Journal: Journal of applied microbiology

Article Title: Lactobacillus salivarius Ren prevent the early colorectal carcinogenesis in 1, 2-dimethylhydrazine-induced rat model.

doi: 10.1111/jam.12499

Figure Lengend Snippet: Figure 3 Structural segregation analysis of gut microbiota in rats from different group. (a) 16s rRNA gene V3 region PCR-denaturing gradient gel electrophoresis (DGGE) profiles of faecal samples obtained from healthy rats (No treatment group), 1, 2-dimethylhydrazine (DMH)-treated rats (DMH alone group) and Lactobacillus salivarius Ren (LS)-treated group (DMH + LS high group). M represents the marker for DGGE analysis. (b) Principal component analysis (PCA) score plots (PC1 vs PC2) based on the PCR–DGGE profiles among no treatment ( ), DMH alone ( ) and DMH +LS high ( ) groups. The first and the second axes explained 1 95 and 122% of total variation, respectively.

Article Snippet: PCR products were examined by denaturing gradient gel electrophoresis (DGGE) (D-code Universal Mutation Detection System, Bio-Rad, Hercules, CA).

Techniques: Denaturing Gradient Gel Electrophoresis, Marker

Journal: Folia microbiologica

Article Title: Unusual oral mucosal microbiota after hematopoietic cell transplantation with glycopeptide antibiotics: potential association with pathophysiology of oral mucositis.

doi: 10.1007/s12223-018-0596-1

Figure Lengend Snippet: Fig. 2 DGGE profiles of amplified 16S rDNA from mucosal bacterial samples of HCT patients. DGGE profiles of amplified 16S rDNA from mucosal bacterial samples of HCT patients are shown. a Quinolone prophylaxis and/or β- lactam monotherapy group. b β- Lactam-glycopeptide combination therapy group. bfr, before HCT sample; aft, after HCT sample. Intense bands (a a– ao, b a–z) were sequenced, and bacterial species identified from the sequence data are shown in Table 2. M, marker

Article Snippet: For DGGE analyses, the amplicons and DGGE marker I (Nippon Gene, Tokyo, Japan) were electrophoresed using a D-code DGGE complete system (Bio-Rad, Hercules, CA) operated at 60 °C for 12 h at 100 V in a linear 25–65% denaturing agent gradient (100% denaturing agent consisted of 7mol/L urea and 40% deionized formamide) with 8% polyacrylamide gels (polyacrylamide gel, ratio of acrylamide HG (Wako Pure Chemical Industries, Osaka, Japan) to bisacrylamide (Wako Pure Chemical Industries), 37.5:1).

Techniques: Amplification, Glycoproteomics, Sequencing, Marker

Journal:

Article Title: Activation of Telomerase RNA Gene Promoter Activity by NF-Y, Sp1, and the Retinoblastoma Protein and Repression by Sp3 1

doi:

Figure Lengend Snippet: (a) hTERC promoter sequence and potential transcription factor recognition sites. A total of 176 bp of the human promoter sequence is shown and potential regulatory motifs, identified by computer analysis, are underlined on the sequence. The transcriptional start site is marked as “+1.” Four potential Sp1 sites are shown and termed Sp1.1 to Sp1.4. Sp1.4 contains two overlapping Sp1 consensus sites. The names of the oligonucleotides used in electrophoresis mobility shift assays (EMSA) are indicated under their respective sites. (b) Oligonucleotides used in EMSA and mutagenesis studies of the hTERC promoter. The sequence of the wild-type oligonucleotides covering potential transcription factor recognition sites are shown. Oligonucleotide h9 covers Sp1.1 and the adjacent TATA-box, h10 covers the CCAAT box, h4 covers Sp1.2 and h11 covers the closely opposed Sp1.3 and Sp1.4 sites. Mutations, h10m1 and h10m2, were introduced into the wild-type oligonucleotide h10 and used in EMSA and in the construction of the mutant reporter construct (hProm176h10m1).

Article Snippet: Electrophoresis Mobility Shift Assay Electrophoresis mobility shift assays (EMSA) were performed by using the EMSA kit (Promega).

Techniques: Sequencing, Electrophoresis, Mobility Shift, Mutagenesis, Construct

Journal:

Article Title: Activation of Telomerase RNA Gene Promoter Activity by NF-Y, Sp1, and the Retinoblastoma Protein and Repression by Sp3 1

doi:

Figure Lengend Snippet: (a) Identification of nuclear proteins binding to the CCAAT box. HeLa nuclear extract was mixed with radiolabeled oligonucleotide probe and analyzed by EMSA. Specific DNA-protein complexes are indicated by the arrow on the left. Complexes supershifted by preincubation with antibodies are shown on the right by arrows marked “ss.” The oligonucleotide h10 was used as a probe and the oligonucleotides used as competitors are indicated at the top of lanes 2 to 8. The antibodies used in supershifts are indicated above lanes 9 to 14. (b) Inhibition of hTERC promoter activity by a dominant-negative mutant of NF-YA termed NF-YAm29. 5637 cells were transfected with fixed amount of the hTERC-luciferase plasmid hProm176 and increasing concentrations of the NF-YAm29 dominant-negative vector (black columns) or wild-type NF-YA vector (light grey columns). For each transfection the mean and standard deviation for duplicate samples is shown. (c) Functional analysis of the CCAAT box. Promoter activities of a mutant CCAAT box construct (hProm176h10m1) and shorter promoter construct with deletion of the CCAAT box (hProm120) were assayed by transfection into the bladder carcinoma cell line 5637 and compared to the wild-type promoter activity (hProm176). Promoter activities of the constructs are shown as percentage luciferase activity of the wild-type promoter alone. The pSEAP2-Control vector was used as an internal control for transfection efficiency.

Article Snippet: Electrophoresis Mobility Shift Assay Electrophoresis mobility shift assays (EMSA) were performed by using the EMSA kit (Promega).

Techniques: Binding Assay, Inhibition, Activity Assay, Dominant Negative Mutation, Transfection, Luciferase, Plasmid Preparation, Standard Deviation, Functional Assay, Mutagenesis, Construct, Control

Journal:

Article Title: Activation of Telomerase RNA Gene Promoter Activity by NF-Y, Sp1, and the Retinoblastoma Protein and Repression by Sp3 1

doi:

Figure Lengend Snippet: (a) Identification of nuclear proteins binding to the Sp1 sites. HeLa nuclear extract was mixed with radiolabeled oligonucleotide probe and analyzed by EMSA. The proteins bound to the probe were identified by preincubation of nuclear extracts with antibodies specific for Sp1, Sp3, or control antibodies specific for Ets2 and Ap2. Complexes specific to Sp1 and Sp3 are indicated to the left of the panel. The antibodies used are indicated at the top of the figure. (b) The Sp1 transcription factor upregulates and Sp3 transcription factor downregulates the hTERC promoter. The wild-type hTERC-luciferase plasmid was cotransfected with increasing amounts of either an Sp1 or Sp3 expression vector (0.25 µg to 2.0 µg) into the 5637 cell line. The mean luciferase activity normalized for protein and transfection efficiency is shown with the standard deviation of duplicate samples.

Article Snippet: Electrophoresis Mobility Shift Assay Electrophoresis mobility shift assays (EMSA) were performed by using the EMSA kit (Promega).

Techniques: Binding Assay, Control, Luciferase, Plasmid Preparation, Expressing, Activity Assay, Transfection, Standard Deviation