Alanine scanning mutagenesis of a high-affinity nitrate transporter highlights the requirement for glycine and asparagine residues in the two nitrate signature motifs

Common to all of the nitrate nitrite porter family are two conserved motifs in transmembrane helices 5 and 11 termed NS (nitrate signature) 1 and NS2. Although perfectly conserved substrate-interacting arginine residues have been described in transmembrane helices 2 and 8, the role of NSs has not been investigated. In the present study, a combination of structural modelling of NrtA (nitrate transporter from Aspergillus nidulans) with alanine scanning mutagenesis of residues within and around the NSs has been used to shed light on the probable role of conserved residues in the NSs. Models show that Asn 168 in NS1 and Asn 459 in NS2 are positioned approximately midway within the protein at the central pivot point in close proximity to the substrate-binding residues Arg 368 and Arg 87 respectively, which lie offset from the pivot point towards the cytoplasmic face. The Asn 168 /Arg 368 and Asn 459 /Arg 87 residue pairs are relatively widely separated on opposite sides of the probable substrate translocation pore. The results of the present study demonstrate the critical structural contribution of several glycine residues in each NS at sites of close helix packing. Given the relative locations of Asn 168 /Arg 368 and Asn 459 /Arg 87 pairs, the validity of the models and possible role of the NSs together with the substrate-binding arginine residues are discusse

Thermal activation between Landau levels in the organic superconductor β′′\beta''-(BEDT-TTF)2_{2}SF5_{5}CH2_{2}CF2_{2}SO3_{3}

We show that Shubnikov-de Haas oscillations in the interlayer resistivity of the organic superconductor $\beta''$-(BEDT-TTF)$_{2}$SF$_{5}$ CH$_{2}$CF$_{2}$SO$_{3}$ become very pronounced in magnetic fields $\sim$~60~T. The conductivity minima exhibit thermally-activated behaviour that can be explained simply by the presence of a Landau gap, with the quasi-one-dimensional Fermi surface sheets contributing negligibly to the conductivity. This observation, together with complete suppression of chemical potential oscillations, is consistent with an incommensurate nesting instability of the quasi-one-dimensional sheets.Comment: 6 pages, 4 figure

A simply connected surface of general type with p_g=0 and K^2=2

In this paper we construct a simply connected, minimal, complex surface of general type with p_g=0 and K^2=2 using a rational blow-down surgery and Q-Gorenstein smoothing theory.Comment: 19 pages, 6 figures. To appear in Inventiones Mathematica

Defect segregation facilitates oxygen transport at fluorite UO₂ grain boundaries

Data support article accepted for publication in Philosophical Transactions A. Data includes inputs and outputs for molecular dynamics simulations. Where impractical simulations can be rerun from the inputs provided

Modeling the Halpha line emission around classical T Tauri stars using magnetospheric accretion and disk wind models

Spectral observations of classical T Tauri stars show a wide range of line profiles, many of which reveal signs of matter inflow and outflow. Halpha is the most commonly observed line profile due to its intensity, and it is highly dependent on the characteristics of the surrounding environment of these stars. Our aim is to analyze how the Halpha line profile is affected by the various parameters of our model which contains both the magnetospheric and disk wind contributions to the Halpha flux. We used a dipolar axisymmetric stellar magnetic field to model the stellar magnetosphere and a modified Blandford & Payne model was used in our disk wind region. A three-level atom with continuum was used to calculate the required Hydrogen level populations. We use the Sobolev approximation and a ray-by-ray method to calculate the integrated line profile. Through an extensive study of the model parameter space, we have investigated the contribution of many of the model parameters on the calculated line profiles. Our results show that the Halpha line is strongly dependent on the densities and temperatures inside the magnetosphere and the disk wind region. The bulk of the flux comes, most of the time, from the magnetospheric component for standard classical T Tauri stars parameters, but the disk wind contribution becomes more important as the mass accretion rate, the temperatures and densities inside the disk wind increase. We have also found that most of the disk wind contribution to the Halpha line is emitted at the innermost region of the disk wind. Models that take into consideration both inflow and outflow of matter are a necessity to fully understand and describe classical T Tauri stars.Comment: 15 pages, 9 figures, accepted for publication in Astronomy & Astrophysics. Revised version with English correction

Arginine deprivation alters microglia polarity and synergises with radiation to eradicate non arginine auxotrophic glioblastoma tumors

New approaches for the management of glioblastoma (GBM) are an urgent and unmet clinical need. Here, we illustrate that the efficacy of radiotherapy for GBM is strikingly potentiated by concomitant therapy with the arginine depleting agent ADI-PEG20 in a non-arginine auxotrophic cellular background (Arginine Succinate Synthetase 1 positive). Moreover, this combination led to durable and complete radiological and pathological response with extended disease-free survival in an orthotopic immune competent model of GBM with no significant toxicity. ADI-PEG20 not only enhances the cellular sensitivity of Arginine succinate synthetase 1 positive GBM to ionising radiation by elevated production of nitric oxide (NO) and hence generation of cytotoxic peroxynitrites, but also promotes glioma-associated macrophages/microglia infiltration into tumors and turns their classical anti-inflammatory (pro-tumor) phenotype into a pro-inflammatory (anti-tumor) phenotype. Our results provide an effective, well-tolerated and simple strategy to improve GBM treatment which merits consideration for early evaluation in clinical trials

Single-stranded DNA catenation mediated by human EVL and a type I topoisomerase

The human Ena/Vasp-like (EVL) protein is considered to be a bifunctional protein, involved in both actin remodeling and homologous recombination. In the present study, we found that human EVL forms heat-stable multimers of circular single-stranded DNA (ssDNA) molecules in the presence of a type I topoisomerase in vitro. An electron microscopic analysis revealed that the heat-stable ssDNA multimers formed by EVL and topoisomerase were ssDNA catemers. The ssDNA catenation did not occur when either EVL or topoisomerase was omitted from the reaction mixture. A deletion analysis revealed that the ssDNA catenation completely depended on the annealing activity of EVL. Human EVL was captured from a human cell extract by TOPO IIIα-conjugated beads, and the interaction between EVL and TOPO IIIα was confirmed by a surface plasmon resonance analysis. Purified TOPO IIIα catalyzed the ssDNA catenation with EVL as efficiently as the Escherichia coli topoisomerase I. Since the ssDNA cutting and rejoining reactions, which are the sub-steps of ssDNA catenation, may be an essential process in homologous recombination, EVL and TOPO IIIα may function in the processing of DNA intermediates formed during homologous recombination

Biochemical analysis of the N-terminal domain of human RAD54B

The human RAD54B protein is a paralog of the RAD54 protein, which plays important roles in homologous recombination. RAD54B contains an N-terminal region outside the SWI2/SNF2 domain that shares less conservation with the corresponding region in RAD54. The biochemical roles of this region of RAD54B are not known, although the corresponding region in RAD54 is known to physically interact with RAD51. In the present study, we have biochemically characterized an N-terminal fragment of RAD54B, consisting of amino acid residues 26–225 (RAD54B26–225). This fragment formed a stable dimer in solution and bound to branched DNA structures. RAD54B26–225 also interacted with DMC1 in both the presence and absence of DNA. Ten DMC1 segments spanning the entire region of the DMC1 sequence were prepared, and two segments, containing amino acid residues 153–214 and 296–340, were found to directly bind to the N-terminal domain of RAD54B. A structural alignment of DMC1 with the Methanococcus voltae RadA protein, a homolog of DMC1 in the helical filament form, indicated that these RAD54B-binding sites are located near the ATP-binding site at the monomer–monomer interface in the DMC1 helical filament. Thus, RAD54B binding may affect the quaternary structure of DMC1. These observations suggest that the N-terminal domain of RAD54B plays multiple roles of in homologous recombination

Inhomogeneous Superconductivity in Condensed Matter and QCD

Inhomogeneous superconductivity arises when the species participating in the pairing phenomenon have different Fermi surfaces with a large enough separation. In these conditions it could be more favorable for each of the pairing fermions to stay close to its Fermi surface and, differently from the usual BCS state, for the Cooper pair to have a non zero total momentum. For this reason in this state the gap varies in space, the ground state is inhomogeneous and a crystalline structure might be formed. This situation was considered for the first time by Fulde, Ferrell, Larkin and Ovchinnikov, and the corresponding state is called LOFF. The spontaneous breaking of the space symmetries in the vacuum state is a characteristic feature of this phase and is associated to the presence of long wave-length excitations of zero mass. The situation described here is of interest both in solid state and in elementary particle physics, in particular in Quantum Chromo-Dynamics at high density and small temperature. In this review we present the theoretical approach to the LOFF state and its phenomenological applications using the language of the effective field theories.Comment: RevTex, 83 pages, 26 figures. Submitted to Review of Modern Physic

Induction of oxidative stress and lipid peroxidation in rats chronically exposed to cypermethrin through dermal application

Present study was undertaken to study the effect of cypermethrin on oxidative stress after chronic dermal application. The insecticide was applied dermally at 50 mg/kg body weight in different groups of Wistar rats of either sex weighing 150~200 g. Significant (p < 0.05) increase in catalase activity was observed after 30 days of exposure. However, the superoxide dismutase activity declined significantly after 60 days of exposure. The activity of glutathione peroxidase and blood glutathione levels declined significantly (p < 0.05) after 30 days of cypermethrin dermal application. However, the activity of glutathione S-transferase increased significantly (p < 0.05) in all groups after 60 days of dermal exposure. Significant increase in lipid peroxidation was observed from 30 days onwards and reached a peak after 120 days of application