In situ studies of the decomposition of ammonium uranyl carbonate in an electron microscope

An electron microscope has been used to study the reduction of ammonium uranyl carbonate (AUC) to UO₂. The reactions could be followed both in the diffraction and the lattice image mode. The first intermediate obtained was amorphous UO₃. Depending on the experimental conditions, either crystalline UO₂ was formed directly from this phase, or several other intermediates were indicated.Properties like crystallinity and crystallite size of final UO₂ were found to be a function of experimental conditions. Comparisons with properties of UO₂ from the industrial process have been made.     

Catalytic Encounters at the Molecular Level: Gabor A. Somorjai Award Symposium for Creative Research in Catalysis in Honor of Professor Manos Mavrikakis

Topics in Catalysis -     

Classification of Amyloidosis by Model-Assisted Mass Spectrometry-Based Proteomics

Amyloidosis is a rare disease caused by the misfolding and extracellular aggregation of proteins as insoluble fibrillary deposits localized either in specific organs or systemically throughout the body. The organ targeted and the disease progression and outcome is highly dependent on the specific fibril-forming protein, and its accurate identification is essential to the choice of treatment. Mass spectrometry-based proteomics has become the method of choice for the identification of the amyloidogenic protein. Regrettably, this identification relies on manual and subjective interpretation of mass spectrometry data by an expert, which is undesirable and may bias diagnosis. To circumvent this, we developed a statistical model-assisted method for the unbiased identification of amyloid-containing biopsies and amyloidosis subtyping. Based on data from mass spectrometric analysis of amyloid-containing biopsies and corresponding controls. A Boruta method applied on a random forest classifier was applied to proteomics data obtained from the mass spectrometric analysis of 75 laser dissected Congo Red positive amyloid-containing biopsies and 78 Congo Red negative biopsies to identify novel “amyloid signature” proteins that included clusterin, fibulin-1, vitronectin complement component C9 and also three collagen proteins, as well as the well-known amyloid signature proteins apolipoprotein E, apolipoprotein A4, and serum amyloid P. A SVM learning algorithm were trained on the mass spectrometry data from the analysis of the 75 amyloid-containing biopsies and 78 amyloid-negative control biopsies. The trained algorithm performed superior in the discrimination of amyloid-containing biopsies from controls, with an accuracy of 1.0 when applied to a blinded mass spectrometry validation data set of 103 prospectively collected amyloid-containing biopsies. Moreover, our method successfully classified amyloidosis patients according to the subtype in 102 out of 103 blinded cases. Collectively, our model-assisted approach identified novel amyloid-associated proteins and demonstrated the use of mass spectrometry-based data in clinical diagnostics of disease by the unbiased and reliable model-assisted classification of amyloid deposits and of the specific amyloid subtype.     

Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA

Cellobiohydrolase CbhA from Clostridium thermocellum cellulosome is a multi-modular protein composed starting from the N-terminus of a carbohydrate-binding module (CBM) of family 4, an immunoglobulin(Ig)-like module, a catalytic module of family 9 glycoside hydrolases (GH9), X1(1) and X1(2) modules, a CBM of family 3 and a dockerin module. Deletion of the Ig-like module from the Ig-GH9 construct results in complete inactivation of the GH9 module. The crystal structure of the Ig-GH9 module pair reveals the existence of an extensive module interface composed of over 40 amino acid residues of both modules and maintained through a large number of hydrophilic and hydrophobic interactions. To investigate the importance of these interactions between the two modules, we compared the secondary and tertiary structures and thermostabilities of the individual Ig-like and GH9 modules and the Ig-GH9 module pair using both circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC). Thr230, Asp262 and Asp264 of the Ig-like module are located in the module interface of the Ig-GH9 module pair and are suggested to be important in 'communication' between the modules. These residues were mutated to alanyl residues. The structure, stability and catalytic properties of the native Ig-GH9 and its D264A and T230A/D262A mutants were compared. The results indicate that despite being able to fold relatively independently, the Ig-like and GH9 modules interact and these interactions affect the final fold and stability of each module. Mutations of one or two amino acid residues lead to destabilization and change of the mechanism of thermal unfolding of the polypeptides. The enzymatic properties of native Ig-GH9, D264A and T230A/D262A mutants are similar. The results indicate that inactivation of the GH9 module occurs as a result of multiple structural disturbances finally affecting the topology of the catalytic center.     

Predicting and rationalizing the effect of surface charge distribution and orientation on nano-wire based FET bio-sensors

A single charge screening model of surface charge sensors in liquids (De Vico et al., Nanoscale, 2011, 3, 706-717) is extended to multiple charges to model the effect of the charge distributions of analyte proteins on FET sensor response. With this model we show that counter-intuitive signal changes (e.g. a positive signal change due to a net positive protein binding to a p-type conductor) can occur for certain combinations of charge distributions and Debye lengths. The new method is applied to interpret published experimental data on Streptavidin (Ishikawa et al., ACS Nano, 2009, 3, 3969-3976) and Nucleocapsid protein (Ishikawa et al., ACS Nano, 2009, 3, 1219-1224).     

Upgrading of Raw Gas from Biomass and Waste Gasification: Challenges and Opportunities

The depletion of fossil fuel-based resources and concerns for increasing emissions of CO₂ call for new ways of producing environmentally-friendly substitutes for motor fuels and chemicals. Thermo-chemical conversion of biomass and waste using gasification is a strong candidate to meet these challenges. For efficient and cost-effective application of this technique, novel solutions for hot gas cleaning are needed. This review highlights some important areas for improvement of upgrading technologies for pressurised fluidised bed gasification systems using biomass as a fuel.     

Engineering a mammalian super producer

Mammalian cells are the preferred host for the manufacture of a wide range of biopharmaceuticals, but production costs are high owing to low productivity. A range of rational engineering strategies have been pursued in order to increase volumetric product titres from mammalian cells, such as delaying apoptosis, manipulation of the cell cycle, and improving metabolism and protein processing. Unfortunately, outcomes from these strategies have been mixed, with few instances where significant improvements in product yield have been achieved. This article reviews and contrasts many of the engineering strategies attempted to date, highlighting the variability and context specificity in outcome. The paper argues that this is a reflection of the complexity of mammalian cells, and that a deeper understanding of the biology underpinning protein production for biotechnological purposes is required. Copyright © 2011 Society of Chemical Industry     

Nanopaper membranes from chitin–protein composite nanofibers—structure and mechanical properties

Chitin nanofibers may be of interest as a component for nanocomposites. Composite nanofibers are therefore isolated from crab shells in order to characterize structure and analyze property potential. The mechanical properties of the porous nanopaper structures are much superior to regenerated chitin membranes. The nanofiber filtration‐processing route is much more environmentally friendly than for regenerated chitin. Minerals and extractives are removed using HCl and ethanol, respectively, followed by mild NaOH treatment and mechanical homogenization to maintain chitin–protein structure in the nanofibers produced. Atomic force microscope (AFM) and scanning transmission electron microscope (STEM) reveal the structure of chitin–protein composite nanofibers. The presence of protein is confirmed by colorimetric method. Porous nanopaper membranes are prepared by simple filtration in such a way that different nanofiber volume fractions are obtained: 43%, 52%, 68%, and 78%. Moisture sorption isotherms, structural properties, and mechanical properties of membranes are measured and analyzed. The current material is environmentally friendly, the techniques employed for both individualization and membrane preparation are simple and green, and the results are of interest for development of nanomaterials and biocomposites. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40121.