Additional file 1 of seq-seq-pan: building a computational pan-genome data structure on whole genome alignment

Supplementary Information for “seq-seq-pan”: Building a computational pan-genome data structure on whole genome alignment”. Additional file 1 provides details on implementation of the sequential workflow for whole genome alignment. (PDF 183 kb

Additional file 2: of Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

Table S1. Metadata of the 107 German carbapenemase-producing, clinical Klebsiella isolates, 2008-2014. Isolates were ordered by carbapenemase type. For more information see main text document. (XLSX 54 kb

Additional file 1: of Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

Figure S1. Origin of the 107 German carbapenemase-producing K. pneumoniae isolates. Regions are shown, where isolates originated from. Isolates from Saxony could not be elucidated further due to the lack of additional geographic information. Number of isolates is given by the size of the circle (see legend). Image is from: © Bundesamt für Kartographie und Geodäsie, Frankfurt am Main, Germany. Figure S2. Virulence gene content in 107 carbapenemase-producing K. pneumonaie isolates from Germany. Data are given in % of isolates showing possession of the corresponding gene cluster. The graph shows four most frequent virulence genes identified in more than one single isolate. Figure S3. Detailed view of the ML tree concerning ST258/ST512 – carbapenemase-producing K. pneumoniae isolates from Germany, 2008-2014. The image shows a subtree of Fig. 3 containing 52 isolates of ST258 (light violett) and ST512 (grey). Colour codes of the inner ring designate the corresponding carbapenemase type, the outer designates the wzi allele (see legend). Figure S4. ML tree of NGS-based analysis of German K. pneumoniae isolates and isolates from an international collection - detailed view of the cluster ST258/ST512 isolates. The image shows a subtree of Fig. 4 containing 66 isolates of ST258 and ST512. Colour codes of the inner ring correspond to the origin of strains, the middle ring to the carbapenemase KPC-2 or KPC-3, and the outer ring demonstrates the wzi allele type. (PPTX 1367 kb

Additional file 3: of Genome-based analysis of Carbapenemase-producing Klebsiella pneumoniae isolates from German hospital patients, 2008-2014

Table S2. Names and sequences of used primers for MLST and PCR amplification of virulence genes and β-lactamase genes. Table S3. Identified virulence genes in K. pneumoniae isolate no. 316/15 (ST23, OXA-48). Table S4. Identified wzi alleles from NGS data of 107 carbapenemase-producing K. pneumoniae from Germany. (DOCX 35 kb

<i>Aureolib</i> — A Proteome Signature Library: Towards an Understanding of <i>Staphylococcus aureus</i> Pathophysiology

<div><p>Gel-based proteomics is a powerful approach to study the physiology of <i>Staphylococcus aureus</i> under various growth restricting conditions. We analyzed 679 protein spots from a reference 2-dimensional gel of cytosolic proteins of <i>S. aureus</i> COL by mass spectrometry resulting in 521 different proteins. 4,692 time dependent protein synthesis profiles were generated by exposing <i>S. aureus</i> to nine infection-related stress and starvation stimuli (H₂O₂, diamide, paraquat, NO, fermentation, nitrate respiration, heat shock, puromycin, mupirocin). These expression profiles are stored in an online resource called <i>Aureolib</i> (<a href="http://www.aureolib.de" target="_blank">http://www.aureolib.de</a>). Moreover, information on target genes of 75 regulators and regulatory elements were included in the database. Cross-comparisons of this extensive data collection of protein synthesis profiles using the tools implemented in <i>Aureolib</i> lead to the identification of stress and starvation specific marker proteins. Altogether, 226 protein synthesis profiles showed induction ratios of 2.5-fold or higher under at least one of the tested conditions with 157 protein synthesis profiles specifically induced in response to a single stimulus. The respective proteins might serve as marker proteins for the corresponding stimulus. By contrast, proteins whose synthesis was increased or repressed in response to more than four stimuli are rather exceptional. The only protein that was induced by six stimuli is the universal stress protein SACOL1759. Most strikingly, cluster analyses of synthesis profiles of proteins differentially synthesized under at least one condition revealed only in rare cases a grouping that correlated with known regulon structures. The most prominent examples are the GapR, Rex, and CtsR regulon. In contrast, protein synthesis profiles of proteins belonging to the CodY and σ^B regulon are widely distributed. In summary, <i>Aureolib</i> is by far the most comprehensive protein expression database for <i>S. aureus</i> and provides an essential tool to decipher more complex adaptation processes in <i>S. aureus</i> during host pathogen interaction.</p></div

Studies investigating TPTD and PCA in RRT.

<p>Studies investigating TPTD and PCA in RRT.</p

Boxplots comparing thermodilution derived cardiac index (CItd) values over time.

<p>Boxplots comparing thermodilution derived cardiac index (CItd) values over time.</p

Stress experiments included in the proteome signature library.

1<p>CDM = chemically defined medium.</p

Boxplots comparing global end-diastolic volume index (GEDVI) values over time.

<p>Boxplots comparing global end-diastolic volume index (GEDVI) values over time.</p

Intra-experimental comparison of protein synthesis patterns in response to different stimuli.

<p>Quantification data for all detected protein spots were normalized (total) and standardized (z-score). Significant changes of spot intensities were determined for each experiment (ANOVA, α = 0.1, distribution based on 1000 permutations) and the corresponding expression values were used for hierarchical sample clustering (HCL, Euclidean distance, complete linkage). Accordingly, the stimuli can be divided into two classes: (<b>A</b>) Stimuli causing continuous changes of the protein synthesis pattern and (<b>B</b>) stimuli transiently affecting the protein synthesis pattern.</p