Exploring the biochemistry at the extracellular redox frontier of bacterial mineral Fe(III) respiration

Many species of the bacterial Shewanella genus are notable for their ability to respire in anoxic environments utilizing insoluble minerals of Fe(III) and Mn(IV) as extracellular electron acceptors. In Shewanella oneidensis, the process is dependent on the decahaem electron-transport proteins that lie at the extracellular face of the outer membrane where they can contact the insoluble mineral substrates. These extracellular proteins are charged with electrons provided by an inter-membrane electron-transfer pathway that links the extracellular face of the outer membrane with the inner cytoplasmic membrane and thereby intracellular electron sources. In the present paper, we consider the common structural features of two of these outer-membrane decahaem cytochromes, MtrC and MtrF, and bring this together with biochemical, spectroscopic and voltammetric data to identify common and distinct properties of these prototypical members of different clades of the outer-membrane decahaem cytochrome superfamily

Varieties of vacua in classical supersymmetric gauge theories

We give a simple description of the classical moduli space of vacua for supersymmetric gauge theories with or without a superpotential. The key ingredient in our analysis is the observation that the lagrangian is invariant under the action of the complexified gauge group \Gc. From this point of view the usual $D$-flatness conditions are an artifact of Wess--Zumino gauge. By using a gauge that preserves \Gc invariance we show that every constant matter field configuration that extremizes the superpotential is \Gc gauge-equivalent (in a sense that we make precise) to a unique classical vacuum. This result is used to prove that in the absence of a superpotential the classical moduli space is the algebraic variety described by the set of all holomorphic gauge-invariant polynomials. When a superpotential is present, we show that the classical moduli space is a variety defined by imposing additional relations on the holomorphic polynomials. Many of these points are already contained in the existing literature. The main contribution of the present work is that we give a careful and self-contained treatment of limit points and singularities.Comment: 14 pages, LaTeX (uses revtex.sty

On the classification of Kahler-Ricci solitons on Gorenstein del Pezzo surfaces

We give a classification of all pairs (X,v) of Gorenstein del Pezzo surfaces X and vector fields v which are K-stable in the sense of Berman-Nystrom and therefore are expected to admit a Kahler-Ricci solition. Moreover, we provide some new examples of Fano threefolds admitting a Kahler-Ricci soliton.Comment: 21 pages, ancillary files containing calculations in SageMath; minor correction

The Neron-Severi group of a proper seminormal complex variety

We prove a Lefschetz (1,1)-Theorem for proper seminormal varieties over the complex numbers. The proof is a non-trivial geometric argument applied to the isogeny class of the Lefschetz 1-motive associated to the mixed Hodge structure on H^2.Comment: 16 pages; Mathematische Zeitschrift (2008

Generating multimedia presentations: from plain text to screenplay

In many Natural Language Generation (NLG) applications, the output is limited to plain text – i.e., a string of words with punctuation and paragraph breaks, but no indications for layout, or pictures, or dialogue. In several projects, we have begun to explore NLG applications in which these extra media are brought into play. This paper gives an informal account of what we have learned. For coherence, we focus on the domain of patient information leaflets, and follow an example in which the same content is expressed first in plain text, then in formatted text, then in text with pictures, and finally in a dialogue script that can be performed by two animated agents. We show how the same meaning can be mapped to realisation patterns in different media, and how the expanded options for expressing meaning are related to the perceived style and tone of the presentation. Throughout, we stress that the extra media are not simple added to plain text, but integrated with it: thus the use of formatting, or pictures, or dialogue, may require radical rewording of the text itself

Constructible motivic functions and motivic integration

We introduce a direct image formalism for constructible motivic functions. One deduces a very general version of motivic integration for which a change of variables theorem is proved. These constructions are generalized to the relative framework, in which we develop a relative version of motivic integration. These results have been announced in math.AG/0403349 and math.AG/0403350. Main results and statements unchanged. Many minor slips corrected and some details added.Comment: Final versio

Structure of a bacterial cell surface decaheme electron conduit

Some bacterial species are able to utilize extracellular mineral forms of iron and manganese as respiratory electron acceptors. In Shewanella oneidensis this involves decaheme cytochromes that are located on the bacterial cell surface at the termini of trans-outer-membrane electron transfer conduits. The cell surface cytochromes can potentially play multiple roles in mediating electron transfer directly to insoluble electron sinks, catalyzing electron exchange with flavin electron shuttles or participating in extracellular intercytochrome electron exchange along “nanowire” appendages. We present a 3.2-Å crystal structure of one of these decaheme cytochromes, MtrF, that allows the spatial organization of the 10 hemes to be visualized for the first time. The hemes are organized across four domains in a unique crossed conformation, in which a staggered 65-Å octaheme chain transects the length of the protein and is bisected by a planar 45-Å tetraheme chain that connects two extended Greek key split ß-barrel domains. The structure provides molecular insight into how reduction of insoluble substrate (e.g., minerals), soluble substrates (e.g., flavins), and cytochrome redox partners might be possible in tandem at different termini of a trifurcated electron transport chain on the cell surface

On localization in holomorphic equivariant cohomology

We prove a localization formula for a "holomorphic equivariant cohomology" attached to the Atiyah algebroid of an equivariant holomorphic vector bundle. This generalizes Feng-Ma, Carrell-Liebermann, Baum-Bott and K. Liu's localization formulas.Comment: 16 pages. Completely rewritten, new title. v3: Minor changes in the exposition. v4: final version to appear in Centr. Eur. J. Mat

Characterization of an electron conduit between bacteria and the extracellular environment

A number of species of Gram-negative bacteria can use insoluble minerals of Fe(III) and Mn(IV) as extracellular respiratory electron acceptors. In some species of Shewanella, deca-heme electron transfer proteins lie at the extracellular face of the outer membrane (OM), where they can interact with insoluble substrates. To reduce extracellular substrates, these redox proteins must be charged by the inner membrane/periplasmic electron transfer system. Here, we present a spectro-potentiometric characterization of a trans-OM icosa-heme complex, MtrCAB, and demonstrate its capacity to move electrons across a lipid bilayer after incorporation into proteoliposomes. We also show that a stable MtrAB subcomplex can assemble in the absence of MtrC; an MtrBC subcomplex is not assembled in the absence of MtrA; and MtrA is only associated to the membrane in cells when MtrB is present. We propose a model for the modular organization of the MtrCAB complex in which MtrC is an extracellular element that mediates electron transfer to extracellular substrates and MtrB is a trans-OM spanning ß-barrel protein that serves as a sheath, within which MtrA and MtrC exchange electrons. We have identified the MtrAB module in a range of bacterial phyla, suggesting that it is widely used in electron exchange with the extracellular environment