Os crustáceos do gênero Aegla, endêmicos da América do Sul, são os únicos decápodes anomuros que vivem em ambientes de água doce. A descoberta de fósseis em sedimentos marinhos deixou poucas dúvidas sobre a origem do grupo. Diversos estudos taxonômicos, morfológicos e de distribuição geográfica têm sido realizados sobre os eglídeos. Entretanto, informações filogenéticas baseadas na morfologia do grupo limitam-se, basicamente, aos trabalhos sobre a posição da família Aeglidae na infraordem Anomura e a um trabalho pioneiro, no qual os autores propuseram um cladograma para sete espécies com ocorrência no Chile. A partir de revisões taxonômicas e de uma análise cladística, com base em caracteres morfológicos, das espécies de Aegla que ocorrem nas bacias hidrográficas do Alto Paraná e Alto Uruguai, obteve-se: 1. O não-monofiletismo do clado Alto Paraná-Alto Uruguai; 2. Aegla leptochela relacionada filogeneticamente com outras espécies do Alto Ribeira; 3. Aegla marginata é uma espécie parafilética e forma um complexo com Aegla quilombola n. sp.; 4. Aegla franca e A. perobae são espécies irmãs; 5. Aegla lata, entre outras espécies, aparecem relacionadas com populações de diferentes bacias hidrográficas demonstrando tanto a falta de caracteres derivados dentro de Aeglidae, bem como a possibilidade de existirem mais complexos de diferentes espécies nessa família; 6. A invasão ao ambiente subterrâneo ocorreu mais de uma vez ao longo do tempo e espécies estigobiontes não são irmãs recíprocas exclusivas; 7. Aegla paulensis trata-se de um complexo de sete espécies distintas: Aegla paulensis s. str., A. rosanae, A. lancinhas, A. japi n. sp., A. jaragua n. sp., A. jundiai n. sp. e A. vanini n. sp. Além disso, análises em microscopia eletrônica de varredura dos tubos sexuais de machos de 39 espécies de Aegla, revelaram dois principais tipos, o longo estreito e o curto largo e, ainda, que cada espécie possui um conjunto de características específicas para essa estrutura, podendo, então, ser utilizada como caráter diagnóstico em descrições taxonômicas / The South American endemic genus Aegla represents the only anomuran decapod crustaceans strictly living in freshwaters. Marine fossil records left no doubts regarding the origin of the group. A number of studies on taxonomy, morphology and geographical distribution of aeglid have been carried out. Nevertheless, morphology based phylogenetic information about the group is limited to studies of the positioning of Aeglidae into the Anomuran infraorder and one pioneer work which presented a cladogram for seven species from Chile. Through cladistic analysis based on morphological characters of Aegla species occurring in the upper Paraná and upper Uruguay hydrographic basins the following results were obtained: 1. The non-monophyletic condition of the upper Paraná-upper Uruguay clade; 2. Aegla leptochela phylogenetically related to other species from Alto Ribeira; 3. Aegla marginata is paraphyletic, constituting a complex with Aegla quilombola n. sp.; 4. Aegla franca and A. perobae are sister species; 5. Aegla lata and other species were related with populations from different hydrographic basins, showing the lack of derived characters in Aeglidae and the possibility of existence of other species complexes in this family; 6. Invasion to the underground environments occurred more than once and the stygobiont species are not exclusive reciprocal sisters; 7. Aegla paulensis is a species complex encompassing seven species: Aegla paulensis s. str., A. rosanae, A. lancinhas, A. japi n. sp., A. jaragua n. sp., A. jundiai n. sp. e A. vanini n. sp.. In addition, scanning electron microscopy revealed two main types of sexual tubes (long and narrow; short and wide) in males from 39 Aegla species. Each species has a specific set of characters for this structure, hence indicating it can be used as diagnostic character in taxonomic descriptions

A realização do presente trabalho permitiu o estudo dos micromecanismos de deformação e fratura da liga de titânio Ti-6Al-4V, utilizada comercialmente para a fabricação de biomateriais metálicos. As técnicas empregadas para a análise do material em estudo foram: microscopia eletrônica de varredura (MEV), microscopia eletrônica de transmissão (MET) e a difração de raios X (DRX). Estudar a influência e comportamento das diversas fases existentes em ligas de titânio é importante para se avaliar o comportamento de trincas nas ligas de titânio com alta resistência mecânica, que possuem microestrutura fina, relacionando a presença das fases alfa (α), beta (β) e alfa+beta (α+β) com a resistência do material. A avaliação in situ dos micromecanismos de deformação e fratura foi realizada por MET e também foi feito o estudo das transformações de fase durante o resfriamento em ligas de titânio, por MET, utilizando-se as técnicas de campo claro, campo escuro e difração de elétrons (DEAS), em área selecionada. Após tratamento térmico foram observadas as diferenças entre a quantidade das fases α e β, em relação à microestrutura original do material para diferentes condições utilizadas no tratamento térmico aplicado à liga metálica. Observou-se a presença da microestrutura lamelar, formada durante o resfriamento no campo β, promovendo a transformação de parte da estrutura alfa secundária em beta, que se encontrava retida entre as lamelas de alfa. / This present work allowed the study of deformation and fracture micromechanisms of titanium alloy Ti-6Al-4V, used commercially for the manufacture of metallic biomaterials. The techniques employed for the analysis of the material under study were: scanning electron microscopy (SEM), transmission electron microscopy (TEM) and X-ray diffraction (XRD). The study of the influence and behavior of the phases present in titanium alloys is important to evaluate the behavior of cracks in titanium alloys with high mechanical strength, which have fine alpha (α), beta (β) and alpha+beta (α+β) microstructure, linking the presence of the phases with the strength of the material. The evaluation in situ of deformation and fracture micromechanisms were performed by TEM and was also a study of phase transformations during cooling in titanium alloys, using the techniques of bright field, dark field and diffraction of electrons in the selected area. After heat treatment differences were observed between the amount of in relation to the original microstructure of the β and α phases material for different conditions used in heat treatment applied to the alloy. The presence of lamellar microstructure formed during cooling in the β field was observed, promoting the conversion of part of the secondary alpha structure in β phase, which was trapped between the lamellar of alpha.

by Chan Lap-kong. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1994. / Includes bibliographical references (leaves 77-80). / ABSTRACT / ACKNOWLEDGEMENTS / LIST OF FIGURES / Chapter 1. --- INTRODUCTION --- p.1 / Chapter 1.1 --- Background --- p.1 / Chapter 1.2 --- Problems in Testing VLSI Circuits --- p.3 / Chapter 1.2.1 --- Test-cost-per-gate --- p.3 / Chapter 1.2.2 --- Tester Complexity --- p.3 / Chapter 1.3 --- Tester Based on Terminals Characteristics -Automatic Testing Equipment(ATE) --- p.4 / Chapter 1.4 --- Tester Based on Terminal and Internal Characteristics --- p.6 / Chapter 1.4.1 --- Mechanical Probing Method --- p.6 / Chapter 1.4.2 --- E-beam Probing Method --- p.7 / Chapter 1.5 --- Movitation for this Research --- p.7 / Chapter 1.6 --- Outline of the Remaining Chapters --- p.9 / Chapter 2. --- E-BEAM TESTER --- p.10 / Chapter 2.1 --- State-of-art of E-Beam Tester --- p.10 / Chapter 2.2 --- An Electron-optical Column of a SEM --- p.12 / Chapter 2.3 --- Beam Rastering Methods --- p.13 / Chapter 2.4 --- Voltage Contrast Phenomenon --- p.14 / Chapter 2.5 --- Configuration of an E-Beam Test System --- p.18 / Chapter 2.6 --- Advantages of an E-beam Tester --- p.20 / Chapter 3. --- BASIC PRINCIPLES --- p.21 / Chapter 3.1 --- Single-Stuck-At Fault Model --- p.21 / Chapter 3.2 --- Observability and Controllability --- p.24 / Chapter 3.3 --- Netlist Format --- p.25 / Chapter 3.4 --- Level --- p.27 / Chapter 3.5 --- Reconvergent Fanout --- p.28 / Chapter 4. --- CONVENTIONAL TEST GENERATION --- p.29 / Chapter 4.1 --- Conventional Automatic Test Generation for ATEs --- p.29 / Chapter 4.3 --- Conventional E-Beam Test Generation --- p.31 / Chapter 5. --- TEST AND PROBE POINT GENERATION --- p.32 / Chapter 5.1 --- Wafer Stage E-beam Testing --- p.32 / Chapter 5.2 --- Critical Paths Generation --- p.33 / Chapter 5.3 --- Assumptions of the Test and Probe Point Generation Algorithm --- p.35 / Chapter 5.4 --- Rules of the Test and Probe Point Generation Algorithm --- p.36 / Chapter 5.5 --- Probe Points Selection and Reduction --- p.38 / Chapter 5.6 --- Test and Probe Point Generation Algorithm --- p.40 / Chapter 5.7 --- Propagation and Justification at Fanout Site --- p.42 / Chapter 6. --- EXAMPLES --- p.45 / Chapter 6.1 --- Example of Test and Probe Point Generation for Circuit sc2 --- p.45 / Chapter 6.2 --- Example of Test and Probe Point Generation for Circuit sfc4 --- p.53 / Chapter 7. --- CONCLUSIONS --- p.61 / Chapter 7.1 --- Summary of Results --- p.61 / Chapter 7.2 --- Further Research --- p.63 / APPENDIX / Appendix A: Algorithm to Find Reconvergent Fanouts / Appendix B: Results of Test Generation for Circuit sc1 / Appendix C: Results of Test Generation for Circuit sc3 / REFERENCES --- p.77

Diseases caused by pathogenic bacteria continue to be major health concerns. For example, it is estimated that in the year 2000 typhoid fever caused over 21,000,000 illnesses and ~200,000 deaths (Crump et al., 2004). The disease is caused by S. typhi, a closely-related serotype of S. typhiumurium, the salmonella strain in which BipA was first identified. The CDC estimated that in 2013, multidrug resistant bacteria caused over 2 million infections in the United States, ending in more than 23,000 deaths (CDC, 2013). This number is set to rise as more bacteria become resilient to the collection of conventional antibiotics. The increasing number of multidrug resistant bacterial strains necessitates the development of new antimicrobial drugs. BipA is an attractive target for drug research. As mentioned in Section 2.5.2, BipA is ubiquitous in eubacteria and lower eukaryotes such as protozoa, but is absent from higher-order eukaryotes such as humans. Because the protein is essential for bacterial survival, BipA presents a major vulnerability of pathogenic bacteria. A drug targeting the protein itself or its interactions to the ribosome will disable only the bacteria, but have no effect on the eukaryotic host. A comprehensive model of BipA bound to the 70S ribosome will provide unparalleled insight into BipA's binding site and its mechanism. Toward this goal, cryo-EM techniques were employed to visualize the binding site of BipA on the 70S ribosome, characterize its interactions with the ribosome, and elucidate its mechanism on the ribosome. An X-ray structure of isolated BipA-GMPPNP was elucidated, by collaborators, and used for further molecular modeling of the protein to reveal possible atomic interactions between BipA and 70S ribosome. Additional biochemical studies were performed to fully characterize the specific ribosomal complex that optimizes binding of the factor. Together, the cryo-EM reconstruction, the BipA X-ray structure, the subsequent molecular modeling, and the additional biochemical studies provide a comprehensive model for BipA binding. Over the last years, the introduction of new automated algorithms for particle selection (AutoPicker) and classification (RELION) for the cryo-EM technique has revolutionized the workflow of the entire imaging and reconstruction process. The BipA dataset was primed to be used as a test bed for these algorithms and classification technique, respectively. Using old and new techniques to process the dataset allows a discussion of how the single particle reconstruction process can be vastly improved, with greater automation and efficiency.

Translation is the process by which the cell produces new proteins on the ribosome, as directed by genetic instructions, in all living organisms. Structural studies of the ribosome have shed considerable lights on its mechanism and regulation. Cryogenic electron microscopy (cryo-EM) and single-particle reconstruction technique is one of the major approaches to studying ribosome structure. In this thesis, I report the use of cryo-EM and related new techniques to study the structure of ribosome complexes. This work is divided into three parts. First, in Chapter 3, I describe the development of a computational method in the classification of cryo-EM data. Recently developed classification methods have enabled resolving multiple structures/conformations of the molecules from cryo-EM data obtained on a heterogeneous biological sample. However, the classification methods all involve various amounts of arbitrary decisions made by researchers, which can limit the use of these methods by inexperienced users. As a step toward fully automated classification, I worked with colleagues to develop a "jumper analysis" to determine the number of distinguishable classes of 3D reconstruction, based on the statistics of cryo-EM particles. Second, in Chapter 4, I document the cryo-EM study of EttA-70S ribosome complex, which provided structural insights into the mechanism of EttA in translation regulation. Energy-dependent translation throttle A (EttA, previously named YjjK in Escherichia coli) is the most prevalent member of ATP-binding cassette F family proteins in eubacteria. Through a collaboration among the Hunt, Frank, and Gonzalez labs, we combined crystallography, biochemical, cryo-EM and single-molecule fluorescence energy transfer techniques to elucidate the function and mechanism of EttA. We demonstrated that EttA gates ribosome entry into the translation elongation cycle through a nucleotide-dependent interaction sensitive to ATP/ADP ratio. We also showed that the ATP-bound form of EttA binds to the ribosomal tRNA-exit site, and restricts the ribosome and tRNA dynamics required for translation. Thirdly, in Chapter 5, I discuss the improvements to a new technique, time-resolved cryo-EM by mixing-spraying, and its application to ribosome studies. The mixing-spraying method can study processes involving two big biological molecules that are in the sub-second time scale. I worked with colleagues to apply this method to studying ribosome subunit association. By mixing the subunits and reacting for 60 ms and 140 ms, we were able to capture the association reaction in a pre-equilibrium state. We detected three 70S ribosome conformations in the system. Quantification of the proportions of particles assuming these conformations suggested that the 70S ribosome can undergo fast conformational changes upon formation, and reaches equilibrium among these conformations earlier than 60 ms. In addition, I present preliminary results of studying translation decoding using the mixing-spraying method. This study, performed before improving the mixing-spraying method, was inconclusive mainly due to the limited size of cryo-EM data. Now that we have demonstrated the capability of the mixing-spraying method to visualize multiple states of molecules in a sub-second reaction, the translation decoding process can be revisited and many other processes, such as translation initiation, can be studied.

The ribosome is a macromolecular machine, present in high copy number in the cell, that synthesizes proteins from information encoded in messenger RNA. It is a universal translator, found in all life forms and in all eras recent enough to bear life. The ribosome is structurally complex and its structure is highly evolutionarily conserved; that conservation reinforces the concept that its function in executing translation is essential. As a subject of study, the ribosome lends itself well to direct imaging, as it is large, asymmetric, dynamic, and it interacts with other heterogeneous agents throughout the translation process; if we are to infer function from structure, then the most certain way to observe the ribosome’s structure is to image it as directly as possible. Cryo-electron microscopy and single particle reconstruction are appropriate tools for this endeavor, as they can produce high-resolution three-dimensional structures of ribosomes or other macromolecular samples, and they can even reveal multiple biologically relevant states of a single sample. Although the ribosome is highly conserved in terms of its presence and core structure and functions, there is considerable variation among taxa, and the function of some of this variation is not yet understood. For example, the ribosome of the unicellular trypanosomatid parasite Leishmania major exhibits unusually large expansion segments of ribosomal RNA, as well as unusual cleavage sites in ribosomal RNA that is otherwise conserved. Here, we present a three-dimensional cryo-electron microscopy reconstruction of the 80S ribosome of Leishmania major and compare it to the available ribosome structures of closely related parasites. There is also structural variation related to the mechanism of translation: certain viruses with RNA genomes employ highly structured segments of RNA called internal ribosome entry sites to initiate translation of viral proteins on host cell ribosomes via noncanonical mechanisms. We explore one instance of this with a reconstruction of the encephalomyocarditis virus internal ribosome entry site bound with necessary protein factors to a eukaryotic 40S ribosomal subunit.

Graphene and other two-dimensional materials can be stacked together to form vander Waals heterostructures: synthetic crystals composed of different atomically thin layers with a bespoke electronic band structure. Structural characterisation of vander Waals heterostructures is difficult using conventional methods as the properties are almost entirely defined by the nature of the buried interfaces between dissimilar crystals. These methods also fall short of resolving the atomic structure of buried defects in van der Waals materials such as graphite. This work demonstrates the refinement and successful application of ion beam specimen preparation to produce cross sectional slices through these unique crystals so that they can be characterised by high resolution scanning transmission electron microscopy (STEM). Cross sectional specimen were prepared using in situ lift-out in a focused ion beam (FIB) dual-beam instrument. The fine polishing steps were optimised to prevent damage to the core of the specimen. High resolution STEM imaging of twin defects in graphene, hexagonal boron ni-tride and MoSe2 revealed that the boundaries are not atomically sharp but extended across many atoms. Advanced processing and analysis of these images uncovered fundamental mechanics which govern their geometry. This technique was further applied to complex transition metal dichalcogenide heterostructures to quantitatively determine the properties of buried interfaces between atomically thin crystals.

Multicellular development in fungi is fundamentally different from that of animals or plants. In filamentous fungi, multicellular structures are formed by aggregation and adhesion of hyphae, followed by septation and specialisation of hyphal compartments within the aggregate. The perithecium, a flask-shaped sexual fruitbody produced by both Neurospora crassa and Sordaria macrospora, provides a model system in which to study fungal multicellular development. This study presents a detailed description of the morphological stages of perithecial morphogenesis in N. crassa and S. macrospora and its early stages, the ascogonial and protoperithecial stages, using a range of microscopical techniques. Details of the development of several mutants impaired in perithecial development are described, including: gene-deletion mutants of all nine mitogen-activated protein (MAP) kinases conserved in N. crassa; and three mutants pro22, pro40 and pro41 of S. macrospora, and their corresponding gene-deletions in N. crassa. The results confirm that all three MAP kinase cascades are required for sexual development. However, only the pheromone response and cell-wall integrity MAP kinase pathways, but not the osmoregulatory MAP kinase pathway, are essential for hyphal cell fusion. Evidence of cell fusion-related processes, regulated through MAP kinase signalling, have been identified as novel features important for the construction of fertilisable protoperithecia. These cell-fusion related processes include extracellular matrix deposition, hyphal attachment and envelopment. A novel phenotype of S. macrospora with defective ascogonial septation is presented. This pro22 mutant also has impaired hyphal cell fusion and produces only small, defective protoperithecia. The pro22 gene encodes a protein that is highly conserved throughout eukaryotes. Live-cell imaging revealed that this PRO22 protein is localised in the dynamic tubular and vesicular vacuolar-network of the colony periphery and in ascogonia. PRO22 is absent from the large spherical vacuoles in the vegetative hyphae of the sub-peripheral region of the colony. This points to a specific role of PRO22 in the tubular and vesicular vacuolar-network. Furthermore, the loss of intercalary septation in ascogonia suggests that PRO22 functions during the initiation of sexual development.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a transmembrane protein that functions as an ion channel. Mutations in this protein cause Cystic Fibrosis. For this reason, it is important to study the structure and function of CFTR. In this study, constructs of CFTR (C-terminii), a CFTR-interacting protein and full-length CFTR were cloned, expressed and purified for structural and functional studies. The purified C-terminal polypeptides of CFTR were soluble and shown to interact with NHERF1 PDZ 1 (a CFTR-interacting protein). The CFTR C-terminus and NHERF1 PDZ 1 domain were co-expressed and co-purified. The purified complex showed a strong interaction that might induces a conformational change. Site-directed mutation of the C-terminus of CFTR was performed in order to examine the effect of removing a potentially flexible amino acid (Arginine) on protein crystallization. Pull-down assay experiments with full-length CFTR demonstrated an interaction between CFTR (in DDM detergent) and NHERF1 PDZ 1(+). No interaction was observed for CFTR in LPG (a relatively denaturing detergent) and NHERF1, implying that the interaction between the PDZ motive of CFTR and NHERF1 requires a stable folded structure for both proteins. In addition, full-length CFTR in DDM has been studied by electron microscopy and Single Particle Analysis in the presence of NHERF1 PDZ 1(+). A 3D structure was generated for the CFTR-NHERF1 PDZ 1(+) complex at a resolution of ~ 18 A. This 3D structure showed a new open conformation of CFTR (V shape). In comparable studies with CFTR alone, a 3D structure was generated at a resolution of 27 A and this structure showed a closed state as previously reported. This new data suggest a possible role for NHERF1 in terms of CFTR channel gating or activation.

Xing, Xiaochen. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2009. / Includes bibliographical references. / Abstract also in Chinese. / Abstract (Chinese) --- p.i / Abstract --- p.iii / Contents --- p.v / Acknowledgement --- p.ix / Chapter Chapter1 --- Introduction and background / Chapter 1.1 --- Overview of Studies in Colloid-Polymer mixture --- p.1 / Chapter 1.2 --- Depletion Force in Colloid-Polymer Mixture --- p.1 / Chapter 1.2.1. --- Depletion Interaction in Monodisperse and Neutral Polymer-Colloid Mixtures: Theory --- p.3 / Chapter 1.2.1.1. --- An Exact Result: the Interaction between Parallel Plates due to Ideal Polymer Chains --- p.3 / Chapter 1.2.1.2. --- Penetrable Hard Sphere (PHS) Approach --- p.4 / Chapter 1.2.2. --- Early Experimental Findings of Depletion Interaction --- p.6 / Chapter 1.3 --- References and Notes --- p.8 / Chapter Chapter2 --- Principle of Total Internal Reflection Microscopy (TIRM) and Instrumentation / Chapter 2.1 --- Introduction of Total Internal Reflection Microscopy (TIRM) --- p.10 / Chapter 2.2 --- The Principle of TIRM Technique --- p.11 / Chapter 2.2.1 --- Total Internal Reflection --- p.11 / Chapter 2.2.2 --- Details on Scattering of the Evanescent Wave --- p.13 / Chapter 2.2.3 --- Data Analysis --- p.16 / Chapter 2.3 --- Instrumentation --- p.20 / Chapter 2.3.1 --- Apparatus --- p.20 / Chapter 2.3.2 --- Optical Tweezer --- p.23 / Chapter 2.3.3 --- Cleaning of the Slide Surface --- p.24 / Chapter 2.3.4 --- A Typical Potential Energy Profile --- p.25 / Chapter 2.4 --- Laser Light Scattering (LLS) --- p.26 / Chapter 2.5 --- Zeta-potential Measurements --- p.27 / Chapter 2.6 --- References and Notes --- p.28 / Chapter Chapter3 --- Depletion Attraction between a Polystyrene Sphere and a Hydrophilic Surface in a Pluronic Aqueous Solution / Chapter 3.1 --- Introduction --- p.30 / Chapter 3.2 --- Experimental Section --- p.34 / Chapter 3.2.1 --- Sample Preparation --- p.34 / Chapter 3.2.2 --- Total Internal Reflection Microscopy --- p.35 / Chapter 3.2.3 --- Laser Light Scattering --- p.36 / Chapter 3.3 --- Results and Discussion --- p.37 / Chapter 3.4 --- Conclusion --- p.48 / Chapter 3.5 --- References and Notes --- p.50 / Chapter Chapter4 --- pH-Controllable Depletion Attraction Induced by Microgel Particles / Chapter 4.1 --- Introduction --- p.53 / Chapter 4.2 --- Experimental Section --- p.54 / Chapter 4.2.1 --- Sample Preparation --- p.54 / Chapter 4.2.2 --- Total Internal Reflection Microscopy --- p.56 / Chapter 4.3 --- Results and Discussion --- p.58 / Chapter 4.4 --- Conclusion --- p.63 / Chapter 4.5 --- References and Notes --- p.64 / Publication List --- p.65