Thesis (Ph. D.)--Cornell University, May, 2007. / Vita. Includes bibliographical references (leaves 101-107).

Thesis (Ph. D.)--University of Hong Kong, 2005.

Thesis (Ph. D.)--Oregon State University, 2007. / Printout. Includes bibliographical references (leaves 86-100). Also available on the World Wide Web.

Molecular imaging involves the development of probes which can specifically label a certain object in the body at cellular or subcellular level. This thesis consists of three parts, each involving the development of novel labelling methods for viruses or virus-like particles with specific applications. Virus-like particles (VLP) derived from the E. coli bacteriophage Qβ are widely employed as a nano-carrier for drugs and vaccines, but a powerful method for tracing its circulation without affecting its structure is yet to be developed. In the first part of the thesis, the electrophilic fluorine source ¹⁹F-Selectfluor^TM was employed for introducing single fluorine atoms on Qβ VLPs. For the 'tag-and-modify' approach, site-selective electrophilic C-F bond formation was achieved on the dehydroalanine (Dha) amino acid tag of VLPs under aqueous conditions. Chemoselective electrophilic aromatic fluorination on tyrosine residues were also achieved using the same reagent by manipulating the amino acid sequence. Similar results were observed in conditions required for ¹⁸F-Selectfluor™ reaction, indicating the potential of this technique for positron emission tomography (PET) imaging. In addition, there is a lack of in situ technique for tracking the functional status of Qβ VLPs and hence the release of cargos. In the second part of the thesis, a simple way to monitor the disassembly of ¹⁹F-labelled Qβ VLPs by ¹⁹F NMR spectrosocpy is reported. Analysis of resonances, using experiments under a range of conditions, allowed determination not only of the intact particle but also the disassembled multimeric species and even smaller peptides upon digestion by cells. This in turn allowed mutational redesign of disassembly and testing in both bacterial and mammalian systems as a strategy for the creation of putative, targeted-VLP delivery systems. In the third part of the thesis, a new type of rhodamine B fluorescent dye functionalised with a 2-imino-2-methoxyethyl (IME) group is reported. The amidine linkage formed between the IME group and lysine residue retains the pKaH of the original side chain, which cannot be achieved using commercially available conjugating dyes. This in turn minimises the change in net charge hence virus infectivity following virus labelling. By employing adenovirus (AV) as an example, the IME dye was shown to be a better choice in retaining virus infectivity compared to dyes linked with other coupling groups. In addition, preliminary experiments on dengue virus with the synthesised dyes were also performed.

abstract: The green fluorescent protein (GFP)-like fluorescent proteins play an important role for the color of reef-building corals. Different colors of extant coral fluorescent proteins (FPs) have evolved from a green ancestral protein. Interestingly, green-to-red photoconversion FPs (Kaede-type Red FPs) are only found in clade D from Scleractinia (Faviina suborder). Therefore, I focus on the evolution of Kaede-type FPs from Faviina suborder ancestral FP. A total of 13 mutations have been identified previously that recapitulate the evolution of Kaede-type red FPs from the ancestral green FP. To examine the effect of each mutation, total ten reconstructed FPs were analyzed and six x-ray crystal structures were solved. These substitutions created a more hydrophilic environment around the carbonyl group of Phe61. Also, they increased the flexibility of the c-terminal chain, which keeps it from interacting with the entrance of the putative solvent channel. The photoconversion reaction shows a twophase kinetics. After the rapid initial phase, the overall reaction followed the firstorder kinetics. Based on the crystal structure analysis, I propose a new mechanism for Kaede-type FP photoconversion process, which a proton transfers via Gln38 to the carbonyl group of Phe61. / Dissertation/Thesis / Ph.D. Chemistry 2012

Hydrogen sulfide (H2S) is an essential small molecule in human physiology. Although quite toxic, H2S is produced endogenously and performs important regulatory functions in the cardiovascular, immune, nervous, and respiratory systems. Varied interactions with intracellular thiols, reactive oxidants, and protein transition-metal centers are highly dynamic and sensitive to fluctuations in redox homeostasis. Furthermore, H2S is implicated in a number of diseases such as cancer, neurodegeneration, and heart disease. Hence, exogenously delivered H2S as a therapeutic agent is an active area of intrigue and research. The complexity and interconnectivity of these processes has stimulated the development of advanced chemical tools with which to study biological H2S, including reaction-based fluorescent probes and slow-releasing H2S donors. Toward these goals, I present several significant advances in the fields of H2S detection and delivery. An azide reduction-based probe, MeRho-Az, provides a rapid >1,000-fold fluorescence response when treated with H2S. MeRho-Az is sufficiently sensitive to detect endogenous H2S in C6 cells and was used to image H2S in live zebrafish larvae using light sheet fluorescence microscopy, representing the first analyte-responsive experiments with this imaging technology. Using a ratiometric dual-fluorophore fragmentation strategy, NBD-Coum simultaneously detects, differentiates, and measures relative concentration ratios of H2S versus cysteine/homocysteine, two important metabolites in H2S biosynthesis. NBD-Coum was used to monitor changes in redox homeostasis in a simulated sulfur pool and is useful for studying H2S-thiol dynamics. The synthesis and amide-coupling conditions of ADT-NH2, a highly sought dithiolethione H2S donor, allow for hydrolytically stable, H2S-releasing non-steroidal anti-inflammatory drug hybrids. Finally, inspired by polysulfide-containing natural products, functionalized tetrasulfides are a new class of accessible, customizable, and versatile H2S donors with controllable H2S release rates. I hope that by using these investigative tools, chemists and biologists are able to refine our understanding of physiological H2S and exploit H2S activities in disease treatments.

abstract: The purpose of this study was to determine the applicability of fluorescent microspheres as a surrogate to measure the removal of Cryptosporidium oocysts through the coagulation, flocculation, sedimentation, and filtration steps of conventional water treatment. In order to maintain accuracy and applicability, a local water treatment facility was chosen as the system to model. The city of Chandler Arizona utilizes conventional treatment methodologies to remove pathogens from municipal drinking water and thus the water, coagulant, polymer, and doses concentrations were sourced directly from the plant. Jar testing was performed on four combinations of coagulant, polymer, and fluorescent microsphere to determine if the log removal was similar to that of Cryptosporidium oocysts. Complications with the material properties of the microspheres arose during testing that ultimately yielded unfavorable but conclusive results. Log removal of microspheres did not increase with added coagulant in the predicted manner, though the beads were seen aggregating, the low density of the particles made the sedimentation step inefficient. This result can be explained by the low density of the microspheres as well as the potential presence of residual coagulant present in the system. Given the unfavorable properties of the beads, they do not appear to be a suitable candidate for the surrogacy of Cryptosporidium oocysts in conventional drinking water treatment. The beads in their current state are not an adequate surrogate; however, future testing has been outlined to modify the experiment in such a way that the microspheres should behave like oocysts in terms of physical transportation. / Dissertation/Thesis / Masters Thesis Civil Engineering 2015

A series of fluorescent probes based on different signal transduction mechanisms for the detection of Fe3+, Zn2+, histidine and pH was designed and synthesized. Their photophysical properties, binding abilities and the further application in cell imaging were fully evaluated. Building on the groundwork of our previous study, molecular scaffold 19 has been appended to spirobenzopyran fluorophore to furnish a highly selective and sensitive Zn2+ sensor. To broaden the application scope of this trifunctional receptive molecule, 19 was incorporated onto rhodamine, antipyrine and coumarin moieties to give 20, 21 and 23, respectively. Probe 20 operative on a chelation-enhanced fluorescence mechanism exhibited highly selective response to Fe3+ with 2:1 stoichiometry of 20-Fe3+ complex. However, a possible tendency of probe 20 to hydrolyze induced by Fe3+ and the unsuccessful attempt of cell imaging would limit its application scope. Probe 21 with O-N-N-N-N-ligand showed a highly selective and sensitive detection of Zn2+. The probe displayed suppressed response to Cd2+ which is the most common interference ion in zinc metal detection. The binding of Zn2+ to probe 21 inhibited the photoinduced electron transfer process originating from the lone pair of the nitrogen atom in the antipyrine moiety to quinoline fluorophore. Therefore, a turn-on fluorescent probe was developed. A moderate binding constant with 1:1 stoichiometry of 21-Zn2+ complex was established by fluorescence titration. The binding mechanism was fully explained by 1H NMR titration. To our delight, probe 21 was successfully applied for recognizing Zn2+ in living cells. The preparation of probe 23 was achieved by appendage of 19 to coumarin derived fluorophore and the probe exhibited a good selectivity and fluorescent turn-off property to Cu2+. The 1:1 stoichiometry of 23-Cu2+ ensemble can serve as an efficient probe for the detection of histidine and biothiols. In the presence of NEM, the influence of biothiols could be eliminated. Furthermore, this sensing ensemble was also used in the detection of histidine in hard-to-transfect U87MG cells with very low cytotoxicity. Based on our group’s previous work on the spiropyran platform, a novel ratiometric near-infrared pH probe 27 operating on an excited-state intramolecular electron transfer mechanism was developed. The pKa was calculated to be 5.9 and the ring-opening/ring-closing mechanism triggered by protons was reasonably explained by 1H NMR titration. However, this spiropyran-based probe was found to be unsuitable for cell imaging. To continue the innovation of pH sensing and extend its application in bioimaging, a series of ratiometric pH probes 32 and 38 characterized by their high quantum yield working in the NIR range was developed. The appendage of N,O-disubstituted hemiaminal ether moiety onto coumarin fluorophore with C=C double bond conferred the sensory material with the ability to display a pH-dependent ratiometric output operating on the ring-opening/ring-closing mechanism. The pKa of 32 and 38 were 6.9 and 5.8 – 6.0, respectively, which rendered them suitable for pH measurement in near-neutral and acidic media. A preliminary work of intracellular pH measurement was also conducted and promising results were obtained

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17541号 / 工博第3700号 / 新制||工||1563(附属図書館) / 30307 / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 清水 芳久, 教授 田中 宏明, 教授 米田 稔 / 学位規則第4条第1項該当

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17600号 / 工博第3759号 / 新制||工||1573(附属図書館) / 30366 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 松田 建児, 教授 秋吉 一成 / 学位規則第4条第1項該当