Information Thermodynamics and Reducibility of Large Gene Networks

Gene regulatory networks (GRNs) control biological processes like pluripotency, differentiation, and apoptosis. Omics methods can identify a large number of putative network components (on the order of hundreds or thousands) but it is possible that in many cases a small subset of genes control the state of GRNs. Here, we explore how the topology of the interactions between network components may indicate whether the effective state of a GRN can be represented by a small subset of genes. We use methods from information theory to model the regulatory interactions in GRNs as cascading and superposing information channels. We propose an information loss function that enables identification of the conditions by which a small set of genes can represent the state of all the other genes in the network. This information-theoretic analysis extends to a measure of free energy change due to communication within the network, which provides a new perspective on the reducibility of GRNs. Both the information loss and relative free energy depend on the density of interactions and edge communication error in a network. Therefore, this work indicates that a loss in mutual information between genes in a GRN is directly coupled to a thermodynamic cost, i.e., a reduction of relative free energy, of the system.     

Compact high‐resolution algorithms for time‐dependent advection on unstructured grids

A technique for constructing monotone, high resolution, multi‐dimensional upwind fluctuation distribution schemes for the scalar advection equation is presented. The method combines the second‐order Lax–Wendroff scheme with the upwind positive streamwise invariant (PSI) scheme via a fluctuation redistribution step, which ensures monotonicity (and which is a generalization of the flux‐corrected transport approach for fluctuation distribution schemes). Furthermore, the concept of a distribution point is introduced, which, when related to the equivalent equation for the scheme, leads to a ‘preferred direction’ for the limiting procedure, and hence to a new distribution of the fluctuation, which retains second‐order accuracy from the Lax–Wendroff scheme, even when the solution contains turning points. Experimental comparisons show that the new method compares favourably in terms of speed, accuracy and robustness with other, similar, techniques. Copyright © 2000 John Wiley & Sons, Ltd.     

A novel polar polymer via romp

We have synthesised poly(2,3-bis(trifluoromethyl)norbornadiene) (PBTFMND) via ring-opening metathesis polymerisation (ROMP) to yield a glassy, highly polar polymer. The high trans polymer is ∼92% tactic and the high cis polymer is ∼75% tactic but the type of tacticity cannot be determined by NMR techniques. Thermally Stimulated Depolarisation (TSD) measurements give relaxed susceptibilities as high as 45 for the high trans material but as low as 3 for the high cis material. These data suggest that both the trans and cis materials are syndiotactic. The high trans material can be poled to yield a maximum polarisation of about 20 mC m⁻² and a pyroelectric coefficient of 6 μC m⁻². Though this is less than that of PVDF, the low room temperature permittivity and loss of PBTFMND results in a pyroelectric figure of merit comparable with that of PVDF.     

Identifying key electrostatic interactions in Rhizomucor miehei lipase: the influence of solvent dielectric

The conformational change associated with the interfacial activation of Rhizomucor miehei lipase involves the displacement of an α-helical lid (residues 82–96) away from the active site on moving from water (high dielectric) to lipid (low dielectric). The presence of two media of very different dielectric properties suggests that electrostatic interactions play an important role in this process. We have used linearized Poisson–Boltzmann calculations to examine the key electrostatic interactions which contribute to lid stability in the closed and open states. It is the two charged residues of the lid, Arg86 and Asp91, that form the strongest electrostatic interactions with the rest of the protein. We identify key residues whose interactions with the lid are significantly perturbed by the change in the dielectric of the medium: Asp61, Arg80, Lys109, Glu117 and the active-site residues Asp203 and Asp256, all of which lie within approximately 20 ? of the lid. We suggest that these residues are good candidates for site-specific mutation studies, which could help elucidate their role in the lipase activation mechanism. Received: 27 May 1998 / Accepted: 17 September 1998 / Published online: 7 December 1998     

1,4,7-Trithiacyclononane as a Tridentate Ligand for Complexation of Heavy-Metal Ions: Synthesis and Complexation Studies of Mesocyclic and Macrocyclic Polythioethers IV

Bis octahedral complexes of 1,4,7-trithiacyclononane (9-ane-S₃) with Group 12 metal ions Zn(II), Cd(II), and Hg(II), as well as Pb(II), have been prepared. Two equivalents of 9-ane-S₃ react with Zn(BF₄)₂·6H₂O, Cd(ClO₄)₂·6H₂O, Hg(ClO₄)₂·3H₂O, and Pb(ClO₄)₂. 3H₂O, respectively, to give stable crystalline complexes of the formula [M(9-ane-S₃)₂]²+ 2X⁻. Single-crystal X-ray structures of the zinc and mercury complexes have been determined. The zinc complex crystallizes in the orthorhombic space group Pbca with four molecules per unit cell (a = 9.219(3) Å, b = 15.400(5) Å, and c = 19.965(10)Å; R = 7.6%) whereas the mercury complex crystallizes in the monoclinic space group P2₁/c with two molecules per unit cell (a = 10.400(3) Å, b = 15.190(4) Å, c = 9.533(3) Å, and p = 99.09(3)°; R = 5.2%). In each structure, the metal atom is located on a crystallographic center of inversion and is octahedrally surrounded by six sulfur atoms provided by the two facially coordinating tridentate ligands. Reaction of 9-ane-S₃ with RuCl₃·xH₂O displaces chloride ions with concomitant reduction of Ru(III) to Ru(II), giving the octahedral thioether complex, [Ru(9-ane-S₃)₂]Cl₂·4H₂O. Reaction of the ligand with RhCl₃, on the other hand, gives (9-ane-S₃)RhCl₃. A single-crystal X-ray structure determination has been done on the Ru(II) complex (triclinic space group P 1 ̅; a = 7.652(1) Å, b = 8.946(1) Å, c = 9.042(1) Å, α = 93.43(1)°, β = 103.43(1)°, and γ = 107.79(1)°; R = 2.8%) and this complex is also octahedral with the metal center at an inversion center.     

Structure and derivatization of the product from carbonylation of lithium triethylborohydride

Treatment of the reactive product from carbonylation of lithium triethylborohydride with the electrophilic reagent chlorotrimethylsilane does not produce the expected α-hydroxyborane derivative. Instead, a borinate arising through migration of a second ethyl group from boron to carbon is obtained. This result is rationalized in terms of the initial product being a borate having two possible constitutions. The borate nature of this initial product is confirmed by ¹¹B NMR.     

Application of low-temperature rapid-scan techniques in the elucidation of inorganic reaction mechanisms

Reactions that occur too rapidly to be monitored by rapid reaction methods at temperatures at or close to ambient can be investigated kinetically by retarding their reaction rates employing very low temperatures. A selection of reactions studied by this approach (low-temperature stopped-flow spectrophotometry) is reported. Details of the reaction mechanisms have been revealed for peroxide activation involving iron(III) porphyrins and cytochrome P450, superoxide activation involving manganese(II) complexes and iron porphyrin complexes, and dioxygen activation and binding by model mono-, and dinuclear copper(I) complexes and dioxygen activation at mono-, and dinuclear non-heme iron complexes. A final section covers progress in unravelling the mechanism of carbon–hydrogen bond activation by platinum complexes.     

Evolution of a lamellar domain structure for an equilibrating lyotropic liquid crystal

Aerosol OT/water exhibits a lamellar phase over a wide range of concentrations. We show, by magnetic resonance (NMR) and scanning electron microscopy (SEM), that the morphology of the lamellar phase varies significantly across that range and that the rate of equilibration depends strongly on concentration (25, 33, and 50 wt %) with, paradoxically, the faster equilibration at higher surfactant concentrations. We find that the 25 wt % sample exhibits a defect-rich local structure, characteristic of a superposed L(3) character. Further into the lamellar region, at 33 wt %, this defect-rich structure persists heterogeneously, while, at 50 wt %, the lamellar phase domains are highly ordered. The NMR methods used here included (2)H spectroscopy and the two-dimensional NMR method, diffusion-diffusion exchange spectroscopy (DEXSY). The latter was used to obtain quantitative information on the domain sizes and defects within the polydomain lamellar mesophase. Comparison of the NMR with the SEM results suggests that, at 25 wt % AOT, bilayer defects play an important role in influencing the (2)H NMR and DEXSY NMR results.     

Effects of radiation damping on Z-spectra

Radiation damping induced by the strong water magnetization in Z-spectroscopy experiments can be sufficient to perturb significantly the resultant Z-spectrum. With a probe tuned to exact electrical resonance the effects are relatively straightforward, narrowing the central feature of the Z-spectrum. Where, as is commonly the case, the probe is tuned sufficiently well to give optimum signal-to-noise ratio and radiofrequency field strength but is not at exact resonance, radiation damping introduces an unexpected asymmetry into the Z-spectrum. This has the potential to complicate the use of Z-spectrum asymmetry to study chemical exchange, for example in the estimation of pH in vivo.     

Strong Short-Range Cooperativity in Hydrogen-Bond Chains

Chains of hydrogen bonds such as those found in water and proteins are often presumed to be more stable than the sum of the individual H bonds. However, the energetics of cooperativity are complicated by solvent effects and the dynamics of intermolecular interactions, meaning that information on cooperativity typically is derived from theory or indirect structural data. Herein, we present direct measurements of energetic cooperativity in an experimental system in which the geometry and the number of H bonds in a chain were systematically controlled. Strikingly, we found that adding a second H-bond donor to form a chain can almost double the strength of the terminal H bond, while further extensions have little effect. The experimental observations add weight to computations which have suggested that strong, but short-range cooperative effects may occur in H-bond chains.