Structure of the molybdenum site in YedY, a sulfite oxidase homologue from Escherichia coli

YedY from Escherichia coli is a new member of the sulfite oxidase family of molybdenum cofactor (Moco)-containing oxidoreductases. We investigated the atomic structure of the molybdenum site in YedY by X-ray absorption spectroscopy, in comparison to human sulfite oxidase (hSO) and to a Mo(IV) model complex. The K-edge energy was indicative of Mo(V) in YedY, in agreement with X- and Q-band electron paramagnetic resonance results, whereas the hSO protein contained Mo(VI). In YedY and hSO, molybdenum is coordinated by two sulfur ligands from the molybdopterin ligand of the Moco, one thiolate sulfur of a cysteine (average Mo-S bond length of ～2.4 ?), and one (axial) oxo ligand (Mo═O, ～1.7 ?). hSO contained a second oxo group at Mo as expected, but in YedY, two species in about a 1:1 ratio were found at the active site, corresponding to an equatorial Mo-OH bond (～2.1 ?) or possibly to a shorter Mo-O(-) bond. Yet another oxygen (or nitrogen) at a ～2.6 ? distance to Mo in YedY was identified, which could originate from a water molecule in the substrate binding cavity or from an amino acid residue close to the molybdenum site, i.e., Glu104, that is replaced by a glycine in hSO, or Asn45. The addition of the poor substrate dimethyl sulfoxide to YedY left the molybdenum coordination unchanged at high pH. In contrast, we found indications that the better substrate trimethylamine N-oxide and the substrate analogue acetone were bound at a ～2.6 ? distance to the molybdenum, presumably replacing the equatorial oxygen ligand. These findings were used to interpret the recent crystal structure of YedY and bear implications for its catalytic mechanism.     

Comparative spectroscopic and mechanistic study of chelation properties of fisetin with iron in aqueous buffered solutions. Implications on in vitro antioxidant activity

Fisetin (3,3',4',7-tetrahydroxyflavone) has been investigated for its ability to bind iron in a wide range of pH values of acetate and phosphate buffered solutions. To assess the relevant interactions of iron with fisetin, combined spectroscopic (UV/visible, Raman, MS) and theoretical approaches were used. The chelation sites, stoichiometry, stability and the dependence of the complexes structures on pH were defined. The results pointed to the formation of two iron-fisetin complexes with stoichiometries of 1 : 1 and 1 : 2, depending on the pH. Results of vibrational analysis and theoretical calculations implicated the 3-hydroxyl-4-carbonyl group as a chelating site in acidic media while catechol (3'-hydroxyl-4'-hydroxyl) group was identified as the chelating group in neutral and alkaline media. Determined relative, conditional, stability constants with iron-fisetin were in the range from 6 × 10(4) dm(3) mol(-1) to 7 × 10(9) dm(6) mol(-2). Competition experiments demonstrated that fisetin bound iron less strongly than EDTA and citric acid under the investigated experimental conditions. Rate constant values calculated for the fast step of the DPPH reduction for fisetin and the iron-fisetin complex are k(1) = 225.75 dm(3) mol(-1) s(-1) and k(1) = 658.00 dm(3) mol(-1) s(-1). These values fit within the interval of the rate constant values which are typical for antioxidants which have a single polyphenolic nucleus. The equilibrium geometries, optimized at the B3LYP/6-311 + G(d,p) and M06/6-311 + G(d,p) levels of theory, predicted structural modifications between the ligand molecule in the free state and in the complex structure. The theoretical model has been validated by both vibrational and electronic spectroscopies.     

Single molecule fluorescence correlation spectroscopy of single apoptotic cells using a red-fluorescent caspase probe

The detection of single molecules in single cells has enabled biochemical analyses to be conducted with high sensitivity and high temporal resolution. In this work, detection of apoptosis was studied by single molecule fluorescence correlation spectroscopy (FCS) in single living cells. Caspase activity was assayed using a new red fluorogenic probe that avoids the spectral overlap of green fluorescent probes and cell autofluorescence. This new probe, 2SBPO-Casp, was synthesized by coupling a water-soluble Nile Blue derivative (2SBPO) to an aspartic acid residue. Upon apoptosis induction and caspase activation, free 2SBPO dye is shown to accumulate inside the cell after probe cleavage. In previous work in our lab, single molecule fluorescence in single apoptotic cells was detected 45 min after induction using a rhodamine 110-based probe. However, significant statistical analysis was needed to exclude false positives. The use of 2SBPO-Casp overcomes the autofluorescence problem and offers a steady fluorescence signal. In our single molecule FCS measurements, Ramos cells were determined apoptotic on the basis of their correlation coefficient value (R(2)). Cells that contain an R(2) ≥ 0.65 were identified as highly correlated and therefore determined to be apoptotic. Single apoptotic cells identified in this manner were found as early as 30 min after induction and the number of apoptotic cells reached a peak value at the 3rd hour, which is consistent with other techniques. Using single molecule techniques and a new apoptosis probe, the temporal dynamics were elucidated with better sensitivity and resolution than in previous studies.     

Spatially selective reagent delivery into cancer cells using a two-layer microfluidic culture system

In this work, we demonstrate a two-layer microfluidic system capable of spatially selective delivery of drugs and other reagents under low shear stress. Loading occurs by hydrodynamically focusing a reagent stream over a particular region of the cell culture. The system consisted of a cell culture chamber and fluid flow channel, which were located in different layers to reduce shear stress on cells. Cells in the center of the culture chamber were exposed to parallel streams of laminar flow, which allowed fast changes to be made to the cellular environment. The shear force was reduced to 2.7 dyn cm⁻² in the two-layer device (vs. 6.0 dyn cm⁻² in a one-layer device). Cells in the side of the culture chamber were exposed to the side streams of buffer; the shear force was further reduced to a greater extent since the sides of the culture chamber were separated from the main fluid path. The channel shape and flow rate of the multiple streams were optimized for spatially controlled reagent delivery. The boundaries between streams were well controlled at a flow rate of 0.1 mL h⁻¹, which was optimized for all streams. We demonstrated multi-reagent delivery to different regions of the same culture well, as well as selective treatment of cancer cells with a built in control group in the same well. In the case of apoptosis induction using staurosporine, 10% of cells remained viable after 24 h of exposure. Cells in the same chamber, but not exposed to staurosporine, had a viability of 90%. This chip allows dynamic observation of cellular behavior immediately after drug delivery, as well as long-term drug treatment with the benefit of large cell numbers, device simplicity, and low shear stress.     

A joint application of spectroscopic, electrochemical and theoretical approaches in evaluation of the radical scavenging activity of 3-OH flavones and their iron complexes towards different radical species

Combined spectroscopic (UV/visible, MS and EPR), electrochemical (CV) and theoretical approaches were used to evaluate the relevant interactions of morin and quercetin, as well as their respective iron(III) complexes with DPPH, tempone, hydroxyl and superoxide radicals. The results on iron complexation specify the stoichiometry and the relevant structural forms entering the chelation of the molecules. The spectroscopic DPPH assay shows better antioxidant activity of quercetin and its iron complex both in terms of EC(50) values and stoichiometry. The results of 2-deoxyribose degradation suggest that antioxidant activities of morin and quercetin may originate from their combined effect of iron chelation and radical scavenging. The distinctive difference in the EPR spectra of morin and quercetin radicals suggests different positions of the radical centers which may account for different sequences of their activities towards investigated radicals. Activity ranking of quercetin and morin, established by cyclic voltammetry, confirms their activity sequence obtained by EPR results and is also in agreement with the results of conformational analysis. The equilibrium geometries, optimized with the M052X functionals and 6-311G(d,p) basis set, predict structural modifications between the ligand molecules in the free state and in the complex structures. The arguments gained through experimental results can also be rationalized in terms of overall molecular geometry and structural features governing antioxidant behavior i.e. substitution pattern of the ring B.     

The copigmentation effect of sinapic acid on malvin: a spectroscopic investigation on colour enhancement

The present paper reports on spectroscopic investigation of copigmentation effect of sinapic acid on the malvin molecule. A reaction of copigmentation was investigated by the use of UV-Vis absorption spectra in the whole range of acidic and moderately acidic buffered aqueous solutions (pH range 1.0-6.0). It was observed that the ratio (A-A0)/A0, as a good measure of the copigment effect, has its maximum value at pH 3.6. The influences of the pH of the medium, molecular concentration, and temperature were investigated. The reaction was thermodynamically defined in terms of deltaH0, deltaG0 and deltaS0 values.     

The Tannaka Representation Theorem for Separable Frobenius Functors

A weak bialgebra is known to be a special case of a bialgebroid. In this paper we study the relationship of this fact with the Tannaka theory of bialgebroids as developed in Phùng H? Hai (Isr J Math 167(1):193–225, 2008). We obtain a Tannaka representation theorem with respect to a separable Frobenius fiber functor.     

A GPU-based incompressible Navier–Stokes solver on moving overset grids

In pursuit of obtaining high fidelity solutions to the fluid flow equations in a short span of time, graphics processing units (GPUs) which were originally intended for gaming applications are currently being used to accelerate computational fluid dynamics (CFD) codes. With a high peak throughput of about 1 TFLOPS on a PC, GPUs seem to be favourable for many high-resolution computations. One such computation that involves a lot of number crunching is computing time accurate flow solutions past moving bodies. The aim of the present paper is thus to discuss the development of a flow solver on unstructured and overset grids and its implementation on GPUs. In its present form, the flow solver solves the incompressible fluid flow equations on unstructured/hybrid/overset grids using a fully implicit projection method. The resulting discretised equations are solved using a matrix-free Krylov solver using several GPU kernels such as gradient, Laplacian and reduction. Some of the simple arithmetic vector calculations are implemented using the CU++: An Object Oriented Framework for Computational Fluid Dynamics Applications using Graphics Processing Units, Journal of Supercomputing, 2013, doi:10.1007/s11227-013-0985-9 approach where GPU kernels are automatically generated at compile time. Results are presented for two- and three-dimensional computations on static and moving grids.     

Behavioral and Antennal Responses of Tribolium confusum to Varronia globosa Essential Oil and Its Main Constituents: Perspective for Their Use as Repellent

Essential oils of aromatic plants represent an alternative to classical pest control with synthetic chemicals. They are especially promising for the alternative control of stored product pest insects. Here, we tested behavioral and electrophysiological responses of the stored product pest Tribolium confusum, to the essential oil of a Brazilian indigenous plant, Varronia globosa, collected in the Caatinga ecosystem. We analyzed the essential oil by GC-MS, tested the effects of the entire oil and its major components on the behavior of individual beetles in a four-way olfactometer, and investigated responses to these stimuli in electroantennogram recordings (EAG). We could identify 25 constituents in the essential oil of V. globosa, with anethole, caryophyllene and spathulenole as main components. The oil and its main component anethole had repellent effects already at low doses, whereas caryophyllene had only a repellent effect at a high dose. In addition, the essential oil abolished the attractive effect of the T. confusum aggregation pheromone. EAG recordings revealed dose-dependent responses to the individual components and increasing responses to the blend and even more to the entire oil. Our study reveals the potential of anethole and the essential oil of V. globosa in the management of stored product pests.