Energy efficiency trade-offs drive nucleotide usage in transcribed regions

Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides 'U' and 'C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides 'A' and 'G' at non-synonymous coding sites

Confinement effects and acid strength in zeolites

Chemical reactivity and sorption in zeolites are coupled to confinement and—to a lesser extent—to the acid strength of Brønsted acid sites (BAS). In presence of water the zeolite Brønsted acid sites eventually convert into hydronium ions. The gradual transition from zeolite Brønsted acid sites to hydronium ions in zeolites of varying pore size is examined by ab initio molecular dynamics combined with enhanced sampling based on Well-Tempered Metadynamics and a recently developed set of collective variables. While at low water content (1–2 water/BAS) the acidic protons prefer to be shared between zeolites and water, higher water contents (n > 2) invariably lead to solvation of the protons within a localized water cluster adjacent to the BAS. At low water loadings the standard free energy of the formed complexes is dominated by enthalpy and is associated with the acid strength of the BAS and the space around the site. Conversely, the entropy increases linearly with the concentration of waters in the pores, favors proton solvation and is independent of the pore size/shape

Accurate adsorption thermodynamics of small alkanes in zeolites. Ab initio theory and experiment for H-chabazite

Heats of adsorption of methane, ethane, and propane in H-chabazite (Si/Al = 14.4) have been measured and entropies have been derived from adsorption isotherms. For these systems quantum chemical ab initio calculations of Gibbs free energies have been performed. The deviations from the experimental values for methane, ethane, and propane are below 3 kJ/mol for the enthalpy, and the Gibbs free energy. A hybrid high-level (MP2/CBS): low-level (DFT+dispersion) method is used to determine adsorption structures and energies. Vibrational entropies and thermal enthalpy contributions are obtained from vibrational partition functions for the DFT+dispersion potential energy surface. Anharmonic corrections have been evaluated for each normal mode separately. One-dimensional Schrödinger equations are solved for potentials obtained by (curvilinear) distortions of the normal modes using a representation in internal coordinates

Umklapp scattering from spin fluctuations in Copper-Oxides

The $\mathbf k$-dependent electronic momentum relaxation rate due to Umklapp scattering from antiferromagnetic spin fluctuations is studied within a renormalized mean-field approach to an extended $t-J$ model appropriate to YBa$_2$Cu$_3$O$_{7-x}$ and other cuprates. Transport coefficients are calculated in a relaxation time approximation. We compare these results with those obtained with the phenomenological assumption that all scattering processes dissipate momentum. We show that the latter, which violates momentum conservation, leads to quite different magnitudes and temperature dependences of resistivities and Hall coefficients.Comment: replaced by LaTeX file (due to problems with PostScript

Does negative auto-regulation increase gene duplicability?

BACKGROUND: A prerequisite for a duplication to spread through and persist in a given population is retaining expression of both gene copies. Yet changing a gene's dosage is frequently detrimental to fitness. Consequently, dosage-sensitive genes are less likely to duplicate. However, in cases where the level of gene product is controlled, via negative feedback, by its own abundance, an increase in gene copy number can in principle be decoupled from an increase in protein while both copies remain expressed. Using data from the transcriptional networks of E. coli and S. cerevisiae, we test the hypothesis that genes under negative auto-regulation show enhanced duplicability. RESULTS: Controlling for several known correlates of duplicability, we find no statistically significant support in either E. coli or S. cerevisiae that transcription factors under negative auto-regulation hold a duplicability advantage over transcription factors with no auto-regulation. CONCLUSION: Based on the analysis of transcriptional networks in E. coli and S. cerevisiae, there is no evidence that negative auto-regulation has contributed, on a genome-wide scale, to the variability in gene family sizes in these species

Oxidative dehydrogenation of propane over niobia supported vanadium oxide catalysts

Oxidative dehydrogenation (ODH) of propane is examined over a series of catalysts, which include Nb2O5 supported monolayer V2O5 catalysts, bulk vanadia-niobia with different vanadium oxide loadings and prepared by four different methods, V2O5and Nb2O5. The intrinsic activity (TOF) of the samples studied indicates that vanadium containing active sites are indispensable for catalytic oxidative dehydrogenation of propane. Variations in the chemical environment of the vanadium ion do not cause significant changes in activity per site and, hence, all samples show similar TOF when the rates are normalised to the concentration of V on the surface. Selectivity to propene on the other hand strongly depends on the nature of the catalyst because readsorption and interaction of propene with the acid sites leads to total oxidation. Optimization of the weak sorption of propene is, therefore, concluded to be the key factor for the design of selective oxidative dehydrogenation catalysts

The role of mutation rate variation and genetic diversity in the architecture of human disease

Background We have investigated the role that the mutation rate and the structure of genetic variation at a locus play in determining whether a gene is involved in disease. We predict that the mutation rate and its genetic diversity should be higher in genes associated with disease, unless all genes that could cause disease have already been identified. Results Consistent with our predictions we find that genes associated with Mendelian and complex disease are substantially longer than non-disease genes. However, we find that both Mendelian and complex disease genes are found in regions of the genome with relatively low mutation rates, as inferred from intron divergence between humans and chimpanzees, and they are predicted to have similar rates of non-synonymous mutation as other genes. Finally, we find that disease genes are in regions of significantly elevated genetic diversity, even when variation in the rate of mutation is controlled for. The effect is small nevertheless. Conclusions Our results suggest that gene length contributes to whether a gene is associated with disease. However, the mutation rate and the genetic architecture of the locus appear to play only a minor role in determining whether a gene is associated with disease