The objective of this thesis is to present the fabrication of a multiphoton microscope and the underlying theory responsible for its proper functioning. A basic introduction to nonlinear optics will give the necessary knowledge to the reader to understand the optical effects involved. Femtosecond laser pulses will be presented and characterized. Each part of the microscope, their integration and the design of the microscope will be discussed. The basic concepts of laser scanning microscopy are also required to explain the design of the scanning optics. Fast scanning problems and their solutions are also briefly viewed. As a working proof, the first images taken with the microscope will be presented. Fluorescent beads, rat tail tendon, gold nanoparticles and pollen grain images using various nonlinear effects will be shown and discussed.

Toxic elements are present in polluted water from mines, industrial outlets, storm water etc. Wetland plants take up toxic elements and increase the pH of the medium. In this thesis was investigated how the shoots of submerged plants and roots of emergent plants affected the pH of the surrounding water in the presence of free toxic ions. The aim was to clarify the mechanisms by which these plants change the surrounding water pH in the presence of toxic ions. The influence of Elodea canadensis shoots on the pH of the surrounding water was studied in the presence of cadmium (Cd) at low initial pH (4-5). The involvement of photosynthetic activity in the pH changes was investigated in the presence and absence of Cd. The cytosolic, vacuolar and apoplasmic pH changes as well as cytosolic Cd changes in E. canadensis were monitored. The influence of Eriophorum angustifolium roots on the pH of the surrounding water was investigated in the presence of a combination of Cd, copper, lead, zinc and arsenic at low initial pH (3.5). Eriophorum angustifolium root exudates were analyzed for organic acids. Elodea canadensis shoots increased the pH of the surrounding water, an effect more pronounced with increasing Cd levels and/or increasing plant biomass and increased plant Cd uptake. The pH increase in the presence of free Cd ions was not due to photosynthesis or proton uptake across the plasmalemma or tonoplast. Cadmium was initially sequestered in the apoplasm of E. canadensis and caused its acidosis. Eriophorum angustifolium roots increased the surrounding water pH and this effect was enhanced in the presence of arsenic and metals. This pH increase was found to depend partly on the release of oxalic acid, formic acid and succinic acid by the plants. In conclusion, E. canadensis shoots and E. angustifolium roots were found to increase the low initial pH of the surrounding water. The pH modulation by these species was enhanced by low levels of free toxic ions in the surrounding water. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 2: Submitted. Paper 3: Submitted. Paper 4: Manuscript.

Thesis (Ph. D.)--University of Washington, 1997. / Vita. Includes bibliographical references (leaves [96]-100).

Thesis (Ph. D.)--University of Western Australia, 2007.

Thesis (Ph. D. in Physics)--Vanderbilt University, May 2006. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--University of Texas at Austin, 2007. / Vita. Includes bibliographical references.

Metal ions play essential roles in biological functions including catalysis, protein stability, DNA-protein interactions and cell signaling. It is estimated that 30% of proteins utilize metals in some fashion. Additionally, methods by which metal ions can be visualized have been utilized to study metal concentrations and localizations in relation to disease. Understanding the roles metals play in biological systems has great potential in medicine and technology. Chapters 1 and 2 of this dissertation analyzes the structure and function of the Mn-dependent enzyme oxalate decarboxylase (OxDc) and Chapter 2 presents a bioinformatic analysis of the cupin superfamily that provides the structural scaffold of the decarboxylase. The X-ray crystal structure of the W132F variant was determined and utilized together with EPR data to develop a computational approach to determining EPR spectra of the enzyme’s two metal-binding centers. Furthermore, a variant in which the catalytic Glu162 was deleted revealed the binding mode of oxalate, the first substrate-bound structure of OxDc. OxDc is a member of the cupin superfamily, which comprises a wide variety of proteins and enzymes with great sequence and functional diversity. A bioinformatics analysis of the superfamily was performed to analyze how sequence variation determines function and metal utilization. Chapters 3 and 4 discuss the expansion of lanthanide-binding tags (LBTs) to in cellulo studies. Lanthanide-binding tags are short sequences of amino acids that have high affinity and selectivity for lanthanide ions. An EGF-LBT construct used to quantify EGF receptors on the surface of A431 and HeLa cells. The results from the LBT quantification are consistent with previous studies of EGFR receptors in these cell types, validating the use of this method for future studies. The potential of using LBTs for X-ray fluorescence microscopy (XFM) was also investigated. LBT-labeled constructs were utilized to investigate if membrane bound as well as cytosolic LBT-containing proteins could be visualized and localized to their cell compartments via XFM; both membrane-localized and cytosolic proteins were successfully visualized. With the high resolution (< 150 Å) obtainable with new synchrotron beamline configurations LBTs could be used to study nanoscale biological structures in their near-native state.

Doctor of Philosophy / Department of Chemistry / Takashi Ito / This dissertation describes single-molecule tracking (SMT) measurements for the quantitative characterization of one-dimensional (1D) nanostructures in 200 nm-thick surfactant-templated mesoporous silica (STMS) and cylinder-forming polystyrene-poly(ethylene oxide) diblock copolymer (CF-PS-b-PEO) films with a μm-scale thickness. SMT is advantageous for the characterization of nanomaterials over conventional methods because it permits the simultaneous and quantitative assessment of the nanoscale and microscale morphologies, and mass-transport properties of the materials with a high nanometer-scale resolution under ambient conditions. It offers a unique means for the assessment and evaluation of the μm-scale nanostructure alignment in polymer films induced by vertical spin-coating (for STMS films), directional solution flow and solvent-vapor penetration (SVP) methods (both for CF-PS-b-PEO films), highly crucial for many potential technological applications using the materials. Through this work, we have identified suitable sample preparation conditions (e.g. solvent, temperature or solution flow rate) for obtaining highly-ordered mesoporous and microdomain structures over a long-range (> 5 μm). For the quantitative assessment of the 1D SMT data, orthogonal regression analysis was employed, providing assessment of the in-plane orientation and size of individual nanostructures with nanometer-scale precision. The analysis of the 1D trajectory data allowed the radius (ca. 11 nm) of cylindrical PEO microdomains to be estimated, yielding results consistent with the AFM results (ca. 14 nm). The distribution of the trajectory angles offered the estimation of the average orientation and order of the nanostructures in domains/grains for a μm-wide region of the polymer films, revealing the higher efficiency of SVP in the nanostructure alignment as compared to the spin coating and solution flow approaches. Systematic SMT measurements across the film depth and along lateral mm-scale distances afforded valuable insights into the shear- and solvent-evaporation-based alignment mechanisms induced by solution flow and SVP/spin coating approaches, respectively. Fluorescence recovery after photobleaching (FRAP) measurements in a SVP-aligned CF-PS-b-PEO film permitted the longer-range mass-transport properties to be probed, reflecting the effective continuity of the aligned cylindrical nanostructures over > 100 μm in length. In this dissertation, FRAP and more importantly SMT methods have provided a unique and useful means for the in-depth characterization of morphology and mass-transport characteristics in thin polymer films under ambient conditions, in confined spaces, and with a nanometer-scale resolution.

abstract: Neurotoxicology has historically focused on substances that directly damage nervous tissue. Behavioral assays that test sensory, cognitive, or motor function are used to identify neurotoxins. But, the outcomes of behavioral assays may also be influenced by the physiological status of non-neural organs. Therefore, toxin induced damage to non- neural organs may contribute to behavioral modifications. Heavy metals and metalloids are persistent environmental pollutants and induce neurological deficits in multiple organisms. However, in the honey bee, an important insect pollinator, little is known about the sublethal effects of heavy metal and metalloid toxicity though they are exposed to these toxins chronically in some environments. In this thesis I investigate the sublethal effects of copper, cadmium, lead, and selenium on honey bee behavior and identify potential mechanisms mediating the behavioral modifications. I explore the honey bees’ ability to detect these toxins, their sensory perception of sucrose following toxin exposure, and the effects of toxin ingestion on performance during learning and memory tasks. The effects depend on the specific metal. Honey bees detect and reject copper containing solutions, but readily consume those contaminated with cadmium and lead. And, exposure to lead may alter the sensory perception of sucrose. I also demonstrate that acute selenium exposure impairs learning and long-term memory formation or recall. Localizing selenium accumulation following chronic exposure reveals that damage to non-neural organs and peripheral sensory structures is more likely than direct neurotoxicity. Probable mechanisms include gut microbiome alterations, gut lining damage, immune system activation, impaired protein function, or aberrant DNA methylation. In the case of DNA methylation, I demonstrate that inhibiting DNA methylation dynamics can impair long-term memory formation, while the nurse-to- forager transition is not altered. These experiments could serve as the bases for and reference groups of studies testing the effects of metal or metalloid toxicity on DNA methylation. Each potential mechanism provides an avenue for investigating how neural function is influenced by the physiological status of non-neural organs. And from an ecological perspective, my results highlight the need for environmental policy to consider sublethal effects in determining safe environmental toxin loads for honey bees and other insect pollinators. / Dissertation/Thesis / Doctoral Dissertation Neuroscience 2016

La majorité des études sur la dynamique des facteurs de transcription en cellules vivantes s'accordent sur une dynamique rapide. Il existe cependant quelques exceptions, comme la dynamique du facteur de transcription HSF « Heat Shock Factor », sur les chromosomes polyténiques de drosophile. Notre projet a consisté à étudier la dynamique d'HSF1 dans des cellules humaines. L'exposition des cellules à un stress tel qu'un choc thermique induit une réponse ubiquitaire et transitoire, dont la fonction est de protéger les cellules contre les effets délétères du stress. Au cours d'un choc thermique, plusieurs phénomènes se produisent : i) un arrêt global de la transcription excepté pour certains gènes tels que ceux codant pour les protéines de choc thermique (HSPs), dont l'expression est sous le contrôle du facteur de transcription HSF1. ii) une activation d'HSF1 qui se relocalise de façon rapide et transitoire sur les corps nucléaires de stress (nSBs), où il induit la transcription des séquences satellite III. Les nSBs forment un site d'activité naturellement amplifié et visible en microscopie. Nous avons utilisé deux techniques complémentaires pour étudier la dynamique d'HSF1 en cellules vivantes : le recouvrement de fluorescence après photoblanchiment (FRAP) et la spectroscopie à corrélation de fluorescence multi-confocale (mFCS), qui permet l'analyse FCS en plusieurs points simultanément. En cellules HeLa, la protéine HSF1-eGFP présente une dynamique rapide qui est significativement ralentie suite à un choc thermique. En mFCS, nous avons obtenu des constantes de diffusion de 14 µm²/s avant choc thermique et de 10 µm²/s après choc thermique. En FRAP, le temps de demi-recouvrement est de 0,2 s avant choc thermique, 2,6 s après choc thermique dans le nucléoplasme et 65 s sur les corps nucléaires de stress. Le ralentissement de la dynamique d'HSF1 s'explique par deux phénomènes : i) la formation de complexes de haut poids moléculaire, ii) une augmentation des interactions avec la chromatine. Pour mieux caractériser le changement de dynamique d'HSF1 après choc thermique, plusieurs mutants ont été analysés. Le domaine de trimérisation est indispensable pour le changement de dynamique après choc thermique, alors que le domaine de liaison à l'ADN et le domaine de transactivation n'ont que peu d'effet sur le changement de dynamique. Il ne peut donc pas être expliqué uniquement par les interactions directes à la chromatine du domaine de liaison à l'ADN, ni même par les liaisons indirectes du domaine de transactivation via d'autres protéines. La protéine HSF1 pourrait interagir de façon aspécifique avec la chromatine lors de la recherche de site de liaison, ou d'autres protéines via d'autres domaines pourraient entrainer des interactions indirectes avec la chromatine. / The majority of studies made on transcription factors dynamics on living cells agree with a fast dynamics process. However, there is some exceptions such as the dynamics of the transcription factor HSF “Heat Shock Factor” on drosophila polytenic chromosome. My project is to study HSF1 dynamics in human living cells. Cells exposure to a stress such as heat shock induces a transient and ubiquitous response that function's to protect cells against the deleterious effect of stress. During the course of a heat shock, several phenomenons take place: i) a global arrest of transcription, with the exception of some genes, such as those coding for the heat shock proteins (hsp), which expression is under the control of HSF1. ii) Activation of HSF1 that relocalize in a fast and transient way to nuclear stress bodies (nSBs), where it induces satellite III transcription. nSBs act as a natural amplification gene array, visible on microscopy. We have used two complementary techniques to look at HSF1 dynamics in living cells: Fluorescence recovery after photobleaching (FRAP) and multiconfocal fluorescence correlation spectroscopy (mFCS) that allow FCS analysis at several position simultaneously. On HeLa cells, HSF1-eGFP protein has a fast dynamics which is significantly slowed down following heat shock. On mFCS, we obtained a diffusion constant of 14 µm²/s before heat shock, and 10 µm²/s after heat shock. On FRAP, the half recovery time is 0.2 s before heat shock, 2.6 s after heat shock in the nucleoplasm and 65 s in nuclear stress bodies. HSF1 dynamics slowing down may be explain by two phenomenons: i) formation of high molecular mass complexes, ii) rise of interaction of HSF1 with chromatin. To better characterize changes in HSF1 dynamics after heat shock, several mutants have been analyzed. The trimerization domain of HSF1 is essential for dynamics changes after heat shock, while DNA binding domain (DBD) and transactivation domain (TAD) have only little effects on dynamics changes. These changes cannot only be explained by direct interaction of DNA binding domain with chromatin, neither by indirect interaction of the transactivation domain with other protein partners. HSF1 could be able to interact non-specifically with chromatin during the search for specific binding sites. Also other proteins via other domains might induce indirect binding to chromatin.