Transcriptional and Proteomic Analysis of a Ferric Uptake Regulator (Fur) Mutant of Shewanella oneidensis: Possible Involvement of Fur in Energy Metabolism, Transcriptional Regulation, and Oxidative Stress

The iron-directed, coordinate regulation of genes depends on the fur (ferric uptake regulator) gene product, which acts as an iron-responsive, transcriptional repressor protein. To investigate the biological function of a fur homolog in the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1, a fur knockout strain (FUR1) was generated by suicide plasmid integration into this gene and characterized using phenotype assays, DNA microarrays containing 691 arrayed genes, and two-dimensional polyacrylamide gel electrophoresis. Physiological studies indicated that FUR1 was similar to the wild-type strain when they were compared for anaerobic growth and reduction of various electron acceptors. Transcription profiling, however, revealed that genes with predicted functions in electron transport, energy metabolism, transcriptional regulation, and oxidative stress protection were either repressed (ccoNQ, etrA, cytochrome b and c maturation-encoding genes, qor, yiaY, sodB, rpoH, phoB, and chvI) or induced (yggW, pdhC, prpC, aceE, fdhD, and ppc) in the fur mutant. Disruption of fur also resulted in derepression of genes (hxuC, alcC, fhuA, hemR, irgA, and ompW) putatively involved in iron uptake. This agreed with the finding that the fur mutant produced threefold-higher levels of siderophore than the wild-type strain under conditions of sufficient iron. Analysis of a subset of the FUR1 proteome (i.e., primarily soluble cytoplasmic and periplasmic proteins) indicated that 11 major protein species reproducibly showed significant (P < 0.05) differences in abundance relative to the wild type. Protein identification using mass spectrometry indicated that the expression of two of these proteins (SodB and AlcC) correlated with the microarray data. These results suggest a possible regulatory role of S. oneidensis MR-1 Fur in energy metabolism that extends the traditional model of Fur as a negative regulator of iron acquisition systems

Ground-state properties of trapped Bose-Fermi mixtures: role of exchange-correlation

We introduce Density Functional Theory for inhomogeneous Bose-Fermi mixtures, derive the associated Kohn-Sham equations, and determine the exchange-correlation energy in local density approximation. We solve numerically the Kohn-Sham system and determine the boson and fermion density distributions and the ground-state energy of a trapped, dilute mixture beyond mean-field approximation. The importance of the corrections due to exchange--correlation is discussed by comparison with current experiments; in particular, we investigate the effect of of the repulsive potential energy contribution due to exchange--correlation on the stability of the mixture against collapse.Comment: 6 pages, 4 figures (final version as published in Physical Review

c-Type Cytochrome-Dependent Formation of U(IV) Nanoparticles by Shewanella oneidensis

Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, are essential for the reduction of U(VI) and formation of extracelluar UO (2) nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC (metal reduction), previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild-type MR-1. Similar to the wild-type, the mutants accumulated UO (2) nanoparticles extracellularly to high densities in association with an extracellular polymeric substance (EPS). In wild-type cells, this UO (2)-EPS matrix exhibited glycocalyx-like properties and contained multiple elements of the OM, polysaccharide, and heme-containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high-resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO (2) nanoparticles with MtrC and OmcA (outer membrane cytochrome). This is the first study to our knowledge to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO (2) nanoparticles. In the environment, such association of UO (2) nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O (2) or transport in soils and sediments

Density Functional Theory of Bosons in a Trap

A time-dependent Kohn-Sham (KS) like theory is presented for N bosons in thre e and lower-dimensional traps. We derive coupled equations, which allow one to calculate the energies of elementary excitations. A rigorous proof is given to show that the KS like equation correctly describes properties of the one-dimensional condensate of impenetrable bosons in a general time-dependent harmonic trap in the larg N limit.Comment: 10 page

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values

Isolation and characterization of multicytochrome gene cluster from Shewanella putrefaciens MR-1 involved in iron and manganese reduction

Dissimilatory Fe(III) and Mn(IV) reduction is an anaerobic respiratory process common to many environments. A large number of bacteria that utilize these metals as terminal electron acceptors have been isolated and identified for the past decade. However, the molecular mechanisms of metal reduction remain unclear despite intensive research in this area. There are no genes or proteins identified, which are directly involved in metal reduction. The major goal of this work is to identify and isolate genes related to Fe(III) and Mn(IV) reduction as well as to determine the specific functions of their products. The organism used in this work is the facultatively anaerobic metal reducer S. putrefaciens MR-1. Transposon mutagenesis was used to generate mutants solely deficient in Fe(III) and Mn(IV) reduction. Analysis of the interrupted regions in two such mutants, SR-8 and SR-21, led to the identification of three genes, designated mtrC, mtrA and mtrB. The deduced amino acid sequence of mtrC and mtrA revealed that these genes encode deca-heme c-type cytochromes. The third gene, mtrB, was shown to encode an outer membrane protein of 679 amino acids. mRNA and Western blot analyses indicated that the three genes are organized in a single operon, mtrCAB, which is expressed constitutively. To elucidate the role of each protein in metal reduction, gene replacement was used to generate strains lacking either mtrC, mtrA or mtrB. Whole-cell suspensions of mtrC−A+B+, mirC+A−B+ and mtrC+A+B− mutants resulted in 4.6-fold, 31-fold and 70-fold decrease in iron reduction rates, respectively. In contrast to whole cells, the levels of iron reductase activity in the crude cell extracts of the mutants were similar to that observed in the wild type. These findings strongly suggest that the products of mtrC, mtrA and mtrB play an important role in metal reduction, however, they may not constitute the terminal metal reductase complex. Analysis of the DNA region upstream of mtrCAB revealed a presence of another multicytochrome gene cluster. Although the identified genes, mtrD, mtrE, mtrF and omcA, exhibited high degree of similarity to the mtrCAB operon, there was no evidence indicating their involvement in Fe(III) and Mn(IV) reduction in S. putrefaciens

Song, H.-S., et al. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review. Processes 2014, 2, 711–752

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Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power

Low Energy Implantation of Carbon into Elastic Polyurethane

Ion modification of polymeric materials requires gentle regimens and subsequent investigation of mechanical and deformation behavior of the surfaces. Polyurethane is a synthetic block copolymer: A fibrillar hard phase is inhomogeneoulsy distributed in a matrix of soft phase. Implantation of carbon ions into this polymer by deep oscillation magnetron sputtering (energy&mdash;0.1&ndash;1 keV and dose of ions&mdash;1014&ndash;1015 ion/cm2) forms graphene-like nanolayer and causes heterogeneous changes in structural and mechanical properties of the surface: Topography, elastic modulus and depth of implantation for the hard/soft phase areas are different. As a result, after certain treatment regimens strain-induced defects (nanocracks in the areas of the modified soft phase, or folds in the hard phase) appear on the surfaces of stretched materials. Treated surfaces have increased hydrophobicity and free surface energy, and in some cases show good deformability without any defects