Results for the five-study simulation data with simulated percent differentially expressed genes <i>p_s</i> = 5%.

<p>a) True integration-driven discovery rate (<i>t</i>IDR) versus levels of posterior probability of differential expression γ ≥0.50, for Model (1) (triangles) and Model (2) (circles); b) The maximum number of true genes discovered versus posterior expected false discovery rate (<i>pe</i>FDR) for Model (1) (triangles), Model (2) (circles), individual analyses of Study 1 (checks), Study 2 (diamonds), Study 3 (pluses), Study 4 (inverted triangles), Study 5 (stars).</p

<i>G. sulfurreducens</i> spotted array and ISO array study data results.

<p>a) Integration-driven discovery rate (IDR) versus levels of posterior probability of differential expression γ ≥0.50, for Model (1) (triangles) and Model (2) (circles); b) The maximum number of genes discovered versus posterior expected false discovery rate (<i>pe</i>FDR) for Model (1) (triangles), Model (2) (circles), separate analyses of the <i>G. sulfurreducens</i> spotted array study (checks) and ISO array study (diamonds).</p

Results for the two-study simulation data with simulated percent differentially expressed genes <i>p_s</i> = 5%.

<p>a) True integration-driven discovery rate (<i>t</i>IDR) versus levels of posterior probability of differential expression γ ≥0.50, for Model (1) (triangles) and Model (2) (circles); b) The maximum number of true genes discovered versus posterior expected false discovery rate (<i>pe</i>FDR) for Model (1) (triangles), Model (2) (circles), individual analyses of Study 1 (checks), Study 2 (diamonds).</p

Data_Sheet_1_Construction of a Geobacter Strain With Exceptional Growth on Cathodes.DOCX

<p>Insoluble extracellular electron donors are important sources of energy for anaerobic respiration in biogeochemical cycling and in diverse practical applications. The previous lack of a genetically tractable model microorganism that could be grown to high densities under anaerobic conditions in pure culture with an insoluble extracellular electron donor has stymied efforts to better understand this form of respiration. We report here on the design of a strain of Geobacter sulfurreducens, designated strain ACL, which grows as thick (ca. 35 μm) confluent biofilms on graphite cathodes poised at -500 mV (versus Ag/AgCl) with fumarate as the electron acceptor. Sustained maximum current consumption rates were >0.8 A/m², which is >10-fold higher than the current consumption of the wild-type strain. The improved function on the cathode was achieved by introducing genes for an ATP-dependent citrate lyase, completing the complement of enzymes needed for a reverse TCA cycle for the synthesis of biosynthetic precursors from carbon dioxide. Strain ACL provides an important model organism for elucidating the mechanisms for effective anaerobic growth with an insoluble extracellular electron donor and may offer unique possibilities as a chassis for the introduction of synthetic metabolic pathways for the production of commodities with electrons derived from electrodes.</p

Reconstruction, analysis, and wet lab validation of carbon fixation pathways in <i>G. metallireducens</i>.

<p>A) A map of the two carbon fixation pathways included in the iAF987 reconstruction and encoded by genes annotated in the updated genome annotation. The two pathways, the reductive citric acid (TCA), and the dicarboxylate–hydroxybutyrate cycles share four reactions in the citric acid cycle. CO₂ fixation (and resulting acetyl-coA generated) and ATP-driven steps are shown in green and red, respectively. B) A graph of phenotypic data that demonstrated the model-predicted growth condition of formate as an electron donor and carbon source with Fe(III) as an electron acceptor is a viable growth condition. Carbon fixation is occurring under these conditions and the specifics of this process can be further elucidated in subsequent “drill-down” studies.</p

Validated and predicted carbon sources and electron donors for <i>G. metallireducens</i>.

†<p>Formate was validated as a carbon source and electron donor experimentally in this study.</p

Subsystem distribution of reactions unique to the <i>G. metallireducens</i> iAF987 reconstruction.

<p>Subsystem distribution of reactions unique to the <i>G. metallireducens</i> iAF987 reconstruction.</p

A model-driven analysis of the electron transport system in <i>G. metallireducens</i>.

<p>A) schematic of the iterative loop process common to model-driven analyses, and (B) the process applied to examine the cost of the electron transport system in <i>G. metallireducens</i>. C) Map of the updated ETS in the iAF987 reconstruction. The functional states of the network components during internal electron transfer to fumarate are shown in green (facilitated by the <i>dcuB</i> strain), additional components active during internal transfer to nitrate are shown in blue, and additional components during external electron transfer (Fe respiration) are shown in brown. Note that the fumarate reductase (FRD2rpp) operates in opposite directions depending on whether the electron acceptor is fumarate or nitrate/Fe(III). Also note that nitrate reductase (NO3R3pp) is not used when Fe(III) is the electron acceptor. Abbreviations are defined in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003575#pcbi.1003575.s002" target="_blank">Dataset S2</a>. The process was started with the bottom-up reconstruction of the updated metabolic network. At each cycle around the loop, optimal performance was calculated as different components of the ETS were isolated, compared to experimental data, and then incorporated into the reconstruction. Ultimately, the final product is a reconstructed ETS consistent with experimental data and an estimate of the cost associated with transferring electrons from the internal membrane cytochrome (focytC) to the extracellular electron acceptor Fe(III) (fe3).</p

OmcZ sequence and identification.

<p>A. Amino acid sequence of OmcZ. The predicted cleavage site for mature OmcZ indicated by arrow. Confirmed heme-binding domains (CXXCH) are enclosed in boxes. OmcZ has 473 amino acid residues and 7 heme binding domains. B. Cytochrome content of loosely bound outer membrane protein-enriched fractions from fumarate and current-harvesting biofilms. Proteins (10 µg/lane) were separated by 12% Tris-Tricine denaturing polyacryamide gel electrophoresis and stained for heme. C. Peptides detected from two different sizes of OmcZs, fragments detected in the 50 KDa OmcZ are indicated in panel A in red; fragments detected in the 30 KDa OmcZ are indicated in panel A in green and fragments detected in both size OmcZ are indicated in blue.</p

Primers used for mutant construction, complementation and RT-PCR analyses.

<p>Primers used for mutant construction, complementation and RT-PCR analyses.</p