The Transmission Electron Microscope

The book "The Transmission Electron Microscope" contains a collection of research articles submitted by engineers and scientists to present an overview of different aspects of TEM from the basic mechanisms and diagnosis to the latest advancements in the field. The book presents descriptions of electron microscopy, models for improved sample sizing and handling, new methods of image projection, and experimental methodologies for nanomaterials studies. The selection of chapters focuses on transmission electron microscopy used in material characterization, with special emphasis on both the theoretical and experimental aspect of modern electron microscopy techniques. I believe that a broad range of readers, such as students, scientists and engineers will benefit from this book

An analytical study on image databases

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.Includes bibliographical references (leaves 87-88).by Francine Ming Fang.M.Eng

A blue light receptor that mediates RNA binding and translational regulation

Sensory photoreceptor proteins underpin light-dependent adaptations in nature and enable the optogenetic control of organismal behavior and physiology. We identified the bacterial light-oxygen-voltage (LOV) photoreceptor PAL that sequence-specifically binds short RNA stem loops with around 20 nM affinity in blue light and weaker than 1 µM in darkness. A crystal structure rationalizes the unusual receptor architecture of PAL with C-terminal LOV photosensor and N-terminal effector units. The light-activated PAL–RNA interaction can be harnessed to regulate gene expression at the RNA level as a function of light in both bacteria and mammalian cells. The present results elucidate a new signal-transduction paradigm in LOV receptors and conjoin RNA biology with optogenetic regulation, thereby paving the way toward hitherto inaccessible optoribogenetic modalities

Molecular, morphological and physiological analyses of Mediophyceae diatoms in Bilbao Estuary

219 p.La evaluación medioambiental de estuarios, ríos o lagos se puede realizar basada en las comunidades de fitoplancton. En el estuario de Bilbao se lleva a cabo un monitoreo rutinario desde el año 2000, con el objetivo de evaluar la calidad del agua. Para realizar esta evaluación, se tienen en cuenta los grupos generales de fitoplancton en términos taxonómicos, creando subgrupos en función del tamaño celular y registrando su abundancia. De acuerdo con este procedimiento, las diatomeas céntricas se clasificaban en tres grupos: 15 ¿m (desde el año 2000 al 2009) y 3-10¿m; 10-15 ¿m; > 15 ¿m (desde 2010 a la actualidad). Ésta evaluación se hacía usando microscopía óptica, la cual no es resolutiva a nivel de especie. Sin embargo, la identificación de estas especies es importante porque se han registrado floraciones de diatomeas céntricas al final de la primavera y el verano durante años, siendo éstas las especies dominantes del estuario. El objetivo de este estudio es demostrar que los grupos de diatomeas establecidos en clases de tamaños y analizados con microscopía óptica, en realidad son grupos heterogéneos que contienen una gran diversidad específica. Para ello se lleva a cabo una exhaustiva identificación de las diferentes cepas de especies de la clase Mediophyceae a nivel morfológico y molecular, que revelarán una gran diversidad, incluyendo la presencia de especies cripticas o complejos de especies (como el caso del género Skeletonema o el complejo de especies de Cyclotella meneghiniana). Estas especies, fueron sometidas, a los análisis anteriormente nombrados y a análisis fisiológicos complementarios para analizar su potencial como especies formadoras de floraciones en el área de estudio

Crystal structure solution of hydrogen bonded systems : a validation and an investigation using historical methodologies followed by a review of crystal structure prediction methodologies to date

There are many chemicals that crystallize into more than one form. This phenomenon is called polymorphism. In each form or polymorph, inter and intra-molecular binding differ to varying degrees. As a result of this structural variation, the physical properties of the solid phases may also differ. Even the smallest of changes at the molecular level can result in a significant change in the final adopted crystal structure. Polymorphism in crystal structures allows studies of structure-property relationships since it is only the packing motifs that differ between polymorphs. In this thesis, a ‘computationally assisted’ approach to crystal structure solution was taken. X-ray powder diffraction was used to generate unit cell dimensions and space groups while historical in-house molecular modelling methods were used to generate possible trial structures that would be the starting point for refinement. Finally, a review of the latest methodologies for crystal structure prediction and consideration of polymorphism within the pharmaceutical industry completes this work

Biochemical characterisation of unusual glycolytic enzymes from the human intestinal parasite Blastocystis hominis

Blastocystis is an important parasite that infects humans and a wide range of animals like rats, birds, reptiles, etc. infecting a sum of 60% of world population. It belongs to the Stramenopiles, a Heterologous group that includes for example the Phythophthora infestans the responsible for the Irish potato famine. Previous work had reported the presence of an unusual fusion protein that is composed of two of the main glycolytic enzymes; Triosephosphate isomerase-glyceraldehyde-3-phosphate dehydrogenase (TPI-GAPDH). Little is known about this protein. Blastocystis TPI-GAPDH and Blastocystis enolase were both characterized biochemically and biophysically in this project. The phylogenetic relationships of those two proteins among other members of either Stramenopiles, or other members of the kingdom of life were examined and found to be grouping within the chromalveolates. Our studies revealed that those two proteins, Blastocystis enolase and Blastocystis TPI-GAPDH, had a peptide signal targeting them to the mitochondria. This was an unusual finding knowing that text books always referred to the glycolytic pathway as a canonical cytoplasmic pathway. Structural studies had also been conducted to unravel the unknown structure of the fusion protein Blastocystis TPI-GAPDH. X-ray crystallography had been conducted to solve the protein structure and the protein was found to be a tetrameric protein composed of a central tetrameric GAPDH protein flanked with two dimmers of TPI protein. Solving its structure would be the starting point towards reviling the role that TPI-GAPDH might play in Blastocystis and other organisms that it was found in as well. Although a fusion protein, the individual components of the fusion were found to contain all features deemed essential for function for TPI and GAPDH and contain all expected protein motifs for these enzymes

Biomolecule interactions on calcium carbonate and stoichiometrically similar biomedical, optical and electronic materials

textA combinatorial approach has been successfully used to characterize peptides that bind to four different surfaces of CaCO3 and six different oxide substrates that are chemically and stoichiometrically similar to CaCO3. A standard screening and a single substrate screening method were employed. Both methods used a bacteriophage combinatorial library with a complexity of 109 different random sequences. While geological (104) calcite screenings do not seem to show strong consensus, peptides screened against geological aragonite exhibit extraordinary consensus. Overall, peptides screened against aragonite were highly basic. Peptides screened against (110) geological aragonite show [LAIVG]P[WF][RKH] and triple [RKH] patterns. The most significant binding peptide, A21 (LPPWKHKTSGVA) was found in 4 separate screenings. The (110) geological aragonite sequences are highly enriched in prolines. Coincidently, peptides screened against the optical material LiNbO3 +Z show patterns similar to those found in the aragonite screenings. Other substrates that did not exhibit strong consensus include powdered LiNbO3, powdered BaTiO3, powdered PbTiO3, single crystal LiNbO3 –Z, and hydroxyapatite. A database and analysis program was written to catalog and evaluate the statistical significance of the many sequences. One peptide that was determined to be extremely significant in binding to aragonite, A20 (LPKWQERQMLSA), was modeled using umbrella sampling molecular dynamics techniques as well as analyzed by NMR. It was determined that there is a good probability that the peptide’s conformation is helical, but it is able to introconvert between α-helical, 3-10 helical and extended conformations fast enough that a stable secondary structure is not detectable by NMR. Engineered phage were constructed to display these significant peptides on the pVIII surface, increasing the expression level and the long range order in the hopes of building an aragonite nucleation surface. Hybrid organic-inorganic materials were grown on the phage resulting in a mixture of the three forms of CaCO3: calcite, vaterite, and aragonite. In addition, hybrid materials were grown on the optical waveguide material LiNbO3. Doubly engineered phage were shown to bind preferentially to the LiNbO3 +Z surface through the interaction of the A1 displayed peptide as well as nucleate semiconducting ZnS particles via the A7 peptide selected previously against ZnS.Chemistry and BiochemistryChemistr

Biomimetic Growth and Morphology Control of Calcium Oxalates

With respect to the principles of biomineralization, it is of interest to study the crystallization of calcium oxalates under various experimental conditions. Calcium oxalates play decisive roles as biominerals in plants and as pathological “urinary/kidney stones” in vertebrates. Calcium oxalate exists in three different hydration states; calcium oxalate monohydrate (COM, monoclinic, a = 6.290(1)Å, b = 14.583(1)Å, c = 10.116(1)Å, β = 109.46°, P21/c), calcium oxalate dihydrate (COD, tetragonal, a = b = 12.371(3)Å, c = 7.357(2)Å, α = β = γ = 90°, I4/m) and calcium oxalate trihydrate (COT, triclinic, a = 6.11(1)Å, b = 7.167(2)Å, c = 8.457(2)Å, α = 76.5(2)°, β = 70.35(2)°, γ = 70.62(2)°, P ). Monoclinic COM and tetragonal COD are the most common phyto-crystals and the main constituents of kidney and urinary stones. The occurrence of calcium oxalates in plants represents a useful biogenesis (protection against herbivores) unlike the devastating occurrence in renal tubules. Therefore, biomineralization can be physiological or pathological. A systematic investigation of the morphological evolution of calcium oxalates in the presence of organic components is essential for understanding the mechanism of “pathological biomineralization”. In order to understand the pathological biomineralization of uroliths, it is necessary grow calcium oxalates comparable in morphology under similar growth conditions. The formation of calcium oxalate stones within a gelatinous state of proteins, polysaccharides, lipids and other biomacromolecules under a flow of supersaturated urine supports the fact that an “organic” gel model can simulate the process of urinary stone formation under in vitro conditions. Furthermore, synthetic polymers with precisely known functions and solution behaviours are better choices to understand the interaction of acidic proteins with calcium oxalates. Therefore, as a first step to unravel the complex pathology of uro/nephro lithiasis, we started to examine the structure and morphology of calcium oxalates crystallized in the presence of organic additives such as the sodium salt of polyacrylic acid (PAA) as well as agar gel. The influence of initial calcium oxalate concentration, pH and concentration of the additives on the formation of hydration states of calcium oxalates have been investigated along with the stated general methods. Apart from the three hydrated forms, calcium oxalate exists also in the anhydrous form (COA). Although three modifications of COA (α, β and γ) are reported in the literatures, the crystal structures and phase transformations were controversially discussed. We have been able to reveal the crystal structure of the β-modification of the anhydrous calcium oxalate by a combination of atomistic simulations and Rietveld refinements on the basis of powder X-ray diffraction pattern. β-COA belongs to the monoclinic system with unit cell parameters, a = 6.1644(3)Å, b = 7.3623(2)Å, c = 9.5371(5)Å, β = 90.24(2)°, P2/m (No. 10). The dehydration of COM was mimicked in silico to receive an initial model of the crystal structure of anhydrous calcium oxalate. This general approach may also be accessible for other decomposition processes ending up with crystalline powders of unknown crystal structure. No evidence for transformations from or to the α- or γ- modifications was found during our investigations. The growth pattern of COD crystals precipitated from aqueous solutions in the presence of PAA is clearly dependent on the concentration of PAA. By increasing the concentration of PAA, the shape of COD has been found to change from tetragonal bi-pyramids with dominant (101) pyramidal faces to tetragonal prisms with dominant (100) prism faces and finally to dumbbells. At still higher PAA concentrations, the morphology is reverted back to rod-like tetragonal prisms. Apart from these experiments, the interaction of PAA with (100) and (101) crystal faces of COD was explored with the aid of atomistic simulations. The simulation confirmed that during the development of the aggregates, strong interactions of PAA with the (100) faces take over control of morphologies. Our investigations show that the inner architecture of all the morphological varieties of COD was found to be dominated by an inner “core” consisting of thin elongated crystallites together with incorporated PAA and an outer “shell” formed as a consequence of secondary nucleation processes. We propose that for all types of COD aggregates, relative proportion of calcium oxalate and PAA dictates the shape and formation of nanometer sized crystallites which then aggregate and align to form the core. Such cores enriched with PAA may act as the sites for secondary nucleation events of calcium oxalate crystallites which then cover the core like a shell. In vitro experimental models for the growth of calcium oxalates can give valuable information on the growth and aggregation of urinary stones. Therefore, the “double diffusion technique” in agar gel matrix has been used for the biomimetic growth of calcium oxalate (COM) stones. A great variety of morphological forms of COM are produced in agar gel matrices (2 wt.-% agar gel of pH 8.5) ranging from platy crystallites to dumbbells and spherulites. The COM dumbbells and spherulites are assumed to be formed by the aggregation of smaller crystallites as a consequence of increased supersaturation inside the gel. Moreover, an increase of the pH value of the agar gel has been found to suppress the growth of COM and favours the growth of COD. The morphology of COD crystals grown in 2 wt.-% agar gel of pH 11.5 includes tetragonal prisms and dumbbells. The system calcium oxalate/ PAA/ H2O is a suitable model system for the investigation of principles of biomineral growth (shape development) in general. Our results demonstrate that the double diffusion technique in agar gel is a convenient route to grow calcium oxalate aggregates showing close resemblance to biogenic calculi and to study their ontogeny