Additional file 7: of Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

Multilocus supertree orthologues and 16S rRNA genes list. List of locus tag identifiers and predicted functions of 596 orthologous protein sequences which were concatenated to generate the multilocus supertree and list of locus tag identifiers used to generate the 16S rRNA tree. (XLSX 34 kb

Additional file 6: of Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

Pearce assay growth curves. Pearce assay growth curves of representative strains; [A] L. lactis subsp. cremoris JM1, [B] L. lactis subsp. cremoris JM4, [C] L. lactis subsp. cremoris JM3, [D] L. lactis subsp. cremoris JM2, [E] L. lactis subsp. lactis 229, [F] L. lactis subsp. lactis UC063, [G] L. lactis subsp. cremoris SK11, [H] L. lactis subsp. cremoris UC109, [I] L. lactis subsp. cremoris 158, [J] L. lactis subsp. lactis UC77, [K] L. lactis subsp. lactis 275, [L] L. lactis subsp. lactis 184. Black lines represent growth under Pearce assay conditions (Temperature: 32 °C for 70 min, 32–38 °C for 30 min, 38 °C for 160 min, 32 °C for 40 min). Red (subsp. cremoris) and blue (subsp. lactis) lines represent controls grown at 30 °C for 300 min. (PPTX 96 kb

Additional file 3: of Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation

Unique gene family list. List of locus tag identifiers and predicted functions of unique gene families identified by MCL clustering. (XLSX 24 kb

Undercooling and rapid solidification of Cu84Co16 alloys under a static magnetic field

Bulk samples of Cu84Co16 composition were undercooled and rapidly solidified using the electromagnetic levitation technique under a static magnetic field of 2 T. A droplet-shaped microstructure was frozen in due to metastable phase separation in the undercooled liquid. A singular droplet size distribution was determined for the minority Co-rich phase, which differed from a bimodal one observed in the samples levitated without the static magnetic field. Such an effect of the magnetic field was found to be similar to that of reduced gravity of parabolic flights

Additional file 7: Figure S4. of Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

B. breve sRNA expression. Artemis plot showing the sRNA transcription in B. breve of a) Ribonuclease P, b) tmRNA, and c) 4.5S SRP RNA. In all cases tiling array signals of forward (red) and reverse (blue) strand are indicated. (PDF 701 kb

Phylogenomics of <i>Lactobacillus rossiae</i> DSM 15814^T.

<p>A) 16S neighbor-joining (NJ) tree, resulting from the alignment of the 16S rRNA-encoding gene of <i>L. rossiae</i> DSM 15814^T and that of 20 selected representatives of the <i>Lactobacillus</i> genus (<i>L. amylovorus</i> GRL 1112, <i>L. acidophilus</i> 30SC, <i>L. kefiranofaciens</i> ZW3, <i>L. crispatus</i> ST1, <i>L. helveticus</i> DPC 4571, <i>L. gasseri</i> ATCC 33323, <i>L. johnsonii</i> NCC 533, <i>L. delbrueckii</i> subsp. <i>bulgaricus</i> ATCC 11842, <i>L. sakei</i> subsp. <i>sakei</i> 23K, <i>L. rhamnosus</i> ATCC 8530, <i>L. paracasei</i> subsp. <i>paracasei</i>, <i>L. casei</i> ATCC334, <i>L. ruminis</i> ATCC 27782, <i>L. salivarius</i> UCC118, <i>L. fermentum</i> IFO 3956, <i>L. reuteri</i> DSM 20016, <i>L. plantarum</i> WCFS1, <i>L. brevis</i> ATCC 367, <i>L. buchneri</i> NRRL B-30929 and <i>L. sanfranciscensis</i> TMW 1.1304). The corresponding 16S rRNA-specifying sequence of <i>Bifidobacterium breve</i> UCC2003 was used as an outgroup. The positioning of <i>L. rossiae</i> DSM 15814^T within the <i>Lactobacillus</i> genus is indicated in red. B) Multilocus supertree resulting from the alignment of the sequence of three housekeeping genes (<i>groEL</i>, <i>dnaK</i> and <i>grpE</i>) of <i>L. rossiae</i> DSM 15814^T and 20 selected representatives of the <i>Lactobacillus</i> genus (see above for the species). The positioning of <i>L. rossiae</i> DSM 15814^T within the <i>Lactobacillus</i> genus is indicated in red. C) Multilocus supertree resulting from the alignment of 96 selected orthologous genes of <i>L. rossiae</i> DSM 15814^T and 20 selected representatives of the <i>Lactobacillus</i> genus (see above for the species). The positioning of <i>L. rossiae</i> DSM 15814^T within the <i>Lactobacillus</i> genus is indicated in red.</p

Luminescence signal of the <i>V. harveyi</i> BB170 biosensor strain in the presence of sterile and neutralized supernatant of <i>B. breve</i> UCC2003, the insertion mutant <i>B. breve</i> UCC2003-luxS and the complemented strain <i>B. breve</i> UCC2003-luxS [pBC1.2luxS].

<p>Data obtained with <i>E. coli</i> DH5α (a strain not producing AI-2) and a medium-only control are included as reference. Data shown are means ± SEM. (*, luminescence is significantly lower than than produced with supernatant of <i>B. breve</i> UCC2003, p<0.05, compared to WT; n = 3).</p

Comparison of the <i>lux</i>S genetic loci of <i>B. breve</i> UCC2003 with corresponding <i>lux</i>S loci from other sequenced bifidobacteria.

<p>Each solid arrow indicates an open reading frame. The lengths of the arrows are proportional to the length of the predicted open reading frame. The colour coding which is indicative of putative function, is indicated within the arrow. Orthologs are marked with the same colour while the amino acid identity of each predicted protein is indicated as a percentage relative to its equivalent protein encoded by <i>B. breve</i> UCC2003.</p

Relative survival of <i>Salmonella</i>-infected <i>C. elegans</i> nematodes to which <i>B. breve</i> UCC2003 WT or mutants UCC2003-bfeU or UCC2003-bfeB were administered (24 h {blue bars} and 48 h {white bars} after <i>Salmonella</i> infection).

<p>Data shown are means ± SEM. Control: infected nematodes that have not been administered any bifidobacteria. (*  =  significantly different as compared to the control, p<0.05; n = 3).</p

Biosynthesis of riboflavin and folate.

<p>Reconstruction of the biosynthesis of riboflavin (A) and folate (B) in <i>L. rossiae</i> DSM 15814^T. Growth and acidification (ΔpH) of DSMZ 15184^T at 30°C for 18 h (C). LDMIIIG, modified semi-defined medium LDMIIIG; vitamin-free, LDMIIIG without added vitamins; folate-free, LDMIIIG without folate; riboflavin-free, LDMIIIG without riboflavin. Data are the means of three separate experiments performed in triplicate.</p