Axisymmetric smoothed particle hydrodynamics with self-gravity

The axisymmetric form of the hydrodynamic equations within the smoothed particle hydrodynamics (SPH) formalism is presented and checked using idealized scenarios taken from astrophysics (free fall collapse, implosion and further pulsation of a sun-like star), gas dynamics (wall heating problem, collision of two streams of gas) and inertial confinement fusion (ICF, -ablative implosion of a small capsule-). New material concerning the standard SPH formalism is given. That includes the numerical handling of those mass points which move close to the singularity axis, more accurate expressions for the artificial viscosity and the heat conduction term and an easy way to incorporate self-gravity in the simulations. The algorithm developed to compute gravity does not rely in any sort of grid, leading to a numerical scheme totally compatible with the lagrangian nature of the SPH equations.Comment: 17 pages, 10 figures, 1 Table. Accepted for publication in MNRA

Constraining deflagration models of Type Ia supernovae through intermediate-mass elements

The physical structure of a nuclear flame is a basic ingredient of the theory of Type Ia supernovae (SNIa). Assuming an exponential density reduction with several characteristic times we have followed the evolution of a planar nuclear flame in an expanding background from an initial density 6.6 10^7 g/cm3 down to 2 10^6 g/cm3. The total amount of synthesized intermediate-mass elements (IME), from silicon to calcium, was monitored during the calculation. We have made use of the computed mass fractions, X_IME, of these elements to give an estimation of the total amount of IME synthesized during the deflagration of a massive white dwarf. Using X_IME and adopting the usual hypothesis that turbulence decouples the effective burning velocity from the laminar flame speed, so that the relevant flame speed is actually the turbulent speed on the integral length-scale, we have built a simple geometrical approach to model the region where IME are thought to be produced. It turns out that a healthy production of IME involves the combination of not too short expansion times, t_c > 0.2 s, and high turbulent intensities. According to our results it could be difficult to produce much more than 0.2 solar masses of intermediate-mass elements within the deflagrative paradigma. The calculations also suggest that the mass of IME scales with the mass of Fe-peak elements, making it difficult to conciliate energetic explosions with low ejected nickel masses, as in the well observed SN1991bg or in SN1998de. Thus a large production of Si-peak elements, especially in combination with a low or a moderate production of iron, could be better addressed by either the delayed detonation route in standard Chandrasekhar-mass models or, perhaps, by the off-center helium detonation in the sub Chandrasekhar-mass scenario.Comment: 9 pages, 5 figures, 2 table

Climate Vulnerability and the Cost of Debt

We use indices from the Notre Dame Global Adaptation Initiative to investigate the impact of climate vulnerability on bond yields. Our methodology invokes panel ordinary least squares with robust standard errors and principal component analysis. The latter serves to address the multicollinearity between a set of vulnerability measures. We find that countries with higher exposure to climate vulnerability, such as the member countries of the V20 climate vulnerable forum, exhibit 1.174 percent higher cost of debt on average. This effect is significant after accounting for a set of macroeconomic controls. Specifically, we estimate the incremental debt cost due to higher climate vulnerability, for the V20 countries, to have exceeded USD 62 billion over the last ten years. In other words, for every ten dollars they pay in interest cost, they pay another dollar for being climate vulnerable. We also find that a measure of social readiness, which includes education and infrastructure, has a negative and significant effect on bond yields, implying that social and physical investments can mitigate climate risk related debt costs and help to stabilize the cost of debt for vulnerable countries

Spillover Events of Infection of Brown Hares (Lepus europaeus) with Rabbit Haemorrhagic Disease Type 2 Virus (RHDV2) Caused Sporadic Cases of an European Brown Hare Syndrome-Like Disease in Italy and Spain

Rabbit haemorrhagic disease virus (RHDV) is a lagovirus that can cause fatal hepatitis (rabbit haemorrhagic disease, RHD) with mortality of 80\u201390% in farmed and wild rabbits. Since 1986, RHDV has caused outbreaks in rabbits (Oryctolagus cuniculus) in Europe, but never in European brown hares (Lepus europaeus, EBH). In 2010, a new RHDV-related virus, called RHDV2, emerged in Europe, causing extended epidemics because it largely overcame the immunity to RHDV present in most rabbit populations. RHDV2 also was identified in Cape hare (Lepus capensis subsp. mediterraneus) and in Italian hare (Lepus corsicanus). Here, we describe two distinct incidents of RHDV2 infection in EBH that occurred in Italy (2012) and Spain (2014). The two RHDV2 strains caused macroscopic and microscopic lesions similar to European brown hare syndrome (EBHS) in hares, and they were genetically related to other RHDV2 strains in Europe. EBHs are common in Europe, often sharing habitat with rabbits. They likely have been exposed to high levels of RHDV2 during outbreaks in rabbits in recent years, yet only two incidents of RHDV2 in EBHs have been found in Italy and Spain, suggesting that EBHs are not a primary host. Instead, they may act as spillover hosts in situations when infection pressure is high and barriers between rabbits and hares are limited, resulting in occasional infections causing EBHS-like lesions. The serological survey of stocked hare sera taken from Italian and Spanish hare populations provided an understanding of naturally occurring RHDV2 infection in the field confirming its sporadic occurrence in EBH. Our findings increase the knowledge on distribution, host range and epidemiology of RHDV2

CCBuilder:An interactive web-based tool for building, designing and assessing coiled-coil protein assemblies

Motivation: The ability to accurately model protein structures at the atomistic level underpins efforts to understand protein folding, to engineer natural proteins predictably and to design proteins de novo . Homology-based methods are well established and produce impressive results. However, these are limited to structures presented by and resolved for natural proteins. Addressing this problem more widely and deriving truly ab initio models requires mathematical descriptions for protein folds; the means to decorate these with natural, engineered or de novo sequences; and methods to score the resulting models. Results: We present CCBuilder, a web-based application that tackles the problem for a defined but large class of protein structure, the α-helical coiled coils. CCBuilder generates coiled-coil backbones, builds side chains onto these frameworks and provides a range of metrics to measure the quality of the models. Its straightforward graphical user interface provides broad functionality that allows users to build and assess models, in which helix geometry, coiled-coil architecture and topology and protein sequence can be varied rapidly. We demonstrate the utility of CCBuilder by assembling models for 653 coiled-coil structures from the PDB, which cover >96% of the known coiled-coil types, and by generating models for rarer and de novo coiled-coil structures. Availability and implementation: CCBuilder is freely available, without registration, at http://coiledcoils.chm.bris.ac.uk/app/cc_builder

Polymorphic Signature of the Anti-inflammatory Activity of 2,2′- {[1,2-Phenylenebis(methylene)]bis(sulfanediyl)}bis(4,6- dimethylnicotinonitrile)

Weak noncovalent interactions are the basic forces in crystal engineering. Polymorphism in flexible molecules is very common, leading to the development of the crystals of same organic compounds with different medicinal and material properties. Crystallization of 2,2′- {[1,2-phenylenebis(methylene)]bis(sulfanediyl)}bis(4,6-dimethylnicotinonitrile) by evaporation at room temperature from ethyl acetate and hexane and from methanol and ethyl acetate gave stable polymorphs 4a and 4b, respectively, while in acetic acid, it gave metastable polymorph 4c. The polymorphic behavior of the compound has been visualized through singlecrystal X-ray and Hirshfeld analysis. These polymorphs are tested for anti-inflammatory activity via the complete Freund’s adjuvant-induced rat paw model, and compounds have exhibited moderate activities. Studies of docking in the catalytic site of cyclooxygenase-2 were used to identify potential anti-inflammatory lead compounds. These results suggest that the supramolecular aggregate structure, which is formed in solution, influences the solid state structure and the biological activity obtained upon crystallization

Mitochondrial ATP synthase: architecture, function and pathology

Human mitochondrial (mt) ATP synthase, or complex V consists of two functional domains: F1, situated in the mitochondrial matrix, and Fo, located in the inner mitochondrial membrane. Complex V uses the energy created by the proton electrochemical gradient to phosphorylate ADP to ATP. This review covers the architecture, function and assembly of complex V. The role of complex V di-and oligomerization and its relation with mitochondrial morphology is discussed. Finally, pathology related to complex V deficiency and current therapeutic strategies are highlighted. Despite the huge progress in this research field over the past decades, questions remain to be answered regarding the structure of subunits, the function of the rotary nanomotor at a molecular level, and the human complex V assembly process. The elucidation of more nuclear genetic defects will guide physio(patho)logical studies, paving the way for future therapeutic interventions

The metastasis-associated protein S100A4 exists in several charged variants suggesting the presence of posttranslational modifications

<p>Abstract</p> <p>Background</p> <p>S100A4 is a metastasis-associated protein which has been linked to multiple cellular events, and has been identified extracellularly, in the cytoplasm and in the nucleus of tumor cells; however, the biological implications of subcellular location are unknown. Associations between a variety of posttranslational protein modifications and altered biological functions of proteins are becoming increasingly evident. Identification and characterization of posttranslationally modified S100A4 variants could thus contribute to elucidating the mechanisms for the many cellular functions that have been reported for this protein, and might eventually lead to the identification of novel drugable targets.</p> <p>Methods</p> <p>S100A4 was immuoprecipitated from a panel of <it>in vitro </it>and <it>in vivo </it>sources using a monoclonal antibody and the samples were separated by 2D-PAGE. Gels were analyzed by western blot and silver staining, and subsequently, several of the observed spots were identified as S100A4 by the use of MALDI-TOF and MALDI-TOF/TOF.</p> <p>Results</p> <p>A characteristic pattern of spots was observed when S100A4 was separated by 2D-PAGE suggesting the presence of at least three charge variants. These charge variants were verified as S100A4 both by western immunoblotting and mass spectrometry, and almost identical patterns were observed in samples from different tissues and subcellular compartments. Interestingly, recombinant S100A4 displayed a similar pattern on 2D-PAGE, but with different quantitative distribution between the observed spots.</p> <p>Conclusion</p> <p>Endogenously expressed S100A4 were shown to exist in several charge variants, which indicates the presence of posttranslational modifications altering the net charge of the protein. The different variants were present in all subcellular compartments and tissues/cell lines examined, suggesting that the described charge variants is a universal phenomenon, and cannot explain the localization of S100A4 in different subcellular compartments. However, the identity of the specific posttranslational modification and its potential contribution to the many reported biological events induced by S100A4, are subject to further studies.</p