Structure determination of protein-ligand complexes by transferred paramagnetic shifts

Rational drug design depends on the knowledge of the three-dimensional (3D) structure of complexes between proteins and lead compounds of low molecular weight. A novel nuclear magnetic resonance (NMR) spectroscopy strategy based on the paramagnetic effects from lanthanide ions allows the rapid determination of the 3D structure of a small ligand molecule bound to its protein target in solution and, simultaneously, its location and orientation with respect to the protein. The method relies on the presence of a lanthanide ion in the protein target and on fast exchange between bound and free ligand. The binding affinity of the ligand and the paramagnetic effects experienced in the bound state are derived from concentration-dependent (1)H and (13)C spectra of the ligand at natural isotopic abundance. Combined with prior knowledge of the crystal or solution structure of the protein and of the magnetic susceptibility tensor of the lanthanide ion, the paramagnetic data define the location and orientation of the bound ligand molecule with respect to the protein from simple 1D NMR spectra. The method was verified with the ternary 30 kDa complex between the lanthanide-labeled N-terminal domain of the epsilon exonuclease subunit from the Escherichia coli DNA polymerase III, the subunit theta, and thymidine. The binding mode of thymidine was found to be very similar to that of thymidine monophosphate present in the crystal structure.     

Computed tomographic X-ray velocimetry for simultaneous 3D measurement of velocity and geometry in opaque vessels

Computed tomographic X-ray velocimetry has been developed for simultaneous three-dimensional measurement of flow and vessel geometry. The technique uses cross-correlation functions calculated from X-ray projection image pairs acquired at multiple viewing angles to tomographically reconstruct the flow through opaque objects with high resolution. The reconstruction is performed using an iterative, least squares approach. The simultaneous measurement of the object’s structure is performed with a limited projection tomography method. An extensive parametric study using Monte Carlo simulation reveals accurate measurements with as few as 3 projection angles, and a minimum required scan angle of only 30°. When using a single/source detector system, the technique is limited to measurement of periodic or steady flow fields; however, with the use of a multiple source/detector system, instantaneous measurement will be possible. Synchrotron experiments are conducted to demonstrate the simultaneous measurement of structure and flow in a complex geometry with strong three-dimensionality. The technique will find applications in biological flow measurement, and also in engineering applications where optical access is limited, such as in mineral processing.     

Anti‐Inflammatory Activity of a Novel Acetylene Isolated from the Roots of Angelica tenuissima Nakai

Three polyacetylenes, one novel and two known, were isolated from the root of Angelica tenuissima. Using ¹H‐ and ¹³C‐NMR, COSY, HMBC, and HMQC, their structures were found to be (3R,8S)‐heptadeca‐1‐en‐4,6‐diyne‐3,8‐diol ( 1 ), falcarindiol ( 2 ), and oplopandiol ( 3 ). Absolute configurations of compound 1 were established using Mosher's esterification. In addition, the polyacetylenes ( 1 – 3 ) were evaluated for their anti‐inflammatory activity. Compounds 1 and 3 showed potent inhibitory activity against lipopolysaccharide‐induced nitric oxide (NO) production in RAW267.7 macrophage cells with IC₅₀ values of 4.31 and 5.06 μm, respectively. Compound 1 strongly inhibited inducible nitric oxide synthase (iNOS) and cyclooxygenase (COX)‐2 in a concentration‐dependent manner.     

Enhanced thermal degradation of 2,2′-dichlorodiethyl sulfide (sulfur mustard,HD) with the presence of metal oxides

Thermal degradation of sulfur mustard (2,2′-dichlorodiethyl sulfide, HD) in the presence of metal oxide adsorbents was investigated by thermal desorption in conjunction with gas chromatography–mass spectrometry (GC-MS). Zr(OH)₄, Al₂O₃, Al₂CoO₄, MgO, CeO₂, and V₂O₅ were used as metal oxide adsorbents. Neat HD was spiked onto the metal oxides packed in glass tubes, which were kept at room temperature and then heated at moderately elevated temperatures of 100°C by a thermal desorption system. The products of thermal degradation were directly transferred and analyzed by GC-MS. 1,4-Dithiane and 1,4-oxathiane were characterized as the major products of the thermal degradation of HD in the presence of Zr(OH)₄, Al₂O₃, Al₂CoO₄, and CeO₂ adsorbents. No effective degradation was observed with MgO and V₂O₅. Of particular note is Zr(OH)₄, which extremely enhanced the thermal degradation of HD.     

Tracking extended mucociliary transport activity of individual deposited particles: longitudinal synchrotron X‐ray imaging in live mice

To assess potential therapies for respiratory diseases in which mucociliary transit (MCT) is impaired, such as cystic fibrosis and primary ciliary dyskinesia, a novel and non‐invasive MCT quantification method has been developed in which the transit rate and behaviour of individual micrometre‐sized deposited particles are measured in live mice using synchrotron phase‐contrast X‐ray imaging. Particle clearance by MCT is known to be a two‐phase process that occurs over a period of minutes to days. Previous studies have assessed MCT in the fast‐clearance phase, ～20 min after marker particle dosing. The aim of this study was to non‐invasively image changes in particle presence and MCT during the slow‐clearance phase, and simultaneously determine whether repeat synchrotron X‐ray imaging of mice was feasible over periods of 3, 9 and 25 h. All mice tolerated the repeat imaging procedure with no adverse effects. Quantitative image analysis revealed that the particle MCT rate and the number of particles present in the airway both decreased with time. This study successfully demonstrated for the first time that longitudinal synchrotron X‐ray imaging studies are possible in live small animals, provided appropriate animal handling techniques are used and care is taken to reduce the delivered radiation dose.     

Formation of [M − nH + mNa](m−n)+ and [M − nH + mK](m−n)+ ions in electrospray mass spectrometry of peptides and proteins

The [M - nH + mNa](m-n)+ and [M - nH + mK](m-n)+ ions are common in the electrospray mass spectra of proteins and peptides. The feasibility of forming these ions in the gas phase via collision activation and/or ion-molecule reaction is investigated. Sodium and potassium affinities of the N-methylacetamide anion, the acetate anion, and the 1-propanamide anion have been calculated using density functional theory at the B3LYP/6-311+ +G(d,p) level of theory. These anions were chosen as models for the functional groups on a protein or peptide. These affinity values are then used to calculate reaction enthalpies of alkali hydroxides, chlorides, and hydrates with N-methylacetamide, acetic acid, the acetate anion, and 1-propanamine, model reactions that may lead to formation of the [M - nH + mNa](m-n) and [M - nH + mK](m-n)+ ions. It is found that a number of these reactions are exothermic or slightly endothermic (deltaH(o) < + 20 kcal/mol) and are accessible after collision activation in the lens region. The potential energy hypersurfaces of model reactions between NaOH and formamide as well as NaCl and formamide show relatively flat surfaces devoid of significant barriers.     

Magnetically-actuated blood filter unit attachable to pre-made biochips

We present a novel blood filter unit that is designed to separate blood plasma from whole blood by simple magnetic actuation. A non-diluted blood sample is dropped into the filter unit and magnetic attraction is applied to squeeze out only blood plasma while blood particles are filtered by membranes stacked in the filter unit. The new filter device yields good filtering performance with nearly perfect filtering efficiency (～99.999%), high plasma recovery (～30%), low blood consumption (<50 μl), and fast operation (～1 min). Because it is simple to operate and is attachable to any kind of pre-made biochip, it has commercial potential in various lab-on-a-chip applications for blood tests.     

On-chip continuous monitoring of motile microorganisms on an ePetri platform

Self-imaging Petri dish platforms with microscopy resolution, which we term 'ePetri', can significantly streamline cell cultures and/or other longitudinal biological studies. In this paper, we demonstrate high-resolution imaging and long-term culture of motile microorganisms in a specialized ePetri platform by taking advantage of the inherent motion. By applying a super-resolution algorithm to a set of low-resolution images of the microorganisms as they move across the sensing area of a complementary metal oxide semiconductor (CMOS) image sensor chip, we can render an improved-resolution image of the microorganisms. We perform a longitudinal study of Euglena gracilis cultured in an ePetri platform, and image-based analysis on the motion and morphology of the cells. As a miniaturized and automated culture monitoring platform, this ePetri technology can greatly improve studies and experiments with motile microorganisms.     

Statistical analysis of model risk concerning temperature residuals and its impact on pricing weather derivatives

In this paper we model the daily average temperature via an extended version of the standard Ornstein Uhlenbeck process driven by a Levy noise with seasonally adjusted asymmetric ARCH process for volatility. More precisely, we model the disturbances with the Normal inverse Gaussian (NIG) and Variance gamma (VG) distribution. Besides modelling the residuals we also compare the prices of January 2010 out of the money call and put options for two of the Slovenian largest cities Ljubljana and Maribor under normally distributed disturbances and NIG and VG distributed disturbances. The results of our numerical analysis demonstrate that the normal model fails to capture adequately tail risk, and consequently significantly misprices out of the money options. On the other hand prices obtained using NIG and VG distributed disturbances fit well to the results obtained by bootstrapping the residuals. Thus one should take extreme care in choosing the appropriate statistical model.     

A BSDE approach to risk-based asset allocation of pension funds with regime switching

An asset allocation problem of a member of a defined contribution (DC) pension fund is discussed in a hidden, Markov regime-switching, economy using backward stochastic differential equations, (BSDEs). A risk-based approach is considered, where the member selects an optimal asset mix with a view to minimizing the risk described by a convex risk measure of his/her terminal wealth. Firstly, filtering theory is adopted to transform the hidden, Markov regime-switching, economy into one with complete observations and to develop, (robust), filters for the hidden Markov chain. Then the optimal asset allocation problem of the member is formulated as a two-person, zero-sum stochastic differential game between the member and the market in the economy with complete observations. The BSDE approach is then used to solve the game problem and to characterize the saddle point of the game problem. An explicit expression for the optimal asset mix is obtained in the case of a convex risk measure with quadratic penalty and it can be considered a generalized version of the Merton ratio. An explicit expression for the optimal strategy of the market is also obtained, which leads to a risk-neutral wealth dynamic and may provide some insights into asset pricing in the economy with inflation risk and regime-switching risk. Numerical examples are provided to illustrate financial implications of the BSDE solution.