MOESM5 of Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824

Additional file 5. Corrected annotated chromosomal genome sequence of ATCC 824

Polymers for binding of the gram-positive oral pathogen <i>Streptococcus mutans</i> - Fig 3

<p>Binding of coumarin 343-tagged a) cationic <b>(3)_25-100%</b> and b) sulfobetaine <b>(4)_25-100%</b> polymers at different degrees of functionalization, to <i>E</i>. <i>coli</i> and <i>S</i>. <i>mutans</i> in bacterial suspensions of OD₆₀₀ 0.1, and 1.0 mg mL^-1 polymer solutions. Area of fluorescence (%) was quantified using ImageJ. Error bars represent standard deviations on independent experiments (N = 3). Fluorescence micrographs are shown for fully functionalised (c, d) cationic and (e, f) sulfobetaine polymers, <b>(3)</b>_<b>100%</b> and <b>(4)</b>_<b>100%</b>, respectively using the 488 nm (green) channel.</p

Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in <i>Clostridium autoethanogenum</i> with Uniformly ¹³C‑Labeled Standards Derived from Spirulina

We have investigated the applicability of commercially available lyophilized spirulina (<i>Arthrospira platensis</i>), a microorganism uniformly labeled with ¹³C, as a readily accessible source of multiple ¹³C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-¹³C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of <i>Clostridium autoethanogenum</i> using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze–thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves (<i>R</i>² ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood–Ljungdahl pathway of <i>C. autoethanogenum</i> grown in continuous culture over 35 days. Using LC-IDMS with U-¹³C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the <i>C. autoethanogenum</i> metabolic pathways active in gas fermentation

The Nearshore Fish Fauna of Bonne Bay, a Fjord within Gros Morne National Park, Newfoundland

A standardized survey of the nearshore fish fauna of Bonne Bay, a fjord within Gros Morne National Park in western Newfoundland, was conducted using beach seines, gill-nets and bottom trawls during the month of June over a seven year period (2002-2008). The survey documents the presence of 31 fish species (in 17 taxonomic families). Sampling sites varied in benthic habitat and associated fish assemblages. Both juvenile and adult life history stages of Atlantic cod (Gadus morhua) were present in Bonne Bay, suggesting the presence of a local population or “bay cod stock”. Acadian redfish (Sebastes fasciatus) live in the bay, and may be members of a genetically differentiable population of redfish. Striped wolfish (Anarhichas lupus), a fish species protected under Canada’s Species at Risk Act (SARA), inhabits Bonne Bay. Surrounded by Gros Morne National Park, this bay with a diverse fish fauna is a focus of local stewardship and conservation efforts

MOESM7 of Microbial solvent formation revisited by comparative genome analysis

Additional file 7: Table S7. General GenBank features

MOESM4 of Microbial solvent formation revisited by comparative genome analysis

Additional file 4: Table S4. Acidogenensis and solventogenesis gene clusters

Polymers for binding of the gram-positive oral pathogen <i>Streptococcus mutans</i> - Fig 4

<p>(A) Binding of coumarin 343-tagged sulfobetaine polymer <b>(4)</b>_<b>100%</b> to <i>E</i>. <i>coli</i>, <i>S</i>. <i>mutans</i>, <i>V</i>. <i>Harveyi</i> and <i>S</i>. <i>Aureus</i> in bacterial suspensions of OD₆₀₀ 0.1, and 1.0 mg mL^-1 polymer solutions (scale bars = 5 μm). Representative fluorescence micrographs are shown using the green channel (488 nm excitation). Area of fluorescence (%) was quantified using ImageJ. Error bars represent standard deviations of three equivalent areas on three different micrographs. (B) Bacterial aggregation mediated by sulfobetaine polymer <b>(4)</b>_<b>100%</b>, as quantified <i>via</i> master sizer (Coulter counter) analysis of polymer—bacteria clusters.</p

インド デ ヌノ オ サワル

<p>(A) Binding of coumarin 343-tagged sulfobetaine polymer <b>(4)</b>_<b>100%</b> to <i>E</i>. <i>coli</i>, <i>S</i>. <i>mutans</i>, <i>V</i>. <i>Harveyi</i> and <i>S</i>. <i>Aureus</i> in bacterial suspensions of OD₆₀₀ 0.1, and 1.0 mg mL^-1 polymer solutions (scale bars = 5 μm). Representative fluorescence micrographs are shown using the green channel (488 nm excitation). Area of fluorescence (%) was quantified using ImageJ. Error bars represent standard deviations of three equivalent areas on three different micrographs. (B) Bacterial aggregation mediated by sulfobetaine polymer <b>(4)</b>_<b>100%</b>, as quantified <i>via</i> master sizer (Coulter counter) analysis of polymer—bacteria clusters.</p

MOESM6 of Microbial solvent formation revisited by comparative genome analysis

Additional file 6: Table S6. Sporulation proteins and σ-factors

Metabolic activity of Caco-2 cell line incubated with (red squares ■) galactosylated (5)_Gal or (green circles ●) mannosylated (5)_Man glycopolymers for 24 hours in a concentration range 0.010–5.0 mg mL^-1 for 24 h.

<p>Cell viability is expressed as a percentage of MTT metabolized by a control group of untreated cells. Experiments were performed in triplicate.</p