Journal: Scientific Reports

Article Title: MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

doi: 10.1038/s41598-020-75960-3

Figure Lengend Snippet: Phage typing of Brucella isolates. Presented are the phage lysis patterns of the B. canis isolates after incubation with the bacteriophages Tb, Wb, BK2, F1, F25, Iz, Fi, and R/C. Black squares indicate lysis of the bacteria, and white squares indicate no lysis; v: variable. The phage lysis patterns of the reference strains B. canis RM6/66, B. melitensis 16 M, B. abortus 544, and B. suis 1330 are shown as determined in our study.

Article Snippet: Assembly quality was analyzed using Quast v4.5 by comparison to the type strain B. canis ATCC 23,365 genome (GenBank file GCF_000018525.1, accession no. NC_010103.1 for chromosome 1 and accession no. NC_010104.1 for chromosome 2 with a genome size of 3,312,769 bp in total).

Techniques: Lysis, Incubation, Bacteria

Journal: Scientific Reports

Article Title: MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

doi: 10.1038/s41598-020-75960-3

Figure Lengend Snippet: Identification of Brucella canis from diseased dogs by MALDI-TOF MS. ( A ) Comparison of pre-processed and normalized spectra of the reference strain B. canis RM 6/66 and a representative isolate from the kennel under investigation in the m/z range 3–12 kDa; ( B ) Gel view depiction of averaged group spectra. Arrows indicate m/z positions with high divergence in either intensity or mass-to-charge ratio between B. canis , B. suis bv 4 and B. suis bv 1; ( C ) A biomarker for discrimination of B. canis and B. suis bv 4 versus B. suis bv 1 found by Karger et al. and its double ( D ) and triple charged ( E ) ions (both from this study); ( F ) The mass peak at m/z 7073 is a unique biomarker for the group B. canis and B. suis bv 4; ( G ) B. canis and B. suis bv 4 may be discriminated from B. suis bv 1 by their higher intensity mass peaks at m/z 7661 (single charged) and ( H ) m/z 3830 (double charged). ( I + J ) Peaks at m/z 5900 and m/z 3926 discriminate B. canis from B. suis bv 4.

Article Snippet: Assembly quality was analyzed using Quast v4.5 by comparison to the type strain B. canis ATCC 23,365 genome (GenBank file GCF_000018525.1, accession no. NC_010103.1 for chromosome 1 and accession no. NC_010104.1 for chromosome 2 with a genome size of 3,312,769 bp in total).

Techniques: Comparison, Biomarker Discovery

Journal: Scientific Reports

Article Title: MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

doi: 10.1038/s41598-020-75960-3

Figure Lengend Snippet: Consensus genome sequence of the Brucella canis outbreak strain from a kennel in São Paulo, Brazil . Shown are the two chromosomes of the B. canis BfR-SPBR-consensus genome derived from whole genome sequencing results of four B. canis isolates. The genomes were sequenced using Illumina NGS technology. The open reading frames (CDS) determined by Prokka v1.12 are presented in the two outer circles with grey (+ strand) and black (-strand) boxes. Positions with nucleotide sequence variations in the B. canis BfR-SPBR-consensus genome compared to the reference strain B. canis ATCC 23365 are depicted in the inner circle and marked with the colors red (stop-loss variants), orange (missense variants), blue (upstream or downstream variants) and green (synonymous variants). Open reading frames affected by missense variants or stop-loss variants are shown in red together with the corresponding protein IDs given as NCBI numbers (WP_xxxxxxxxx.1).

Article Snippet: Assembly quality was analyzed using Quast v4.5 by comparison to the type strain B. canis ATCC 23,365 genome (GenBank file GCF_000018525.1, accession no. NC_010103.1 for chromosome 1 and accession no. NC_010104.1 for chromosome 2 with a genome size of 3,312,769 bp in total).

Techniques: Sequencing, Derivative Assay

Journal: Scientific Reports

Article Title: MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

doi: 10.1038/s41598-020-75960-3

Figure Lengend Snippet: Phylogenetic comparison of the Brucella canis BfR-SPBR-consensus strain newly identified in São Paulo with isolates from worldwide outbreaks. The genetic relationship between the outbreak strain B. canis BfR-SPBR-consensus and previously sequenced B. canis strains was determined by SNP analysis. The genome sequences were analyzed with ParSNP, FastTree2 and iTol. The B. suis outgroup strain and the B. canis outbreak strain under study are marked in bold. Shown is a neighbor-joining phylogenetic tree with the branch length displaying the relative genetic distance. All bootstrap support values were either below 0.5 or above 0.8.

Article Snippet: Assembly quality was analyzed using Quast v4.5 by comparison to the type strain B. canis ATCC 23,365 genome (GenBank file GCF_000018525.1, accession no. NC_010103.1 for chromosome 1 and accession no. NC_010104.1 for chromosome 2 with a genome size of 3,312,769 bp in total).

Techniques: Comparison

Journal: Scientific Reports

Article Title: MALDI-TOF MS and genomic analysis can make the difference in the clarification of canine brucellosis outbreaks

doi: 10.1038/s41598-020-75960-3

Figure Lengend Snippet: Distribution of single-nucleotide polymorphisms (SNPs) in South American Brucella canis isolates. The positions of SNPs in the genomes of South American B. canis strains are shown in comparison to the reference strain B. canis ATCC 23365. The two chromosomes of the B. canis isolates are color-coded and the background colors show the geographical origin for each strain. The strains are presented in the following order from inside to outside: 10469 (1), B. canis BfR-SPBR-consensus (2), 07-2859-6070 (3), CNBG 1324 (4), 07-2859-6071 (5), CNGB 513 (6), SCL (7), Oliveri (8), CNGB 1172 (9) and ATCC 23365 (10). SNPs are shown as colored strokes in red (stop-loss variants), in light pink (stop-gain variants), orange (missense variants), blue (upstream or downstream variants) and green (synonymous variants).

Article Snippet: Assembly quality was analyzed using Quast v4.5 by comparison to the type strain B. canis ATCC 23,365 genome (GenBank file GCF_000018525.1, accession no. NC_010103.1 for chromosome 1 and accession no. NC_010104.1 for chromosome 2 with a genome size of 3,312,769 bp in total).

Techniques: Comparison

Journal: BMC Plant Biology

Article Title: An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches

doi: 10.1186/1471-2229-9-101

Figure Lengend Snippet: Types and frequency of complex T-DNA insertion events within the SK population . Complex T-DNA integration events fell into ten classes, differentiated by the number of times a border sequence was present, the presence of Ti plasmid or internal T-DNA sequence and the strand orientation. Red and blue boxes indicate the left and right border sequences, respectively. Green boxes represent pSKI015 backbone sequence, and the arrowhead shows the priming site that generated the observed FST sequence.

Article Snippet: For each SK-FST line the DNA sequencing trace files were warehoused in APED http://sourceforge.net/projects/aped .

Techniques: Sequencing, Plasmid Preparation, Generated

Journal: BMC Plant Biology

Article Title: An archived activation tagged population of Arabidopsis thaliana to facilitate forward genetics approaches

doi: 10.1186/1471-2229-9-101

Figure Lengend Snippet: Web interface for the display of FST sequence features in the context of the A. thaliana genome http://aafc-aac.usask.ca/fst/ . A 5 kb view around a T-DNA insertion harboured by the SK6478 line is shown. FST sequences are visualized using a standard GBrowse genome viewer (A). Users may obtain detailed sequence information (B) from our sequence portal including sequence traces (C).

Article Snippet: For each SK-FST line the DNA sequencing trace files were warehoused in APED http://sourceforge.net/projects/aped .

Techniques: Sequencing