Light-induced flipping of a conserved glutamine sidechain and its orientation in the AppA BLUF domain

The AppA BLUF domain is a blue light photoreceptor containing flavin. Conserved glutamine 63 is necessary for the photocycle of the protein, and its side chain has been proposed to flip in response to blue light illumination. Recently published crystal structures of AppA WT and the AppA mutant C20S describe contradictory conclusions regarding the orientation of the conserved glutamine 63 side chain in the dark. Here, we present evidence from NMR spectroscopy confirming light-induced flipping of the glutamine side chain to form a strong hydrogen bond between the glutamine 63 side chain carbonyl group and the tyrosine 21 side chain hydroxyl proton in the light-induced state. Our conclusions are consistent with published data from UV/vis absorbance and FTIR spectroscopy, as well as the crystal structure of AppA WT.     

Functionalized magnetic micro- and nanoparticles: optimization and application to micro-chip tryptic digestion

The preparation of an easily replaceable protease microreactor for micro-chip application is described. Magnetic particles coated with poly(N-isopropylacrylamide), polystyrene, poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate), poly(glycidyl methacrylate), [(2-amino-ethyl)hydroxymethylen]biphosphonic acid, or alginic acid with immobilized trypsin were utilized for heterogeneous digestion. The properties were optimized, with the constraint of allowing immobilization in a microchannel by a magnetic field gradient. To obtain the highest digestion efficiency, sub-micrometer spheres were organized by an inhomogeneous external magnetic field perpendicularly to the direction of the channel. Kinetic parameters of the enzyme reactor immobilized in micro-chip capillary (micro-chip immobilized magnetic enzyme reactor (IMER)) were determined. The capability of the proteolytic reactor was demonstrated by five model (glyco)proteins ranging in molecular mass from 4.3 to 150 kDa. Digestion efficiency of proteins in various conformations was investigated using SDS-PAGE, HPCE, RP-HPLC, and MS. The compatibility of the micro-chip IMER system with total and limited proteolysis of high-molecular-weight (glyco)proteins was confirmed. It opens the route to automated, high-throughput proteomic micro-chip devices.     

Numerical Analysis of Thermally Coupled Flow Problems with Interfaces and Phase-change Effects

In this work a fixed mesh finite element approach is presented to solve thermally coupled flow problems including moving interfaces between immiscible fluids and phase-change effects. The weak form of the full incompressible Navier-Stokes equations is obtained using a generalized streamline operator (GSO) technique that enables the use of equal order interpolation of the primitive variables of the problem: velocity, pressure and temperature. The interfaces are defined with a mesh of marker points whose motion is obtained applying a Lagrangian scheme. Moreover, a temperature-based formulation is considered to describe the phase-change phenomena. The proposed methodology is used in the analysis of a filling of a step mould and a gravity-driven flow of an aluminium alloy in an obstructed vertical channel.     

Optimized thermal desorption for improved sensitivity in trace explosives detection by ion mobility spectrometry

In this work we evaluate the influence of thermal desorber temperature on the analytical response of a swipe-based thermal desorption ion mobility spectrometer (IMS) for detection of trace explosives. IMS response for several common high explosives ranging from 0.1 ng to 100 ng was measured over a thermal desorber temperature range from 60 °C to 280 °C. Most of the explosives examined demonstrated a well-defined maximum IMS signal response at a temperature slightly below the melting point. Optimal temperatures, giving the highest IMS peak intensity, were 80 °C for trinitrotoluene (TNT), 100 °C for pentaerythritol tetranitrate (PETN), 160 °C for cyclotrimethylenetrinitramine (RDX) and 200 °C for cyclotetramethylenetetranitramine (HMX). By modifying the desorber temperature, we were able to increase cumulative IMS signal by a factor of 5 for TNT and HMX, and by a factor of 10 for RDX and PETN. Similar signal enhancements were observed for the same compounds formulated as plastic-bonded explosives (Composition 4 (C-4), Detasheet, and Semtex). In addition, mixtures of the explosives exhibited similar enhancements in analyte peak intensities. The increases in sensitivity were obtained at the expense of increased analysis times of up to 20 seconds. A slow sample heating rate as well as slower vapor-phase analyte introduction rate caused by low-temperature desorption enhanced the analytical sensitivity of individual explosives, plastic-bonded explosives, and explosives mixtures by IMS. Several possible mechanisms that can affect IMS signal response were investigated such as thermal degradation of the analytes, ionization efficiency, competitive ionization from background, and aerosol emission.     

Structural first-order transformation in La2/3Ba1/3MnO3: ESR study

We have studied by the electron-spin resonance (ESR) and static magnetic field techniques, the La_2/3Ba_1/3MnO₃ perovskite, which was previously shown to exhibit a martensitic phase transformation in the vicinity of T_s∼200 K [Physical Review B 68, 054109 (2003)], leading to its structural phase-segregated state. Resonant absorptions reveal that in the temperature interval from 100 K to 340 K the compound represents a mixture of two ferromagnetic phases possessing different magnetizations, in varying proportions depending on the temperature, and a small amount of a paramagnetic phase. The results agree well with the previous neutron diffraction study. Applied in the ESR experiments, magnetic fields (2–6 kOe) strongly affect the magnetization curves: even magnetic field as high as 700 Oe modifies the anomaly in the phase transformation region and removes the difference between the zero-field cooled and field-cooled magnetization curves, which implies that the difference in the magnetic susceptibility of the coexisting phases is small and the magnetic domain configuration can be easily changed.     

Monotonicity testing and shortest-path routing on the cube

We study the problem of monotonicity testing over the hypercube. As previously observed in several works, a positive answer to a natural question about routing properties of the hypercube network would imply the existence of efficient monotonicity testers. In particular, if any set of source-sink pairs on the directed hypercube (with all sources and all sinks distinct) can be connected with edge-disjoint paths, then monotonicity of functions $f:\{ 0,1\} ^n \to \mathcal{R}$ can be tested with O(n/∈) queries, for any totally ordered range $\mathcal{R}$ . More generally, if at least a µ(n) fraction of the pairs can always be connected with edge-disjoint paths then the query complexity is O(n/(∈µ(n))). We construct a family of instances of Ω(2 ⁿ ) pairs in n-dimensional hypercubes such that no more than roughly a $\frac{1} {{\sqrt n }}$ fraction of the pairs can be simultaneously connected with edge-disjoint paths. This answers an open question of Lehman and Ron [16], and suggests that the aforementioned appealing combinatorial approach for deriving query-complexity upper bounds from routing properties cannot yield, by itself, query-complexity bounds better than ≈ n ^3/2. Additionally, our construction can also be used to obtain a strong counterexample to Szymanski’s conjecture about routing on the hypercube. In particular, we show that for any δ > 0, the n-dimensional hypercube is not $n^{\tfrac{1} {2} - \delta }$ -realizable with shortest paths, while previously it was only known that hypercubes are not 1-realizable with shortest paths. We also prove a lower bound of Ω(n/∈) queries for one-sided non-adaptive testing of monotonicity over the n-dimensional hypercube, as well as additional bounds for specific classes of functions and testers.     

Influence of Catalyses on the Preparation of YVO<Subscript>4</Subscript>:Eu<Superscript>3+</Superscript> Phosphors by the Sol–gel Methodology

YVO(4):Eu(3+) phosphors have been prepared by the hydrolytic sol-gel methodology, with and without alkaline catalyst. The solid powder was obtained by reaction between yttrium III chloride and vanadium alkoxides; the europium III chloride was used as structural probe. The powder was treated at 100, 400, 600, or 800 °C for 4 h. The samples were characterized by X-ray diffraction, thermal analysis, and photoluminescence. The XRD patterns revealed YVO(4) crystalline phase formation for the sample prepared without the catalyst and heat-treated at 600 °C and for the sample prepared in the presence of ammonium as catalyst and heat-treated at 100 °C. The average nanosized crystallites were estimated by the Scherrer equation. The sample which was produced via alkaline catalysis underwent weight loss in two stages, at 100 and 400 °C, whereas the sample obtained without catalyst presented four stages of weight loss, at 150, 250, 400, and 650 °C. The excitation spectra of the samples treated at different temperatures displayed the charge transfer band (CTB) at 320 nm. PL data of all the samples revealed the characteristic transition bands arising from the (5)D(0) → (5)F(J) (J = 0, 1, 2, 3, and 4) manifolds under maximum excitation at 320, 394, and 466 nm in all cases. The (5)D(0) → (7)F(2) transition often dominates the emission spectra, indicating that the Eu(3+) ion occupies a site without inversion center. The long lifetime suggests that the matrix can be applied as phosphors. In conclusion, the sol-gel methodology is a very efficient approach for the production of phosphors at low temperature.     

Studies regarding the formation from metal nitrates and diol of NiM 2 III O4 spinels, inside a silica matrix

The present study deals with preparation and characterization of spinel mixed oxide systems NiM ₂ ^III O₄, where M^III?=?Fe^III, Cr^III. In order to obtain 50% NiFe₂O₄/50% SiO₂ and 50% NiCr₂O₄/50% SiO₂ nanocomposite, we have used a versatile route based on the thermal decomposition inside the SiO₂ matrix, of some particular precursors, coordination compounds of the involved M^II and M^III cations with dicarboxylate ligands. The ligands form in the redox reaction between metal nitrates mixture and 1,3-propanediol at the heating around 140?°C of the gels (tetraethylorthosilicate?Cmetal nitrates?C1,3-propanediol?Cwater). The as-obtained precursors, embedded in silica gels, have been characterized by FT-IR spectrometry and thermal analysis. Both precursors thermally decompose up to 350?°C leading to the formation of the corresponding metal oxides inside the silica matrix. X-ray diffraction of the annealed powders have evidenced the formation of NiFe₂O₄ starting with 600?°C, and NiCr₂O₄ starting with 400?°C. This behavior can be explained by the fact that, by thermal decomposition of the Fe(III) carboxylate at 300?°C, the spinelic phase ??-Fe₂O₃ is formed, which interacts with the NiO, forming the ferrite nuclei. By thermal decomposition of chromium carboxylate, a nonstoichiometric chromium oxide (Cr₂O_3+x ) is formed. In the range 380?C400?°C, Cr₂O_3+x turns into Cr₂O₃ which immediately interacts with NiO leading to the formation of nickel chromites nuclei inside the pores of silica matrix. Both spinels have been obtained as nanocrystalites homogenously dispersed as resulted from XRD and TEM data.     

Hydrogen-bonded coordination network in crystal structures of [Cu(3-PM)4Cl2] and [Cu(4-PM)4Cl]Cl, (PM = pyridylmethanol)

The crystal and molecular structures of [Cu(3-PM)₄Cl₂] (1) and [Cu(4-PM)₄Cl]Cl (2) have been determinated by X-ray crystallography. Complex 1 crystallizes in the triclinic system, space group P–1, with lattice parameters a = 7.972(2) Å, b = 8.293(2) Å, c = 10.707(2) Å, = 105.73(3)°, = 90.04(3)°, = 110.38(3)°, and Z = 1 at 100 K. The coordination geometry of each Cu atom is approximately octahedral formed by four nitrogen atoms of pyridine rings of 3-pyridylmethanol molecules in the equatorial plane and two chlorine atoms occupying the axial positions. The O—HsO, C—HsCl, and O—HsCl intermolecular hydrogen bonds and s stacking link the molecules in 3-D hydrogen-bonded coordination network. Complex 2 crystallizes in the tetragonal system, space group P4/n, with lattice parameters a = 10.464(1) Å, c = 11.339(2) Å, and Z = 2 at 217 K and a = 10.352(1) Å, c = 11.201(2) Å, and Z = 2 at 293 K. The coordination geometry of Cu atom in the [Cu(4-PM)₄Cl]⁺ ion is approximately square pyramidal formed by four nitrogen atoms of pyridine rings of 4-pyridylmethanol molecules in equatorial plane and one chlorine atom in axial position. The O—HsCl and C—HsCl intermolecular hydrogen bonds link the molecules in 2-D hydrogen-bonded coordination network.     

Aminoquinolones and Their Benzoquinone Dimer Hybrids as Modulators of Prion Protein Conversion

Prion Diseases or Transmissible Spongiform Encephalopathies are neurodegenerative conditions associated with a long incubation period and progressive clinical evolution, leading to death. Their pathogenesis is characterized by conformational changes of the cellular prion protein—PrP^C—in its infectious isoform—PrP^Sc—which can form polymeric aggregates that precipitate in brain tissues. Currently, there are no effective treatments for these diseases. The 2,5-diamino-1,4-benzoquinone structure is associated with an anti-prion profile and, considering the biodynamic properties associated with 4-quinolones, in this work, 6-amino-4-quinolones derivatives and their respective benzoquinone dimeric hybrids were synthesized and had their bioactive profile evaluated through their ability to prevent prion conversion. Two hybrids, namely, 2,5-dichloro-3,6-bis((3-carboxy-1-pentyl-4-quinolone-6-yl)amino)-1,4-benzoquinone (8e) and 2,5-dichloro-3,6-bis((1-benzyl-3-carboxy-4-quinolone-6-yl)amino)-1,4-benzoquinone (8f), stood out for their prion conversion inhibition ability, affecting the fibrillation process in both the kinetics—with a shortening of the lag phase—and thermodynamics and their ability to inhibit the formation of protein aggregates without significant cytotoxicity at ten micromolar.