A tetramethyl rhodamine (Tamra) phosphoramidite facilitates solid-phase-supported synthesis of 5'-Tamra DNA

5-Carboxy Tamra 1 was conjugated to 4-hydroxypiperidine with BOP and N-methylmorpholine, and the resulting 5-(N-pipyridyl-4-hydroxy)-Tamra carboxamide 2 was treated with 2-cyanoethyl tetraisopropylphosphorodiamidite to give 5-[N-pipyridyl-4-O-(2-cyanoethyl diisopropylphosphoramidite)]-Tamra carboxamide 3. Solutions of 3 were coupled onto the 5'-hydroxyl of solid-phase-supported DNA fragments with standard amidite coupling techniques. Cleavage and deprotection with aqueous tert-butylamine cocktail gave 5-Tamra-functionalized DNA as well as an additional compound without the Tamra chromophore. A mass spectrum of this product showed the incorporation of tert-butylamine. The extra product was completely suppressed by including a 5 min acetylation step after coupling. A model study of 3 coupled onto thymidine-functionalized CPG showed similar results. NMR and mass spectra of cleaved products confirmed the addition of tert-butylamine to the minor product. Coupling a Tamra active ester onto T CPG which was previously coupled with N-(4-methoxytrityl)piperidyl-4-O-(2-cyanoethyl diisopropylphosphoramidite) 4 produced the same major Tamra-bearing product, which coeluted on reverse phase HPLC with the major product generated with 3.     

A network modelling approach for assessing the efficiency of prevention strategies

Survey data and a simulation model based on a stochastic pair formation process are used to construct networks of sexual contacts. We model heterosexual partnerships which can be steady or casual depending on their average duration. Transmission of an infectious disease can take place in pairs of a susceptible and an infected individual. We study networks of sexual contacts accumulated during 1 year for different types of mixing patterns. The networks are constructed on the basis of data from a survey in The Netherlands. We analyze the network structure for different mixing patterns and investigate the relationship between network structure and disease spread; furthermore we study the effect of prevention measures on the structure of the network.     

Photo-reduction of flavin mononucleotide to semiquinone form in LOV domain mutants of blue-light receptor phot from Chlamydomonas reinhardtii

The photo-excitation dynamics of the mutants LOV1-C57S and LOV2-C250S of the LOV-domains of the phototropin photoreceptor phot from the green alga Chlamydomonas reinhardtii is investigated by absorption and fluorescence studies. The LOV domains fused to a maltose binding protein (MBP) are expressed in Escherichia coli. The mutants were studied under aerobic conditions in aqueous solution at pH 8. Blue-light exposure reduced the fully oxidized flavin mononucleotide, FMN(ox), to FMN semiquinone, FMNH*, (quantum efficiency around 1%) which further reduced to FMN hydroquinone, FMN(red)H(2) or FMN(red)H(-) (quantum efficiency ca. 3 x 10(-5)). In the dark both reduced forms recovered back to the oxidized form on a minute timescale. Besides photoreduction, blue-light photo-excitation of the mutants resulted in photoproduct formation (efficiency in the 2 x 10(-4) - 10(-3) range). Photo-reaction schemes for the mutants are discussed.     

Transport properties of 2F <==> F2 in a temperature gradient as studied by molecular dynamics simulations

We calculate transport properties of a reacting mixture of F and F(2) from results of non-equilibrium molecular dynamics simulations. The reaction investigated is controlled by thermal diffusion and is close to local chemical equilibrium. The simulations show that a formulation of the transport problem in terms of classical non-equilibrium thermodynamics theory is sound. The chemical reaction has a large effect on the magnitude and temperature dependence of the thermal conductivity and the interdiffusion coefficient. The increase in the thermal conductivity in the presence of the chemical reaction, can be understood as a response to an imposed temperature gradient, which reduces the entropy production. The heat of transfer for the Soret stationary state was more than 100 kJ mol(-1), meaning that the Dufour and Soret effects are non-negligible in reacting mixtures. This sheds new light on the transport properties of reacting mixtures.     

Numerical simulation and flow visualization using soap film of the self-organized vortex structure in the wake of an array of cylinders

Abstract  

With the aid of computational fluid dynamics (CFD) and simple flow visualization technique using flowing soap-film, we present here the wake structures behind an array of cylinders for Reynolds numbers corresponding to both laminar and turbulent flow regimes. The image results illustrate interesting vortex interactions past these equally spaced cylinders; for low Reynolds number flow, well-organized wake pattern persists and manifests unsteadily to different symmetry states. An increase of free stream flow velocity causes the wake transition, resulting in the formation of asymmetric flow wake with chaotic mixing at the far wake. Observations from both the numerical simulations and soap-film are in good agreement at least qualitatively.     

Unraveling the flavin-catalyzed photooxidation of benzylic alcohol with transient absorption spectroscopy from sub-pico- to microseconds

Flavin-mediated photooxidations have been described for applications in synthetic organic chemistry for some time and are claimed to be a route to the use of solar energy. We present a detailed investigation of the involved photophysical and photochemical steps in methoxybenzyl alcohol oxidation on a timescale ranging from sub-picoseconds to tens of microseconds. The results establish the flavin triplet state as the key intermediate for the photooxidation. The initial step is an electron transfer from the alcohol to the triplet state of the flavin catalyst with (3)k(ET)≈ 2 × 10(7) M(-1) s(-1), followed by a proton transfer in ～6 μs. In contrast, the electron transfer involving the singlet state of flavin is a loss channel. It is followed by rapid charge recombination (τ = 50 ps) without significant product formation as seen when flavin is dissolved in pure benzylic alcohol. In dilute acetonitrile/water solutions of flavin and alcohol the electron transfer is mostly controlled by diffusion, though at high substrate concentrations >100 mM we also find a considerable contribution from preassociated flavin-alcohol-aggregates. The model including a productive triplet channel and a competing singlet loss channel is confirmed by the course of the photooxidation quantum yield as a function of substrate concentration: We find a maximum quantum yield of 3% at 25 mM of benzylic alcohol and significantly smaller values for both higher and lower alcohol concentrations. The observations indicate the importance to perform flavin photooxidations at optimized substrate concentrations to achieve high quantum efficiencies and provide directions for the design of flavin photocatalysts with improved performance.     

Boundary data immersion method for Cartesian-grid simulations of fluid-body interaction problems

A new robust and accurate Cartesian-grid treatment for the immersion of solid bodies within a fluid with general boundary conditions is described. The new approach, the Boundary Data Immersion Method (BDIM), is derived based on a general integration kernel formulation which allows the field equations of each domain and the interfacial conditions to be combined analytically. The resulting governing equation for the complete domain preserves the behavior of the original system in an efficient Cartesian-grid method, including stable and accurate pressure values on the solid boundary. The kernel formulation allows a detailed analysis of the method, and it is demonstrated that BDIM is consistent, obtains second-order convergence relative to the kernel width, and is robust with respect to the grid and boundary alignment. Formulation for no-slip and free slip boundary conditions are derived and numerical results are obtained for the flow past a cylinder and the impact of blunt bodies through a free surface. The BDIM predictions are compared to analytic, experimental and previous numerical results confirming the properties, efficiency and efficacy of this new boundary treatment for Cartesian grid methods.     

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.