A retrotransposon-inserted VvmybA1a allele has been spread among cultivars of Vitis vinifera but not North American or East Asian Vitis species

Research Note

Depth-dependent ordering, two-length-scale phenomena and crossover behavior in a crystal featuring a skin-layer with defects

Structural defects in a crystal are responsible for the "two length-scale" behavior, in which a sharp central peak is superimposed over a broad peak in critical diffuse X-ray scattering. We have previously measured the scaling behavior of the central peak by scattering from a near-surface region of a V2H crystal, which has a first-order transition in the bulk. As the temperature is lowered toward the critical temperature, a crossover in critical behavior is seen, with the temperature range nearest to the critical point being characterized by mean field exponents. Near the transition, a small two-phase coexistence region is observed. The values of transition and crossover temperatures decay with depth. An explanation of these experimental results is here proposed by means of a theory in which edge dislocations in the near-surface region occur in walls oriented in the two directions normal to the surface. The strain caused by the dislocation lines causes the ordering in the crystal to occur as growth of roughly cylindrically shaped regions. After the regions have reached a certain size, the crossover in the critical behavior occurs, and mean field behavior prevails. At a still lower temperature, the rest of the material between the cylindrical regions orders via a weak first-order transition.Comment: 12 pages, 8 figure

Oscillator neural network model with distributed native frequencies

We study associative memory of an oscillator neural network with distributed native frequencies. The model is based on the use of the Hebb learning rule with random patterns ($\xi_i^{\mu}=\pm 1$), and the distribution function of native frequencies is assumed to be symmetric with respect to its average. Although the system with an extensive number of stored patterns is not allowed to get entirely synchronized, long time behaviors of the macroscopic order parameters describing partial synchronization phenomena can be obtained by discarding the contribution from the desynchronized part of the system. The oscillator network is shown to work as associative memory accompanied by synchronized oscillations. A phase diagram representing properties of memory retrieval is presented in terms of the parameters characterizing the native frequency distribution. Our analytical calculations based on the self-consistent signal-to-noise analysis are shown to be in excellent agreement with numerical simulations, confirming the validity of our theoretical treatment.Comment: 9 pages, revtex, 6 postscript figures, to be published in J. Phys.

SPINT2 deregulation in prostate carcinoma

SPINT2 is a tumor suppressor gene that inhibits proteases implicated in cancer progression, like HGFA, hepsin and matriptase. Loss of SPINT2 expression in tumors has been associated with gene promoter hypermethylation; however, little is known about the mechanisms of SPINT2 deregulation in prostate cancer (PCa). We aimed to analyze SPINT2 expression levels and understand the possible regulation by SPINT2 promoter hypermethylation in PCa. In a cohort of 57 cases including non-neoplastic and PCa tissues, SPINT2 expression and promoter methylation was analyzed by immunohistochemistry and methylation-specific PCR, respectively. Methylation status of the SPINT2 promoter was also evaluated by bisulfite sequencing and 5-aza-2’-deoxycytidine treatment. Oncomine and TCGA databases were used to perform in silico PCa analysis of SPINT2 mRNA and methylation levels. A reduction in SPINT2 expression levels from nonneoplastic to PCa tissues was observed; however, none of the cases exhibited SPINT2 promoter methylation. Both bisulfite sequencing and 5-aza demonstrated that SPINT2 promoter is not methylated in PCa cells. Bioinformatics approaches did not show downregulation of SPINT2 at the mRNA level and, in corroboration with our results, SPINT2 promoter region is reported to be unmethylated. Our study suggests an involvement of SPINT2 in PCa tumorigenesis, probably in association with a post-translational regulation of SPINT2.The authors disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This study was supported by the ICVS internal research funds of participating authors and by FCT project, ref. PTDC/SAUONC/115513/2009. F.P. received fellowship from the FCT, ref. SFRH/BD/81369/2011 and M.VP from the ON.2 SR&TD Integrated Program (N-01-01-01-24-01-07), ref. UMINHO/ BPD/36/2013

Universal neural field computation

Turing machines and G\"odel numbers are important pillars of the theory of computation. Thus, any computational architecture needs to show how it could relate to Turing machines and how stable implementations of Turing computation are possible. In this chapter, we implement universal Turing computation in a neural field environment. To this end, we employ the canonical symbologram representation of a Turing machine obtained from a G\"odel encoding of its symbolic repertoire and generalized shifts. The resulting nonlinear dynamical automaton (NDA) is a piecewise affine-linear map acting on the unit square that is partitioned into rectangular domains. Instead of looking at point dynamics in phase space, we then consider functional dynamics of probability distributions functions (p.d.f.s) over phase space. This is generally described by a Frobenius-Perron integral transformation that can be regarded as a neural field equation over the unit square as feature space of a dynamic field theory (DFT). Solving the Frobenius-Perron equation yields that uniform p.d.f.s with rectangular support are mapped onto uniform p.d.f.s with rectangular support, again. We call the resulting representation \emph{dynamic field automaton}.Comment: 21 pages; 6 figures. arXiv admin note: text overlap with arXiv:1204.546

First principles simulations of liquid Fe-S under Earth's core conditions

First principles electronic structure calculations, based upon density functional theory within the generalized gradient approximation and ultra-soft Vanderbilt pseudopotentials, have been used to simulate a liquid alloy of iron and sulfur at Earth's core conditions. We have used a sulfur concentration of $\approx 12$wt, in line with the maximum recent estimates of the sulfur abundance in the Earth's outer core. The analysis of the structural, dynamical and electronic structure properties has been used to report on the effect of the sulfur impurities on the behavior of the liquid. Although pure sulfur is known to form chains in the liquid phase, we have not found any tendency towards polymerization in our liquid simulation. Rather, a net S-S repulsion is evident, and we propose an explanation for this effect in terms of the electronic structure. The inspection of the dynamical properties of the system suggests that the sulfur impurities have a negligible effect on the viscosity of Earth's liquid core.Comment: 24 pages (including 8 figures

Scaling Limits for Internal Aggregation Models with Multiple Sources

We study the scaling limits of three different aggregation models on Z^d: internal DLA, in which particles perform random walks until reaching an unoccupied site; the rotor-router model, in which particles perform deterministic analogues of random walks; and the divisible sandpile, in which each site distributes its excess mass equally among its neighbors. As the lattice spacing tends to zero, all three models are found to have the same scaling limit, which we describe as the solution to a certain PDE free boundary problem in R^d. In particular, internal DLA has a deterministic scaling limit. We find that the scaling limits are quadrature domains, which have arisen independently in many fields such as potential theory and fluid dynamics. Our results apply both to the case of multiple point sources and to the Diaconis-Fulton smash sum of domains.Comment: 74 pages, 4 figures, to appear in J. d'Analyse Math. Main changes in v2: added "least action principle" (Lemma 3.2); small corrections in section 4, and corrected the proof of Lemma 5.3 (Lemma 5.4 in the new version); expanded section 6.

Direct Sensing of Endothelial Oxidants by Vascular Endothelial Growth Factor Receptor-2 and c-Src

BACKGROUND: ADPH oxidase-derived reactive oxygen species (ROS) play important roles in redox homeostasis and signal transduction in endothelial cells (ECs). We previously demonstrated that c-Src plays a key role in VEGF-induced, ROS-dependent selective activation of PI3K-Akt but not PLCγ-1-ERK1/2 signaling pathways. The aim of the present study was to understand how VEGFR-2-c-Src signaling axis 'senses' NADPH oxidase-derived ROS levels and couples VEGF activation of c-Src to the redox state of ECs. METHODOLOGY/PRINCIPAL FINDINGS: Using biotinylated probe that detects oxidation of cysteine thiol (cys-OH) in intracellular proteins, we demonstrate that VEGF induced oxidative modification in c-Src and VEGFR-2, and that reduction in ROS levels using siRNA against p47(phox) subunit of Rac1-dependent NADPH oxidase inhibited this phenomenon. Co-immunoprecipitation studies using human coronary artery ECs (HCAEC) showed that VEGF-induced ROS-dependent interaction between VEGFR-2 and c-Src correlated with their thiol oxidation status. Immunofluorescence studies using antibodies against internalized VEGFR-2 and c-Src demonstrated that VEGF-induced subcellular co-localization of these tyrosine kinases were also dependent on NADPH oxidsase-derived ROS. CONCLUSION/SIGNIFICANCE: These results demonstrate that VEGF induces cysteine oxidation in VEGFR-2 and c-Src in an NADPH oxidase-derived ROS-dependent manner, suggesting that VEGFR-2 and c-Src can 'sense' redox levels in ECs. The data also suggest that thiol oxidation status of VEGFR-2 and c-Src correlates with their ability to physically interact with each other and c-Src activation. Taken together, these findings suggest that prior to activating downstream c-Src-PI3K-Akt signaling pathway, VEGFR-2-c-Src axis requires an NADPH oxidase-derived ROS threshold in ECs

Mouse models for preeclampsia: disruption of redox-regulated signaling

The concept that oxidative stress contributes to the development of human preeclampsia has never been tested in genetically-defined animal models. Homozygous deletion of catechol-Omethyl transferase (Comt-/-) in pregnant mice leads to human preeclampsia-like symptoms (high blood pressure, albuminurea and preterm birth) resulting from extensive vasculo-endothelial pathology, primarily at the utero-fetal interface where maternal cardiac output is dramatically increased during pregnancy. Comt converts estradiol to 2-methoxyestradiol 2 (2ME2) which counters angiogenesis by depleting hypoxia inducible factor-1 alpha (HIF-1 alpha) at late pregnancy. We propose that in wild type (Comt++) pregnant mice, 2ME2 destabilizes HIF-1 alpha by inhibiting mitochondrial superoxide dismutase (MnSOD). Thus, 2ME2 acts as a pro-oxidant, disrupting redox-regulated signaling which blocks angiogenesis in wild type (WT) animals in physiological pregnancy. Further, we suggest that a lack of this inhibition under normoxic conditions in mutant animals (Comt-/-) stabilises HIF-1 alpha by inactivating prolyl hydroxlases (PHD). We predict that a lack of inhibition of MnSOD, leading to persistent accumulation of HIF-1 alpha, would trigger inflammatory infiltration and endothelial damage in mutant animals. Critical tests of this hypothesis would be to recreate preeclampsia symptoms by inducing oxidative stress in WT animals or to ameliorate by treating mutant mice with Mn-SOD-catalase mimetics or activators of PHD

A broad distribution of the alternative oxidase in microsporidian parasites

Microsporidia are a group of obligate intracellular parasitic eukaryotes that were considered to be amitochondriate until the recent discovery of highly reduced mitochondrial organelles called mitosomes. Analysis of the complete genome of Encephalitozoon cuniculi revealed a highly reduced set of proteins in the organelle, mostly related to the assembly of ironsulphur clusters. Oxidative phosphorylation and the Krebs cycle proteins were absent, in keeping with the notion that the microsporidia and their mitosomes are anaerobic, as is the case for other mitosome bearing eukaryotes, such as Giardia. Here we provide evidence opening the possibility that mitosomes in a number of microsporidian lineages are not completely anaerobic. Specifically, we have identified and characterized a gene encoding the alternative oxidase (AOX), a typically mitochondrial terminal oxidase in eukaryotes, in the genomes of several distantly related microsporidian species, even though this gene is absent from the complete genome of E. cuniculi. In order to confirm that these genes encode functional proteins, AOX genes from both A. locustae and T. hominis were over-expressed in E. coli and AOX activity measured spectrophotometrically using ubiquinol-1 (UQ-1) as substrate. Both A. locustae and T. hominis AOX proteins reduced UQ-1 in a cyanide and antimycin-resistant manner that was sensitive to ascofuranone, a potent inhibitor of the trypanosomal AOX. The physiological role of AOX microsporidia may be to reoxidise reducing equivalents produced by glycolysis, in a manner comparable to that observed in trypanosome