a baumannii atcc 17978 genome sequence  (ATCC)

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: Overview of transcriptional responses to iron starvation . The A. baumannii ATCC 17978 transcriptome was compared under iron replete and iron limiting conditions (200 μM DIP). All 3367 genes of the A. baumannii ATCC 17978 genome are represented on the X-axis, ordered according locus tag. Differential expression levels between iron replete and iron limiting conditions are displayed in Log -values on the Y-axis. Up- and down-regulated genes under iron limiting conditions are displayed in the green and red sections, respectively. Gene names or functions have been provided for various highly differentially expressed genes, such as siderophore biosynthesis genes and the fumarases. The putative FUR binding sites displayed in the top section were identified as described in Methods and the nucleotide sequences are listed in Additional file .

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques: Expressing, Binding Assay

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: Putative FUR binding sequences in the ATCC 17978 genome

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques: Binding Assay, Sequencing

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: The optimized A. baumannii FUR motif . Per position, the size of the nucleotide (T in red, A in green, C in blue and G in black) indicates its prevalence in the 22 included sequences from Table 1. The motif shows a palindrome with a central non-conserved nucleotide in position 13 which is indicated by the star. The figure of the A. baumannii ATCC 17978 FUR motif was created using WebLogo 3.0 .

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques:

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: Transcriptional profiling of three siderophore gene clusters identified in A. baumannii ATCC 17978 . Transcriptional alteration of the three siderophore gene clusters to low iron conditions are shown, (A) siderophore gene cluster 1 (A1S_1647-1657), (B) siderophore cluster 2 (A1S_2562-2581) and (C) the acinetobactin gene cluster (A1S_2372-2392). The top arrows show predicted gene function; siderophore biosynthesis in purple, receptors and uptake mechanisms in light orange, efflux pumps in orange and genes of unknown function in white. The relative transcriptional differences between A. baumannii grown under iron replete and iron limiting conditions are depicted in the bottom set of arrows according to the green color scale bar, all values are in times-fold difference. Genes depicted in white were not differentially expressed and those in dark green were overexpressed more than 25-fold. No significant down-regulation was observed within the siderophore gene clusters. Putative FUR boxes are shown as black arrows.

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques:

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: Swarming of A. baumannii ATCC 17978 . A. baumannii colony material was spotted on Luria-Bertani medium containing 0.25% agar. Swarming motility (A) is visible as the channel-like growth around the dense white colony material. The absence of halo growth around the colony (B) indicates lack of swarming motility of A. baumannii when available iron is limited.

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques:

Journal: BMC Genomics

Article Title: Investigation of the human pathogen Acinetobacter baumannii under iron limiting conditions

doi: 10.1186/1471-2164-12-126

Figure Lengend Snippet: Comparison of siderophore cluster 1 in sequenced Acinetobacter isolates . The alignment of siderophore cluster 1 between strain ATCC 17978, ADP1 and SDF. Arrows indicate open reading frames, in black genes with high homology (> 50% identity) and in grey genes with low homology (< 50% identity). White genes represent a 3.5 Kb transposon insertion, which replaced the A1S_1648-1656 orthologs in strain SDF.

Article Snippet: At least four 60 mer DNA oligonucleotides with an average GC % of 41.5, were incorporated into the design for each of the protein coding genes annotated in the ATCC 17978 genome sequence [ ].

Techniques:

Journal: bioRxiv

Article Title: An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus

doi: 10.1101/2022.05.19.492579

Figure Lengend Snippet:

Article Snippet: Further inspection using MLST revealed that the genome belongs to sequence type ST2 in the Institut Pasteur scheme, rather than ST437 as for all other ATCC 17978 genome sequences.

Techniques: