The All-Data-Based Evolutionary Hypothesis of Ciliated Protists with a Revised Classification of the Phylum Ciliophora (Eukaryota, Alveolata)

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Mitochondrial targeting adaptation of the hominoid-specific glutamate dehydrogenase driven by positive Darwinian selection

Many new gene copies emerged by gene duplication in hominoids, but little is known with respect to their functional evolution. Glutamate dehydrogenase (GLUD) is an enzyme central to the glutamate and energy metabolism of the cell. In addition to the single, GLUD-encoding gene present in all mammals (GLUD1), humans and apes acquired a second GLUD gene (GLUD2) through retroduplication of GLUD1, which codes for an enzyme with unique, potentially brain-adapted properties. Here we show that whereas the GLUD1 parental protein localizes to mitochondria and the cytoplasm, GLUD2 is specifically targeted to mitochondria. Using evolutionary analysis and resurrected ancestral protein variants, we demonstrate that the enhanced mitochondrial targeting specificity of GLUD2 is due to a single positively selected glutamic acid-to-lysine substitution, which was fixed in the N-terminal mitochondrial targeting sequence (MTS) of GLUD2 soon after the duplication event in the hominoid ancestor ~18–25 million years ago. This MTS substitution arose in parallel with two crucial adaptive amino acid changes in the enzyme and likely contributed to the functional adaptation of GLUD2 to the glutamate metabolism of the hominoid brain and other tissues. We suggest that rapid, selectively driven subcellular adaptation, as exemplified by GLUD2, represents a common route underlying the emergence of new gene functions

Measurement of K∗(892)0K^*(892)^0 and K0K^0 mesons in Al+Al collisions at 1.9AA GeV

New measurement of sub-threshold $K^*(892)^0$ and $K^0$ production is presented. The experimental data complete the measurement of strange particles produced in Al+Al collisions at 1.9$A$ GeV measured with the FOPI detector at SIS/GSI. The $K^*(892)^0$ / $K^0$ yield ratio is found to be $0.0315\pm 0.006 (\mathrm{stat.})\pm 0.012 (\mathrm{syst.})$ and is in good agreement with the UrQMD model prediction. These measurements provide information on in-medium cross section of $K^+$ - $\pi^-$ fusion which is the dominant process on sub-threshold $K^*(892)^0$ production.Comment: 5 pages, 4 figures, accepted for publication in Phys. Rev.

A novel determination of density, temperature and symmetry energy for nuclear multi-fragmentation through primary fragment yield reconstruction

For the first time primary hot isotope distributions are experimentally reconstructed in intermediate heavy ion collisions and used with antisymmetrized molecular dynamics (AMD) calculations to determine density, temperature and symmetry energy coefficient in a self-consistent manner. A kinematical focusing method is employed to reconstruct the primary hot fragment yield distributions for multifragmentation events observed in the reaction system $^{64}$Zn + $^{112}$Sn at 40 MeV/nucleon. The reconstructed yield distributions are in good agreement with the primary isotope distributions of AMD simulations. The experimentally extracted values of the symmetry energy coefficient relative to the temperature, $a_{sym}/T$, are compared with those of the AMD simulations with different density dependence of the symmetry energy term. The calculated $a_{sym}/T$ values changes according to the different interactions. By comparison of the experimental values of $a_{sym}/T$ with those of calculations, the density of the source at fragment formation was determined to be $\rho /\rho_{0} = (0.63 \pm 0.03 )$. Using this density, the symmetry energy coefficient and the temperature are determined in a self-consistent manner as $a_{sym} = (24.7 \pm 1.9) MeV$ and $T=(4.9 \pm 0.2)$ Me

Strange meson production in Al+Al collisions at 1.9A GeV

The production of K$^+$, K$^-$ and $\varphi$(1020) mesons is studied in Al+Al collisions at a beam energy of 1.9A GeV which is close or below the production threshold in NN reactions. Inverse slopes, anisotropy parameters, and total emission yields of K$^{\pm}$ mesons are obtained. A comparison of the ratio of kinetic energy distributions of K$^-$ and K$^+$ mesons to the HSD transport model calculations suggests that the inclusion of the in-medium modifications of kaon properties is necessary to reproduce the ratio. The inverse slope and total yield of $\phi$ mesons are deduced. The contribution to K$^-$ production from $\phi$ meson decays is found to be [17 $\pm$ 3 (stat) $^{+2}_{-7}$ (syst)] %. The results are in line with previous K$^{\pm}$ and $\phi$ data obtained for different colliding systems at similar incident beam energies.Comment: 16 pages, 11 figure

Electronic Structure of the Cuprate Superconducting and Pseudogap Phases from Spectroscopic Imaging STM

We survey the use of spectroscopic imaging STM to probe the electronic structure of underdoped cuprates. Two distinct classes of electronic states are observed in both the d-wave superconducting (dSC) and the pseudogap (PG) phases. The first class consists of the dispersive Bogoliubov quasiparticle excitations of a homogeneous d-wave superconductor, existing below a lower energy scale E=Delta0. We find that the Bogoliubov quasiparticle interference signatures of delocalized Cooper pairing are restricted to a k-space arc which terminates near the lines connecting k=\pm(pi/a0,0) to k=\pm(pi/a0). This arc shrinks continuously with decreasing hole density such that Luttinger's theorem could be satisfied if it represents the front side of a hole-pocket which is bounded behind by the lines between k=\pm(pi/a0,0) and k=\pm(0,pi/a0). In both phases the only broken symmetries detected for the |E|<Delta0 states are those of a d-wave superconductor. The second class of states occurs proximate to the pseudogap energy scale E=Delta1. Here the non-dispersive electronic structure breaks the expected 90o-rotational symmetry of electronic structure within each unit cell, at least down to 180o-rotational symmetry. This Q=0 electronic symmetry breaking was first detected as an electronic inequivalence at the two oxygen sites within each unit cell by using a measure of nematic (C2) symmetry. Incommensurate non-dispersive conductance modulations, locally breaking both rotational and translational symmetries, coexist with this intra-unit-cell electronic symmetry breaking at E=Delta1. Their characteristic wavevector Q is determined by the k-space points where Bogoliubov quasiparticle interference terminates and therefore changes continuously with doping. The distinct broken electronic symmetry states (Q=0 and finite Q) coexisting at E~Delta1 are found to be indistinguishable in the dSC and PG phases.Comment: 32 pages with 10 figure

Centrality dependence of subthreshold ϕ\phi meson production in Ni+Ni collisions at 1.9A GeV

We analysed the $\phi$ meson production in central Ni+Ni collisions at the beam kinetic energy of 1.93A GeV with the FOPI spectrometer and found the production probability per event of $[8.6 ~\pm~ 1.6 ~(\text{stat}) \pm 1.5 ~(\text{syst})] \times 10^{-4}$. This new data point allows for the first time to inspect the centrality dependence of the subthreshold $\phi$ meson production in heavy-ion collisions. The rise of $\phi$ meson multiplicity per event with mean number of participants can be parameterized by the power function with exponent $\alpha = 1.8 \pm 0.6$. The ratio of $\phi$ to $\text{K}^-$ production yields seems not to depend within the experimental uncertainties on the collision centrality, and the average of measured values was found to be $0.36 \pm 0.05$.Comment: 9 pages, 5 figure

Inter-cluster reactivity of Metallo-aromatic and anti-aromatic Compounds and Their Applications in Molecular Electronics: A Theoretical Investigation

Local reactivity descriptors such as the condensed local softness and Fukui function have been employed to investigate the inter-cluster reactivity of the metallo-aromatic (Al4Li- and Al4Na-) and anti-aromatic (Al4Li4 and Al4Na4) compounds. We use the concept of group softness and group Fukui function to study the strength of the nucleophilicity of the Al4 unit in these compounds. Our analysis shows that the trend of nucleophilicity of the Al4 unit in the above clusters is as follows; Al4Li- > Al4Na- > Al4Li4 > Al4Na 4 For the first time we have used the reactivity descriptors to show that these clusters can act as electron donating systems and thus can be used as a molecular cathode.Comment: 23 pages, 1 figure and 1 table of conten

Experimental Implementation of the Deutsch-Jozsa Algorithm for Three-Qubit Functions using Pure Coherent Molecular Superpositions

The Deutsch-Jozsa algorithm is experimentally demonstrated for three-qubit functions using pure coherent superpositions of Li$_{2}$ rovibrational eigenstates. The function's character, either constant or balanced, is evaluated by first imprinting the function, using a phase-shaped femtosecond pulse, on a coherent superposition of the molecular states, and then projecting the superposition onto an ionic final state, using a second femtosecond pulse at a specific time delay

Non-Parametric Approximations for Anisotropy Estimation in Two-dimensional Differentiable Gaussian Random Fields

Spatially referenced data often have autocovariance functions with elliptical isolevel contours, a property known as geometric anisotropy. The anisotropy parameters include the tilt of the ellipse (orientation angle) with respect to a reference axis and the aspect ratio of the principal correlation lengths. Since these parameters are unknown a priori, sample estimates are needed to define suitable spatial models for the interpolation of incomplete data. The distribution of the anisotropy statistics is determined by a non-Gaussian sampling joint probability density. By means of analytical calculations, we derive an explicit expression for the joint probability density function of the anisotropy statistics for Gaussian, stationary and differentiable random fields. Based on this expression, we obtain an approximate joint density which we use to formulate a statistical test for isotropy. The approximate joint density is independent of the autocovariance function and provides conservative probability and confidence regions for the anisotropy parameters. We validate the theoretical analysis by means of simulations using synthetic data, and we illustrate the detection of anisotropy changes with a case study involving background radiation exposure data. The approximate joint density provides (i) a stand-alone approximate estimate of the anisotropy statistics distribution (ii) informed initial values for maximum likelihood estimation, and (iii) a useful prior for Bayesian anisotropy inference.Comment: 39 pages; 8 figure