Journal: Bioengineered

Article Title: Assembly of evolved ligninolytic genes in Saccharomyces cerevisiae

doi: 10.4161/bioe.29167

Figure Lengend Snippet: Figure 4. In vivo assembly of synthetic genes by IVOE. Each overlapping region allowed crossover events to occur between fragments giving rise to an autonomously repaired vector containing single and double expression cassettes in the correct orientation. ( A ) and ( B ) Single expression cassettes are constructed in pESC by engineering specific primers containing overhangs to foster in vivo cloning with the linearized plasmid in yeast (pJRoC30 was used as template for Vp or Lac amplifications). ( C ) and ( D ) The pESC constructs obtained in ( A ) and ( B ) were used as scaffolds to assemble Lac and Vp genes under the control of different promoter/terminator pairs. Primers used: (1)-MCS1- Vp / Lac -α-BamHI, (2)-MCS2- Vp -ter-NheI, (3)-MCS2- Lac -ter-NheI, (4)-MCS1- Vp / Lac -α-SpeI, (5)-MCS1- Lac -ter-SacI and (6)-MCS1- Vp -ter-SacI. Black arrows indicate the direction of the transcription process.

Article Snippet: The ura3 -deficient S. cerevisiae strain BJ5465 ( α ura3–52 trp1 leu2Δ1 his3Δ200 pep4::HIS2 prb1Δ1.6R can1 GAL1 ) was obtained from LGCPromochem, the NucleoSpin Plasmid kit was purchased from Macherey-Nagel, and the restriction enzymes BamHI, NheI, SpeI, SacI, and NotI from New England Biolabs.

Techniques: In Vivo, Plasmid Preparation, Expressing, Construct, Clone Assay

Journal: AMB Express

Article Title: Alkane biosynthesis by Aspergillus carbonarius ITEM 5010 through heterologous expression of Synechococcus elongatus acyl-ACP/CoA reductase and aldehyde deformylating oxygenase genes

doi: 10.1186/s13568-016-0321-x

Figure Lengend Snippet: FAR/FADO gene copy number determination in the selected TDR transformant. a Hybridization probe used for the Southern blot analysis; FADO fatty aldehyde deformylating oxygenase; TrpC_T terminator region of TrpC ; Tef1_P promoter region of Tef1 ; FAR fatty acyl-ACP/CoA reductase; BamHI, NdeI, PstI restriction enzyme cut sites. b Southern blot analysis. Lane 1 contains 1 kb DNA ladder (size in base pairs); lanes 2–4 shows the hybridization of the probe to the BamHI, PstI and NdeI digested gDNA of the TDR transformant; lanes 5–7 shows the hybridization of the probe to the BamHI, PstI and NdeI digested gDNA of the parent strain

Article Snippet: Genomic DNA of the transformants was extracted as described above and digested with restriction enzymes BamHI, PstI, and NdeI (all purchased from Thermo Scientific, Rockford, IL, USA).

Techniques: Hybridization, Southern Blot

Journal: Jundishapur Journal of Microbiology

Article Title: Zinc Finger Nuclease: A New Approach to Overcome Beta-Lactam Antibiotic Resistance

doi: 10.5812/jjm.29384

Figure Lengend Snippet: Confirmation of Self-Ligated pP15A, kana R by Digestion Lane 2: digestion of pP15A, kana R vector with BamHI ; lane 3, xbaI; Lane 4, double digestion with BamHI-XbaI; Lane 5, undigested pP15A, kana R vector; Lanes 1 and 6, GeneRuler DNA ladder mix (Thermo Scientific, Waltham, MA, USA).

Article Snippet: The pTZ57R plasmid was extracted using a GeneJET™ Plasmid Miniprep Kit (Thermo Scientific, Waltham, MA, USA) and was digested using EcoRI and BamHI restriction enzymes (Thermo Scientific, Waltham, MA, USA).

Techniques: Plasmid Preparation

Journal: PLoS ONE

Article Title: DNA Methylation and Expression of the EgDEF1 Gene and Neighboring Retrotransposons in mantled Somaclonal Variants of Oil Palm

doi: 10.1371/journal.pone.0091896

Figure Lengend Snippet: Determination of copy number by Southern blot. A: EgDEF1 gene; B: gypsy retroelement. One L2T-related genotype (left: LMC343 or LMC51) is compared to one non-L2T-related genotype (right: FC2317 or FC2318). Lowercase letters signal the hybridizing bands that are predicted by the in silico digestion of the Eg133H20 BAC sequence with the appropriate restriction enzyme (a: 4,069 bp EcoRI fragment; b: 4,841 bp HindIII fragment; c: 6,251 BamHI fragment; d: 6,138 bp HindIII fragment; e: 13,132 bp BamHI fragment), asterisks indicate supernumerary bands.

Article Snippet: Southern blot Seven micrograms of oil palm genomic DNA extracts were digested in parallel by either EcoRI, HindIII or BamHI restriction enzymes (Promega) according to the manufacturer's instructions.

Techniques: Southern Blot, In Silico, BAC Assay, Sequencing