Additional file 7: Figure S4. of More than 2500 years of oil exposure shape sediment microbiomes with the potential for syntrophic degradation of hydrocarbons linked to methanogenesis

Distribution and abundance of prokaryotic taxa at different depths of the NE and HE sites. The ten most abundant phyla are depicted as distinct colors. Individual data points represent different orders; the size indicates the order’s abundance while the position on the plot shows the proportion in the three depths. (PDF 42 kb

Additional file 1: Figure S1. of Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation

(Related to Fig. 1) Ezh2 expression is lost from E10.5. Figure S2. (related to Fig. 2) Ezh2 ablation results in increased neurogenesis. Figure S3. (related to Fig. 3) Gene ontology analysis. Figure S4. (related to Fig. 4) Expression levels of forebrain transcription factors in Ezh2 cko midbrain do not reach those of wildtype forebrain. Figure S5. (related to Fig. 4) Incomplete Cre-mediated recombination in the dorsal midbrain. Figure S6. (related to Fig. 5) Ezh2 ablation does not affect early midbrain patterning. Figure S7. (related to Fig. 6) Pax6 does not directly repress Pax3 and Pax7. Table S1. (related to Fig. 3) Differentially expressed genes of E10.5 control and Ezh2 cko midbrains. Table S2. Primers used for the generation of in situ probes by in vitro transcription. Table S3. Primers used for quantitative real-time PCR on embryo tissue samples. Table S4. Primers used for quantitative real-time PCR on DNA fragments isolated in H3K27me3 ChIP assay. (PDF 4989 kb

Predicted functional consequences of SNP polymorphisms on the translational level.

<p>¹silent mutation</p><p>The SNP numbers (#), positions in the reference and the respective variant alleles for the SNP (Mut.) and the reference (Ref.) are shown as well as the potential amino acid (AA.) changes in the affected gene products and the gene designations.</p

SNPs in Pollino isolates detected by whole genome sequencing.

<p>SNPs are numbered according to their position in the reference genome¹ (<i>B</i>. <i>anthracis</i> Ames Ancestor; GenBank accession: AE017334). The bases at the respective positions are shown for Pollino isolates and the reference². SNPs are highlighted in italics.</p

Temperature-dissociation (melt) curve derivatives of HRM-SNP.

<p>The relative fluorescence signal is plotted against the melting temperature (°C) for each SNP. Curves showing ancestral alleles (same base as predominant Pollino allele) are displayed in green. Curves indicating derived alleles (variant allele at the SNP-position) are displayed in red. The respective bases at the SNP position (“G” or “A”) are indicated for each allele group. Inconsistent curves (“?”) are displayed in blue. Negative controls (“NC”) are displayed in light-blue.</p

Hypothesis on an active life cycle of <i>B</i>. <i>anthracis</i> in soil environments.

<p>Soil surrounding the carcass at the lower part of the figure harbors a very high spore burden. The left part of the panel predicts massive soil proliferation of <i>B</i>. <i>anthracis</i> (hypothesis). In this case of an active near-surface life cycle, local accumulation of spores is suggested to be due to repeated rounds of germination, replication and sporulation in the near-surface soil environment. During genome amplification random mutations occur resulting in derived genotypes compared to the genotypes of the initial spore population within the carcass. The right part of the panel depicts events if there was no soil-borne life cycle of the pathogen (competing hypothesis). Inert spores are supposed to accumulate in rainwater depressions. Genotypes differing from the original animal-infecting population cannot be observed in near-surface isolates.</p

Oligonucleotides used for high resolution melting analysis of Pollino-SNPs.

<p>¹with reference to <i>B</i>. <i>anthracis</i> strain Ames Ancestor</p><p>Oligonucleotides used for high resolution melting analysis of Pollino-SNPs.</p

Location and details of sampling sites in southern Italy.

<p>Panel A indicates the locations of burial sites in Southern Italy (left) and positions of burial sites A, B and C at Pollino National Park (right). Panel B shows burial site C after sampling at positions 1, 2 and 3 (holes, approx. 50 cm apart).</p

Modified (synthesis) model for <i>B</i>. <i>anthracis</i> genotype dynamics in soil of Pollino burial sites.

<p>Soil surrounding the carcass at the lower part of the figure harbors a very high endospore burden. Genetically diverse genotypes, which can be found near-carcass and near-surface, are the result of either multiple genotype infection or mutations during the course of host infection. Endospores reach the surface and accumulate via physical diffusion. Sporadic germination in soil or possibly in transient vectors, replication and sporulation under favorable conditions can lead to genetically diverse genotypes that can be found in near-surface soil.</p

SNR sub-genotypes according to length differences in markers HM1 and HM2.

<p>SNR sub-genotypes according to length differences in markers HM1 and HM2.</p