Journal: PLoS ONE

Article Title: Molecular Correlates of Host Specialization in Staphylococcus aureus

doi: 10.1371/journal.pone.0001120

Figure Lengend Snippet: showing (from outside) 1) Scale in basepairs, 2) Mobile elements (red = conserved island, blue = pathogenicity island, pink = putative phage), 3) Ribosomal RNA operons (arrowheads), 4) Homology to other SA genomes, from outside and with color code, dark purple = MRSA252, light purple = MSA553, red = NCTC8325, orange = COL, yellow = Mu50, green = N315, teal = MW2, light blue = MSSA476, 5) ORF homology of ET3-1; navy blue = strong homolog to other SA, light blue = intermediate homolog to other SA, green = weak homolog to other SA, red = non-SA homolog, yellow = no GenBank matches (e-value>10 −5 ), 6) Location of tRNAs (small arrows), 7) ORF direction, light teal = forward strand, dark teal = reverse strand, 8) Microarray data from bovine isolates; light green inner portion = similar ET3 bovine isolates and dark green (outer) = non-ET3 bovine isolates. Yellow lines indicate insertion elements and transposases. 9) GC content = red graph line.

Article Snippet: Probes were synthesized by Illumina (San Diego, CA); dried oligos were resuspended in 3XSSC and spotted in triplicate onto Corning Gaps II aminosaline-coated microarray slides (Corning, Big Flats NY) using a BioRobotics Microgrid II Array Spotter (Genomic Solutions, Ann Arbor MI).

Techniques: Microarray

Journal: PLoS ONE

Article Title: Molecular Correlates of Host Specialization in Staphylococcus aureus

doi: 10.1371/journal.pone.0001120

Figure Lengend Snippet: The ET3-1 genome (blue/multi) was aligned with the microarray probe data from the 10 bovine SA isolates (top section of green histograms) and the Smith-Waterman alignment of the microarray probe with the 8 completely sequenced human SA isolates (bottom section of green histograms). The scale, in nucleotides, is shown in blue. Mobile genetic elements are annotated above each histogram block and ribosomal RNA operons are represented as large white gaps in the green histograms. The purple histogram above the ET3-1 genome representation shows the orientation of the ORFs. For the green microarray and Smith-Waterman alignment histograms, green = present, yellow = divergent, red = absent. For the blue/multi histogram showing ORF homology of ET3-1; navy blue = strong homolog to other SA, light blue = intermediate homolog to other SA, green = weak homolog to other SA, red = non-SA homolog, yellow = no GenBank matches (blastp e-value>10 −5 ).

Article Snippet: Probes were synthesized by Illumina (San Diego, CA); dried oligos were resuspended in 3XSSC and spotted in triplicate onto Corning Gaps II aminosaline-coated microarray slides (Corning, Big Flats NY) using a BioRobotics Microgrid II Array Spotter (Genomic Solutions, Ann Arbor MI).

Techniques: Microarray, Blocking Assay

Journal: PLoS ONE

Article Title: Molecular Correlates of Host Specialization in Staphylococcus aureus

doi: 10.1371/journal.pone.0001120

Figure Lengend Snippet: In total, 47 microarray probes corresponded to gene sequences that are unique to ET3-1 among the sequenced S. aureus genomes. Nearly 94% of these genes were conserved in all of the ET3 isolates, while only 2 of these ‘unique’ genes were conserved among all 11 isolates of bovine origin.

Article Snippet: Probes were synthesized by Illumina (San Diego, CA); dried oligos were resuspended in 3XSSC and spotted in triplicate onto Corning Gaps II aminosaline-coated microarray slides (Corning, Big Flats NY) using a BioRobotics Microgrid II Array Spotter (Genomic Solutions, Ann Arbor MI).

Techniques: Microarray

Journal: PLoS ONE

Article Title: Molecular Correlates of Host Specialization in Staphylococcus aureus

doi: 10.1371/journal.pone.0001120

Figure Lengend Snippet: In the MLST-based cladogram generated by PAUP , at the left, “B” denotes a strain originally isolated from a bovine; “H” denotes isolation from a human. All data associated with “B” strains and MSA553 A are microarray hybridization data; all remaining “H” strains show the results of in silico Smith-Waterman alignment of the 70mer microarray probe to the genome sequence. Red = absent, yellow = indeterminable/variable, green = present. OPtrans = oligopeptide transporter island and Ebh = region of probes representing the ebh gene or gene remnants+probes for 6 gene insertion in ET3-1. The white boxes within the SaPIbov1 and SaPIbov3 islands show gene clusters that were consistently absent from strains associated with human infection and largely conserved in strains recovered from bovine sources, including those that more closely resemble the isolates from humans.

Article Snippet: Probes were synthesized by Illumina (San Diego, CA); dried oligos were resuspended in 3XSSC and spotted in triplicate onto Corning Gaps II aminosaline-coated microarray slides (Corning, Big Flats NY) using a BioRobotics Microgrid II Array Spotter (Genomic Solutions, Ann Arbor MI).

Techniques: Generated, Isolation, Microarray, Hybridization, In Silico, Sequencing, Infection