Journal: eLife

Article Title: Activation of the CaMKII-Sarm1-ASK1-p38 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria

doi: 10.7554/eLife.73557

Figure Lengend Snippet:

Article Snippet: Commercial assay, kit , 1 kb DNA Ladder , Promega , Cat# G571A , .

Techniques: Recombinant, Generated, Marker, Mutagenesis, Software

Journal: eLife

Article Title: Activation of the CaMKII-Sarm1-ASK1-p38 MAP kinase pathway protects against axon degeneration caused by loss of mitochondria

doi: 10.7554/eLife.73557

Figure Lengend Snippet:

Article Snippet: Commercial assay, kit , 1 kb DNA Ladder , Promega , Cat# G571A , .

Techniques: Recombinant, Control, Generated, Marker, Mutagenesis, Software

Journal: BMC Genomics

Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

doi: 10.1186/s12864-018-4748-0

Figure Lengend Snippet: Controlling of partial cleavage of genomic DNAs by TthHB27I under cofactor/analogue-induced ‘star’ activity conditions. E. coli and λ genomic DNAs were digested with TthHB27I under cofactor/analogue-induced ‘star’ conditions, while varying: temperature, incubation time and TthHB27I amount. 0.5 μg of DNAs were digested with TthHB27I in REase buffer supplemented with 100 μM SIN and 25% (v/v) DMSO. a Cleavage control by reaction temperature. Reactions conducted with E. coli DNA digested with 2 U of TthHB27I for 1 h at temperatures from 30 °C to 80 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction at 30 °C; lane 2, 35 °C; lane 3, 40 °C; lane 4, 45 °C; lane 5, 50 °C; lane 6, 55 °C; lane 7, 60 °C; lane 8, 65 °C; lane 9, 70 °C; lane 10, 75 °C; lane 11, 80 °C. b The same as ( a ), except that λ DNA was used. c Cleavage control by reaction time. E. coli DNA was digested at 65 °C at times ranging from 7.5 min to 16 h. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction conducted for 7.5 min; lane 2, 15 min; lane 3, 30 min; lane 4, 1 h; lane 5, 2 h; lane 6, 4 h; lane 7, 8 h; lane 8, 16 h. d The same as ( c ), except that λ DNA was used. e Cleavage control by the enzyme amount. E. coli DNA was digested at 65 °C with TthHB27I. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, DNA digested with 8 U TthHB27I; lane 2, 4 U; lane 3, 2 U; lane 4, 1 U; lane 5, 0.5 U; lane 6, 0.25 U; lane 7, 0.12 U; lane 8, 0.06 U. f The same as ( e ), except that λ DNA was used

Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

Techniques: Activity Assay, Incubation

Journal: BMC Genomics

Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

doi: 10.1186/s12864-018-4748-0

Figure Lengend Snippet: TthHB27I digestion patterns comparison in the presence of DMSO and cofactor SAM or its analogues. 0.5 μg of 1789 bp PCR DNA substrate (see Additional file ) was incubated with 2 U of TthHB27I for 1 h at 65 °C in REase buffer with increasing amount of DMSO. Reaction mixtures were precipitated and electrophoresed in 1.3% agarose/TBE gels. The pictures on the right side of the figure show the theoretical arrangement of the DNA bands in an agarose gel after digesting the substrate DNA with TthHB27I under standard conditions. a Digestions performed only with the addition of DMSO, without any cofactor. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested PCR fragment; lane 1, 0% ( v /v) DMSO present in the reaction mixture; lane 2, with 5% (v/v) DMSO; lane 3, with 10% (v/v) DMSO; lane 4, with 15% (v/v) DMSO; lane 5, with 20% (v/v) DMSO; lane 6, with 25% (v/v) DMSO; lane 7, with 30% (v/v) DMSO. As in ( a ), but in the presence of 100 μM SAM ( b ); 100 μM SIN ( c ); 100 μM SAC ( d ); 100 μM SAH ( e ); 100 μM ATP ( f )

Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

Techniques: Incubation, Agarose Gel Electrophoresis

Journal: BMC Genomics

Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

doi: 10.1186/s12864-018-4748-0

Figure Lengend Snippet: TthHB27I cofactor/analogue-induced ‘star’ activity towards methylated or non-methylated substrate DNA. 0.5 μg of methylated or non-methylated PCR DNA fragment (see Additional file ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the DNA bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence

Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

Techniques: Activity Assay, Methylation, Agarose Gel Electrophoresis, Sequencing

Journal: BMC Genomics

Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

doi: 10.1186/s12864-018-4748-0

Figure Lengend Snippet: Cleavage of λ DNA under TthHB27I specificity relaxation conditions. a Cleavage pattern of λ DNA digested with TthHB27I under various conditions. 0.5 μg of DNA substrate was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM SAM and/or 25% (v/v) DMSO for 4 h at 65 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, digestion in the presence of SAM; lane 2, digestion in the presence of DMSO; lane 3, digestion in the presence of both SAM and DMSO. b The same as ( a ), but SIN was used instead of SAM. c Distribution of insert lengths in 200 clones randomly selected from TthHB27I/DMSO/SAM-generated λ DNA library. d The same as ( c ), but for TthHB27I/DMSO/SIN-generated λ DNA library

Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

Techniques: Clone Assay, Generated