Journal: Applied and Environmental Microbiology

Article Title: Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

doi: 10.1128/AEM.01159-15

Figure Lengend Snippet: Characteristics of strains examined in this study a

Article Snippet: Selective filtering of variable orthologs identified 143 clade-specific genes that were present in at least 7 out of 8 available C. sporogenes -clade genomes (strains 11579, 85-3852, 88-0163, ATCC 15579, 87-0535, PA3679, Osaka05, and Okyama2011) and absent in the genomes associated with the group I C. botulinum clade ( ).

Techniques: Mutagenesis

Journal: Applied and Environmental Microbiology

Article Title: Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

doi: 10.1128/AEM.01159-15

Figure Lengend Snippet: C. sporogenes clade-specific gene signatures

Article Snippet: Selective filtering of variable orthologs identified 143 clade-specific genes that were present in at least 7 out of 8 available C. sporogenes -clade genomes (strains 11579, 85-3852, 88-0163, ATCC 15579, 87-0535, PA3679, Osaka05, and Okyama2011) and absent in the genomes associated with the group I C. botulinum clade ( ).

Techniques: Modification, Histone Deacetylase Assay

Journal: Applied and Environmental Microbiology

Article Title: Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

doi: 10.1128/AEM.01159-15

Figure Lengend Snippet: Core gene phylogenetic trees of C. sporogenes and C. botulinum genomes. An initial tree was based on the maximum-likelihood distance calculated from the alignment of 179 shared orthologous genes of C. sporogenes and C. botulinum groups I, II, and III. The tree in the inset was based on the maximum-likelihood distance calculated from the alignment of 1,451 shared orthologous genes restricted to C. sporogenes and group I C. botulinum. Specific clades discussed in the text are labeled. The BoNT produced by each strain in indicated in brackets (NT, nontoxic). Genomes sequenced in this study are in red. Additional genome sequences were retrieved from GenBank.

Article Snippet: Selective filtering of variable orthologs identified 143 clade-specific genes that were present in at least 7 out of 8 available C. sporogenes -clade genomes (strains 11579, 85-3852, 88-0163, ATCC 15579, 87-0535, PA3679, Osaka05, and Okyama2011) and absent in the genomes associated with the group I C. botulinum clade ( ).

Techniques: Labeling, Produced

Journal: Applied and Environmental Microbiology

Article Title: Implications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy

doi: 10.1128/AEM.01159-15

Figure Lengend Snippet: Hierarchical clustering based on the presence or absence of variable orthologs. (A) The presence (yellow) or absence (black) of variable orthologs (n = 16,412) in C. sporogenes and C. botulinum group I genomes was used to perform hierarchical clustering using a complete linkage across a centered Pearson correlation. (B) Identification of 143 orthologs genes that are present in the genomes of 7 out of 8 C. sporogenes strains and 91 genes that are present in 11 out of 13 group I C. botulinum strains.

Article Snippet: Selective filtering of variable orthologs identified 143 clade-specific genes that were present in at least 7 out of 8 available C. sporogenes -clade genomes (strains 11579, 85-3852, 88-0163, ATCC 15579, 87-0535, PA3679, Osaka05, and Okyama2011) and absent in the genomes associated with the group I C. botulinum clade ( ).

Techniques:

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Distinction between the Cfr Methyltransferase Conferring Antibiotic Resistance and the Housekeeping RlmN Methyltransferase

doi: 10.1128/AAC.00448-13

Figure Lengend Snippet: Origin of cfr -like and rlmN -like genes and modification activities at A2503 in 23S RNA

Article Snippet: Gene label Protein name Host organism a Modification(s) Reference(s) cfr Cfr Staphylococcus ( Ec ) m 8 A2503 and m 2 A2503 1 , 9 clba ClBa Bacillus amyloliquefaciens ( Ec ) m 8 A2503 b 7 clbc ClBc Bacillus clausii ( Ec ) m 8 A2503 b 7 clbb ClBb Brevibacillus brevis NBRC 100599 ( Ec ) m 8 A2503 b 7 clcs ClCs Clostridium sporogenes ATCC 15579 c ( Ec ) None This study clpa ClPa Paenibacillus sp. Y412MC10 c (Ec ) m 8 A2503 This study rlmN/yfgB RlmN E. coli m 2 A2503 2 , 11 , 37 Staphylococcus aureus NWMN_1128 mA2503 d 2 Thermus thermophilus HB8 m 2 A2503 36 , this study Bacillus subtilis subsp. subtilis 168 m 2 A2503 This study Deinococcus radiodurans m 2 A2503 35 nlbb NlBb Brevibacillus brevis NBRC 100599 ( Ec ) m 2 A2503 e This study Open in a separate window a Ec is added in parentheses if the modification was investigated in E. coli . b Based on phenotype and primer extension, no information on additional m 2 A2503 modification. c The gene sequences have been modified to suit codon usage in E. coli for optimal expression. d Methylation assignment based on the primer extension stop. e C-2 methylation is assumed as it is an adenine methylation but not m 8 A.

Techniques: Modification