Additional file 2: of Understanding key features of bacterial restriction-modification systems through quantitative modeling

Model of EcoRV regulation and dynamics. (DOCX 198 kb

Additional file 1: of Understanding key features of bacterial restriction-modification systems through quantitative modeling

Model of AhdI regulation and dynamics. (PDF 415 kb

Schematic representation of the infectious clones derived from the stool and BAL isolates and their derivatives and assessment of their replication efficiency in Vero versus SH-SY5Y cells.

<p>(A) Representation of the infectious clones. (B–C) Vero cells (I–IV) and SH-SY5Y cells (V–VIII) were infected with infectious clones derived from the clinical isolates. (B) Replication was assessed by immunofluorescence with an anti-EV71 monoclonal antibody. The cell type and residue at positions VP1₉₇ and 2B₃₈ are indicated on the left and bottom of the figure, respectively. The TCID50/ml performed after 5 days on the SH-SY5Y infected cell supernatant is indicated with a bar on the left side of each panel. (C) Increase in viral RNA load as quantified by real-time RT-PCR at different time points post infection with the four derivatives. Vertical bars indicate minimum/maximum values. Key for (A) +, positive charge, − negative charge, o neutral; * sequence corresponding to that of the BAL samples, ** sequence corresponding to that of the stool samples.</p

Competition between the stool and BAL infectious clone derivatives.

<p>Vero cells, Caco-2 cells (A), and SH-SY5Y cells (B) were transfected by equimolar amounts of the stool and BAL infectious clone derivatives and virus present in the cell supernatant was analysed by sequencing post-transfection and repassage at different times. Substitutions are marked by red arrows and correspond to nucleotide (nt) and amino acid (aa) positions of the EV71 VP1 coding sequence (GenBank accession number: AAB39968.1).</p

EV71 VP1 substitution locations relative to known receptors and capsid symmetry.

<p>(A) EV71 VP1 model highlighting the BC loop (green) and positions of VP1_97R (red circle) and VP1_167E (orange circle) relative to known receptors (gray). Eight known picornavirus VP1-receptor complexes (PDB codes along their sides) were structurally aligned to our model using the VP1 coordinates in each structure file. The distance (∼12 Å) between EV71 VP1 residue 97 and receptor surfaces is marked by vertical black dotted lines (distance between VP1 residue 97 and the 3dpr receptor, also ∼12 Å, is not marked). (B) Five EV71 VP1_97R model monomers arranged in capsid symmetry based on poliovirus capsid VP1 orientations (PDB 3epf). BC loops (green) and positions of residue 97 (red circles) and residue 167 (orange circles) are highlighted. (C) Side view of VP1_97R capsid assembly in B, rotated 80° on the plane of this page. The curvature and thickness of the capsid surface (based on PDB 3epf capsid assembly, VIPERdb) is represented as a light gray arc. (D) Sequence alignment of VP1 clinical isolates, EV71 substrain BrCr (Genbank U22521), and polivirus (PV1 (Genbank V01149), PV2 (M12197), PV3 (K01392)) surrounding EV71 VP1₉₇ and VP1₁₆₇ substitutions. Index numbers refer to EV71 VP1 residue positions.</p

Genome evolution at the nucleotide and amino-acid level according to the time and site of sampling.

<p>Positions of nucleotide and amino acid substitutions are listed in reference to both the full-length EV71 polyprotein (number on left of column) and within the affected protein (in parenthesis). BAL: bronchoalveolar lavage sample; CSF: cerebrospinal fluid sample; nt: nucleotide position; aa: amino acid position.</p>*<p>Positions are indicated relative to EV71 BrCr strain (GenBank accession number: U22521).</p><p>Of note, real-time RT-PCR performed on plasma samples collected at days 1, 5 and 7 presented 27, 32 and 45 ct values, respectively, and immunoglobulins were injected at day 5.</p

Seroneutralization assay with the patient's serum.

*<p>smaller dilution not tested;</p>**<p>Patient serum was toxic for cells at a dilution <1∶5.</p><p>d4: patient serum sampled at day 4.</p><p>BAL: bronchoalveolar lavage.</p

EV71 binding assay.

<p>SH-SY5Y cells (A) and Vero cells (B) were used to compare the cell-binding capacity of pCIVP1_97R2B_38A and pCIVP1_97L2B_38V. Two conditions were assessed: undiluted (1∶1) and 2-fold diluted (1∶2) standardized viral stocks. Quantification of bound virus was measured by the Entero/Ge/08 real-time RT-PCR assay and expressed relative to pCIVP1_97R2B_38A (1∶1 condition). Vertical bars indicate minimum/maximum values.</p

Additional file 2: of Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle–plant interface

Large supporting tables. (XLSX 344 kb

RAD tag (SgrAI) derived SNPs from Bombus impatiens

RAD tag (SgrAI) derived SNPs from Bombus impatiens from Sadd et al. (2015) "The genomes of two key bumblebee species with primitive eusocial organisation