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  • 1
    Language: English
    In: PLoS ONE, 2009, Vol.4(5), p.e5440
    Description: Calculating the metabolome size of species by genome-guided reconstruction of metabolic pathways misses all products from orphan genes and from enzymes lacking annotated genes. Hence, metabolomes need to be determined experimentally. Annotations by mass spectrometry would greatly benefit if peer-reviewed public databases could be queried to compile target lists of structures that already have been reported for a given species. We detail current obstacles to compile such a knowledge base of metabolites. ; As an example, results are presented for rice. Two rice () subspecies have been fully sequenced, and . Several major small molecule databases were compared for listing known rice metabolites comprising PubChem, Chemical Abstracts, Beilstein, Patent databases, Dictionary of Natural Products, SetupX/BinBase, KNApSAcK DB, and finally those databases which were obtained by computational approaches, i.e. RiceCyc, KEGG, and Reactome. More than 5,000 small molecules were retrieved when searching these databases. Unfortunately, most often, genuine rice metabolites were retrieved together with non-metabolite database entries such as pesticides. Overlaps from database compound lists were very difficult to compare because structures were either not encoded in machine-readable format or because compound identifiers were not cross-referenced between databases. ; We conclude that present databases are not capable of comprehensively retrieving all known metabolites. Metabolome lists are yet mostly restricted to genome-reconstructed pathways. We suggest that providers of (bio)chemical databases enrich their database identifiers to PubChem IDs and InChIKeys to enable cross-database queries. In addition, peer-reviewed journal repositories need to mandate submission of structures and spectra in machine readable format to allow automated semantic annotation of articles containing chemical structures. Such changes in publication standards and database architectures will enable researchers to compile current knowledge about the metabolome of species, which may extend to derived information such as spectral libraries, organ-specific metabolites, and cross-study comparisons.
    Keywords: Research Article ; Biotechnology -- Plant Biotechnology ; Biotechnology -- Small Molecule Chemistry ; Chemical Biology -- Chemical Biology Of The Cell ; Chemical Biology -- Small Molecule Chemistry ; Chemistry -- Organic Chemistry ; Chemistry -- Reprographic Processes ; Computational Biology -- Literature Analysis ; Computational Biology -- Metabolic Networks ; Computational Biology -- Systems Biology ; Computational Biology -- Bio-ontology
    E-ISSN: 1932-6203
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  • 2
    Language: English
    In: Journal of Catalysis, 2011, Vol.277(2), pp.196-207
    Description: The catalytic performance of VZrON and novel P-containing VZrPON oxynitrides is compared in the ammoxidation of 3-picoline. Due to higher VO dispersion, lower V valence state and a pronounced formation of P N instead of V N bonds VZrPON catalysts are less active but slightly more selective. ► P incorporation raises V dispersion, forms P N and suppresses V N moieties. ► P lowers activity and improves selectivity only slightly. ► 3-CP selectivity rises with rising N surface concentration. ► Impact of N surface sites on selectivity dominates over surface acidity. Novel P-containing oxynitrides VZrPON were tested besides their VZrPO oxide precursors in the ammoxidation of 3-picoline and compared with P-free VZrON catalysts for analysing the influence of both incorporated P and N on the catalytic performance. Results of XRD, XPS, P and V MAS NMR as well as of simultaneous in situ-EPR/UV–vis/Raman studies during nitridation have shown that the incorporation of phosphorus enhances the V dispersion, reduces vanadium partially even down to V and leads to the formation of a crystalline ZrV P O phase for Zr/V ⩾ 0.5 with V sites surrounded by four O atoms only. N is preferentially incorporated in the vicinity of P, thus, suppressing the formation of V N moieties. These facts may be a reason why the incorporation of P does not markedly improve the catalytic performance of VZrPON catalysts.
    Keywords: Vanadium Zirconium Phosphorus Oxynitrides ; In Situ-Epr/Uv–Vis/Raman Spectroscopy ; Ammoxidation ; 3-Picoline ; Engineering ; Chemistry
    ISSN: 0021-9517
    E-ISSN: 1090-2694
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  • 3
    Language: English
    In: The Journal of biological chemistry, 09 March 2012, Vol.287(11), pp.7956-68
    Description: Calcineurin B-like proteins (CBLs) represent a family of calcium sensor proteins that interact with a group of serine/threonine kinases designated as CBL-interacting protein kinases (CIPKs). CBL-CIPK complexes are crucially involved in relaying plant responses to many environmental signals and in regulating ion fluxes. However, the biochemical characterization of CBL-CIPK complexes has so far been hampered by low activities of recombinant CIPKs. Here, we report on an efficient wheat germ extract-based in vitro transcription/translation protocol that yields active full-length wild-type CIPK proteins. We identified a conserved serine residue within the C terminus of CBLs as being phosphorylated by their interacting CIPKs. Remarkably, our studies revealed that CIPK-dependent CBL phosphorylation is strictly dependent on CBL-CIPK interaction via the CIPK NAF domain. The phosphorylation status of CBLs does not appear to influence the stability, localization, or CIPK interaction of these calcium sensor proteins in general. However, proper phosphorylation of CBL1 is absolutely required for the in vivo activation of the AKT1 K(+) channel by CBL1-CIPK23 and CBL9-CIPK23 complexes in oocytes. Moreover, we show that by combining CBL1, CIPK23, and AKT1, we can faithfully reconstitute CBL-dependent enhancement of phosphorylation of target proteins by CIPKs in vitro. In addition, we report that phosphorylation of CBL1 by CIPK23 is also required for the CBL1-dependent enhancement of CIPK23 activity toward its substrate. Together, these data identify a novel general regulatory mechanism of CBL-CIPK complexes in that CBL phosphorylation at their flexible C terminus likely provokes conformational changes that enhance specificity and activity of CBL-CIPK complexes toward their target proteins.
    Keywords: Arabidopsis -- Metabolism ; Arabidopsis Proteins -- Metabolism ; Calcium-Binding Proteins -- Metabolism ; Multiprotein Complexes -- Metabolism ; Potassium Channels -- Metabolism ; Protein-Serine-Threonine Kinases -- Metabolism
    E-ISSN: 1083-351X
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  • 4
    Language: English
    In: Biochemical and Biophysical Research Communications, 2005, Vol.329(2), pp.616-623
    Description: The adhesion of highly activated neutrophils to cerebral microvascular endothelial cells (MVECs) may contribute to disruption and hyperpermeability of the blood–brain barrier (BBB) after cardiac surgery with prolonged cardiopulmonary bypass (CPB). A correlation between CPB duration and neutrophil-mediated BBB damage has not been investigated on the cellular level yet. Therefore, we studied the effects of neutrophils from cardiac surgery patients with CPB time 〈80 min (group I; = 8) and 〉80 min (group II; = 8) on the integrity of cultured porcine MVEC. Ex vivo, neutrophils of group II but not of group I significantly degraded the molecule β-catenin whereas VE-cadherin and occludin were not modified. The transendothelial electric resistance as a measure for the integrity of the endothelial monolayers was reduced over time in both groups. In conclusion, prolonged CPB time entails neutrophil-mediated decrease in MVEC β-catenin expression, and thus may be an important trigger for BBB disruption.
    Keywords: Blood–Brain Barrier ; Junction Molecule Complexes ; Cardiac Surgery ; Neutrophils ; Biology ; Chemistry ; Anatomy & Physiology
    ISSN: 0006-291X
    E-ISSN: 1090-2104
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  • 5
    In: Organic & Biomolecular Chemistry, 2013, Vol.11(4), pp.549-554
    Description: The electrophilic nature of chalcones (1,3-diphenylprop-2-en-1-ones) and many other ,-unsaturated carbonyl compounds is crucial for their biological activity, which is often based on thiol-mediated regulation processes. To better predict their biological activity a simple screening assay for the assessment of the second-order rate constants ( k 2 ) in thia-Michael additions was developed. Hence, a clear structureactivity relationship of 16 differentially decorated hydroxy-alkoxychalcones upon addition of cysteamine could be established. Moreover, amongst other naturally occurring ,-unsaturated carbonyl compounds k 2 values for curcumin and cinnamaldehyde were gained while cinnamic acids or esters gave no or very slow reactions.
    Keywords: Chalcones -- Chemistry ; Sulfhydryl Compounds -- Chemistry;
    ISSN: 1477-0520
    E-ISSN: 1477-0539
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  • 6
    In: Physical Chemistry Chemical Physics, 2012, Vol.14(29), pp.10187-10195
    Description: We compare results from single crystal X-ray diffraction and FTIR spectroscopy to elucidate the nature of hydrogen bonding in -9-anthracene carboxylic acid (-9AC, C 15 H 10 O 2 ). The crystallographic studies indicate a disorder for the protons in the cyclic hydrogen bond. This disorder allows the determination of the energy difference between two proton sites along the hydrogen bond. The temperature dependent Fourier transform infrared spectroscopy (FTIR) underpins the crystallographic results. The combination of both methods allows the estimation of a one-dimensional potential curve describing the OH-stretching motion. The dynamical properties of the proton transfer along the hydrogen bond are extracted from this potential. The work presented here has profound implication on future studies of photochemical dynamics of crystalline -9AC, which can deliver a deeper understanding of the mechanism of photochemical driven molecular machines and the optical and electronic properties of molecular organic semiconductors.
    Keywords: Crystal Structure ; Crystallography ; Disorders ; Dynamic Tests ; Dynamics ; Hydrogen Bonds ; Photochemical ; Spectroscopy ; Miscellaneous Sciences (So);
    ISSN: 1463-9076
    E-ISSN: 1463-9084
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  • 7
    Language: English
    In: Surface & Coatings Technology, 15 December 2016, Vol.307, pp.565-573
    Description: In this work, interdiffusion between a polycrystalline nickel-base superalloy (René 80) and two MCrAlY bond coats, each with a different chemical composition, is investigated. Of primary interest is the evolution of Kirkendall porosity, which can form at the interface of substrate and bond coat and depends largely on the chemical composition of the coating and substrate, as well as on the coating deposition process. Severe formation of porosity at the interface causes a degradation of the bonding strength between substrate and coating, with functional breakdown of the coating system as worst result. To investigate the influence of the deposition process, the MCrAlY bond coats were applied using two different spraying processes, high velocity oxygen fuel spraying (HVOF) and low-pressure plasma spraying (LPPS). After coating deposition, the samples were annealed at 1050 °C for varying test periods up to 2000 h. Microstructural and compositional analyses were performed to determine and to evaluate the Kirkendall porosity. The results reveal a strong influence of both the spraying process and the chemical composition. Bond coats applied by means of LPPS show less Kirkendall porosity than bond coats applied by HVOF. Furthermore, the location of Kirkendall porosity formation shifts, depending on the spraying process used, from the substrate-side of the interface (LPPS) to the coating-side of the interface (HVOF). It is hypothesized that accelerated element diffusion, especially of aluminum, from coating to substrate is the main factor for these observations. Results indicate that matching the chromium activity in coating and substrate will result in lower amounts of Kirkendall porosity because of chromium accumulation at the interface.
    Keywords: Interdiffusion ; Mcraly Coating ; Kirkendall Porosity ; Thermo-Calc ; Dictra ; Engineering ; Chemistry
    ISSN: 0257-8972
    E-ISSN: 1879-3347
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  • 8
    Language: English
    In: Nature, 2015, Vol.520(7545), pp.78-81
    Description: Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion(1,2). Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in...
    Keywords: Natural Sciences ; Physical Sciences ; Naturvetenskap ; Fysik ; Fysik ; Physics ; Naturvetenskap ; Natural Sciences
    ISSN: 0028-0836
    E-ISSN: 14764687
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  • 9
    Language: English
    In: Journal of Colloid And Interface Science, 15 October 2017, Vol.504, pp.346-355
    Description: The formation of perovskite oxide nanoparticles supported on ordered mesoporous silica with different pore geometry is here presented. Systematic study was performed varying both pore shape (gyroidal, cylindrical, spherical) and size (7.5, 12, 17 nm) of the hosts. LaFeO , PrFeO and LaCoO were chosen as target guest structures. The distribution of the oxide nanoparticles on silica was comprehensively assessed using a multi-technique approach. It could be shown that the pore geometry plays a determining role in the conversion of the infiltrated metal nitrates to metal oxide. In particular, slow degradation kinetic was observed in highly curved pores, which fostered nucleation and crystallization of the guest species. In spherical pore systems the enhancement of pore size caused a remarkable delay of the decomposition of the metal salts, but at the same time improved the homogeneous distribution of the oxide particles in the matrix.
    Keywords: Confinement ; Heterogeneous Catalysis ; Perovskite ; Nanocasting ; Ink-Bottle Pores ; Engineering ; Chemistry
    ISSN: 0021-9797
    E-ISSN: 1095-7103
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  • 10
    Language: English
    In: Surface & Coatings Technology, 25 January 2016, Vol.286, pp.119-128
    Description: In this work, the delamination toughness and the sintering behavior of modern double-layer thermal barrier coatings of type gadolinium zirconate (GZO)/yttrium-stabilized zirconia (YSZ) are investigated in detail. These properties mainly determine the strain tolerance and thus the performance of thermal barrier coatings (TBCs). The delamination toughness was determined using a modified four-point bending setup. It is shown that the delamination behavior differs significantly from conventional monolayer coatings and is highly dependent on the specific microstructure of the GZO layer. The stiffness and sintering behavior of freestanding GZO layers were determined using impulse excitation, a test method sensitive to the global stiffness of the ceramic coating. The increase in stiffness is thereby correlated to microstructural changes, explicitly the healing of micro-cracks and the sintering of inter-lamellar cracks and unmolten particles. The results reveal that the specific spray structure of GZO has a great influence on the sinter stability which results in a characteristic temperature dependency. In this case the GZO coatings have an advantage in comparison to conventional YSZ coatings at temperatures above 1300 °C.
    Keywords: Double-Layer Thermal Barrier Coatings ; Gadolinium Zirconate ; Mixed Mode Interfacial Fracture Toughness ; Delamination Behavior ; Sintering Behavior ; Engineering ; Chemistry
    ISSN: 0257-8972
    E-ISSN: 1879-3347
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