The fox Operon from Rhodobacter Strain SW2 Promotes Phototrophic Fe(II) Oxidation in Rhodobacter capsulatus SB1003

Anoxygenic photosynthesis based on Fe(II) is thought to be one of the most ancient forms of metabolism and is hypothesized to represent a transition step in the evolution of oxygenic photosynthesis. However, little is known about the molecular basis of this process because, until recently (Y. Jiao and D. K. Newman, J. Bacteriol. 189:1765-1773, 2007), most phototrophic Fe(II)-oxidizing bacteria have been genetically intractable. In this study, we circumvented this problem by taking a heterologous-complementation approach to identify a three-gene operon (the foxEYZ operon) from Rhodobacter sp. strain SW2 that confers enhanced light-dependent Fe(II) oxidation activity when expressed in its genetically tractable relative Rhodobacter capsulatus SB1003. The first gene in this operon, foxE, encodes a c-type cytochrome with no significant similarity to other known proteins. Expression of foxE alone confers significant light-dependent Fe(II) oxidation activity on SB1003, but maximal activity is achieved when foxE is expressed with the two downstream genes foxY and foxZ. In SW2, the foxE and foxY genes are cotranscribed in the presence of Fe(II) and/or hydrogen, with foxZ being transcribed only in the presence of Fe(II). Sequence analysis predicts that foxY encodes a protein containing the redox cofactor pyrroloquinoline quinone and that foxZ encodes a protein with a transport function. Future biochemical studies will permit the localization and function of the Fox proteins in SW2 to be determined

Characterization of the Arsenate Respiratory Reductase from Shewanella sp. Strain ANA-3

Microbial arsenate respiration contributes to the mobilization of arsenic from the solid to the soluble phase in various locales worldwide. To begin to predict the extent to which As(V) respiration impacts arsenic geochemical cycling, we characterized the expression and activity of the Shewanella sp. strain ANA-3 arsenate respiratory reductase (ARR), the key enzyme involved in this metabolism. ARR is expressed at the beginning of the exponential phase and persists throughout the stationary phase, at which point it is released from the cell. In intact cells, the enzyme localizes to the periplasm. To purify ARR, a heterologous expression system was developed in Escherichia coli. ARR requires anaerobic conditions and molybdenum for activity. ARR is a heterodimer of ~131 kDa, composed of one ArrA subunit (~95 kDa) and one ArrB subunit (~27 kDa). For ARR to be functional, the two subunits must be expressed together. Elemental analysis of pure protein indicates that one Mo atom, four S atoms associated with a bis-molybdopterin guanine dinucleotide cofactor, and four to five [4Fe-4S] are present per ARR. ARR has an apparent melting temperature of 41°C, a Km of 5 µM, and a Vmax of 11,111 µmol of As(V) reduced min–1 mg of protein–1 and shows no activity in the presence of alternative electron acceptors such as antimonite, nitrate, selenate, and sulfate. The development of a heterologous overexpression system for ARR will facilitate future structural and/or functional studies of this protein family

Statistics of Certain Models of Evolution

In a recent paper, Newman surveys the literature on power law spectra in evolution, self-organised criticality and presents a model of his own to arrive at a conclusion that self-organised criticality is not necessary for evolution. Not only did he miss a key model (Ecolab) that has a clear self-organised critical mechanism, but also Newman's model exhibits the same mechanism that gives rise to power law behaviour as does Ecolab. Newman's model is, in fact, a ``mean field'' approximation of a self-organised critical system. In this paper, I have also implemented Newman's model using the Ecolab software, removing the restriction that the number of species remains constant. It turns out that the requirement of constant species number is non-trivial, leading to a global coupling between species that is similar in effect to the species interactions seen in Ecolab. In fact, the model must self-organise to a state where the long time average of speciations balances that of the extinctions, otherwise the system either collapses or explodes. In view of this, Newman's model does not provide the hoped-for counter example to the presence of self-organised criticality in evolution, but does provide a simple, almost analytic model that can used to understand more intricate models such as Ecolab.Comment: accepted in Phys Rev E.; RevTeX; See http://parallel.hpc.unsw.edu.au/rks/ecolab.html for more informatio

MgB2 tunnel junctions with native or thermal oxide barriers

MgB2 tunnel junctions (MgB2/barrier/MgB2) were fabricated using a native oxide grown on the bottom MgB2 film as the tunnel barrier. Such barriers therefore survive the deposition of the second electrode at 300oC, even over junction areas of ~1 mm2. Studies of such junctions, and those of the type MgB2/native or thermal oxide/metal (Pb, Au, or Ag) show that tunnel barriers grown on MgB2 exhibit a wide range of barrier heights and widths.Comment: 9 pages, 3 figure

Effect of stoichiometry on oxygen incorporation in MgB2 thin films

The amount of oxygen incorporated into MgB2 thin films upon exposure to atmospheric gasses is found to depend strongly on the material's stoichiometry. Rutherford backscattering spectroscopy was used to monitor changes in oxygen incorporation resulting from exposure to: (a) ambient atmosphere, (b) humid atmospheres, (c) anneals in air and (d) anneals in oxygen. The study investigated thin-film samples with compositions that were systematically varied from Mg0.9B2 to Mg1.1B2. A significant surface oxygen contamination was observed in all of these films. The oxygen content in the bulk of the film, on the other hand, increased significantly only in Mg rich films and in films exposed to humid atmospheres.Comment: 10 pages, 6 figures, 1 tabl

The Brownian Web: Characterization and Convergence

The Brownian Web (BW) is the random network formally consisting of the paths of coalescing one-dimensional Brownian motions starting from every space-time point in ${\mathbb R}\times{\mathbb R}$. We extend the earlier work of Arratia and of T\'oth and Werner by providing characterization and convergence results for the BW distribution, including convergence of the system of all coalescing random walkssktop/brownian web/finale/arXiv submits/bweb.tex to the BW under diffusive space-time scaling. We also provide characterization and convergence results for the Double Brownian Web, which combines the BW with its dual process of coalescing Brownian motions moving backwards in time, with forward and backward paths ``reflecting'' off each other. For the BW, deterministic space-time points are almost surely of ``type'' $(0,1)$ -- {\em zero} paths into the point from the past and exactly {\em one} path out of the point to the future; we determine the Hausdorff dimension for all types that actually occur: dimension 2 for type $(0,1)$, 3/2 for $(1,1)$ and $(0,2)$, 1 for $(1,2)$, and 0 for $(2,1)$ and $(0,3)$.Comment: 52 pages with 4 figure

Small But Slow World: How Network Topology and Burstiness Slow Down Spreading

Communication networks show the small-world property of short paths, but the spreading dynamics in them turns out slow. We follow the time evolution of information propagation through communication networks by using the SI model with empirical data on contact sequences. We introduce null models where the sequences are randomly shuffled in different ways, enabling us to distinguish between the contributions of different impeding effects. The slowing down of spreading is found to be caused mostly by weight-topology correlations and the bursty activity patterns of individuals