Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: General genomic characteristics of sequenced genomes of B. animalis subspecies

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: progressiveMauve alignments of sequenced strains of B. animalis. Pairwise alignments with the genome of B. animalis subsp. lactis ATCC 27673 were made using progressiveMauve. All strains are B. animalis subsp. lactis, except for ATCC 25527, which is B. animalis subsp. animalis. All sequences used in this analysis are complete and publicly available. Boxes 1 to 6, genomic islands 1 to 6, respectively.

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: Shared and unique genes between three groups of B. animalis. Unique genes were identified as having less than 60% amino acid similarity between any pair of strains. On the basis of the similarity of the sequenced B. animalis subsp. lactis genomes, Bl-04 was chosen as a representative of the group.

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: Genomic islands present in B. animalis subsp. lactis ATCC 27673. Genomic islands identified in B. animalis subsp. lactis ATCC 27673 (bottom row in each section) were compared to those identified in B. animalis subsp. lactis Bl-04 (top row in each section). Red arrows, sugar transport genes; green arrows, mobile genetic elements; black arrows, CRISPR-associated genes; white arrows, hypothetical genes or genes not specified. Aligned genes from Bl-04 and ATCC 27673 represent the gene homology flanking the genomic islands. Data for other genomic islands are presented in Fig. S3 in the supplemental material.

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques: CRISPR

Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: Total SNPs identified between strains of B. animalis subsp. lactis

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques:

Journal: Applied and Environmental Microbiology

Article Title: Bifidobacterium animalis subsp. lactis ATCC 27673 Is a Genomically Unique Strain within Its Conserved Subspecies

doi: 10.1128/AEM.01777-13

Figure Lengend Snippet: (Top) CRISPR-cas system of B. animalis subsp. lactis ATCC 27673 and comparison to similar systems. Gene similarity represents the percent amino acid similarity between genes of the same assigned function. (Bottom) In addition, repeats from the CRISPR array were aligned with matches to ATCC 27673, highlighted by connecting lines. ATCC 27673, B. animalis subsp. lactis ATCC 27673; ATCC 25527, B. animalis subsp. animalis ATCC 25527; DSM 20098, B. angulatum DSM 20098.

Article Snippet: Three homologs of these genes were identified in the genome of Bifidobacterium dentium Bd1 by BLAST analysis of the nonredundant database (BDP_125, BDP_126, and BDP_127), as Blac_00780 and Blac_00785 share a high degree of similarity to BDP_125 ( 35 ). fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Fig 3 caption a7 Genomic islands present in B. animalis subsp. lactis ATCC 27673.

Techniques: CRISPR

Journal: bioRxiv

Article Title: Clathrin-coated Pits are Shredded Organelles Presorting Receptors in the Plasma Membrane

doi: 10.1101/491670

Figure Lengend Snippet: (A-J) TIRFM images of EGFP-CLC and JF549-labeled SNAP-adaptors (CLC, Cav1, AP2μ2, FCHO, Epsin2, EPS15, EPS8, PICALM, HIP1R and GRB2) ( upper panels ) for the analysis of colocalization between CCPs and the clusters of each adaptor in a single living cell. The individual clusters of each adaptor objectively detected using the particle detection algorithm (magenta dots) are displayed ( lower panels ). (K) The quantitative analysis of the colocalization ratios of CCPs with the clusters of each adaptor. The colocalization ratio of CCPs with EGFRs is shown (a red dashed line). (L) A histogram for the colocalization ratio of CCPs with EGFR after the knock-down of the indicated adaptors. (M, N) Maps showing conditional probability of the CCP subsets containing PICALM (red dots), given the subset containing EGFR (blue circles) (M) or vice versa (N). (O) An independence test for the events between the CCP subsets containing EGFR and the indicated adaptors, respectively. Error bars denote s.e.m. at the single-cell level (n > 5). Scale bars, 5 μm. *p < 0.01 (Student’s t -test).

Article Snippet: Eps15-mCherry (Addgene plasmid #27696), AP2μ2-mCherry (Addgene plasmid #27672), FCHo1-mCherry (Addgene plasmid #27690), Epsin2-mCherry (Addgene plasmid #27673), Eps8-mCherry (Addgene plasmid # 29779), and Hip1R-tDimerRFP (Addgene plasmid #27700) were a gift from Christien Merrifield.

Techniques: Labeling