Annotation and pathway analysis for both up- and down-regulated genes for T4-C4.

<p>ID: MetaCyc identifier. #: number of up- or down-regulated genes annotated with a particular pathway in relation to the number of genes annotated with that pathway.</p

Differential expression of transporter encoding genes.

<p>Stacked percentage bar chart, showing the numbers of up- and down-regulated (putative) transporter encoding genes for T4-C4 (left) and T1-C1 (right), respectively, relative to the total numbers of (putative) transporter encoding genes within the <i>P. larvae</i> genome. The latter are indicated between square brackets. Round brackets: GO term numbers. GO terms were assigned with Blast2GO. White bars: down-regulation for T4-C4. Dark grey bars: up-regulation for T4-C4. Light grey bars: down-regulation for T1-C1. Black bars: up-regulation for T1-C1. Arrow heads: arbitrary GO term hierarchy (◂>⊲><>\raster(90%)="rg3"<>).</p

General overview of the microarray experiment, showing the total number of up- and down-regulated genes, for three selection criteria (columns) and four comparisons (rows).

<p>T1: test sample collected one hour after spiking with larval bodily fluid. T4: test sample collected four hours after spiking with larval bodily fluid. C1: control sample collected one hour after spiking with BHIT broth. C4: control sample collected four hours after spiking with BHIT broth. P: p-value. FC: fold change. Hyb: at least 75% of the different, hybridized probes for the same gene shows differential expression for a particular comparison.</p

Effect of honey bee larval bodily fluid on <i>Paenibacillus larvae</i> growth.

<p>Effect of different concentrations of honey bee larval bodily fluid on the <i>in vitro</i> growth of <i>P. larvae</i> bacterial cells, expressed as the optical density measured at a wavelength of 590 nm (OD₅₉₀) in function of time (hours). Growth alterations were determined for six bodily fluid concentrations, expressed as the fold dilution in BHIT broth cultures: 10× dilution (♦), 25× dilution (▪), 50× dilution (▴), 100× dilution (⋄), 250× dilution (□), 500× dilution (▵), control (○). Each point in the graph displays the mean of three independent replicates, with the error bars being the standard deviations. Time 0 represents the time of spiking. Trend lines are calculated with DMfit. No OD measurements were performed during lag phase.</p

Differential expression of metabolic genes.

<p>Stacked percentage bar chart, showing the numbers of up- and down-regulated (putative) metabolic genes for T4-C4 (left) and T1-C1 (right), respectively, relative to the total numbers of (putative) metabolic genes within the <i>P. larvae</i> genome. C: carbohydrate metabolism. The latter are indicated between square brackets. Round brackets: KO numbers (KEGG pathways). KEGG pathways were assigned with KAAS. White bars: down-regulation for T4-C4. Dark grey bars: up-regulation for T4-C4. Light grey bars: down-regulation for T1-C1. Black bars: up-regulation for T1-C1. E: energy metabolism. L: lipid metabolism. N: nucleotide metabolism. A: amino acid metabolism. ∼: KO:00061; KO:00071; KO:00592; KO:01040. *: KO:00360; KO:00350; KO:00380. °: KO:00410; KO:00430; KO:00450; KO:00460; KO:00480. ?: KO:00740; KO:00770; KO:00780; KO:00670; KO:00860; KO:00130. ‘:KO:00900; KO:00903; KO:00281; KO:00523; KO:01053; KO:01055; KO:00940; KO:00311; KO:00521. ‘’: KO:00362; KO:00627; KO:00625; KO:00622; KO:00633; KO:00642; KO:00643; KO:00930; KO:00363; KO:00621; KO:00626.</p

Effect of honey bee larval bodily fluid on <i>Paenibacillus larvae</i> bacterial density.

<p>OD590 (white bars) and CFU/ml (black bars) for T1, C1, T4 and C4. T1 (n = 12): test sample collected one hour after spiking with 5% larval fluids. T4 (n = 12): test sample collected four hours after spiking with 5% larval fluids. C1 (n = 11): control sample collected one hour after spiking with BHIT-broth. C4 (n = 12): control sample collected four hours after spiking with BHIT-broth. Between brackets (n): number of independent replicates. Error bars: standard deviations.</p

Numbers of genes that are differentially expressed per subset.

<p>Stacked percentage bar chart, showing the numbers of up- and down-regulated genes for T4-C4 (left) and T1-C1 (right), respectively, relative to the total numbers of genes within the <i>P. larvae</i> genome. The latter are indicated between square brackets. Round brackets: COG functional category label. C: cellular processes and signaling. I: information storage and processing. M: metabolism. P: poorly characterized. White bars: down-regulation for T4-C4. Dark grey bars: up-regulation for T4-C4. Light grey bars: down-regulation for T1-C1. Black bars: up-regulation for T1-C1.</p

GO-enrichment analysis for comparison T4–C4, showing the most specific over- and under-represented biological process GO-terms for both up- and down-regulation.

<p>NS, FE, P-value: see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0089175#pone-0089175-t002" target="_blank">Table 2</a>.</p

Saanich_TimeSeries_Historical_O2_DATA

Historical dissolved oxygen winkler measurements at Station S3 in Saanich Inlet from 1953 to 2007. This data includes, geographical coordinates, date (year and month), depth (meters), temperature (celcius degrees), salinity (PSU), density (sigma-theta), oxygen (milliliter per liter and micromolar). For detailed methods see the manuscript

Saanich_TimeSeries_Chemical

Chemical bottle data collected from Station S3 (-123.505, 48.59166667) in Saanich Inlet, BC, Canada. This data includes unique geographical coordinates for sampling station (Decimal degrees), Numerical identifier of individual cruises (Numeric string), Date of cruise (YY-MM-DD), Sampling depth (Meters), Oxygen concentration calculated from CTD SBE (Micromolar), Phosphate (Bran Luebbe AutoAnalyser - colorimetric) (Micromolar), Silicate (Bran Luebbe AutoAnalyser - colorimetric) (Micromolar), Nitrate (Bran Luebbe AutoAnalyser - colorimetric) (Micromolar), Average Ammonium (fluorometric) (Micromolar), Average Nitrite (colorimetric) (Micromolar), Average Hydrogen sulfide (colorimetric) (Micromolar), Cell counts value quantified by flow cytometry (Number of cells per millilitre (cells/mL)), Average concentration of Nitrogen gas (headspace) (Micromolar), Standard deviation for Nitrogen gas, Average concentration of Oxygen (headspace) (Micromolar), Standard deviation for Oxygen, Average concentration of Carbon dioxide (headspace) (Micromolar), Standard deviation for Carbon dioxide, Average concentration of Nitrous oxide (headspace or automated purge-and-trap) (Micromolar), Standard deviation for Nitrous oxide, Average concentration of Methane (headspace or automated purge-and-trap) (Nanomolar), Standard deviation for Methane. For detailed description of methods see manuscript