Journal: RNA Biology

Article Title: Conserved small mRNA with an unique, extended Shine-Dalgarno sequence

doi: 10.1080/15476286.2016.1256534

Figure Lengend Snippet: Putative rreB homologs in Rhodobacterales . (A) Multiple sequence alignment of sequences corresponding to the putative small mRNAs containing homologous sORFs of 18 codons (named rreR ) and preceded by a region with extended complementarity to the 3′-end of 16 sRNA (Extended SD region). Canonical SD, GTG start codon and stop codons are highlighted in gray. For other descriptions see (Fig. 2A . (B) Multiple sequence alignment of the small proteins RreR encoded by the sORFs shown in A). O.ar.238, Octadecabacter arcticus 238; O.an.307, Octadecabacter antarcticus 307; J.sp.1, Jannaschia sp CCS 1; Ros.e.19469, Roseibacterium elongatum DSM 19469; Ro.d.114, Roseobacter denitrificans OCh 114; Ro.l.149, Roseobacter litoralis Och 149; D.s.12, Dinoroseobacter shibae DFL 12; P.t.23, Planktomarina temperata RCA 23; Ph.g.26640, Phaeobacter gallaeciensis DSM 26640; Ph.i.17395, Phaeobacter inhibens DSM 17395; Pa.a.7686, Paracoccus aminophilus JCM 7686; R.c.1003, Rhodobacter capsulatus SB 1003; Pa.d 1222, Paracoccus denitrificans PD 1222; Rh.s.2351, Rhodovulum sulfidophilum DSM 2351; C.i.P73, Celeribacter indicus strain P73; R.s.2.4.1., Rhodobacter spaheroides ATCC 2.4.1. (C) Predicted spatial structure of RreR from D. shibae DFL 12.

Article Snippet: O.ar.238, Octadecabacter arcticus 238; O.an.307, Octadecabacter antarcticus 307; J.sp.1, Jannaschia sp CCS 1; Ros.e.19469, Roseibacterium elongatum DSM 19469; Ro.d.114, Roseobacter denitrificans OCh 114; Ro.l.149, Roseobacter litoralis Och 149; D.s.12, Dinoroseobacter shibae DFL 12; P.t.23, Planktomarina temperata RCA 23; Ph.g.26640, Phaeobacter gallaeciensis DSM 26640; Ph.i.17395, Phaeobacter inhibens DSM 17395; Pa.a.7686, Paracoccus aminophilus JCM 7686; R.c.1003, Rhodobacter capsulatus SB 1003; Pa.d 1222, Paracoccus denitrificans PD 1222; Rh.s.2351, Rhodovulum sulfidophilum DSM 2351; C.i.P73, Celeribacter indicus strain P73; R.s.2.4.1., Rhodobacter spaheroides ATCC 2.4.1. (C) Predicted spatial structure of RreR from D. shibae DFL 12.

Techniques: Sequencing

Journal: Studies in Mycology

Article Title: What can comparative genomics tell us about species concepts in the genus Aspergillus ?

doi: 10.3114/sim.2007.59.02

Figure Lengend Snippet: Major characteristics and genetic diversity of the Aspergillus genomes.

Article Snippet: Strain/Isolate , Af293 , A1163 , ATCC 1015 , CBS 513.88 , NRLL 3357 , ATCC 42149 , Af293 , NRRL 181.

Techniques:

Journal: PLoS ONE

Article Title: Plasmidome Interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum Converts Strains of Independent Lineages into Distinctly Different Pathogens

doi: 10.1371/journal.pone.0107777

Figure Lengend Snippet: Representation of plasmid groups and the plasmid distribution in analyzed strains.

Article Snippet: Libraries of strains BKT75002, BKT2873, 16868, CCUG 7971, NCTC 9693, NCTC 8350, NCTC 9691, ATCC 27606, K25 and DC5 were prepared using the Nextera XT DNA Sample Preparation kit (Illumina, San Diego, USA) and paired-end sequenced (2×250 bp) on an Illumina MiSeq Benchtop Sequencer, with approximately 300 bp inserts.

Techniques: Plasmid Preparation

Journal: Scientia Pharmaceutica

Article Title: Synthesis and Anticancer Activity of 2-(Alkyl-, Alkaryl-, Aryl-, Hetaryl-)-[1,2,4]triazolo[1,5- c ]quinazolines

doi: 10.3797/scipharm.1211-08

Figure Lengend Snippet: Percentage of in vitro tumor cell lines growth at 10 μM for compounds

Article Snippet: 5.10 , , 57.02 , −10.11–120.31 , 25.07 (A549/ATCC/nscLC), 56.27 (HOP-62/nscLC), 11.95 (HOP-92/nscLC), 58.89 (NCI-H23/nscLC), 20.32 (NCI-H460/nscLC), 40.58 (NCI-H522/nscLC), 44.03 (HCT-116/ColC), 43.63 (HCT-15/ColC), 47.67 (HT29/ColC), 42.78 (KM12/ColC), 32.84 (SW-620/ColC), 58.28 (BT-549/BC), 29.74 (MCF7/BC), 64.37 (MDA-MB-231/ATCC/BC), −10.11 (MDA-MB-435/BC), 21.67 (NCI/ADR-RES/BC), 46.30 (IGROV1/OV), 34.97 (OVCAR-3/OV), 23.63 (OVCAR-8/OV), 64.14 (CCRF-CEM/L), 59.79 (HL-60(TB)/L), 30.84 (K-562/L), 47.76 (RPMI-822/L), 14.20 (SR/L), 66.99 (786-0/RC), 44.33 (CAKI-1/RC), 10.54 (RXF 393/RC), 65.31 (UO-31/RC), 57.67 (LOX IMVI/M), 55.63 (M14/M), 57.27 (SK-M EL-28/M), 28.78 (SK-MEL-5/M), 60.50 (UACC-257/M), 65.67 (UACC-62/M), 58.40 (SF-268/CNSC), 29.74 (SF-295/CNSC), 65.45 (SF-539/CNSC), 67.66 (SNB-19/CNSC), 41.59 (SNB-75/CNSC).

Techniques: In Vitro

Journal: Scientia Pharmaceutica

Article Title: Synthesis and Anticancer Activity of 2-(Alkyl-, Alkaryl-, Aryl-, Hetaryl-)-[1,2,4]triazolo[1,5- c ]quinazolines

doi: 10.3797/scipharm.1211-08

Figure Lengend Snippet: The influence of compounds on the growth of individual tumor cell lines (GI 50 ≤1.00 μM)

Article Snippet: 5.10 , , 57.02 , −10.11–120.31 , 25.07 (A549/ATCC/nscLC), 56.27 (HOP-62/nscLC), 11.95 (HOP-92/nscLC), 58.89 (NCI-H23/nscLC), 20.32 (NCI-H460/nscLC), 40.58 (NCI-H522/nscLC), 44.03 (HCT-116/ColC), 43.63 (HCT-15/ColC), 47.67 (HT29/ColC), 42.78 (KM12/ColC), 32.84 (SW-620/ColC), 58.28 (BT-549/BC), 29.74 (MCF7/BC), 64.37 (MDA-MB-231/ATCC/BC), −10.11 (MDA-MB-435/BC), 21.67 (NCI/ADR-RES/BC), 46.30 (IGROV1/OV), 34.97 (OVCAR-3/OV), 23.63 (OVCAR-8/OV), 64.14 (CCRF-CEM/L), 59.79 (HL-60(TB)/L), 30.84 (K-562/L), 47.76 (RPMI-822/L), 14.20 (SR/L), 66.99 (786-0/RC), 44.33 (CAKI-1/RC), 10.54 (RXF 393/RC), 65.31 (UO-31/RC), 57.67 (LOX IMVI/M), 55.63 (M14/M), 57.27 (SK-M EL-28/M), 28.78 (SK-MEL-5/M), 60.50 (UACC-257/M), 65.67 (UACC-62/M), 58.40 (SF-268/CNSC), 29.74 (SF-295/CNSC), 65.45 (SF-539/CNSC), 67.66 (SNB-19/CNSC), 41.59 (SNB-75/CNSC).

Techniques:

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Alignment of the chromosomes of strains TX07-7308 (top) and ATCC 25017 (bottom) using MAUVE 2. Identically colored boxes, known as locally collinear blocks (LCBs), depict homologous regions in the two chromosomes. The edges of LCBs indicate chromosome rearrangements due to recombination, insertions, and/or inversions. Sequences of strain ATCC 25017 inverted in relation to those of strain TX07-7308 are shown as blocks below the horizontal line. The vertical lines connecting the LCBs point to regions of homology among the two chromosomes. Numbers above the maps indicate nucleotide positions within the respective chromosomes.

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques:

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Synteny plot of the chromosomes of strains TX07-7308 and ATCC 25017 generated by NUCmer. This plot shows regions of identity between the two chromosomes based on pair-wise alignments. Strain TX07-7308 sequence is represented on the X-axis. Strain ATCC 25017 sequence is represented on the Y-axis. Plus strand matches are slanted from the bottom left to the upper right corner and are shown in red. Minus strand matches are slanted from the upper left to the lower right and are shown in blue. The number of dots/lines shown in the plot is the same as the number of exact matches found by NUCmer. Numbers indicate nucleotide positions within the respective chromosomes.

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques: Generated, Sequencing

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Venn diagram depicting the shared (orthologs) and unique protein coding genes in the genomes of Francisella spp. strain TX07-7308, F. philomiragia strains ATCC 25017, and F. novicida strain U112. Numbers in parenthesis indicate the total number of protein coding genes in the genomes of each of the three strains. Strains ATCC 25017 and TX07-7308 had 1719 orthologous protein coding genes, strains ATCC 25017 and U112 had 1507 orthologous protein coding genes, whereas strains TX07-7308 and U112 had 1522 orthologous protein coding genes.

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques:

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Identification of pilus biosynthesis, oligopeptide transport, glucuronate metabolism, and lactose metabolism genes

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques: Blocking Assay

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Comparison of arsenic resistance loci of F. philomiragia strain ATCC 25017 (A and C) and Francisella spp. strain TX07-7308 (B and D). The relevant ORFs marked in A and C are: Fphi_1740, transposase X; Fphi_1741 and 1750, integrase catalytic subunit; Fphi_1742, transposase; Fphi_1743, transposase; Fphi_1744, invertase/recombinase-like protein; Fphi_1745, truncated ArsB arsenite/antimonite exporter; Fphi_1746, arsenate reductase; Fphi_1747, sulfate transporter; Fphi_1748, hypothetical protein; Fphi_1749, mechanosensitive ion channel family protein; Fphi_1817, ArsR family transcriptional regulator; Fphi_1818, ArsB arsenite/antimonite exporter. The relevant ORFs marked in B and D are: F7308_0309, ArsR family transcriptional regulator; F7308_0310, Arsenical-resistance protein ACR3; F7308_1298, Arsenical-resistance protein ACR3; F7308_1299, ArsR family transcriptional regulator. t1, t2, and t3 are tRNA genes. The numbers on either side of the maps refer to the nucleotide positions in the respective chromosomes.

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques:

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: A Summary of important genetic traits among strains TX07-7308, ATCC 25015, ATCC 25017, 3523, Fx1, U112, and Schu S4. ArsRB. Arsenic resistance locus, GlcUA. Glucuronate metabolism locus, Lac. Lactose metabolism locus, Opp. Oligopeptide ABC transporter locus, Thi. Thiamine biosynthesis locus. + indicates the presence and – indicates the absence of a particualr locus in each strain. B . Neighbor joining tree using succinate dehydrogenase ( sdhA ) genes. Phylogenetic relationships among strains TX07-7308, ATCC 25015, ATCC 25017, U112, and eleven other Francisella isolates based on SdhA sequences are shown. Nodes with bootstrap support greater than 70% are indicated. C . As in Figure B, but using full-length 16S rRNA genes.

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques:

Journal: BMC Genomics

Article Title: Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

doi: 10.1186/1471-2164-13-422

Figure Lengend Snippet: Comparison of the genomes of five different strains within the genus Francisella

Article Snippet: Furthermore, the homolog of FTN_1314, which encodes a hypothetical protein in F. novicida strain U112, was truncated in strain TX07-7308 (F7308_1011) and homologs of FTN_1318-FTN_1320 (encoding a hypothetical protein, a pathogenicity determinant protein, and a hypothetical protein, respectively) were absent in strains ATCC 25017 and TX07-7308.

Techniques:

Journal: BMC Microbiology

Article Title: Amylase production by Preussia minima , a fungus of endophytic origin: optimization of fermentation conditions and analysis of fungal secretome by LC-MS

doi: 10.1186/1471-2180-14-55

Figure Lengend Snippet: Effect of pH and temperature on specific amylase activity of EL-14 and standard. (A) EL-14 was grown at different pH and specific amylase activity was determined. (B) EL-14 was grown at different temperatures and specific amylase activity was determined. (C) standards ( A. oryzae and A. niger ) were grown at the same conditions to compare their activity with P. minima . The crude extracellular sample (EL-14) exhibited the highest activity at 25°C and pH 9, significantly more than standard. Means followed by the same letter within a column are not significantly different at P < 0.01 according to the Duncan multiple range test.

Article Snippet: The same procedures were used for standard fungi Aspergillus oryzae (ATCC 10124) and A. niger (ATCC 10577) as controls at 25°C and pH 9.

Techniques: Activity Assay

Journal: BMC Microbiology

Article Title: Amylase production by Preussia minima , a fungus of endophytic origin: optimization of fermentation conditions and analysis of fungal secretome by LC-MS

doi: 10.1186/1471-2180-14-55

Figure Lengend Snippet: Qualitative assessment of amylase activity by zymography. Zymography was performed to confirm that α-amylase activity at pH 9 and 25°C was optimal, in comparison with standards ( A. oryzae and A. niger ). M = molecular weight markers. A common band was detected at around 70 kDa for P. minima .

Article Snippet: The same procedures were used for standard fungi Aspergillus oryzae (ATCC 10124) and A. niger (ATCC 10577) as controls at 25°C and pH 9.

Techniques: Activity Assay, Zymography, Molecular Weight

Journal: BMC Microbiology

Article Title: Amylase production by Preussia minima , a fungus of endophytic origin: optimization of fermentation conditions and analysis of fungal secretome by LC-MS

doi: 10.1186/1471-2180-14-55

Figure Lengend Snippet: Proteins in the secretome of Preussia minima identified by LC MS/MS and compared to proteins in the NCBI database 1 by BLAST searching

Article Snippet: The same procedures were used for standard fungi Aspergillus oryzae (ATCC 10124) and A. niger (ATCC 10577) as controls at 25°C and pH 9.

Techniques:

Journal: PLoS ONE

Article Title: DNA Polymorphisms and Biocontrol of Bacillus Antagonistic to Citrus Bacterial Canker with Indication of the Interference of Phyllosphere Biofilms

doi: 10.1371/journal.pone.0042124

Figure Lengend Snippet: Bacterial strains and plasmids used in this study.

Article Snippet: BCRC 11601 , B. amyloliquefaciens type strain ATCC 23350, DSM7 , BCRC.

Techniques: Sequencing, Isolation, Plasmid Preparation, Clone Assay