The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. ...IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M's data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).
Alzheimer's disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies ...revealed that structural variation in Aβ fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate Aβ aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote Aβ fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on Aβ42 amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a change in the peptide secondary structure from random-coil to β-turn structures with subsequent generation of predominantly β-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 likely interacts with an amyloidogenic Aβ42 intermediate species leading to a possible formation of GM1-modified Aβ42 fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between Aβ42 fibrils and GM1-tweaked Aβ42 aggregates. Moreover, GM1-modified Aβ42 aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of Aβ, Aβ40, and Aβ42.
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•Interaction of non-micellar GM1 with Aβ42 induces a β-turn conformation with subsequent generation of soluble β-sheet species.•GM1 likely amends the Aβ42 primary nucleus leading to the generation of GM1-modified fibrils.•No significant statistical difference in the cytotoxicity of Aβ42 fibrils and GM1-incubated Aβ42 fibrils to human neuroblastoma cells.•Aβ42 fibrils formed in the presence of GM1 exhibit prion-like properties by catalyzing the conversion of soluble Aβ42 and Aβ40.
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•The classification of surface nitrates currently used by consensus is misleading.•Nitrates on ceria, thought to be monodentate, are actually tridentate.•Isotopic exchange with 18O ...helps distinguishing different nitrate coordination.•Bidentate nitrates on ceria are bridging and chelating simultaneously.•Bi/tridentate nitrates on ceria are converted to monodentate in presence of water.
Nitrates formed on ceria surface were investigated by FTIR spectroscopy and DFT methods. Isotope labelling (15N, 18O) was utilized to strengthen the conclusions. We found that the structures usually associated with monodentate nitrates (IR bands at ca. 1460, 1300 and 1030 cm−1), although bound to surface most strongly via one oxygen atom, are tridentate nitrates with C2v symmetry. The bidentate nitrates, as a rule, simultaneously bridge and chelate cerium cations. The spectral difference between these species is due to the binding geometry and symmetry reduction. An experimental approach is proposed to distinguish between different nitrate coordination. It is based on the split of the higher frequency IR band (1650–1450 cm−1) upon partial exchange with 18O: one new band appears for bidentate nitrates and two new bands for monodentate and the observed tridentate nitrates.
The variety of functionalities and porous structures inherent to metal-organic frameworks (MOFs) together with the facile tunability of their properties makes these materials suitable for a wide ...range of existing and emerging applications. Many of these applications are based on processes involving interaction of MOFs with guest molecules. To optimize a certain process or successfully design a new one, a thorough knowledge is required about the physicochemical characteristics of materials and the mechanisms of their interaction with guest molecules. To obtain such important information, various complementary analytical techniques are applied, among which vibrational spectroscopy (IR and Raman) plays an important role and is indispensable in many cases. In this review, we critically examine the reported applications of IR and Raman spectroscopies as powerful tools for initial characterization of MOF materials and for studying processes of their interaction with various gases. Both the advantages and the limitations of the technique are considered, and the cases where IR or Raman spectroscopy is preferable are highlighted. Peculiarities of MOFs interaction with specific gases and some inconsistent band assignments are also emphasized. Summarizing the broad analytical possibilities of the IR and Raman spectroscopies, we conclude that it can be applied in combinations with other techniques to explicitly establish the structure, properties, and reactivity of MOFs.
Abstract
The Integrated Microbial Genome/Virus (IMG/VR) system v.2.0 (https://img.jgi.doe.gov/vr/) is the largest publicly available data management and analysis platform dedicated to viral genomics. ...Since the last report published in the 2016, NAR Database Issue, the data has tripled in size and currently contains genomes of 8389 cultivated reference viruses, 12 498 previously published curated prophages derived from cultivated microbial isolates, and 735 112 viral genomic fragments computationally predicted from assembled shotgun metagenomes. Nearly 60% of the viral genomes and genome fragments are clustered into 110 384 viral Operational Taxonomic Units (vOTUs) with two or more members. To improve data quality and predictions of host specificity, IMG/VR v.2.0 now separates prokaryotic and eukaryotic viruses, utilizes known prophage sequences to improve taxonomic assignments, and provides viral genome quality scores based on the estimated genome completeness. New features also include enhanced BLAST search capabilities for external queries. Finally, geographic map visualization to locate user-selected viral genomes or genome fragments has been implemented and download options have been extended. All of these features make IMG/VR v.2.0 a key resource for the study of viruses.
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► XPS and XAS were used in situ to study the formation of Pd/CeO2 catalyst. ► Formation of mixed PdxCe1−xO2−δ surface phase occurs during the catalyst synthesis. ► Catalytic ...performance depends on Pd-ceria interaction. ► Treatment of the catalysts with hydrogen leads to a sharp increase in the activity.
The formation of Pd0.05Ce0.95O2 catalysts for the low-temperature oxidation of CO by the thermal decomposition of Ce(NO3)3 and Pd(NO3)2 with oxygen was studied by X-ray photoelectron spectroscopy (XPS) and X-ray absorption spectroscopy (XAS) directly in the preparation chamber of a spectrometer. Palladium is represented by two species on the surface of the catalysts: solid solutions of PdxCe1−xO2−δ and palladium clusters. Pd clusters can be formed in an oxidized or reduced state depending on the reaction conditions. Treatment of the catalysts with hydrogen leads to a sharp increase in CO conversion because of the reduction of parts of the palladium accompanying the formation of the metallic clusters. The testing of “real” and model catalysts was conducted in a light-off mode. The correlation between the activity of the Pd/CeO2 catalysts and the states of the palladium was proposed.
The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and ...reviewing the structural and functional annotations of genomes in a comparative context. IMG's data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG's annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).
Abstract Background Studies comparing the efficacy of dawn simulation to conventional bright light for the treatment of seasonal affective disorder (in parallel groups) have yielded conflicting ...results. This crossover study investigated treatment outcomes and long-term treatment preference. Methods Forty winter depressives were treated for a week with bright light (4.300 lx for 30–45 min shortly after awakening) or dawn simulation (gradually increasing light during the last 30 min of sleep achieving 100 lx before alarm beep, with the dawn simulator placed closer to the open eyes for a further 15 min: 250 lx). The depression level was self-rated using SIGH-SAD-SR. Results Depression scores reduced similarly following bright light and dawn simulation: for 43.8% and 42.2% (medians), respectively; efficacy ratio was 23:17. The preference was also similar (21:19). Among those who preferred bright light, the most common reason was that they perceived the bright light to be more effective (19/21; it was more effective, p =0.0096; this subgroup tended to have more severe depression) and ease of use (6/21). Among those who preferred the dawn simulator, the reasons were a more “natural” action (9/19), device compactness and/or time-saving (10/19) and in 4 cases where bright light caused eyestrain. Limitations Not overhead naturalistic light for dawn simulation, self-rating of depression. Conclusions Dawn simulation is similarly effective to bright light in the treatment of winter depression. Patients with more severe depression tended to report greater improvement with bright light; in such cases, this would outweigh the non-clinical advantages of dawn simulation.
The synthesis of buta‐1,3‐diene from ethanol has been studied over metal‐containing (M=Ag, Cu, Ni) oxide catalysts (MOx=MgO, ZrO2, Nb2O5, TiO2, Al2O3) supported on silica. Kinetic study of a wide ...range of ethanol conversions (2–90 %) allowed the main reaction pathways leading to butadiene and byproducts to be determined. The key reaction steps of butadiene synthesis were found to involve ethanol dehydrogenation, acetaldehyde condensation, and the reduction of crotonaldehyde with ethanol into crotyl alcohol. Catalyst design included the selection of active components for each key reaction step and merging of these components into multifunctional catalysts and adjusting the catalyst functions to achieve the highest selectivity. The best catalytic performance was achieved over the Ag/ZrO2/SiO2 catalyst, which showed the highest selectivity towards butadiene (74 mol %).
Losing H2: Metal‐promoted oxides supported on silica are efficient catalysts for butadiene synthesis from ethanol. The metal promoters allow ethanol dehydrogenation, the metal oxide components are efficient in acetaldehyde condensation and reduction of crotonaldehyde with ethanol, whereas the silica support allows the dehydration steps. The optimized catalyst provides 74 mol % selectivity to butadiene at 88 % ethanol conversion at 593 K.
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