The aim of this thesis is to provide a thorough characterization of the photosynthetic machinery from the heterocysts of Nostoc punctiforme strain ATCC 29133. In this thesis I describe the protocols I have optimized for the isolation of thylakoids from vegetative cells, the purification of heterocysts and the isolation of thylakoids from the purified heterocysts. The composition of the thylakoid membranes was studied by two dimensional electrophoresis and mass-spectrometry. Further insight into the functionality of the photosynthetic complexes was obtained by EPR, electron transport measurements through Photosystem II (PSII), and fluorescence spectroscopy. The proteome of the heterocysts thylakoids compared to that of the vegetative cell was found to be dominated by Photosystem I (PSI) and ATP-synthase complexes, both essential for keeping high nitrogenase activities. Surprisingly, we found a significant amount of assembled monomeric PSII complexes in the heterocysts thylakoid membranes. We measured in vitro light-driven electron transfer from PSII in heterocysts using an artificial electron donor, suggesting that under certain circumstances heterocysts might activate PSII. Parallel to my main research I also worked in a collaboration to elucidate the total proteome of Nostoc sp. strain 7120 and Nostoc punctiforme using quantitative shotgun proteomics. Several hundred proteins were quantified for both species. It was possible to trace the detailed changes that occurred in the energy and nitrogen metabolism of a heterocyst after differentiation. Moreover, the presence of PSII proteins identified in our membrane proteome was also confirmed and extended. Lastly, I studied how the heterocysts are capable of responding to variations in light quality as compared to vegetative cells. Using 77 K fluorescence spectroscopy on heterocysts and vegetative cells previously illuminated with light at specific wavelengths, I was able to demonstrate that heterocysts still possess a possibly modified but functional antenna system, capable of harvesting light and transferring energy preferentially to PSI. The characterization of the membrane and total proteome permitted to draw a more comprehensive and integrated picture of the interplay between the distinct metabolic processes that are carried out in each cell type at the same time; from oxygenic photosynthesis and carbon fixation in the vegetative cells to the anoxygenic cyclic photophosphorylation essential to power nitrogen assimilation in the heterocysts.

Research toward a multiplexed nucleic acid biosensor that uses quantum dots (QDs) as donors in a fluorescence resonance energy transfer (FRET) assay is described. Optical fibers were modified with mixed films composed of different colours of QDs and different oligonucleotide probes that served as scaffolds for the hybridization of the corresponding target nucleic acid sequences. Fluorescent dyes that were suitable as acceptors for each QD donor were associated with hybridization and provided an analytical signal through FRET-sensitized emission. Different detection channels were achieved through the combination of different donors and acceptors: green emitting QDs with Cyanine 3 or Rhodamine Red-X; and red emitting QDs with Alexa Fluor 647. A detection channel that used the direct excitation of Pacific Blue complemented the FRET pairs. One-plex, two-plex, three-plex and four-plex hybridization assays were demonstrated. A sandwich assay format was adopted to avoid target labeling. Detection limits were 1-10 nM (1-12 pmol) and analysis times were 1-4 h. Single nucleotide polymorphisms were discriminated in multiplexed assays, and the potential for reusability was also demonstrated. Non-selective interactions between QDs and oligonucleotides were characterized, and routes toward the optimization of the QD-FRET hybridization assays were identified. A basic model for multiple FRET pathways in a mixed film was also developed. In addition to the advantages of solid-phase assays, the combination of QDs and FRET was advantageous because it permitted multiplexed detection using a single excitation source and a single substrate, in the ensemble, and via ratiometric signals. Spatial registration or sorting methods, imaging or spatial scanning, and single molecule spectroscopy were not required. The research in this thesis is expected to enable new chip-based biosensors in the future, and is an original contribution to both bioanalytical spectroscopy and the bioanalytical applications of nanomaterials.

More than one-third of all Magnetic Resonance Imaging (MRI) scans employ image-enhancing contrast agents to increase the differential signal intensity between diseased and normal tissue. Because current clinical contrast agents exhibit low relaxivity (mM-1 s-1), low dose efficiency, and rapid secretion, we have designed a group of protein-based MRI contrast agents with multiple gadolinium binding sites. In this study, the developed purification method for Class ProCA-3 agents allows for a quick and cost-effective way to abstract up to 109 mg of pure, soluble protein from a 1L E. Coli cell pellet devoid of DNA or RNA “contamination” for extensive animal studies. Circular dichroism far-UV spectra ensure the metal stability of the agents, revealing maintenance of their native α-helical structure in the presence and absence of metal ions. Furthermore, substantial evidence supports the high dose efficiency of these agents, exhibiting up to five folds higher relaxivity than their analogous commercial competitors.

Mn-doped II-VI semiconductor nanocrystals exhibit bright dopant photoluminescence that has potential usefulness for light emitting devices, temperature sensing, and biological imaging. The bright luminescence comes from the 4T1→6A1 transition of the Mn2+ d electrons after the exciton-dopant energy transfer, which reroutes the exciton relaxation through trapping processes. The driving force of the energy transfer is the strong exchange coupling between the exciton and Mn2+ due to the confinement of exciton in the nanocrystal. The exciton-Mn spatial overlap affecting the exchange coupling strength is an important parameter that varies the energy transfer rate and the quantum yield of Mn luminescence. In this dissertation, this correlation is studied in radial doping location-controlled Mn-doped CdS/ZnS nanocrystals. Energy transfer rate was found decreasing when increasing the doping radius in the nanocrystals at the same core size and shell thickness and when increasing the size of the nanocrystals at a fixed doping radius. In addition to the exciton-Mn energy transfer discussed above, two consecutive exciton-Mn energy transfers can also occur if multiple excitons are generated before the relaxation of Mn (lifetime ~10^-4 - 10^-2 s). The consecutive exciton-Mn energy transfer can further excite the Mn2+ d electrons high in conduction band and results in the quenching of Mn luminescence. The highly excited electrons show higher photocatalytic efficiency than the electrons in undoped nanocrystals. Finally, the effect of local lattice strain on the local vibrational frequency and local thermal expansion was observed via the temperature-dependent Mn luminescence spectral linewidth and peak position in Mn-doped CdS/ZnS nanocrystals. The local lattice strain on the Mn2+ ions is varied using the large core/shell lattice mismatch (~7%) that creates a gradient of lattice strain at various radial locations. When doping the Mn2+ closer to the core/shell interface, the stronger lattice strain softens the vibrational frequency coupled to the 4T1→6A1 transition of Mn2+ (Mn luminescence) by ~50%. In addition, the lattice strain also increases the anharmonicity, resulting in larger local thermal expansion observed from the nearly an order larger thermal shift of the Mn luminescence compared to the Mn-doped ZnS nanocrystals without the core/shell lattice mismatch.

Research toward a multiplexed nucleic acid biosensor that uses quantum dots (QDs) as donors in a fluorescence resonance energy transfer (FRET) assay is described. Optical fibers were modified with mixed films composed of different colours of QDs and different oligonucleotide probes that served as scaffolds for the hybridization of the corresponding target nucleic acid sequences. Fluorescent dyes that were suitable as acceptors for each QD donor were associated with hybridization and provided an analytical signal through FRET-sensitized emission. Different detection channels were achieved through the combination of different donors and acceptors: green emitting QDs with Cyanine 3 or Rhodamine Red-X; and red emitting QDs with Alexa Fluor 647. A detection channel that used the direct excitation of Pacific Blue complemented the FRET pairs. One-plex, two-plex, three-plex and four-plex hybridization assays were demonstrated. A sandwich assay format was adopted to avoid target labeling. Detection limits were 1-10 nM (1-12 pmol) and analysis times were 1-4 h. Single nucleotide polymorphisms were discriminated in multiplexed assays, and the potential for reusability was also demonstrated. Non-selective interactions between QDs and oligonucleotides were characterized, and routes toward the optimization of the QD-FRET hybridization assays were identified. A basic model for multiple FRET pathways in a mixed film was also developed. In addition to the advantages of solid-phase assays, the combination of QDs and FRET was advantageous because it permitted multiplexed detection using a single excitation source and a single substrate, in the ensemble, and via ratiometric signals. Spatial registration or sorting methods, imaging or spatial scanning, and single molecule spectroscopy were not required. The research in this thesis is expected to enable new chip-based biosensors in the future, and is an original contribution to both bioanalytical spectroscopy and the bioanalytical applications of nanomaterials.

The aim of this diploma work is to improve selectivity and sensitivity in DNA-chips by utilizing fluorescence resonance energy transfer (FRET) between conjugated polyelectrolytes (CPEs) and fluorophores. Leclerc and co-workers have presented successful results from studies of super FRET between fluorophore tagged DNA and a CPE during hybridisation of the double strand. Orwar and co-workers have constructed a DNA-chip using standard photo lithography creating a pattern of the hydrophobic photoresist SU-8 and cholesterol tagged DNA (chol-DNA). This diploma work will combine and modify these two ideas to fabricate a improved DNA-chip. Immobilizing of DNA onto surface has been done by using soft lithography. Hydrophobic pattern arises from the poly(dimethylsiloxane) (PDMS) stamp. The hydrophobic pattern will attract chol-DNA that is adsorbed to the chip. Different sets of fluorophores are covalently bound to the DNA and adding CPEs to the complex will make FRET occur between CPE and bound fluorophore. We will here show that the specificity in DNA hybridization by using PDMS patterning was high. FRET clearly occurred, especially with the CPEs as donor to the fluorophore Cy5. The intensity of FRET was higher when the fluorophore and the CPE were conjugated to the same DNA strand. The largest difference in FRET intensity between double stranded and single stranded complexes was observed with the CPE tPOMT. Super FRET has been observed but not yet fully proved. The FRET efficiency was lower with the fluorophore Alexa350 as donor compared to the Cy5/CPE complex. Most of the energy transferred from Alexa350 was extinguished by quenching.

<p>A clinically viable brain-machine interface (BMI) requires a fully-implanted wireless neural acquisition system to limit the impediments of percutaneous connections. For an implanted system with an appreciable telemetry range, and where significant</p><p>neural signal processing is performed continuously, a major obstacle for clinical application is the need for a power source. Existing battery technology and wireless power delivery systems have not addressed the need for a mid-range power supply, capable</p><p>of 1-3 W delivery, that limits both induced noise and temperature rise. These factors are crucial for the succesful operation of a fully-implanted neural acquisition system. This work seeks to fill this void, and presents both a wireless power solution suitable for a neural recording device, and a system capable of real time monitoring of tissue temperature rise.</p><p>During this research, a 2 W transcutaneous energy transfer system (TETS) was designed, built and tested. The TETS was designed specifically for a 96-channel implanted neural data acquisition system, which requires continuous power. The major design constraints were tolerance to coil misalignment, low induced noise,</p><p>and reasonable efficiency. The design of the primary circuit consists of an H-bridge switching network driving a planar spiral Litz wire primary coil. The primary also incoporates a novel circuit for detecting the presence of the secondary. The implanted secondary components include a complimentary planar spiral coil connected to a voltage doubling rectifier. The key approach to mitigating axial coil misalignments was the use of step-down switching regulators in the secondary. With this approach, link efficiency remained nearly constant at 40%, for axial coil displacements of up to 2 cm.</p><p>Noise in the recorded neural signals was minimized using two techniques. First, the 250 kHz operating frequency of the system was tuned, such that the aliased harmonics of the switching frequency lay above the bandwidth of the amplifier used for neural recording. The second approach was to limit the impact of induced displacement currents in the body by physically separating the recording front end from the power supply components. A large titanium enclosure was used to house some of the secondary electronics, and provided a low impedance return path for further</p><p>reduction of current-induced noise.</p><p>Limiting the temperature rise of internal components was also a critical design constraint. The need for real time temperature information led to the design of a six channel temperature measurement system and incorporation of the temperature data into the acquisition system data transmission scheme. This system consisted of bead thermistor temperature transducers, and an off-the-shelf microcontroller with a built-in instrumentation amplifier.</p><p>The TETS and temperature system was fully tested in an ovine model during several acute studies. Recorded temperature rise was limited to approximately 5.5&deg C when the system was implanted at an adequate depth in muscle. The TETS was able to successfully power the 2 W neural acquisition system during a data processing task. Received rectified voltage in the secondary ranged from 14.86 V to 20.2 V, while link efficiency remained virtually constant. Acquired neural data was examined for TETS switching noise. The measured RMS noise increased by less than 1 &mu V, averaged over several experiments. These results demonstrate the first mid-range TETS solution for powering a fully implanted neural acquisition system.</p> / Dissertation

We prove the existence and linear stability of quasi-periodic breather solutions in a 1d Hamiltonian lattice of identical, weakly-coupled, anharmonic oscillators with general on-site potentials and under the effect of long-ranged interaction, via de KAM technique. We prove the persistence of finite-dimensional tori which correspond in the uncoupled limit to N arbitrary lattice sites initially excited. The frequencies of the invariant tori of the perturbed system are only slightly deformed from the frequencies of the unperturbed tori.

Molecular photoabsorption enhancement under ambient solar radiations can improve efficiency substantially in renewable energy production. Here, we explore the theoretical basis and experimental evidences that nanostructured molecular assemblies exhibit an unprecedented property of synergistic photon absorption enhancement. The molecular mechanism of this enhancement phenomenon originates from the combined effect of the photon-molecule interaction and the electronic energy transfer between two adjacent molecular assemblies. For a natural system, the synergistic photon absorption enhancement factor of green algae (Chlorella vulgaris) in vivo at 632.8 nm was determined to be 103. This enhanced photon absorption process in nanostructured molecular assemblies opens a doorway to create entangled double excitons by incoherent solar radiations.

A set of three through-bond energy transfer cassettes based on BODIPY as a donor and cyanine dyes as acceptors has been prepared via Sonogashira couplings, and their photophysical properties were examined. These cassettes fluoresce around 600 to 800 nm and are resolved by approximately 100 nm. This property is an important factor for multiplexing study in cellular imaging. Several useful fluorescent probes such as 5- and 6-carboxyfluorescein, water-soluble BODIPY, and water-soluble Nile Blue dyes, have also been synthesized and their photophysical properties studied. We have also attempted to develop a method for protein mono-labeling via a solidphase approach. The labeling of protein with one fluorescent dye facilitates quantification and single molecule imaging in biological applications. Various solidsupports such as PEGA, CPG, and BSA-coated CPG, were tested. Photolabile and chemically cleavable linkers were prepared to connect solid-supports and fluorophores. Unfortunately, our approach to the fluorescent mono-labeling of native proteins did not give us any conclusive results.