Laser-based techniques have become essential tools for probing biological molecules in systems that demand high spatial and temporal control. This dissertation presents the development of micro-analytical techniques based on multiphoton excitation (MPE) to promote highly localized, three-dimensional (3D) photochemistry of biologically relevant molecules on submicron dimensions. Strategies based on capillary electrophoresis (CE) have been developed for the rapid separation and spectroscopic analysis of short-lived photochemical reaction products. High-speed separation and analysis are achieved through a combination of very high electric fields and a laser-based optical system that uses MPE for both the generation and detection of hydroxyindole photoproducts on the time scale of microseconds. MPE was also used for the development of photolithographic techniques for the creation of microstructured protein-based materials with highly defined three-dimensional (3D) topographies. Specifically, a multiphoton lithographic (MPL) technique was developed that used a low-cost microchip laser for the rapid prototyping of 3D microarchitectures when combined with dynamic optical masking. Furthermore, MPL was used to create novel “smart” biomaterials that reproducibly respond with tunable actuation to changes in the local chemical and thermal environment. The utility of these materials for creating biocompatible cellular microenvironments was demonstrated and presents a novel approach for studying small populations of microorganisms. Finally, through the development of a multifocal approach that used multiple laser beams to promote the photocrosslinking of biological molecules, the speed and versatility of MPL was extended to allow both the parallel fabrication of 3D microstructures and the rapid creation of large-scale biomaterials with highly defined spatial features. / text

Thesis (Ph. D.)--Duke University, 2007. / Includes bibliographical references.

Optical manipulation covers a wide range of techniques to guide and trap cells using only the forces exerted by light. Another optical tool is photoporation, the technique of injecting membrane-impermeable molecules using light, which has become an important alternative to other injection techniques. Together they provided sterile tools for manipulation and molecule delivery at the single-cell level. In this thesis, the properties of low Reynolds fluid flows are exploited to guide cells though a femtosecond Bessel beam. This design allows for high-throughput optical injection of cells without the need to individually target cells. A method of 'off-chip' hydrodynamic focusing was evaluated and was found to confine 95.6% of the sample within a region which would receive a femtosecond dose compared to 20% without any hydrodynamic focusing. The system was tested using two cell lines to optically inject the membrane-impermeable dye, propidium iodide. This resulted in an increase of throughput by an order of magnitude compared to the previous microfluidic design (to up to 10 cells per second). Next optical trapping and photoporation were combined to create a multimodal workstation. The system provides 3D beam control using spatial light modulators integrated into a custom user interface. The efficiency of optical injection of adherent cells and trapping capabilities were tested. The development of the system provides the groundwork for exploration of the parameters required for photoporation of non-adherent cells. Finally optical trapping is combined with temporally focused multiphoton illumination for scanless imaging. The axial resolution of the system was measured using different microscope objectives before imaging cells stained with calcein. Both single and a pair of recently trypsinised cells were optically trapped and imaged. The position of the trapped cells was manipulated using a spatial light modulator in order to obtain a z-stack of images without adjusting the objective position.

In this thesis two previously separate fields of study are brought together: optical micromanipulation and ultrashort laser research. Here, the benefits of combining the high peak powers of ultrashort pulsed lasers and conventional optical micromanipulation techniques are explored. As optical trapping has been studied extensively, the focus of this research is on optical guiding. Moreover, the emphasis is on the use of Bessel beams as these have been shown to offer greater guiding distances than comparable Gaussian beams. The studies within this thesis show that optical guiding in Bessel and Gaussian beams is governed by the average power of the laser. However, the benefits of guiding with ultrashort pulsed lasers to exploit multi-photon processes become evident as the demonstration of simultaneous optical guiding and second harmonic generation in microscopic nonlinear crystal fragments is detailed. This work is developed by using ultrashort pulses to induce two-photon excitation-induced fluorescence in the guiding medium. This allows direct visualisation of the beam-particle interaction and measurement of the reconstruction of the Bessel beam around an object. Some studies using two-photon excitation to investigate Bessel beam penetration through turbid media are discussed. Finally, the work is concluded by exploring the use of pulsed white-light lasers in optical guiding. The wavelength-dependent propagation and reconstruction properties of the white-light Bessel beam are studied before some preliminary optical guiding experiments are discussed. From this, the broad bandwidth of the supercontinuum source is found to offer extended guiding distances in Gaussian beams thereby negating the need for Bessel beams.

Development of a three dimensional (3D) HYBROT model with targeted in vivo like intact cellular circuitry in thick brain slices for multi-site stimulation and recording will provide a useful in vitro model to study neuronal dynamics at network level. In order to make this in vitro model feasible, we need to develop several associated technologies. These technologies include development of a thick organotypic brain slice culturing method, a three dimensional (3D) micro-fluidic multielectrode Neural Interface system (µNIS) and the associated electronic interfaces for stimulation and recording of/from tissue, development of targeted stimulation patterns for closed-loop interaction with a robotic body, and a deep-tissue non-invasive imaging system. To make progress towards this goal, I undertook two projects: (i) to develop a method to culture thick organotypic brain slices, and (ii) construct a multiphoton imaging system that allows long-term and deep-tissue imaging of two dimensional and three dimensional cultures. Organotypic brain slices preserve cytoarchitecture of the brain. Therefore, they make more a realistic reduced model for various network level investigations. However, current culturing methods are not successful for culturing thick brain slices due to limited supply of nutrients and oxygen to inner layers of the culture. We developed a forced-convection based perfusion method to culture viable 700µm thick brain slices. Multiphoton microscopy is ideal for imaging living 2D or 3D cultures at submicron resolution. We successfully fabricated a custom-designed high efficiency multiphoton microscope that has the desired flexibility to perform experiments using multiple technologies simultaneously. This microscope was used successfully for 3D and time-lapse imaging. Together these projects have contributed towards the progress of development of a 3D HYBROT. ----- 3D Hybrot: A hybrid system of a brain slice culture embodied with a robotic body.

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Multiphoton fluorescence excitation microscopy (MPM) is an invaluable tool for studying processes in tissue in live animals by enabling biologists to view tissues up to hundreds of microns in depth. Unfortunately, imaging depth in MPM is limited to less than a millimeter in tissue due to spherical aberration, light scattering, and light absorption. Spherical aberration is caused by refractive index mismatch between the objective immersion medium and sample. Refractive index heterogeneities within the sample cause light scattering. We investigate the effects of refractive index mismatch on imaging depth in MPM. Methods: The effects of spherical aberration on signal attenuation and resolution degradation with depth are characterized with minimal light absorption and scattering using sub-resolution microspheres mounted in test sample of agarose with varied refractive index. The effects of light scattering on signal attenuation and resolution degradation with depth are characterized using sub-resolution microspheres in kidney tissue samples mounted in optical clearing media to alter the refractive index heterogeneities within the tissue. Results: The studies demonstrate that signal levels and axial resolution both rapidly decline with depth into refractive index mismatched samples. Interestingly, studies of optical clearing with a water immersion objective show that reducing scattering increases reach even when it increases refractive index mismatch degrading axial resolution. Scattering, in the absence of spherical aberration, does not degrade axial resolution. The largest improvements in imaging depth are obtained when both scattering and refractive index mismatch are reduced. Conclusions: Spherical aberration, caused by refractive index mismatch between the immersion media and sample, and scattering, caused by refractive index heterogeneity within the sample, both cause signal to rapidly attenuate with depth in MPM. Scattering, however, seems to be the predominant cause of signal attenuation with depth in kidney tissue. Kenneth W. Dunn, Ph.D., Chair

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / The sympathetic nervous system strongly modulates the contractile and electrical function of the heart. The anatomical underpinnings that enable a spatially and temporally coordinated dissemination of sympathetic signals within the cardiac tissue are only incompletely characterized. In this work we took the first step of unraveling the in situ 3D microarchitecture of the cardiac sympathetic nervous system. Using a combination of two-photon excitation fluorescence microscopy and computer-assisted image analyses, we reconstructed the sympathetic network in a portion of the left ventricular epicardium from adult transgenic mice expressing a fluorescent reporter protein in all peripheral sympathetic neurons. The reconstruction revealed several organizational principles of the local sympathetic tree that synergize to enable a coordinated and efficient signal transfer to the target tissue. First, synaptic boutons are aligned with high density along much of axon-cell contacts. Second, axon segments are oriented parallel to the main, i.e., longitudinal, axes of their apposed cardiomyocytes, optimizing the frequency of transmitter release sites per axon/per cardiomyocyte. Third, the local network was partitioned into branched and/or looped sub-trees which extended both radially and tangentially through the image volume. Fourth, sub-trees arrange to not much overlap, giving rise to multiple annexed innervation domains of variable complexity and configuration. The sympathetic network in the epicardial border zone of a chronic myocardial infarction was observed to undergo substantive remodeling, which included almost complete loss of fibers at depths >10 µm from the surface, spatially heterogeneous gain of axons, irregularly shaped synaptic boutons, and formation of axonal plexuses composed of nested loops of variable length. In conclusion, we provide, to the best of our knowledge, the first in situ 3D reconstruction of the local cardiac sympathetic network in normal and injured mammalian myocardium. Mapping the sympathetic network connectivity will aid in elucidating its role in sympathetic signal transmisson and processing.

Although amorphous dielectrics feature localized states in the conduction band, electrons excited by highly intense laser radiation are usually considered as nearly free. However, localized or nearly free electrons would result in significantly different optical properties of the material. Therefore, this thesis investigates the transient complex refractive index of amorphous fused silica during the interaction with ultrashort pulsed laser radiation by applying spectroscopic imaging pump-probe ellipsometry. A Drude model, describing the excited electrons as a nearly free electron gas, and a Lorentz model, which considers the excited electrons as bound in localized states, are then approximated to the measured transient complex refractive index. The Lorentz model replicates the experimental data very well in the considered temporal range up to 200 fs after irradiation, whereas the Drude model significantly differs. Hence, the electrons are excited into localized states first, and are not describable as nearly free upon irradiation. / Obwohl amorphe Dielektrika lokalisierte Zustände im Leitungsband aufweisen, werden Elektronen, die durch hoch intensive Laserstrahlung angeregt werden, üblicherweise als quasifrei betrachtet. Im Gegensatz zu quasifreien Elektronen würden lokalisierte Elektronen jedoch zu deutlich anderen transienten optischen Eigenschaften des Materials führen. Daher wird in dieser Arbeit der transiente komplexe Brechungsindex von amorphem Quarzglas während der Wechselwirkung mit ultrakurz gepulster Laserstrahlung mittels spektroskopischer, abbildender Pump-Probe Ellipsometrie untersucht. Jeweils ein Drude-Modell, das die angeregten Elektronen als ein quasifreies Elektronengas beschreibt, und ein Lorentz-Modell, welches die angeregten Elektronen als in lokalisierten Zuständen gebunden betrachtet, werden anschließend mit dem gemessenen transienten komplexen Brechungsindex verglichen. Das Lorentz-Modell repliziert die experimentellen Daten im betrachteten Zeitbereich bis zu 200 fs nach der Bestrahlung sehr gut, während das Drude-Modell deutlich abweicht. Demnach werden die Elektronen zunächst in lokalisierte Zustände angeregt und können während und kurz nach der Bestrahlung nicht als quasifrei beschrieben werden.

Indiana University-Purdue University Indianapolis (IUPUI) / Advancements in human genomics have simultaneously enhanced our basic understanding of the human body and ability to combat debilitating diseases. Historically, research has shown that there have been many hindrances to realizing this medicinal revolution. One hindrance, with particular regard to the kidney, has been our inability to effectively and routinely delivery genes to various loci, without inducing significant injury. However, we have recently developed a method using hydrodynamic fluid delivery that has shown substantial promise in addressing aforesaid issues. We optimized our approach and designed a method that utilizes retrograde renal vein injections to facilitate widespread and persistent plasmid and adenoviral based transgene expression in rat kidneys. Exogenous gene expression extended throughout the cortex and medulla, lasting over 1 month within comparable expression profiles, in various renal cell types without considerably impacting normal organ function. As a proof of its utility we by attempted to prevent ischemic acute kidney injury (AKI), which is a leading cause of morbidity and mortality across among global populations, by altering the mitochondrial proteome. Specifically, our hydrodynamic delivery process facilitated an upregulated expression of mitochondrial enzymes that have been suggested to provide mediation from renal ischemic injury. Remarkably, this protein upregulation significantly enhanced mitochondrial membrane potential activity, comparable to that observed from ischemic preconditioning, and provided protection against moderate ischemia-reperfusion injury, based on serum creatinine and histology analyses. Strikingly, we also determined that hydrodynamic delivery of isotonic fluid alone, given as long as 24 hours after AKI is induced, is similarly capable of blunting the extent of injury. Altogether, these results indicate the development of novel and exciting platform for the future study and management of renal injury.