Additional file 1: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

NCBI accession numbers of downloaded DT sequences (Table S1) and SRA accession numbers of analysed WGS data (Table S2). (DOCX 28 kb

Additional file 2: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

Detected tox, dtxR, prophage and PAI coordinates, annotations and GC content (Table S3): For each of the 137 isolates, coordinates of tox and dtxR genes are given along with their species affiliation and their tox status analysed by qPCR and modified Elek test. All detected prophage sequences and PAIs are shown one line per region. For prophages and PAIs, information about region type and their overlapping or non-overlapping behavior in regard to the tox gene is indicated. For detected prophages, results from the prophage annotation software PHASTER [31] are given. For the alternative PAI, genomic start coordinates of the individual CDS sequences and structural annotations are indicated as well. Average GC content of the draft genome and the specific prophage/PAI regions is given. (XLSX 88 kb

Additional file 3: of NGS-based phylogeny of diphtheria-related pathogenicity factors in different Corynebacterium spp. implies species-specific virulence transmission

Tax IDs used for the generation of the Corynebacterium spp. annotation database in prokka [29]. (DOCX 21 kb

Additional file 4 of Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models

Additional file 4: Fig. S3. Progression of CPE on Calu-3. Cells were infected at an MOI of 0.0001 for 96 h. Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. CPE was considered as: (–) no CPE, (+) emerging CPE, (++) intermediate CPE, (+++) strong CPE, as indicated in the upper right corner of every microscopy picture

Additional file 2 of Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models

Additional file 2: Fig. S1. Progression of CPE on Vero E6. Cells were infected at an MOI of 0.0001 for 96 h. Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. CPE was considered as: (–) no CPE, (+) emerging CPE, (++) intermediate CPE, (+++) strong CPE, as indicated in the upper right corner of every microscopy picture

Additional file 3 of Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models

Additional file 3: Fig. S2. Absence of CPE on Caco-2 Cells were infected at an MOI of 0.0001 for 96 h. Images were taken at all time points from 2 to 96 h p.i.. For 72, 80, and 96 h p.i., representative images of SARS-CoV-2 non-VOC, the five VOCs, and an uninfected control are shown to illustrate the difference in CPE development and progression between different virus strains. CPE was considered as: (–) no CPE, (+) emerging CPE, (++) intermediate CPE, (+++) strong CPE, as indicated in the upper right corner of every microscopy picture

Additional file 1 of Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models

Additional file 1. SNP analysis cell line authentication report

3D-model showing the four lead structures of designed peptides.

<p>Four leading structures (I–IV) were designed differing in charge, hydrophobicity, location and size of the hydrophobic and charged cluster. Amino acids with hydrophobic and positively charged side chains are marked in red and blue, respectively. Three-dimensional modelling was performed using the SWISS PdbViewer (ExPASy website. Available: <a href="http://http://spdbv.vital-it.ch/" target="_blank">http://http://spdbv.vital-it.ch/</a>. Accessed 2013 July 12) with the helical structures of IsCT derivative (PDB code: 1T52) and magainin II (PDB code: 2MAG) as template.</p

Antibacterial activity of synthetic peptides in presence of apoplast fluid and in tomato fruits.

<p>(A) Approximately 10⁵ cfu/ml bacteria (<i>P. syringae</i> pv <i>tomato</i>) were incubated with 0 or 10 µg/ml peptide in the presence or absence of different concentrations (10 µg/ml or 30 µg/ml) of tomato apoplastic fluid. After 14–16 h the bacterial growth was determined by measuring OD_{600 nm}. APO, tomato apoplastic fluid. Values represent the mean of at least three biological replicates ± standard error of the mean. *indicates significantly different in comparison to the corresponding control treatment, <i>P</i><0.05. **indicates significantly different in comparison to the corresponding control treatment, <i>P</i><0.01. (B) <i>X. vesicatoria</i> (0.5×10⁵ cfu/ml) were treated with different concentrations of peptide SP10-5 and immediately injected into tomato fruits. After incubation for 5 d at room temperature infection symptoms were monitored. Above the values of incidence of infection symptoms is given in percentage. The total number of inoculation sides of three biological replicates were 22.</p

Sequences and structural-chemical properties of peptides of the 2^nd generation.

a<p>Estimated using the program Vector NTI 9.1 (Invitrogen).</p>b<p>Calculated using ProtParam tool (<a href="http://www.expasy.org/tools/protparam.html" target="_blank">http://www.expasy.org/tools/protparam.html</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071687#pone.0071687-Gasteiger1" target="_blank">[30]</a>), H [peptide], grand average hydrophobicity of full peptide.</p>c<p>H [cluster], hydrophobicity of the hydrophobic cluster of the peptides with the calculation based on the hydrophobicity scales for amino acids <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071687#pone.0071687-Eisenberg1" target="_blank">[29]</a>. pI, isoelectric point. Special features: Important alterations in comparison to the leading structure are highlighted.>increased,</p