Pharmacodynamic assay of thymidylate synthase activity in peripheral blood mononuclear cells

A simple, selective, and sensitive method utilizing tritium (³H) release from ³H-deoxyuridine 5′-monophosphate (dUMP) substrate for accurate and precise determination of the low basal thymidylate synthase activity (TSA) in normal healthy peripheral blood mononuclear cells (PBMCs) was developed and validated. The method is based on the removal of the remaining substrate after the TSA reaction by absorption onto activated carbon and measurement of the supernatant fluid by liquid scintillation counting. The method background was substantially decreased by using lyophilized substrate and optimized binding conditions of remaining substrate onto carbon after TSA reaction. The concentration of cofactor N ₅,N ₁₀ methylene-(6R,S)-tetrahydrofolate was increased to obtain maximal TSA. Method sensitivity was further increased by omission of ethylenediaminetetraacetic acid from the reaction mix and by using longer reaction times. The validation parameters included specificity, linearity, sensitivity, precision, and stability. The lower limit of quantification was 25 μg PBMC cytosolic lysate, which released 1.4 pmol?³H/h. TSA was stable in PBMC pellets stored for 6 months at ?80 °C. The applicability of the method was demonstrated by the successful determination of TSA in PBMC cytosolic lysates from ten healthy volunteers with and without the specific TSA inhibitor FdUMP.

Enantioselective Enzymes by Computational Design and In Silico Screening

Computational enzyme design holds great promise for providing new biocatalysts for synthetic chemistry. A strategy to design small mutant libraries of complementary enantioselective epoxide hydrolase variants for the production of highly enantioenriched (S,S)‐diols and (R,R)‐diols is developed. Key features of this strategy (CASCO, catalytic selectivity by computational design) are the design of mutations that favor binding of the substrate in a predefined orientation, the introduction of steric hindrance to prevent unwanted substrate binding modes, and ranking of designs by high‐throughput molecular dynamics simulations. Using this strategy we obtained highly stereoselective mutants of limonene epoxide hydrolase after experimental screening of only 37 variants. The results indicate that computational methods can replace a substantial amount of laboratory work when developing enantioselective enzymes.     

DNA‐Based Oligochromophores as Light‐Harvesting Systems

The chromophores ethynyl pyrene as blue, ethynyl perylene as green and ethynyl Nile red as red emitter were conjugated to the 5‐position of 2′‐deoxyuridine via an acetylene bridge. Using phosphoramidite chemistry on solid phase labelled DNA duplexes were prepared that bear single chromophore modifications, and binary and ternary combinations of these chromophore modifications. The steady‐state and time‐resolved fluorescence spectra of all three chromophores were studied in these modified DNA duplexes. An energy‐transfer cascade occurs from ethynyl pyrene over ethynyl perylene to ethynyl Nile red and subsequently an electron‐transfer cascade in the opposite direction (from ethynyl Nile red to ethynyl perylene or ethynyl pyrene, but not from ethynyl perylene to ethynyl pyrene). The electron‐transfer processes finally provide charge separation. The efficiencies by these energy and electron‐transfer processes can be tuned by the distances between the chromophores and the sequences. Most importantly, excitation at any wavelength between 350 and 700 nm finally leads to charge separated states which make these DNA samples promising candidates for light‐harvesting systems.     

Nonlinear dynamics and chaos regularization of one-dimensional pulsating detonations with small sinusoidal density perturbations

In this work, we explore the effect of initial density variation in the combustible mixture on the nonlinear dynamics of one-dimensional gaseous detonation propagation. Studies of nonlinear dynamical behavior of one-dimensional pulsating detonation are frequently based upon the reactive Euler simulations with one-step Arrhenius chemistry. In regions of the control parameters space, i.e., activation energy E_a, the 1-D detonation dynamics are shown to exhibit chaotic behavior at values of 28.5 and 30.0. Using small sinusoidal initial density perturbations, this investigation shows the emergence of various nonlinear temporal patterns as a function of the perturbation wavelength. It demonstrates that the cooperative behavior between the intrinsic instability and imposed small perturbation can lead to regularization of chaotic oscillations in one-dimensional gaseous pulsating detonation. Hence, by means of a small perturbation, an otherwise chaotic motion is rendered more stable and predictable. This result thus has implications for how intrinsically unstable detonation dynamics can be controlled.     

Mechanics and full-field deformation study of the Ring Hoop Tension Test

We investigate the mechanics of the Ring Hoop Tension Test (RHTT), as a means to assess the properties of anisotropic tubes in the hoop direction. This test involves placing a ring extracted from the tube over two close-fitting D-shaped mandrels that are then parted using a universal testing machine. Since the curvature of the ring does not change during loading, the ring undergoes only stretching. We determine the effects of contact pressure, radial stress, and friction between the tube and mandrels using FEA simulations. The effects of the pre-existing thickness eccentricity and of the specimen-making procedure on the recorded RHTT response are also assessed with a combination of experiments and analysis. We tested tubes from Al-6061-T4 with a diameter/thickness ratio of 20. We found that as the friction increases beyond 0.1–0.15, the state of uniaxial tension is deteriorated, indicating that care must be taken to minimize the tube-mandrel friction. We determined that although these tubes have a relatively large thickness eccentricity (±4% of the nominal thickness), this had no effect on the recorded results. We showed that the tubes should not be turned to remove that eccentricity, as the machining process induces damage that is noticeable in the results. We found that the contact pressure and the contact-induced radial stress cause limited deviations from uniaxial tension, comparable to the case of a tube under axial load and internal pressure which is often used for assessing the material properties in the hoop direction. Central in our analyses is the knowledge of the hoop strain field, which was assessed using 3D Digital Image Correlation. We propose a data reduction procedure for RHTT that accounts for all the above effects. Finally, with all effects accounted for, we establish the anisotropy of the extruded Al-6061-T4 tubes studied.     

Experimental investigation of vibration attenuation using nonlinear tuned mass damper and pendulum tuned mass damper in parallel

The present paper experimentally and numerically explores the response attenuation of a hardening Düffing oscillator using a nonlinear tuned mass damper (NTMD) and an adaptive-length pendulum tuned mass damper (APTMD). The three degrees-of-freedom system is excited by harmonic ground motions. The cubic nonlinearity of the primary structure is obtained using an adaptive passive stiffness (APS) device. When an NTMD is used alone, a high amplitude detached resonance branch in the lower frequency range is identified in the experiment, which validates the results reported in earlier numerical research. In order to attenuate this high amplitude resonance branch, an APTMD with an adaptive frequency realized by means of a variable pendulum length is used in parallel with the NTMD. In the experiment, length of the APTMD is adjusted such that its natural frequency matches the dominant frequency of the harmonic ground motions. Results indicate that the high amplitude resonance branch in the case of an NTMD alone can be greatly attenuated using the APTMD, and significant attenuation of the structural responses over a large frequency range can be obtained. In addition, the APTMD can prevent the occurrence of the “jump phenomenon” existing in the forcing response curve of the nonlinear dynamic system, thereby protecting the primary nonlinear structure effectively when the forcing amplitude varies. Therefore, the present paper provides an effective and viable solution to control the hazardous bifurcations in a Düffing oscillator-NTMD dynamic system.     

Applying nonlinear dynamic theory to one-dimensional pulsating detonations

The dynamical behaviour of one-dimensional pulsating detonations was investigated in detail, with the aid of nonlinear theory tools such as phase plots and correlation dimension. The period-doubling cascade, as routes to deterministic chaos, is depicted through the transformations of the shapes of the attractors. Using a correlation dimension method, the dimension of the attractors is determined and we show that the chaos within a one-dimensional pulsating detonation is deterministic.     

M. Nath,S. Phokaria,X. Song,G. Eng,M. Gielen,M. Kemmer,M. Biesemans,R. Willem and D. de Vos, ‘New organotin(IV) derivatives of dipeptides as models for metal–protein interactions: in vitro anti‐tumour activity’ Applied Organometallic Chemistry 2003; 17(5): 305–314

The original article to which these Errata refer was published in the journal Applied Organometallic Chemistry 2003; 17 (5): 305–314. Copyright © 2003 John Wiley & Sons, Ltd.     

Multidimensional solid‐state NMR studies of the structure and dynamics of pectic polysaccharides in uniformly 13C‐labeled Arabidopsis primary cell walls

Plant cell wall (CW) polysaccharides are responsible for the mechanical strength and growth of plant cells; however, the high‐resolution structure and dynamics of the CW polysaccharides are still poorly understood because of the insoluble nature of these molecules. Here, we use 2D and 3D magic‐angle‐spinning (MAS) solid‐state NMR (SSNMR) to investigate the structural role of pectins in the plant CW. Intact and partially depectinated primary CWs of Arabidopsis thaliana were uniformly labeled with ¹³C and their NMR spectra were compared. Recent ¹³C resonance assignment of the major polysaccharides in Arabidopsis thaliana CWs allowed us to determine the effects of depectination on the intermolecular packing and dynamics of the remaining wall polysaccharides. 2D and 3D correlation spectra show the suppression of pectin signals, confirming partial pectin removal by chelating agents and sodium carbonate. Importantly, higher cross peaks are observed in 2D and 3D ¹³C spectra of the depectinated CW, suggesting higher rigidity and denser packing of the remaining wall polysaccharides compared with the intact CW. ¹³C spin–lattice relaxation times and ¹H rotating‐frame spin–lattice relaxation times indicate that the polysaccharides are more rigid on both the nanosecond and microsecond timescales in the depectinated CW. Taken together, these results indicate that pectic polysaccharides are highly dynamic and endow the polysaccharide network of the primary CW with mobility and flexibility, which may be important for pectin functions. This study demonstrates the capability of multidimensional SSNMR to determine the intermolecular interactions and dynamic structures of complex plant materials under near‐native conditions. Copyright © 2012 John Wiley & Sons, Ltd.