The dynamics of alternative pathways to compensatory substitution

The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have received considerable attention, most studies have focused on the case when natural selection is very strong against deleterious intermediates. In the biologically-plausible scenario of weak to moderate selection there exist two alternate pathways for compensatory substitution. In one pathway, a deleterious mutation becomes fixed prior to occurrence of the compensatory mutation. In the other, the two loci are simultaneously polymorphic. The rates of compensatory substitution along these two pathways and their relative probabilities are functions of the population size, selection strength, mutation rate, and recombination rate. In this paper these rates and path probabilities are derived analytically and verified using population genetic simulations. The expected time durations of these two paths are similar when selection is moderate, but not when selection is weak. The effect of recombination on the dynamics of the substitution process are explored using simulation. Using the derived rates, a phylogenetic substitution model of the compensatory evolution process is presented that could be used for inference of population genetic parameters from interspecific data.Comment: 17 pages, 9 figures, 1 table. Accepted to RECOMB Comparative Genomics Meeting 2013, to be published in BMC Bioinformatic

The effect of yttrium and thorium on the oxidation behavior of Ni-Cr-Al alloys

The effect of quaternary additions of 0.5% Y, 0.5 and 1.0% Th to a base alloy of Ni-10CR-5Al on the oxidation behavior and mechanism was studied during oxidation in air over the range of 1000 to 1200 C. The presence of yttrium decreased the oxidation kinetics slightly, whereas, the addition of thorium caused a slight increase. Oxide scale adherence was markedly improved by the addition of the quaternary elements. Although a number of oxides formed on yttrium containing alloys, quantitative X-ray diffraction clearly showed that the rate-controlling step was the diffusion of aluminum through short circuit paths in a thin layer of alumina that formed parabolically with time. Although the scale adherence of the yttrium containing alloy was considerably better than the base alloys, spalling did occur that was attributed to the formation of the voluminous YAG particles which grew in a mushroom-like manner, lifting the protective scale off the subrate locally. The YAG particles formed primarily at grain boundaries in the substrate in which the yttrium originally existed as YNi9

In Vivo Detection of Residues Required for Ligand-Selective Activation of the S-Locus Receptor in Arabidopsis

SummaryThe self-incompatibility response of crucifers is a barrier to fertilization in which arrest of pollen tube development is mediated by allele-specific interactions between polymorphic receptors and ligands encoded by the S-locus haplotype. Activation of stigma-expressed S-locus receptor kinase (SRK) [1] by pollen coat-localized S-locus cysteine-rich (SCR) ligand [2–5] and the resulting rejection of pollen occurs only if receptor and ligand are encoded by the same S haplotype [4, 6–8]. To identify residues within the SRK extracellular domain (eSRK) that are required for its ligand-selective activation, we assayed chimeric receptors and receptor variants containing substitutions at polymorphic sites in Arabidopsis thaliana [9, 10]. We show that only a small number of the ∼100 polymorphic residues in eSRK are required for ligand-specific activation of self-incompatibility in vivo. These essential residues occur in two noncontiguous clusters located at equivalent positions in the two variants tested. They also correspond to sites showing elevated levels of substitutions in other SRKs, suggesting that these residues could define self-incompatibility specificity in most SRKs. The results demonstrate that the majority of eSRK residues that show signals of positive selection and previously surmised to function as specificity determinants are not essential for specificity in the SRK-SCR interaction

Cancer: Linking Powerhouses to Suicidal Bags.

Membrane-bound organelles are integrated into cellular networks and work together for a common goal: regulating cell metabolism, cell signaling pathways, cell fate, cellular maintenance, and pathogen defense. Many of these interactions are well established, but little is known about the interplay between mitochondria and lysosomes, and their deregulation in cancer. The present review focuses on the common signaling pathways of both organelles, as well as the processes in which they both physically interact, their changes under pathological conditions, and the impact on targeting those organelles for treating cancer

Pimavanserin Treatment Increases Plasma Brain-Derived Neurotrophic Factor Levels in Rats

BACKGROUND: Pimavanserin, a serotonin 5HT-2A receptor inverse agonist is the first-line, FDA-approved treatment of hallucinations and delusions associated with Parkinson\u27s Disease psychosis (PDP), which occurs in up to 50% of PD patients. The neurobiological mechanism underlying the therapeutic effectiveness of Pimavanserin in PDP remains unknown. Several earlier studies have shown that treatment with 5HT-2A antagonists and other drugs acting on the serotonergic system such as SSRIs increase Brain derived neurotrophic factor (BDNF) levels in rodents. BDNF is synthesized as the precursor proBDNF, that undergoes cleavage intra or extracellularly to produce a mature BDNF (mBDNF) protein. mBDNF is believed to play a key role in neuroplasticity and neurogenesis. The present study tested the hypothesis that treatment with Pimavanserin is associated with higher and sustained elevations of mBDNF. METHODS: Adult Sprague-Dawley male rats were treated with Pimavanserin, Fluoxetine or vehicle for 4 weeks (chronic) or 2 h (acute). BDNF levels were determined by enzyme-linked Immunosorbent assay (ELISA). RESULTS: We found significant increases in plasma mBDNF levels in rats following chronic Pimavanserin treatment, but not in Fluoxetine-treated rats. No significant changes in mBDNF levels were found in the prefrontal cortex or hippocampus following Pimavanserin or Fluoxetine treatment. CONCLUSION: These findings suggest that increase in mBDNF levels could be a contributing mechanism for the neuroprotective potential of Pimavanserin

Density Functional Theory Study of the Partial Oxidation of Methane to Methanol on Au and Pd Surfaces

The partial oxidation of methane to methanol has been a goal of heterogeneous catalysis for many years. Recent experimental investigations have shown how AuPd nanoparticle catalysts can give good selectivity to methanol with only limited total oxidation of CH4 using hydrogen peroxide as an oxidant in aqueous media. Interestingly, the use of colloidal nanoparticles alone, without a support material, leads to efficient use of the oxidant and the possibility of introducing oxygen from O2(g) into the CH3O2H primary product. This observation indicates that a radical mechanism is being initiated by H2O2 but then the oxygen addition step, catalyzed by these nanoparticles, can incorporate O2(ads). In this contribution, we use density functional theory (DFT) to study the elementary steps in the partial oxidation of methane to methanol using H2O2 as a radical initiator and molecular oxygen as an oxidant over the low index surfaces of Pd and Au. We are able to show that pure Pd nanoparticles are prone to oxidation by O2(g), whereas the competitive adsorption of water on Au surfaces limits the availability of O2(ads). Calculations with Au added to Pd or vice versa show that both effects can be alleviated by using mixed metal surfaces. This provides a rationalization of the need to use alloy nanoparticles experimentally, and the insights from these results will aid future catalyst development

The Goldberger-Treiman Discrepancy

The Golberger- Treiman discrepancy is related to the asymptotic behaviour of the pionic form factor of the nucleon obtained from baryonic QCD sum rules. The result is .015<=Delta_{GT}<=.022Comment: References updated and minor correction

Up and down quark masses from Finite Energy QCD sum rules to five loops

The up and down quark masses are determined from an optimized QCD Finite Energy Sum Rule (FESR) involving the correlator of axial-vector divergences, to five loop order in Perturbative QCD (PQCD), and including leading non-perturbative QCD and higher order quark mass corrections. This FESR is designed to reduce considerably the systematic uncertainties arising from the (unmeasured) hadronic resonance sector, which in this framework contributes less than 3-4% to the quark mass. This is achieved by introducing an integration kernel in the form of a second degree polynomial, restricted to vanish at the peak of the two lowest lying resonances. The driving hadronic contribution is then the pion pole, with parameters well known from experiment. The determination is done in the framework of Contour Improved Perturbation Theory (CIPT), which exhibits a very good convergence, leading to a remarkably stable result in the unusually wide window $s_0 = 1.0 - 4.0 {GeV}^2$, where $s_0$ is the radius of the integration contour in the complex energy (squared) plane. The results are: $m_u(Q= 2 {GeV}) = 2.9 \pm 0.2$ MeV, $m_d(Q= 2 {GeV}) = 5.3 \pm 0.4$ MeV, and $(m_u + m_d)/2 = 4.1 \pm 0.2$ Mev (at a scale Q=2 GeV).Comment: Additional references to lattice QCD results have been adde