Eukaryotic genomes must be folded and compacted to fit within the restricted volume of the nucleus. This folding, and the subsequent organization of the genome, reflects both the transcription profile of the cell and of the specific cell type. A dispersed, mesh-like chromatin configuration, for example, is characteristic of a pluripotent stem cell. Here we show that the acquisition of the pluripotent state during somatic cell reprogramming is coincident with the disruption of compact heterochromatin domains. Using Electron Spectroscopic Imaging (ESI), I made the surprising observation that the heterochromatin domains of the induced pluripotent and of the parental somatic cell contained 10 nm chromatin fibres. Since ESI generates projection images, the precise three-dimensional organization of all chromatin fibres within these domains could not be elucidated. To circumvent this limitation, I developed an electron microscopy technique that combines ESI with tomography. Using this approach, I found that both heterochromatin domains and the surrounding euchromatin of murine pluripotent cells, fibroblasts, and somatic tissues are in fact organized entirely as 10 nm chromatin fibres. This challenges the current paradigm that most, if not all, of the genome exists as 30 nm and higher-order chromatin fibre assemblies. Rather than transitions between 10 nm and 30 nm fibres, I propose that the organization and thus the regulation of the genome is achieved by the bending and folding of 10 nm chromatin fibres into discrete domains in a cell type-specific manner.

Eukaryotic genomes must be folded and compacted to fit within the restricted volume of the nucleus. This folding, and the subsequent organization of the genome, reflects both the transcription profile of the cell and of the specific cell type. A dispersed, mesh-like chromatin configuration, for example, is characteristic of a pluripotent stem cell. Here we show that the acquisition of the pluripotent state during somatic cell reprogramming is coincident with the disruption of compact heterochromatin domains. Using Electron Spectroscopic Imaging (ESI), I made the surprising observation that the heterochromatin domains of the induced pluripotent and of the parental somatic cell contained 10 nm chromatin fibres. Since ESI generates projection images, the precise three-dimensional organization of all chromatin fibres within these domains could not be elucidated. To circumvent this limitation, I developed an electron microscopy technique that combines ESI with tomography. Using this approach, I found that both heterochromatin domains and the surrounding euchromatin of murine pluripotent cells, fibroblasts, and somatic tissues are in fact organized entirely as 10 nm chromatin fibres. This challenges the current paradigm that most, if not all, of the genome exists as 30 nm and higher-order chromatin fibre assemblies. Rather than transitions between 10 nm and 30 nm fibres, I propose that the organization and thus the regulation of the genome is achieved by the bending and folding of 10 nm chromatin fibres into discrete domains in a cell type-specific manner.

Thesis (Ph. D.)--Lehigh University, 1999. / Includes vita. Bibliography: leaves 145-153.

Thesis (Ph. D.)--Lehigh University, 2004. / Includes vita. Includes bibliographical references (leaves 184-195).

No description available.

Evaluation of several methods of fixing chicken skin for scanning electron microscopy (SEM) indicated standard chemical fixation using glutaraldehyde and osmium tetroxide followed by chemical dehydration with 2,2-dimethoxypropane to be the method of choice. SEM revealed that chicken skin has a convoluted surface. Two types of chicken skin, distinguishable on the basis of chemical composition and appearance were observed. Type I has a filamentous surface with 55% moisture and 25% fat, whereas Type II skin has a globular appearance, 52% fat and 33% moisture. The fatty acid profiles of Types I and II skin are the same. Bacteria have greater affinity for Type II than Type I skin. Attachment studies indicated that Salmonella typhimurium quickly attach to the skin surface and cannot be removed easily by washing with water or with water containing a surfactant. / Land and Food Systems, Faculty of / Graduate

The characterization of nanomaterials involved in dynamic processes are conventionally conducted using microscopy, spectroscopy and other physical/chemical methods through the pseudo-dynamic approach. In details, the dynamics processes are recorded by repeating or terminating the process multiple times. However, the above approach can lead to missing important transition information and inducing contamination for mechanistic studies. This motivates the efforts to develop real time characterization techniques which can probe the dynamic change of nanoparticles in their native operating environments. With the capability of probing structural change at the nanoscale, in situ transmission electron microscopy, has shown great potential in studies and applications of various processes. Targeting at conducting precise analysis, which has been limited by many uncertainties from electron beam effects and the miniaturized reaction cell used for TEM, the work presented herein pursues a quantitative characterization of a few electrochemical and biological processes through in situ liquid-phase transmission electron microscopy. In this work, the in situ transmission electron microscopy system is evaluated by comparing the in situ results with those from standard experiments to show its capabilities in studying dynamic processes. The in situ system is quantitatively calibrated to obtain the optimized observation conditions to avoid detectable electron beam interference, solution depletion and achieve sufficient resolution for analysis through micrometer thick liquid. These form the fundamentals for the in situ studies. Moreover, a comprehensive analysis protocol is established by incorporating multiple ex situ and post situ characterizations. Using this optimized in situ system, the mechanism of electrodeposition of gold on carbon electrode is studied. The in situ results allow quantitative analysis of the growth process. The prevailing diffusion limited three dimensional growth model is examined. A study of the effect of supporting electrolyte on the electrodeposition of palladium is also conducted. The self-limiting, surface diffusion and aggregation/recrystallization growth model is found to describe the early stage of growth, rather than the classical Volmer-Weber growth model. A further study is conducted on the structural evolution of palladium nanoparticles under electrochemical cycling. The mechanisms involved in this process, including electrodeposition, dissolution, hydrogen co-deposition and hydrogen desorption, are studied. The supporting electrolyte, HCl, is found to enhance the dissolution of deposited palladium clusters and induce movements and aggregation of the deposits during the hydrogen interaction process to form chain-like and irregular clusters, which provide direct experimental proof on the morphology formation of palladium with hydrogen involvement. Ultimately, the in situ technique is applied to the study of calcium phosphate biomineralization. Combined with multiple post situ characterization techniques, the study provides direct experimental evidence of the non-classical pre-nucleation and attachment growth of calcium phosphate structures. This demonstrates the potential of the in situ technique for studying the mechanisms involved in biological processes. / Dissertation / Doctor of Philosophy (PhD) / Nanostructured materials have been widely used in various fields. In situ transmission electron microscopy, a technique used to characterize nanomaterials involved in different dynamic processes in their operating environments, is an advanced tool over the traditional characterization methods such as ex situ microscopy and spectroscopy. However, there are several challenges in applying this in situ technique to processes occurring in liquid media. In this thesis, an in situ transmission electron microscopy system is applied to study the mechanisms of structural changes during different processes in liquids with both high spatial and temporal resolution. Protocols to evaluate and optimize the in situ system are developed to provide results comparable with those from their actual applications. Then in situ studies on the structural evolution of nanomaterials during electrochemical processes are performed and different theoretical models are applied to describe these processes. Finally, this technique is extended to investigate biomineralization to show its capabilities in future studies on biological processes.

Liquid cell electron microscopy has been proven to provide high spatial and temporal resolution for studying liquid layers and the solid-liquid interface at the micro and nano scale. The in situ environment allows for spatial and spectral characterization and quantification of the dynamics and kinetics involved with structural and chemical changes of nanostructures, which has seen application is fields of materials science, electrochemistry, corrosion, biomaterials, and nanophysics. The rapid growth of in situ liquid cell electron microscopy has motivated the fabrication of a custom liquid cell for improved control over the experimental conditions, including cell dimensions and materials. In this work, the process flow and micro-fabrication of a custom liquid cell system are proposed and executed, with proof of operation through the in situ imaging of suspended gold nanoparticles and electrochemical characterization. The in situ TEM system is improved upon by forming 1μm diameter holes through the viewing membranes, removing the background noise contribution from imaging electrons through the windows. This allows for high resolution liquid cell imaging. This improved system is used to study the oxidative etching conditions for palladium nanocrystals, which are commonly used as catalysis for hydrogen fuel cells. The dendritic etching is studied through native etching under exposure to hydrochloric acid without the presence of oxidizing species, followed by the radiolytic generation of oxidizing radicals via the microscope electron beam, and finally by the application of electrical biasing. / Thesis / Master of Applied Science (MASc) / Characterization of nanomaterials has been available for several decades and has aided in the improvement of material design, such as steel strength and corrosion resistance, electrical systems such as those involved in computers and smartphones, and biological sensing and detection. Observation of dynamic process which occur at the interface between solid and liquid phases, or purely within liquid layers, has always been a challenging topic due to the difficulty of finding a stable environment for both solids and liquids to exist at the nano scale within a measurement device. In situ liquid cell electron microscopy offers the ability to image this interface with real-time data acquisition for recording of dynamics and kinetics at the nano scale. Previous work has shown the liquid cell to provide high spatial and temporal resolution of systems in an environment which mimics their native operating conditions. This thesis addresses current developments for in situ systems and works to develop a custom liquid cell to further the applications of the liquid cell and provide improved control over experimental conditions. The work then aims to improve on current technology by increasing the spatial resolution obtainable. Finally, the technique is applied to study the structural changes of nanocrystals under various etching conditions as a demonstration of its’ capabilities.

No description available.

Phase-transformation-induced microstructures, including twin domains, anti-phase domains and inversion domains have been analyzed using the scanning and transmission electron microscopy for BaTiO3, BaCeO3 and CaTiO3 of the perovskite structure. Differential etching rate was taken to identify the ferroelectric domains in tetragonal (t-) BaTiO3. Space group Pbnm (No. 62) usually adopted for the orthorhombic crystals by materials scientists is assumed throughout this research to avoid confusion of the plane and direction indices. Traditional contrast analysis was adopted for determining dislocation Burgers vectors (b) and fault vectors (R) in deformed and phase-transformed perovskites, synthetic ceramics (BaTiO3, BaCeO3 and CaTiO3) as well as natural minerals (CaTiO3), polycrystalline (BaTiO3, BaCeO3 and CaTiO3) as well as single crystal (CaTiO3). Atomic images for the structures of twin boundaries and anti-phase boundaries were taken by high resolution technique and image contrast enhancement was performed using fast Fourier transform. Failure of Friedel¡¦s law is adopted for determining if the crystal belongs to non-centrosymmetric point groups. Whether the twins are £_-, £\- or £k-type (i.e. anti-phase domain boundaries) is analysed from the contrast of extreme fringe patterns. Tilting experiments were performed on selected area diffraction patterns containing un-split row of reflections to ensure that the twin boundaries are the reflection or rotation type. Transformation twinning in all perovskites studied here follows the prediction by the relation of point group symmetries between the high- and low-symmetry phases, assuming continuous, diffusionless, second-order transitions that obey the restrictions imposed by the Landau theory of phase transition. Although such predictions of transformation-induced twinning are only permitted when crystallographic group-subgroup relationship exists and structural coherence retains between the high- and low-symmetry phases, experimental observations for r (rhombohedral) ¡÷ o-BaCeO3 and t ¡÷ o in CaTiO3 that are not related by group-subgroup, c (cubic) ¡÷ t (tetragonal) in CaTiO3 and and c (cubic) ¡÷ t (tetragonal) in BaTiO3 that are related by group-subgroup, are all consistent with the predictions from loss of point group symmetry elements and change of unit cell volume. In order that the Landau theory is conformed, however, an intermediate phase of either the lowest common supergroup (cubic Pm m) or highest common subgroup (monoclinic C2/c), with phase transition experiencing multistage pathways suggested by Christy and assumption of non-disruption conditions proposed by Guymont, was identified to bridge between two structures, such as rhombohedral and orthorhombic that are not group-subgroup related. Both the 90o and 180o ferroelectric twin domains in t-BaTiO3 are the reflection type and have been identified in pressureless-sintered ceramics. Further, fault vectors (R = £`<110]) for such domain boundaries were determined, boundary planes of {110) for the former, {100) and {220) for the latter deduced accordingly. The polar c-direction between adjacent domains was determined by differential etching rate across domain boundaries, convergent beam electron diffraction was also adopted for identification and confirmation of the c-axis for two types of domains in t-BaTiO3. Plastic deformation resulting from the thermodynamic driving force for sintering (?p) intensified by a multiplication factor £p) was evidenced microstructurally from analysing dislocations in pressureless-sintered BaTiO3 where a Frank-Read source was observed. Slip systems are activated for the effective stress acting on the slip plane along the slip direction has exceeded the critical value of resolved shear stress (£nCRSS) and yielding occurs. It has contributed to densification, i.e. the overall system shrinkage of a green powder compact, although if such contribution is at all significant requires studies of sintering kinetics to ascertain. Dislocation dissociation into the scallop-shaped half partials according to the following reactions is determined from analysing corresponding Burgers vectors. [010] + [001] ¡÷ [011] [001] + [10 ] ¡÷ [100] [001] + [110] ¡÷ [111] Both transformation twins lying in {110) and {112) and anti-phase domain boundaries with R = 1/2<111> are detected in o-BaCeO3. For orthorhombic (o-) BaCeO3, fault vectors of the latter R = 1/2<111> determined by contrast analysis was confirmed by high-resolution imaging, but on the contrary, fault vectors the former R = £`<110] and £`<021], respectively, could not be determined from such images. Utilizing the technique of large-angle convergent beam electron diffraction, such fault vectors and dislocation Burgers vectors determined by traditional contrast analysis have been confirmed. Both twinning and dislocations were observed in hot-pressed CaTiO3 prepared in a multi-anvil apparatus. Such twins are deformation twins since hot-pressing was conducted in the orthorhombic stable phase field at 1000oC under 8 GPa. Since fault vectors R = £`<110] determined for {112) and {110) twins are different from the transformation-induced twins in o-CaTiO3, R = £`<021] determined for the {112) twinning in natural perovskite may serve as a diagnostic feature for the deformation twins. Plastic deformation in hot-pressured sample was contributed by both slip and twinning. Slip occurred via slip systems with dislocations of b = [110] gliding in (110) is therefore {110}o <1 0>o (equivalent to {100}pc <001>pc, where pc for pseudo-cubic) often found in perovskites deformed at high temperatures. Another set of dislocations with b = [001] in screw orientation was also determined. APB with R = 1/2<111> detected in natural minerals suggests that the phase transition sequence in CaTiO3 is better described by: (c) ¡÷ t (I4/mcm) ¡÷ o (Pbnm) and such APB are generated from loss of the lattice point at I-centre (1/2,1/2,1/2) in the absence of a second orthorhombic Cmcm between t-I4/mcm and o-Pbnm reported before from neutron and X-ray powder diffraction studies.