Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection

<p>Abstract</p> <p>Background</p> <p>The pentatricopeptide repeat (PPR) is a degenerate 35 amino acid motif that occurs in multiple tandem copies in members of a recently recognized eukaryotic gene family. Most analyzed eukaryotic genomes contain only a small number of PPR genes, but in plants the family is greatly expanded. The factors that underlie the expansion of this gene family in plants are not as yet understood.</p> <p>Results</p> <p>We show that the location of PPR genes is highly variable in comparisons between orthologous, closely related, and otherwise co-linear chromosomal regions of the <it>Brassica rapa </it>or radish and <it>Arabidopsis thaliana</it>. This observation also pertains to paralogous duplicated segments of the genomes of <it>Arabidopsis thaliana </it>and <it>Brassica rapa</it>. In addition, we show that PPR genes that seem closely linearly aligned in these comparisons are not generally found to be closely related to one another at the nucleotide and amino acid sequence level. We observe a relatively high level of non-synonomous vs synonomous changes among a group tandemly repeated radish PPR genes, suggesting that these, and possibly other PPR genes, are subject to diversifying selection. We also show that a duplicated region of the <it>Arabidopsis </it>genome possesses a relatively high density of PPR genes showing high similarity to restorers of fertility of cytoplasmic male sterile (CMS) systems of petunia, radish and rice. The PPR genes in these regions, together with the restorer genes, are more highly similar to one another, in sequence as well as in structure, than to other PPR genes, even within the same sub-family.</p> <p>Conclusion</p> <p>Our results suggest are consistent with a model in which at least some PPR genes undergo a "birth and death" process that involves transposition to unrelated chromosomal sites. PPR genes hold certain features in common with disease resistance genes (R genes), and their "nomadic" character suggests that their evolutionary expansion in plants may have involved novel molecular processes and selective pressures.</p

Neurobehavioral Symptoms in Mild Primary Hyperparathyroidism: Related to Hypercalcemia but not Improved by Parathyroidectomy

The neurobehavioral symptomatology of severe primary hyperparathyroidism (PHPT) has been thoroughly described. Less is known about more mild cases. We evaluated 34 patients with mild PHPT and followed 19 for an average of six months. Of those cases followed, ten had parathyroidectomy (PTX). Patients with no neurobehavioral abnormalities had the lowest serum calcium levels (10.9 ± 0.88 mg/dL), patients with signs of affective disorder had intermediate levels (11.25 ± 0.66 mg/dL), and patients with signs of cerebral dysfunction had the highest levels (12.17 ± 1.17 mg/dL). Serum calcium significantly correlated with motor speed, psychomotor speed, fluid intelligence, and short term memory. However, in the follow-up of patients, PTX seemed to have no effect on their behavior Serum calcium correlates with both type and severity of the neurobehavioral abnormalities found in mild PHPT. However, most of the evidence indicates that PTX does not produce any improvement of these abnormalities, even when the hypercalcemia elevation is corrected

Statistical Entropy of Schwarzschild Black Strings and Black Holes

The statistical entropy of a Schwarzschild black string in five dimensions is obtained by counting the black string states which form a representation of the near-horizon conformal symmetry with a central charge. The statistical entropy of the string agrees with its Bekenstein-Hawking entropy as well as that of the Schwarzschild black hole in four dimensions. The choice of the string length which gives the Virasoro algebra also reproduces the precise value of the Bekenstein-Hawking entropy and lies inside the stability bound of the string.Comment: 8 pages, Late

Isolation and Phase-Space Energization Analysis of the Instabilities in Collisionless Shocks

We analyze the generation of kinetic instabilities and their effect on the energization of ions in non-relativistic, oblique collisionless shocks using a 3D-3V simulation by $\texttt{dHybridR}$, a hybrid particle-in-cell code. At sufficiently high Mach number, quasi-perpendicular and oblique shocks can experience rippling of the shock surface caused by kinetic instabilities arising from free energy in the ion velocity distribution due to the combination of the incoming ion beam and the population of ions reflected at the shock front. To understand the role of the ripple on particle energization, we devise the new instability isolation method to identify the unstable modes underlying the ripple and interpret the results in terms of the governing kinetic instability. We generate velocity-space signatures using the field-particle correlation technique to look at energy transfer in phase space from the isolated instability driving the shock ripple, providing a viewpoint on the different dynamics of distinct populations of ions in phase space. We generate velocity-space signatures of the energy transfer in phase space of the isolated instability driving the shock ripple using the field-particle correlation technique. Together, the field-particle correlation technique and our new instability isolation method provide a unique viewpoint on the different dynamics of distinct populations of ions in phase space and allow us to completely characterize the energetics of the collisionless shock under investigation.Comment: 32 pages, 14 figures, accepted by the Journal of Plasma Physic

Langevin Simulation of Thermally Activated Magnetization Reversal in Nanoscale Pillars

Numerical solutions of the Landau-Lifshitz-Gilbert micromagnetic model incorporating thermal fluctuations and dipole-dipole interactions (calculated by the Fast Multipole Method) are presented for systems composed of nanoscale iron pillars of dimension 9 nm x 9 nm x 150 nm. Hysteresis loops generated under sinusoidally varying fields are obtained, while the coercive field is estimated to be 1979 $\pm$ 14 Oe using linear field sweeps at T=0 K. Thermal effects are essential to the relaxation of magnetization trapped in a metastable orientation, such as happens after a rapid reversal of an external magnetic field less than the coercive value. The distribution of switching times is compared to a simple analytic theory that describes reversal with nucleation at the ends of the nanomagnets. Results are also presented for arrays of nanomagnets oriented perpendicular to a flat substrate. Even at a separation of 300 nm, where the field from neighboring pillars is only $\sim$ 1 Oe, the interactions have a significant effect on the switching of the magnets.Comment: 19 pages RevTeX, including 12 figures, clarified discussion of numerical technique

Non-abelian magnetic black strings versus black holes

We present $d+1-$dimensional pure magnetic Yang-Mills (YM) black strings (or $1-$branes) induced by the $d-$dimensional Einstein-Yang-Mills-Dilaton black holes. Born-Infeld version of the YM field makes our starting point which goes to the standard YM field through a limiting procedure. The lifting from black holes to black strings, (with less number of fields) is by adding an extra, compact coordinate. This amounts to the change of horizon topology from $S^{d-2}$ to a product structure. Our black string in $5-$dimensions is a rather special one, with uniform Hawking temperature and non-asymptotically flat structure. As the YM charge becomes large the string gets thinner to tend into a breaking point and transform into a $4-$% dimensional black hole.Comment: 5 pages no figure; Final version to appear in EPJ

Numerical Confirmation of Late-time t^{1/2} Growth in Three-dimensional Phase Ordering

Results for the late-time regime of phase ordering in three dimensions are reported, based on numerical integration of the time-dependent Ginzburg-Landau equation with nonconserved order parameter at zero temperature. For very large systems ($700^3$) at late times, $t \ge 150,$ the characteristic length grows as a power law, $R(t) \sim t^n$, with the measured $n$ in agreement with the theoretically expected result $n=1/2$ to within statistical errors. In this time regime $R(t)$ is found to be in excellent agreement with the analytical result of Ohta, Jasnow, and Kawasaki [Phys. Rev. Lett. {\bf 49}, 1223 (1982)]. At early times, good agreement is found between the simulations and the linearized theory with corrections due to the lattice anisotropy.Comment: Substantially revised and enlarged, submitted to PR