Journal: Oncotarget

Article Title: Expression of truncated bile salt-dependent lipase variant in pancreatic pre-neoplastic lesions

doi: 10.18632/oncotarget.11777

Figure Lengend Snippet: Genetic alterations within the DNA sequence of BSDL A. Sequences encoding BSDL were amplified from the RNA extracted from pancreatic tumor SOJ-6 cells using RT-PCR and specific primers. The PCR was performed in a personal Robocycler Gradient 96 (Stratagene). Following PCR, migration on agarose gel was performed to visualize amplified fragments. B. Amplicons were purified and their amino-acid sequences deduced after Sanger sequencing. The BSDL-WT amino-acid sequence corresponds to the 2.2 kb amplicon associated with the BSDL-Mut1 sequence, and the BSDL-Mut2 to that of the 1.8 kb band. Star symbol indicates the identical amino-acids. Only the C-terminal sequences are shown.

Article Snippet: Amplicon purification and sequencing The amplicons obtained were then purified using the DNA extraction kit (Millipore) after electrophoretic migration on agarose gel, according to the protocol recommended by the supplier.

Techniques: Sequencing, Amplification, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Migration, Agarose Gel Electrophoresis, Purification

Journal:

Article Title: CFTR gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR)

doi:

Figure Lengend Snippet: Schematic of small DNA fragment (SDF) generation and PCR analysis of SFHR A. SDF (783bp) containing the ΔF508 mutation and a KpnI restriction enzyme cleavage site was synthesized using primers mCF1 and mCF15, localized within introns 9 and 10

Article Snippet: Before transfection the SDF was used, always gel and ethanol purified (DNA gel extraction kit; Millipore, Bedford, MA).

Techniques: Polymerase Chain Reaction, Mutagenesis, Synthesized

Journal: World Journal of Gastroenterology : WJG

Article Title: Helicobacter species and gut bacterial DNA in Meckel's diverticulum and the appendix

doi: 10.3748/wjg.v17.i36.4104

Figure Lengend Snippet: Microscopic analysis of the Helicobacter pullorum positive Meckel´s diverticulum case. Low power view of a histological section from Meckel´s diverticulum, positive for Helicobacter pullorum ( H. pullorum ) DNA, in the heterotopic area. There is an unusually well developed lymphatic tissue with germinal centres and a predominance of lymphocytes in the non-heterotopic area. Plasma cells were mainly found in the heterotopic area. The small arrows in the big square, point to a small strip of gastric heterotopia. This area displays at higher magnification in the inset. Large arrows point to gastric glands of corpus type. Blue without arrows in the photo indicates intestinal mucus. Alcian blue-PAS staining pH 2.5.

Article Snippet: Helicobacter specific PCR products were purified from agarose gels using the Montage DNA Gel Extraction Kit (Millipore, Bedford, MA, United States), according to the manufacturer’s instructions.

Techniques: Stripping Membranes, Staining

Journal: Annals of Surgery

Article Title: Trauma-Hemorrhagic Shock Mesenteric Lymph Induces Endothelial Apoptosis That Involves Both Caspase-Dependent and Caspase-Independent Mechanisms

doi: 10.1097/01.sla.0000129341.94219.cf

Figure Lengend Snippet: FIGURE 2. (A) T/HS lymph but not T/SS lymph or medium induced DNA fragmentation. HUVECs were incubated with lymph for 4 hours, after which genomic DNA was isolated, fractionated on a 1.5% agarose gel and stained with ethidium bromide. The hallmark DNA step-laddering pattern characteristic of apoptosis is present only in the HUVECS incubated with T/HS lymph. These results are representative of 3 independent studies (M, marker). (B) The number of free nucleosomes generated in HUVECs after 4-hour incubation with T/HS lymph was increased compared with HUVECs incubated in medium or T/SS lymph. Nuclear extracts were prepared using a Nucleosome ELISA kit (Oncogene Research). Optical density (OD) correlates with the number of free nucleosomes. Data expressed as mean ± SD. * P

Article Snippet: Using a DNA Isolation Kit (Oncogene Research Products, Boston MA) low molecular weight DNA extracts were prepared.

Techniques: Incubation, Isolation, Agarose Gel Electrophoresis, Staining, Marker, Generated, Enzyme-linked Immunosorbent Assay

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Synergistic Efficacy of Aedes aegypti Antimicrobial Peptide Cecropin A2 and Tetracycline against Pseudomonas aeruginosa

doi: 10.1128/AAC.00686-17

Figure Lengend Snippet: The binding activities of cecropin A2 to bacterial LPS and DNA. (A) The affinities of cecropin A2 and control reagents to P. aeruginosa LPS were determined using the BODIPY TR cadaverine displacement method. (B) Interaction of cecropin A2 and control reagents with P. aeruginosa genomic DNA. To highlight the effects of high concentrations of cecropin A2 on its DNA-binding activity, we ran multiple gels that demonstrated a decreasing intensity of DNA bands from cells that were treated with a high concentration of the peptide (representative bands from two different gels with complete pictures of the gels included in Fig. S1 in the supplemental material). (C) The DNA-binding ability of cecropin A2. DNA bands were quantified with ImageJ software and DNA binding (%) was defined as the ratio of nonmigrating DNA to total genomic DNA.

Article Snippet: P. aeruginosa strain PA14 genomic DNA was extracted using the bacterial genomic DNA extraction kit (Sigma-Aldrich Biotechnology, St. Louis, MO), and 20 μl of the purified genomic DNA was incubated with cecropin A2, LL-37, or tetracycline for 1 h at room temperature.

Techniques: Binding Assay, Activity Assay, Concentration Assay, Software