Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: General features of NRG857c genome and other E. coli strains

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques: Plasmid Preparation

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Phylogenetic analysis of NRG857c compared with representative strains of other enteric bacteria . (A) A phylogenetic tree based on the unweighted pair group method with arithmetic mean was constructed from the optimal map data and in silico Nco I restriction digests of other enteric bacterial chromosomes. (B) MLST-based analysis of NRG857c with other enteric bacteria was performed as described in the Methods and sequence data was used to construct a phylogenetic tree. Numbers on the tree branches represent bootstrap support from 1000 bootstrap replicates with a minimum cut-off of 65%. Accession numbers for gene sequences can be found in Additional File , Table S1.

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques: Bacteria, Construct, In Silico, Sequencing

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Comparative genome atlas of NRG857c . The chromosome of NRG857c (two outermost rings are CDS on forward and reverse strand) was compared with those of selected E. coli strains, starting from the outer layer LF82 (AIEC; pale green), APEC-O1 (APEC; blue), CFT073 (UPEC; yellow), MG1655 (K12/commensal; purple) and enterohemorrhagic E. coli O157:H7 Sakai (EHEC, red). Genomic islands were plotted on the NRG857c chromosome (grey blocks). The G+C content and G/C skew are also plotted as indicated.

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques:

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Genomic islands in NRG857c . Genomic islands in the NRG857c chromosome (A) and plasmid (B) were predicted using stringent bioinformatics criteria as described in the Methods. Genomic islands are plotted to scale in blue and labelled clockwise on the genome maps. On the plasmid, genes involved in antimicrobial resistance are indicated in red.

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques: Plasmid Preparation

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Putative virulence factors in NRG857c genome

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques: Membrane, Lysis, Binding Assay, Plasmid Preparation

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Type VI secretion system core proteins in NRG857c

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques:

Journal: BMC Genomics

Article Title: Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

doi: 10.1186/1471-2164-11-667

Figure Lengend Snippet: Iron uptake by the aerobactin system is important for intracellular survival and for mouse colonization . (A) J774.A1 macrophage cells were infected with wild type NRG857c or iutA mutant cells. The survival of intracellular bacteria was determined at various times after infection. Data are the mean survival of intracellular bacteria with standard deviation. (*, P < 0.05, Mann Whitney) (B) The aerobactin iron transport system improves colonization in vivo . Groups of mice were infected orally with wild type NRG857c or iutA mutants. Colonization of the small intestine by NRG857c AIEC was determined three days after infection by enumerating the number of cfu in tissue homogenates. Data are the means with standard errors. (**, P < 0.005, Mann Whitney).

Article Snippet: Unweighted Pair-Group Method using Arithmetic averages (UPGMA) similarity clustering of the restriction fragments generated in the whole genome optical map of NRG857c with in silico maps of publicly available E. coli isolates was performed using MapSolver version 2.1.1 (OpGen Inc., Madison, WI).

Techniques: Infection, Mutagenesis, Bacteria, Standard Deviation, MANN-WHITNEY, In Vivo