Networks of rigid molecules

Networks of rigid molecules do not fit into the paradigm of classical theories of rubber elasticity. Some experimental properties of rigid polyamide networks are summarised, and the basis for a theoretical understanding of such systems is discussed and elaborated in terms of the properties such as the existence of several conformational states and twist of such network elements.     

Force localization in contracting cell layers

Epithelial cell layers on soft elastic substrates or pillar arrays are commonly used as model systems for investigating the role of force in tissue growth, maintenance, and repair. Here we show analytically that the experimentally observed localization of traction forces to the periphery of the cell layers does not necessarily imply increased local cell activity, but follows naturally from the elastic problem of a finite-sized contractile layer coupled to an elastic foundation. For homogeneous contractility, the force localization is determined by one dimensionless parameter interpolating between linear and exponential force profiles for the extreme cases of very soft and very stiff substrates, respectively. If contractility is sufficiently increased at the periphery, outward directed displacements can occur at intermediate positions. We also show that anisotropic extracellular stiffness can lead to force localization in the stiffer direction, as observed experimentally.     

Production of 13C labelled pea flour for use in human digestion and fermentation studies

Stable isotope breath tests offer a new approach to the study of digestion and fermentation of carbohydrates in man. In this study, 13C labelled peas were grown by pulsing 250 ml 13CO2 into a sealed growth chamber. A second pulse was added to a portion of the peas to increase the 13C enrichment. This generated pea flour with an enrichment of 2.36 at.% excess (range 2.09-2.71 n = 3) and 8.64 atom % excess (range 7.37-9.78 n = 3) respectively. This represented incorporation of an absolute yield of 3.8% of the 13CO2 into peas in the 'once-labelled' treatment and 7.5% in the 'twice-labelled' treatment. Ingestion of a mixture of the labelled pea flour (300 mg) by two volunteers generated measurable 13CO2 excretion for breath test analysis. The profile of breath 13CO2 enrichment increased to a maximum within three hours after consuming the pea flour followed by a decrease almost back to baseline by 13 hours. Breath 13CO2 appeared to rise again after this apparent nadir at 13 hours until the end of the sampling period. Mathematical analysis of the data suggested that two peaks best described the profile of breath 13CO2 up to 13 hours. A third peak was necessary to describe the late rise in breath 13CO2 enrichment. This use of 13C enriched pea flour may provide a useful non invasive method for measurement of digestion and fermentation in vivo.     

Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch

The tetracycline aptamer is an in vitro selected RNA that binds to the antibiotic with the highest known affinity of an artificial RNA for a small molecule (Kd approximately 0.8 nM). It is one of few aptamers known to be capable of modulating gene expression in vivo. The 2.2 A resolution cocrystal structure of the aptamer reveals a pseudoknot-like fold formed by tertiary interactions between an 11 nucleotide loop and the minor groove of an irregular helix. Tetracycline binds within this interface as a magnesium ion chelate. The structure, together with previous biochemical and biophysical data, indicates that the aptamer undergoes localized folding concomitant with tetracycline binding. The three-helix junction, h-shaped architecture of this artificial RNA is more complex than those of most aptamers and is reminiscent of the structures of some natural riboswitches.     

Digital imaging considerations for gel electrophoresis analysis systems

Gel analysis system purchasers have a large variety of digital imaging products to choose from today. Understanding the specifications presented by the manufacturers is important to ensure that the system fits the needs ofthe researcher using the system. The background information contained in this paper explains the terminology and many of the specifications along with their significance.     

Study on the transesterification of methyl aryl phosphorothioates in methanol promoted by Cd(II), Mn(II), and a synthetic Pd(II) complex

Methanol solutions containing Cd(II), Mn(II), and a palladacycle, (dimethanol bis(N,N-dimethylbenzylamine-2C,N)palladium(II) (3), are shown to promote the methanolytic transesterification of O-methyl O-4-nitrophenyl phosphorothioate (2b) at 25 °C with impressive rate accelerations of 10(6)-10(11) over the background methoxide promoted reaction. A detailed mechanistic investigation of the methanolytic cleavage of 2a-d having various leaving group aryl substitutions, and particularly the 4-nitrophenyl derivative (2b), catalyzed by Pd-complex 3 is presented. Plots of k(obs) versus palladacycle [3] demonstrate strong saturation binding to form 2b:3. Numerical fits of the kinetic data to a universal binding equation provide binding constants, K(b), and first order catalytic rate constants for the methanolysis reaction of the 2b:3 complex (k(cat)) which, when corrected for buffer effects, give corrected (k(cat)(corr)) rate constants. A sigmoidal shaped plot of log(k(cat)(corr)) versus (s)(s)pH (in methanol) for the cleavage of 2b displays a broad (s)(s)pH independent region from 5.6 ≤ (s)(s)pH ≤ 10 with a k(minimum) = (1.45 ± 0.24) × 10(-2) s(-1) and a [lyoxide] dependent wing plateauing above a kinetically determined (s)(s)pK(a) of 12.71 ± 0.17 to give a k(maximum) = 7.1 ± 1.7 s(-1). Br?nsted plots were constructed for reaction of 2a-d at (s)(s)pH 8.7 and 14.1, corresponding to reaction in the midpoints of the low and high (s)(s)pH plateaus. The Br?nsted coefficients (β(LG)) are computed as -0.01 ± 0.03 and -0.86 ± 0.004 at low and high (s)(s)pH, respectively. In the low (s)(s)pH plateau, and under conditions of saturating 3, a solvent deuterium kinetic isotope effect of k(H)/k(D) = 1.17 ± 0.08 is observed; activation parameters (ΔH(Pd)(++) = 14.0 ± 0.6 kcal/mol and ΔS(Pd)(++)= -20 ± 2 cal/mol·K) were obtained for the 3-catalyzed cleavage reaction of 2b. Possible mechanisms are discussed for the reactions catalyzed by 3 at low and high sspH. This catalytic system is shown to promote the methanolytic cleavage of O,O-dimethyl phosphorothioate in CD3OD, producing (CD3O)2P═O(S(-)) with a half time for reaction of 34 min.