Gauged vortices in a background

We discuss the statistical mechanics of a gas of gauged vortices in the canonical formalism. At critical self-coupling, and for low temperatures, it has been argued that the configuration space for vortex dynamics in each topological class of the abelian Higgs model approximately truncates to a finite-dimensional moduli space with a Kaehler structure. For the case where the vortices live on a 2-sphere, we explain how localisation formulas on the moduli spaces can be used to compute explicitly the partition function of the vortex gas interacting with a background potential. The coefficients of this analytic function provide geometrical data about the Kaehler structures, the simplest of which being their symplectic volume (computed previously by Manton using an alternative argument). We use the partition function to deduce simple results on the thermodynamics of the vortex system; in particular, the average height on the sphere is computed and provides an interesting effective picture of the ground state.Comment: Final version: 22 pages, LaTeX, 1 eps figur

Slow Schroedinger dynamics of gauged vortices

Multivortex dynamics in Manton's Schroedinger--Chern--Simons variant of the Landau-Ginzburg model of thin superconductors is studied within a moduli space approximation. It is shown that the reduced flow on M_N, the N vortex moduli space, is hamiltonian with respect to \omega_{L^2}, the L^2 Kaehler form on \M_N. A purely hamiltonian discussion of the conserved momenta associated with the euclidean symmetry of the model is given, and it is shown that the euclidean action on (M_N,\omega_{L^2}) is not hamiltonian. It is argued that the N=3 flow is integrable in the sense of Liouville. Asymptotic formulae for \omega_{L^2} and the reduced Hamiltonian for large intervortex separation are conjectured. Using these, a qualitative analysis of internal 3-vortex dynamics is given and a spectral stability analysis of certain rotating vortex polygons is performed. Comparison is made with the dynamics of classical fluid point vortices and geostrophic vortices.Comment: 22 pages, 2 figure

Superoxide reductase from Giardia intestinalis: structural characterization of the first sor from a eukaryotic organism shows an iron centre that is highly sensitive to photoreduction

Superoxide reductase (SOR), which is commonly found in prokaryotic organisms, affords protection from oxidative stress by reducing the superoxide anion to hydrogen peroxide. The reaction is catalyzed at the iron centre, which is highly conserved among the prokaryotic SORs structurally characterized to date. Reported here is the first structure of an SOR from a eukaryotic organism, the protozoan parasite Giardia intestinalis (GiSOR), which was solved at 2.0 Å resolution. By collecting several diffraction data sets at 100 K from the same flash-cooled protein crystal using synchrotron X-ray radiation, photoreduction of the iron centre was observed. Reduction was monitored using an online UV-visible microspectrophotometer, following the decay of the 647 nm absorption band characteristic of the iron site in the glutamate-bound, oxidized state. Similarly to other 1Fe-SORs structurally characterized to date, the enzyme displays a tetrameric quaternary-structure arrangement. As a distinctive feature, the N-terminal loop of the protein, containing the characteristic EKHxP motif, revealed an unusually high flexibility regardless of the iron redox state. At variance with previous evidence collected by X-ray crystallography and Fourier transform infrared spectroscopy of prokaryotic SORs, iron reduction did not lead to dissociation of glutamate from the catalytic metal or other structural changes; however, the glutamate ligand underwent X-ray-induced chemical changes, revealing high sensitivity of the GiSOR active site to X-ray radiation damage

Structural Basis of RICs Iron Donation for Iron-Sulfur Cluster Biogenesis

Funding Information: We thank L?gia S. Nobre and Joana M. Baptista for contribution at the initial stage of the work, and Cl?udia S. Freitas for technical support. We also thank Professor Miguel Teixeira of ITQB-NOVA for critical reading of the manuscript. We thank the XALOC staff and floor coordinators at the synchrotron ALBA for the YtfEM data collection. We acknowledge the ESRF for provision of synchrotron radiation facilities and we would like to thank Gianluca Santoni for assistance using the beamline ID30A-3 for the YtfEM-E159L data collection. We also thank Diamond Light Source for beamtime and the staff of beamline I04 for assistance with crystal testing and data collection of YtfEM-E125L. Funding. This work was financially supported by Funda??o para a Ci?ncia e Tecnologia (Portugal) through fellowship SFRH/BD/118545/2016 (LOS) and R&D unit LISBOA-01-0145-FEDER007660 (MostMicro) co-funded by FCT/MCTES and FEDER funds under the PT2020 Partnership Agreement. This work was partially supported by PPBI ? Portuguese Platform of BioImaging (PPBI-POCI-01-0145-FEDER-022122) co-funded by national funds from OE ? ?Or?amento de Estado? and by European funds from FEDER ? ?Fundo Europeu de Desenvolvimento Regional.? We also acknowledge funding from the European Union?s Horizon 2020 Research and Innovation Program under grant agreement no. 810856. Publisher Copyright: © Copyright © 2021 Silva, Matias, Romão and Saraiva. Copyright: Copyright 2021 Elsevier B.V., All rights reserved.Escherichia coli YtfE is a di-iron protein of the widespread Repair of Iron Centers proteins (RIC) family that has the capacity to donate iron, which is a crucial component of the biogenesis of the ubiquitous family of iron-sulfur proteins. In this work we identify in E. coli a previously unrecognized link between the YtfE protein and the major bacterial system for iron-sulfur cluster (ISC) assembly. We show that YtfE establishes protein-protein interactions with the scaffold IscU, where the transient cluster is formed, and the cysteine desulfurase IscS. Moreover, we found that promotion by YtfE of the formation of an Fe-S cluster in IscU requires two glutamates, E125 and E159 in YtfE. Both glutamates form part of the entrance of a protein channel in YtfE that links the di-iron center to the surface. In particular, E125 is crucial for the exit of iron, as a single mutation to leucine closes the channel rendering YtfE inactive for the build-up of Fe-S clusters. Hence, we provide evidence for the key role of RICs as bacterial iron donor proteins involved in the biogenesis of Fe-S clusters.publishersversionpublishe

Stabilized least squares finite element method for 2D and 3D convection-diffusion

In this study, a computational code has been developed based into Finite Elements Method in the version of LSFEM (Least Squares Finite Element Method). The numeric development of this method has as a main advantage, the obtaining of an always symmetrical and defined positive algebraic system, independently of the considered partial-differential equation system. The computational code was applied in the solution of two-dimensional and three-dimensional convection-diffusion problems, through domain discretization of structured meshes of quadratic elements. Obtained numerical results showed a good concordance with available results, showing the developed model validity9455

NUMERICAL SIMULATION OF INCOMPRESSIBLE FLOWS BY THE STABILIZED FINITE ELEMENT METHOD

The fast progress has been observed in the development of numerical and analytical techniques for solving convection-diffusion and fluid mechanics problems. Here, a numerical approach, based in Galerkin Finite Element Method with Finite Difference Method is presented for the solution of a class of non-linear transient convection-diffusion problems. Using the analytical solutions and the L2 and L∞ error norms, some applications is carried and valuated with the literature

Genomic diversity of Oenococcus oeni from different winemaking regions of Portugal

Oenococcus oeni is an alcohol-tolerant, acidophilic lactic acid bacterium that plays an important role in the elaboration of wine. It is often added as a starter culture to carry out malolactic conversion. Given the economic importance of this reaction, the taxonomic structure of this species has been studied in detail. In the present work, phenotypic and molecular approaches were used to identify 121 lactic acid bacteria strains isolated from the wines of three winemaking regions of Portugal. The strains were differentiated at the genomic level by M13-PCR fingerprinting. Twenty-seven genomic clusters represented by two or more isolates and 21 single-member clusters, based on an 85% similarity level, were recognized by hierarchic numerical analysis. M13-PCR fingerprinting patterns revealed a high level of intraspecific genomic diversity in O. oeni. Moreover, this diversity could be partitioned according to the geographical origin of the isolates. Thus, M13-PCR fingerprint analysis may be an appropriate methodology to study the O. oeni ecology of wine during malolactic fermentation as well as to trace new malolactic starter cultures and evaluate their dominance over the native microbiota

Insights into the role of three Endonuclease III enzymes for oxidative stress resistance in the extremely radiation resistant bacterium Deinococcus radiodurans

The extremely radiation and desiccation resistant bacterium Deinococcus radiodurans possesses three genes encoding Endonuclease III-like enzymes (DrEndoIII1, DrEndoIII2, DrEndoIII3). In vitro enzymatic activity measurements revealed that DrEndoIII2 is the main Endonuclease III in this organism, while DrEndoIII1 and 3 possess unusual and, so far, no detectable EndoIII activity, respectively. In order to understand the role of these enzymes at a cellular level, DrEndoIII knockout mutants were constructed and subjected to various oxidative stress related conditions. The results showed that the mutants are as resistant to ionizing and UV-C radiation as well as H2O2 exposure as the wild type. However, upon exposure to oxidative stress induced by methyl viologen, the knockout strains were more resistant than the wild type. The difference in resistance may be attributed to the observed upregulation of the EndoIII homologs gene expression upon addition of methyl viologen. In conclusion, our data suggest that all three EndoIII homologs are crucial for cell survival in stress conditions, since the knockout of one of the genes tend to be compensated for by overexpression of the genes encoding the other two