-rays and to the Keratinocyte cell line induced by UV irradiation. Cerium oxide nanoparticles were also found to be neuroprotective to adult rat spinal cord and retinal neurons. We propose that cerium oxide nanoparticles act as free radical scavenger (via redox reactions on its surface) to decrease the ROS induced cellular damages. Additionally, UV-visible spectroscopic studies indicated that cerium oxide nanoparticles possess auto-regenerative property by switching its oxidation state between Ce3+ and Ce4+. The auto-regenerative antioxidant property of these nanoparticles appears to be a key component in all the biological applications discussed in the present study.