Structured Review

TaKaRa bmp 4
Change in the mRNA expression of BMP-2 (top), <t>BMP-4</t> (middle), and the type IA BMP receptor (bottom) with time after mid-diaphyseal femoral fracture in rats at 6 weeks (younger) and 15 months (older) of age. The data are presented as in Fig. 1 .
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1) Product Images from "Delayed union of femoral fractures in older rats:decreased gene expression"

Article Title: Delayed union of femoral fractures in older rats:decreased gene expression

Journal: BMC Musculoskeletal Disorders

doi: 10.1186/1471-2474-2-2

Change in the mRNA expression of BMP-2 (top), BMP-4 (middle), and the type IA BMP receptor (bottom) with time after mid-diaphyseal femoral fracture in rats at 6 weeks (younger) and 15 months (older) of age. The data are presented as in Fig. 1 .
Figure Legend Snippet: Change in the mRNA expression of BMP-2 (top), BMP-4 (middle), and the type IA BMP receptor (bottom) with time after mid-diaphyseal femoral fracture in rats at 6 weeks (younger) and 15 months (older) of age. The data are presented as in Fig. 1 .

Techniques Used: Expressing, IA

2) Product Images from "Suppressor of Cytokine Signaling (SOCS) Genes Are Silenced by DNA Hypermethylation and Histone Deacetylation and Regulate Response to Radiotherapy in Cervical Cancer Cells"

Article Title: Suppressor of Cytokine Signaling (SOCS) Genes Are Silenced by DNA Hypermethylation and Histone Deacetylation and Regulate Response to Radiotherapy in Cervical Cancer Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0123133

Effect of DNA methylation inhibitor and DNMT1 gene knockdown on SOCS gene expression. CaSki (A,D), HeLa (B,E), and ME-180 (C,F) cells were treated with 10 μM of 5-Azacytosine (5-Aza) for 72 h (A-C) or infected with control lentivirus (shSCR) or lentivirus expressing shRNA targeting DNMT1 (shDNMT1) (D-F). Knock-down of DNMT1 and SOCS gene expression was examined with qRT-PCR. Asterisk (*), statistically significant ( p
Figure Legend Snippet: Effect of DNA methylation inhibitor and DNMT1 gene knockdown on SOCS gene expression. CaSki (A,D), HeLa (B,E), and ME-180 (C,F) cells were treated with 10 μM of 5-Azacytosine (5-Aza) for 72 h (A-C) or infected with control lentivirus (shSCR) or lentivirus expressing shRNA targeting DNMT1 (shDNMT1) (D-F). Knock-down of DNMT1 and SOCS gene expression was examined with qRT-PCR. Asterisk (*), statistically significant ( p

Techniques Used: DNA Methylation Assay, Expressing, Infection, shRNA, Quantitative RT-PCR

DNA methylation analysis of SOCS gene promoter. (A) Methyl-specific PCR analysis. Bisulfite-treated genomic DNA was amplified with unmethylated (U) or methylated (M) DNA specific primers. (B-D) Bisulfite sequencing of SOCS1 (B), SOCS3 (C), and SOCS5 (D). Unmethylated CpG site in amplified promoter region was showed as an open circle and methylated CpG as a closed circle.
Figure Legend Snippet: DNA methylation analysis of SOCS gene promoter. (A) Methyl-specific PCR analysis. Bisulfite-treated genomic DNA was amplified with unmethylated (U) or methylated (M) DNA specific primers. (B-D) Bisulfite sequencing of SOCS1 (B), SOCS3 (C), and SOCS5 (D). Unmethylated CpG site in amplified promoter region was showed as an open circle and methylated CpG as a closed circle.

Techniques Used: DNA Methylation Assay, Polymerase Chain Reaction, Amplification, Methylation, Methylation Sequencing

3) Product Images from "Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars"

Article Title: Distribution of photoperiod-insensitive alleles Ppd-B1a and Ppd-D1a and their effect on heading time in Japanese wheat cultivars

Journal: Breeding Science

doi: 10.1270/jsbbs.61.405

Ppd-B1 genotype and heading date of wheat cultivars on the pedigree of extra early wheat cultivars. ●: Carrier of Ppd-B1a . ○: Carrier of Ppd-B1b. Ppd-1 genotype and heading date of ‘Kinki 14’ and ‘Chukei 4010’ and heading date of ‘Jessore’ and ’Konosu 4’ were not tested. The average of heading date for three growing seasons is indicated by calendar date. The year of registration was shown in italics. *1 shows the pedigree of ‘Kinki 14’.
Figure Legend Snippet: Ppd-B1 genotype and heading date of wheat cultivars on the pedigree of extra early wheat cultivars. ●: Carrier of Ppd-B1a . ○: Carrier of Ppd-B1b. Ppd-1 genotype and heading date of ‘Kinki 14’ and ‘Chukei 4010’ and heading date of ‘Jessore’ and ’Konosu 4’ were not tested. The average of heading date for three growing seasons is indicated by calendar date. The year of registration was shown in italics. *1 shows the pedigree of ‘Kinki 14’.

Techniques Used:

4) Product Images from "Pentraxin 3 (PTX3) promoter methylation associated with PTX3 plasma levels and neutrophil to lymphocyte ratio in coronary artery disease"

Article Title: Pentraxin 3 (PTX3) promoter methylation associated with PTX3 plasma levels and neutrophil to lymphocyte ratio in coronary artery disease

Journal: Journal of Geriatric Cardiology : JGC

doi: 10.11909/j.issn.1671-5411.2016.08.010

Association between the NLR and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with NLR in male patients ( r = −0.58, P = 0.002). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.
Figure Legend Snippet: Association between the NLR and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with NLR in male patients ( r = −0.58, P = 0.002). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.

Techniques Used: Methylation

Association between PTX3 levels and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with plasma PTX3 levels ( r = −0.29, P = 0.02). PTX3: Pentraxin 3.
Figure Legend Snippet: Association between PTX3 levels and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with plasma PTX3 levels ( r = −0.29, P = 0.02). PTX3: Pentraxin 3.

Techniques Used: Methylation

PTX3 levels and levels of PTX3 promoter methylation according to CAD occurrence. (A): PTX3 levels in the CAD-free group were 3.65 ± 2.14 ng/mL ( n = 25), lower than the CAD group ( n = 39); (B): the levels of PTX3 promoter methylation in the CAD-free group were 72.45% ± 11.84% ( n = 25), higher than the CAD group (62.69% ± 20.57%, n = 39). CAD: coronary artery disease; PTX3: Pentraxin 3.
Figure Legend Snippet: PTX3 levels and levels of PTX3 promoter methylation according to CAD occurrence. (A): PTX3 levels in the CAD-free group were 3.65 ± 2.14 ng/mL ( n = 25), lower than the CAD group ( n = 39); (B): the levels of PTX3 promoter methylation in the CAD-free group were 72.45% ± 11.84% ( n = 25), higher than the CAD group (62.69% ± 20.57%, n = 39). CAD: coronary artery disease; PTX3: Pentraxin 3.

Techniques Used: Methylation

Association between the NLR and PTX3 levels. NLR was not correlated with PTX3 levels ( r = 0.11, P = 0.48). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.
Figure Legend Snippet: Association between the NLR and PTX3 levels. NLR was not correlated with PTX3 levels ( r = 0.11, P = 0.48). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.

Techniques Used:

5) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

Journal: Scientific Reports

doi: 10.1038/s41598-019-38809-y

Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p
Figure Legend Snippet: Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p

Techniques Used: Luciferase, Plasmid Preparation, Construct, Transfection, Activity Assay

Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p
Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p

Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.
Figure Legend Snippet: The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.

Techniques Used: Binding Assay, Labeling, Methylation, Incubation

6) Product Images from "The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion"

Article Title: The positive feedback loop between ILF3 and lncRNA ILF3-AS1 promotes melanoma proliferation, migration, and invasion

Journal: Cancer Management and Research

doi: 10.2147/CMAR.S186777

ILF3-AS1 epigenetically activates ILF3 expression. Notes: ( A ) The specific binding of EZH2 to ILF3 promoter and H3K27me3 levels at ILF3 promoter in ILF3-AS1 stably overexpressed and control A375 cells were determined by ChIP assays followed by qRT-PCR. ( B ) The specific binding of EZH2 to ILF3 promoter and H3K27me3 levels at ILF3 promoter in ILF3-AS1 stably depleted and control A375 cells were determined by ChIP assays followed by qRT-PCR. ( C ) ILF3 mRNA levels in ILF3-AS1 stably overexpressed and control A375 cells were determined by qRT-PCR. ( D ) ILF3 mRNA levels in ILF3-AS1 stably depleted and control A375 cells were determined by qRT-PCR. ( E ) ILF3 protein levels in ILF3-AS1 stably overexpressed and control A375 cells were determined by Western blot. ( F ) ILF3 protein levels in ILF3-AS1 stably depleted and control A375 cells were determined by Western blot. Results are presented as mean ± SD based on at least three independent experiments. ** P
Figure Legend Snippet: ILF3-AS1 epigenetically activates ILF3 expression. Notes: ( A ) The specific binding of EZH2 to ILF3 promoter and H3K27me3 levels at ILF3 promoter in ILF3-AS1 stably overexpressed and control A375 cells were determined by ChIP assays followed by qRT-PCR. ( B ) The specific binding of EZH2 to ILF3 promoter and H3K27me3 levels at ILF3 promoter in ILF3-AS1 stably depleted and control A375 cells were determined by ChIP assays followed by qRT-PCR. ( C ) ILF3 mRNA levels in ILF3-AS1 stably overexpressed and control A375 cells were determined by qRT-PCR. ( D ) ILF3 mRNA levels in ILF3-AS1 stably depleted and control A375 cells were determined by qRT-PCR. ( E ) ILF3 protein levels in ILF3-AS1 stably overexpressed and control A375 cells were determined by Western blot. ( F ) ILF3 protein levels in ILF3-AS1 stably depleted and control A375 cells were determined by Western blot. Results are presented as mean ± SD based on at least three independent experiments. ** P

Techniques Used: Expressing, Binding Assay, Stable Transfection, Chromatin Immunoprecipitation, Quantitative RT-PCR, Western Blot

ILF3 is increased in melanoma and correlated with poor prognosis. Notes: ( A ) ILF3 expression levels in 37 benign nevi and 60 primary melanoma tissues were determined by qRT-PCR. Results are presented as median with IQR; P
Figure Legend Snippet: ILF3 is increased in melanoma and correlated with poor prognosis. Notes: ( A ) ILF3 expression levels in 37 benign nevi and 60 primary melanoma tissues were determined by qRT-PCR. Results are presented as median with IQR; P

Techniques Used: Expressing, Quantitative RT-PCR

ILF3 physically binds and increases the stability of ILF3-AS1 transcript. Notes: ( A ) RIP assays followed by qRT-PCR revealed the specific enrichment of ILF3-AS1 with ILF3-specific antibody compared with nonspecific IgG. β-Actin mRNA was used as a negative control. LincIN was used as a positive control. ( B ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, ILF3 protein levels were determined by Western blot. ( C ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, ILF3 protein levels were determined by Western blot. ( D ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, the cells were treated with 50 µM α-amanitin to block new RNA synthesis, and then, the stability of ILF3-AS1 transcript over time was determined by qRT-PCR. 18S rRNA, a product of RNA polymerase I that is unchanged by α-amanitin, was used as endogenous control. ( E ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, the cells were treated with 50 µM α-amanitin to block new RNA synthesis and, then, the stability of ILF3-AS1 transcript over time was determined by qRT-PCR. 18S rRNA, a product of RNA polymerase I that is unchanged by α-amanitin, was used as endogenous control. ( F ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, ILF3-AS1 transcript levels were determined by qRT-PCR. ( G ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, ILF3-AS1 transcript levels were determined by qRT-PCR. Results are presented as mean ± SD based on at least three independent experiments. ** P
Figure Legend Snippet: ILF3 physically binds and increases the stability of ILF3-AS1 transcript. Notes: ( A ) RIP assays followed by qRT-PCR revealed the specific enrichment of ILF3-AS1 with ILF3-specific antibody compared with nonspecific IgG. β-Actin mRNA was used as a negative control. LincIN was used as a positive control. ( B ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, ILF3 protein levels were determined by Western blot. ( C ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, ILF3 protein levels were determined by Western blot. ( D ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, the cells were treated with 50 µM α-amanitin to block new RNA synthesis, and then, the stability of ILF3-AS1 transcript over time was determined by qRT-PCR. 18S rRNA, a product of RNA polymerase I that is unchanged by α-amanitin, was used as endogenous control. ( E ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, the cells were treated with 50 µM α-amanitin to block new RNA synthesis and, then, the stability of ILF3-AS1 transcript over time was determined by qRT-PCR. 18S rRNA, a product of RNA polymerase I that is unchanged by α-amanitin, was used as endogenous control. ( F ) Forty-eight hours after transiently transfecting ILF3 overexpression plasmid into SK-MEL-2 cells, ILF3-AS1 transcript levels were determined by qRT-PCR. ( G ) Forty-eight hours after transiently transfecting two independent ILF3-specific shRNAs into A375 cells, ILF3-AS1 transcript levels were determined by qRT-PCR. Results are presented as mean ± SD based on at least three independent experiments. ** P

Techniques Used: Quantitative RT-PCR, Negative Control, Positive Control, Over Expression, Plasmid Preparation, Western Blot, Blocking Assay

7) Product Images from "Aberrant methylation of the 3q25 tumor suppressor gene PTX3 in human esophageal squamous cell carcinoma"

Article Title: Aberrant methylation of the 3q25 tumor suppressor gene PTX3 in human esophageal squamous cell carcinoma

Journal: World Journal of Gastroenterology : WJG

doi: 10.3748/wjg.v17.i37.4225

The mRNA expression of pentraxin 3 was restored after treatment with demethylation agent 5-aza-2'-deoxycytidine in esophageal squamous cell carcinoma cell lines. PTX3: Pentraxin 3; GAPDH: Glyceraldehyde-3-phosohate dehydrogenase.
Figure Legend Snippet: The mRNA expression of pentraxin 3 was restored after treatment with demethylation agent 5-aza-2'-deoxycytidine in esophageal squamous cell carcinoma cell lines. PTX3: Pentraxin 3; GAPDH: Glyceraldehyde-3-phosohate dehydrogenase.

Techniques Used: Expressing

Decreased expression of PTX3 protein in ESCC
Figure Legend Snippet: Decreased expression of PTX3 protein in ESCC

Techniques Used: Expressing

Pentraxin 3 expression assessed by immunohistochemistry staining in esophageal squamous cell carcinoma tumor tissues and adjacent nontumor tissues. A: Significant expression of PTX3 was detected in adjacent nontumor tissues (x 40); B: Negative or weak
Figure Legend Snippet: Pentraxin 3 expression assessed by immunohistochemistry staining in esophageal squamous cell carcinoma tumor tissues and adjacent nontumor tissues. A: Significant expression of PTX3 was detected in adjacent nontumor tissues (x 40); B: Negative or weak

Techniques Used: Expressing, Immunohistochemistry, Staining

Promoter methylation contributes to pentraxin 3 downregulation in esophageal squamous cell carcinoma cell lines. A: Pentraxin 3 (PTX3) mRNA expression was detected by reverse transcription polymerase chain reaction; B: The methylation status of PTX3 promoter
Figure Legend Snippet: Promoter methylation contributes to pentraxin 3 downregulation in esophageal squamous cell carcinoma cell lines. A: Pentraxin 3 (PTX3) mRNA expression was detected by reverse transcription polymerase chain reaction; B: The methylation status of PTX3 promoter

Techniques Used: Methylation, Expressing, Reverse Transcription Polymerase Chain Reaction

8) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

Journal: Scientific Reports

doi: 10.1038/s41598-019-38809-y

Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p
Figure Legend Snippet: Luciferase assay of Kaiso regulatory region of the Ctse gene. ( A ) Nucleotide sequences of CGCG motif in Kaiso regulatory region expanding chromosome 1: 131641487–131642069, and AGGAG motif in PU.1 promoter region expanding chromosome 1: 131661764–131662059 in prepared pGL4.10 [ luc2 ] Vector constructs. ( B ) pGL4.10 [ luc2 ] Vector constructs (1 μg) were transfected into EL4 cells with pRL-TK plasmid and Firefly/Renilla ratio of pGL4.10 (empty vector) was set as 1.0. MRL/MRL construct showed significantly higher luciferase activity compared with pGL4.10-B6/B6 construct (***p

Techniques Used: Luciferase, Plasmid Preparation, Construct, Transfection, Activity Assay

Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p
Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p

Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.
Figure Legend Snippet: The binding of Kaiso on the mCGCG motif of Kaiso regulatory region of Ctse gene. ( A ) Biotin-labeled and methylated probe (B6-Me) was incubated with 28 μg of nuclear protein from EL4 cells, and putative Kaiso and DNA complexes is indicated by asterisk in lane 2. The formation of Kaiso and DNA complexes was inhibited by excess amounts of unlabeled competitor (lane 3). The Kaiso and DNA complexes demonstrated supershift by the addition of 4 μg of anti-Kaiso Ab (arrow head in lane 4). ( B ) Biotin-labeled, unmethylated (MRL), and methylated (MRL-Me) probes were incubated with 28 μg of nuclear protein from EL4 cells. The putative Kaiso and DNA complexes are indicated by asterisks in lanes 2 and 7 and they reveal no supershift with anti-Kaiso Ab and anti-HDAC3 Ab.

Techniques Used: Binding Assay, Labeling, Methylation, Incubation

Expression of Il10 in EL4 cells transfected with siRNA for Ctse and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of Ctse in EL4 cells transfected with 5 μM control siRNA (si-Control) or Ctse siRNA (si-CTSE). *p
Figure Legend Snippet: Expression of Il10 in EL4 cells transfected with siRNA for Ctse and CD4+ T cells isolated from B6 and MRL mice. ( A ) The knockdown and mRNA expression of Ctse in EL4 cells transfected with 5 μM control siRNA (si-Control) or Ctse siRNA (si-CTSE). *p

Techniques Used: Expressing, Transfection, Isolation, Mouse Assay

The expression and methylation status of Ctse gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of Ctse in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p
Figure Legend Snippet: The expression and methylation status of Ctse gene in CD4+ T cells isolated from MRL/lpr lupus-prone (MRL) and C57BL/6 (B6) mice. ( A ) mRNA expression of Ctse in CD4+, CD8+, B cells and macrophages in B6 and MRL mice. *** p

Techniques Used: Expressing, Methylation, Isolation, Mouse Assay

9) Product Images from "High expression of interleukin-1? in the corneal epithelium of MRL/lpr mice is under the control of their genetic background"

Article Title: High expression of interleukin-1? in the corneal epithelium of MRL/lpr mice is under the control of their genetic background

Journal: Clinical and Experimental Immunology

doi: 10.1111/j.1365-2249.2004.02428.x

RT-PCR analyses of IL-1β and MMP-1 expression in the corneas of various strains of mice. The PCR products from 0·5 mg of total RNA extracted from corneas pooled from 10 eyes of each strain were electrophoresed through 2% agarose gels and detected by ethidium bromide staining. Amplified PCR fragment sizes with specific primers for IL-1β, TGF-β, and G3PDH were confirmed with 563, 525, and 983 bp fragments, respectively, of φX174/Hae III.
Figure Legend Snippet: RT-PCR analyses of IL-1β and MMP-1 expression in the corneas of various strains of mice. The PCR products from 0·5 mg of total RNA extracted from corneas pooled from 10 eyes of each strain were electrophoresed through 2% agarose gels and detected by ethidium bromide staining. Amplified PCR fragment sizes with specific primers for IL-1β, TGF-β, and G3PDH were confirmed with 563, 525, and 983 bp fragments, respectively, of φX174/Hae III.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Expressing, Mouse Assay, Polymerase Chain Reaction, Staining, Amplification

10) Product Images from "A Highly Sensitive Telomerase Activity Assay that Eliminates False-Negative Results Caused by PCR Inhibitors"

Article Title: A Highly Sensitive Telomerase Activity Assay that Eliminates False-Negative Results Caused by PCR Inhibitors

Journal: Molecules

doi: 10.3390/molecules181011751

( A ) Fluorescence spectra with probe 1 in the absence or presence of RNase H, MSTP or both; ( B ) Fluorescence at 520 nm with probes 1–4 in the absence or presence of MSTP. Each value is the average calculated from the three replicate data sets and each error bar represents the standard deviation; ( C ) Plots of fluorescence at 520 nm with probe 1 or probe 2  vs.  MSTP concentration. Each data pint is the average calculated from the three replicate data sets and each error bar represents the standard deviation.
Figure Legend Snippet: ( A ) Fluorescence spectra with probe 1 in the absence or presence of RNase H, MSTP or both; ( B ) Fluorescence at 520 nm with probes 1–4 in the absence or presence of MSTP. Each value is the average calculated from the three replicate data sets and each error bar represents the standard deviation; ( C ) Plots of fluorescence at 520 nm with probe 1 or probe 2 vs. MSTP concentration. Each data pint is the average calculated from the three replicate data sets and each error bar represents the standard deviation.

Techniques Used: Fluorescence, Standard Deviation, Concentration Assay

11) Product Images from "Upregulation of DAB2IP Inhibits Ras Activity and Tumorigenesis in Human Pancreatic Cancer Cells"

Article Title: Upregulation of DAB2IP Inhibits Ras Activity and Tumorigenesis in Human Pancreatic Cancer Cells

Journal: Technology in Cancer Research & Treatment

doi: 10.1177/1533033819895494

The messenger RNA (mRNA) expression levels of 16 Ras GTPase-activating proteins (GAPs) in 6 pancreatic cancer cell lines and a normal pancreatic ductal cell line. The RasGAPs superfamily includes 16 members: RASAL3, RASA2, RASA3, IQGAP2, IQGAP3, SYNGAP1, GAPVD1, IQGAP1, ARHGAP5, RASAL2, RASA4, G3BP1, NF1, DAB2IP, RASAL1, and RASA1. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the RasGAPs mRNA levels in pancreatic cancer cells (expressing wild-type KRAS: Bxpc-3; expressing mutant KRAS: Capan-2, Sw1990, CFPAC-1, Aspc-1, Panc-1) and normal H6C7 cells. # P
Figure Legend Snippet: The messenger RNA (mRNA) expression levels of 16 Ras GTPase-activating proteins (GAPs) in 6 pancreatic cancer cell lines and a normal pancreatic ductal cell line. The RasGAPs superfamily includes 16 members: RASAL3, RASA2, RASA3, IQGAP2, IQGAP3, SYNGAP1, GAPVD1, IQGAP1, ARHGAP5, RASAL2, RASA4, G3BP1, NF1, DAB2IP, RASAL1, and RASA1. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to analyze the RasGAPs mRNA levels in pancreatic cancer cells (expressing wild-type KRAS: Bxpc-3; expressing mutant KRAS: Capan-2, Sw1990, CFPAC-1, Aspc-1, Panc-1) and normal H6C7 cells. # P

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Mutagenesis

12) Product Images from "Serum Anti-BPAG1 Auto-Antibody Is a Novel Marker for Human Melanoma"

Article Title: Serum Anti-BPAG1 Auto-Antibody Is a Novel Marker for Human Melanoma

Journal: PLoS ONE

doi: 10.1371/journal.pone.0010566

Expression of BPAG1 in normal human melanocytes and human melanoma cell lines. (A) The expression of BPAG1 and BPAG2 mRNA was quantified by RT-PCR in normal human melanocytes (NHM) and human melanoma cell lines A375 and G361. Normal human keratinocyte (NHK) mRNA was used as a positive control. β-actin was amplified as a loading control for cDNA. NTC; no template control. (B) The expression of BPAG1 protein was detected by IP-western blotting in human melanoma cell lines A375 and G361. A431 was used as positive control for BPAG1. The arrow indicates BPAG1.
Figure Legend Snippet: Expression of BPAG1 in normal human melanocytes and human melanoma cell lines. (A) The expression of BPAG1 and BPAG2 mRNA was quantified by RT-PCR in normal human melanocytes (NHM) and human melanoma cell lines A375 and G361. Normal human keratinocyte (NHK) mRNA was used as a positive control. β-actin was amplified as a loading control for cDNA. NTC; no template control. (B) The expression of BPAG1 protein was detected by IP-western blotting in human melanoma cell lines A375 and G361. A431 was used as positive control for BPAG1. The arrow indicates BPAG1.

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Positive Control, Amplification, Western Blot

13) Product Images from "DNA elements for constitutive androstane receptor- and pregnane X receptor-mediated regulation of bovine CYP3A28 gene"

Article Title: DNA elements for constitutive androstane receptor- and pregnane X receptor-mediated regulation of bovine CYP3A28 gene

Journal: PLoS ONE

doi: 10.1371/journal.pone.0214338

ChIP in control BFH12 cells to quantify the binding of CAR to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO for 6 hours. Chromatin was then isolated, subjected to ChIP using anti-human CAR antibody and quantified by qPCR as described in S1 File . Results for both ER6 and DR5 DNA regions are reported. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.
Figure Legend Snippet: ChIP in control BFH12 cells to quantify the binding of CAR to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO for 6 hours. Chromatin was then isolated, subjected to ChIP using anti-human CAR antibody and quantified by qPCR as described in S1 File . Results for both ER6 and DR5 DNA regions are reported. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Isolation, Real-time Polymerase Chain Reaction, Derivative Assay, Immunoprecipitation, Negative Control

ChIP in control and treated BFH12 cells to quantify the binding of RXRα to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO and 100 μM RU486 for 6 hours. Chromatin was isolated, subjected to ChIP using anti-human RXRα antibody and quantified by qPCR as described in S1 File . Results for ER6 and DR5 DNA regions are reported in panels A and B, respectively. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.
Figure Legend Snippet: ChIP in control and treated BFH12 cells to quantify the binding of RXRα to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO and 100 μM RU486 for 6 hours. Chromatin was isolated, subjected to ChIP using anti-human RXRα antibody and quantified by qPCR as described in S1 File . Results for ER6 and DR5 DNA regions are reported in panels A and B, respectively. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Isolation, Real-time Polymerase Chain Reaction, Derivative Assay, Immunoprecipitation, Negative Control

14) Product Images from "Math6 expression during kidney development and altered expression in a mouse model of glomerulosclerosis"

Article Title: Math6 expression during kidney development and altered expression in a mouse model of glomerulosclerosis

Journal: Developmental dynamics : an official publication of the American Association of Anatomists

doi: 10.1002/dvdy.20934

Characterization of Math6 mRNA and protein expression. A. Northern analysis of altered Math6 expression between normal mouse (wild type, WT) podocytes and normal podocytes infected with a virus (WT+HIV) containing the HIV-1 proviral construct used to make the transgenic mouse model (ribosomal s14 as control). B. Math6 RT/PCR using RNA isolated from normal mouse podocytes (WT); podocytes from the HIV-1 transgenic mouse model (Tg26); E11.5 mouse metanephric mesenchyme (MM) cell line; and E11.5 mouse ureteric bud (UB) cell line. Glyceraldehyde-3-phosphate dehydrogenase (GAP) as control. C. Multi-tissue Northern blot from adult mouse demonstrating the restricted distribution and variable expression level in different adult tissues. D. Expression of Math6 during kidney development. Mouse total kidney RNA was harvested at various days during embryonic and post-natal development (GAP expression is used as a control). E. Semi-quantitative RT/PCR of Math6 expression in glomeruli isolated from normal and HIV-1 transgenic (Tg26) mouse kidneys. Example of a single animal comparison is shown at left using serial dilutions of input template. Quantification of replicas (mean±SD; normal n=4, and Tg26 n=6) is shown in graph at right and was statistical significant ( P =0.014). F. Characterization of Math6 antibody by Western blotting. Lane 1, HEK293T cells. Lane 2, HEK293T cells transfected with a Math6 expression plasmid. Lane 3, HEK293T cells transfected with a Math6 expression plasmid of the cDNA cloned in the reverse orientation.
Figure Legend Snippet: Characterization of Math6 mRNA and protein expression. A. Northern analysis of altered Math6 expression between normal mouse (wild type, WT) podocytes and normal podocytes infected with a virus (WT+HIV) containing the HIV-1 proviral construct used to make the transgenic mouse model (ribosomal s14 as control). B. Math6 RT/PCR using RNA isolated from normal mouse podocytes (WT); podocytes from the HIV-1 transgenic mouse model (Tg26); E11.5 mouse metanephric mesenchyme (MM) cell line; and E11.5 mouse ureteric bud (UB) cell line. Glyceraldehyde-3-phosphate dehydrogenase (GAP) as control. C. Multi-tissue Northern blot from adult mouse demonstrating the restricted distribution and variable expression level in different adult tissues. D. Expression of Math6 during kidney development. Mouse total kidney RNA was harvested at various days during embryonic and post-natal development (GAP expression is used as a control). E. Semi-quantitative RT/PCR of Math6 expression in glomeruli isolated from normal and HIV-1 transgenic (Tg26) mouse kidneys. Example of a single animal comparison is shown at left using serial dilutions of input template. Quantification of replicas (mean±SD; normal n=4, and Tg26 n=6) is shown in graph at right and was statistical significant ( P =0.014). F. Characterization of Math6 antibody by Western blotting. Lane 1, HEK293T cells. Lane 2, HEK293T cells transfected with a Math6 expression plasmid. Lane 3, HEK293T cells transfected with a Math6 expression plasmid of the cDNA cloned in the reverse orientation.

Techniques Used: Expressing, Northern Blot, Infection, Construct, Transgenic Assay, Reverse Transcription Polymerase Chain Reaction, Isolation, Quantitative RT-PCR, Western Blot, Transfection, Plasmid Preparation, Clone Assay

15) Product Images from "A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis"

Article Title: A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0022900

Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.
Figure Legend Snippet: Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.

Techniques Used: Polymerase Chain Reaction, Amplification, Concentration Assay, Marker

16) Product Images from "Diverse pathways of escape from all well-characterized VRC01-class broadly neutralizing HIV-1 antibodies"

Article Title: Diverse pathways of escape from all well-characterized VRC01-class broadly neutralizing HIV-1 antibodies

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1007238

Construction of a HIV-1 proviral library with a soft-randomized Env . ( A ) A representation of the HIV-1 env gene. Regions containing CD4 binding sites (colored boxes)—Loop D, CD4 binding loop, bridging sheet and V5—are expanded with NIH45-46 epitopes indicated by filled red ovals. Residues of Loop D and V5 regions of the HIV-1 isolate ADA, soft randomized in this study, are shown below. ( B ) Sequences of primers used to soft-randomize the Loop D and V5 regions of ADA Env are shown. Amino-acid numbers are based on HXB2 numbering. Soft randomizing primers were synthesized by hand mixing 88% of the original nucleotide and 4% each of the other three nucleotides (88:4:4:4) for the first two codon positions (nucleotides in lower case) of Loop D residues, and 91:3:3:3 ratio for the first two codon positions of V5 residues. For wobble positions of Loop D residues, an equimolar mix (50:50) of G and T (indicated as K) was used for 4- and 6-codon amino acids. For V5 primer, because it is anti-sense, C and A (indicated as M) were used. Nucleotides subject to soft randomization are colored in red. Both the 5’ and 3′ of the primers outside the randomized regions were extended (shown in green) to have a melting temperature matching the pairing primers (shown in blue).
Figure Legend Snippet: Construction of a HIV-1 proviral library with a soft-randomized Env . ( A ) A representation of the HIV-1 env gene. Regions containing CD4 binding sites (colored boxes)—Loop D, CD4 binding loop, bridging sheet and V5—are expanded with NIH45-46 epitopes indicated by filled red ovals. Residues of Loop D and V5 regions of the HIV-1 isolate ADA, soft randomized in this study, are shown below. ( B ) Sequences of primers used to soft-randomize the Loop D and V5 regions of ADA Env are shown. Amino-acid numbers are based on HXB2 numbering. Soft randomizing primers were synthesized by hand mixing 88% of the original nucleotide and 4% each of the other three nucleotides (88:4:4:4) for the first two codon positions (nucleotides in lower case) of Loop D residues, and 91:3:3:3 ratio for the first two codon positions of V5 residues. For wobble positions of Loop D residues, an equimolar mix (50:50) of G and T (indicated as K) was used for 4- and 6-codon amino acids. For V5 primer, because it is anti-sense, C and A (indicated as M) were used. Nucleotides subject to soft randomization are colored in red. Both the 5’ and 3′ of the primers outside the randomized regions were extended (shown in green) to have a melting temperature matching the pairing primers (shown in blue).

Techniques Used: Binding Assay, Synthesized

Soft randomization introduces a controlled number of amino-acid substitutions into a specific target region. ( A ) The distributions of the number of amino-acid substitutions in the Loop D and V5 regions are shown. Pie charts are generated based on the data from approximately 600,000 next generation sequence reads. ( B ) Amino acid substitutions in Loop D and V5 regions of the parental virus library are shown in 2-dimensional heat maps. The relative frequency of the substitutions of each residue is represented by a red gradient. The original amino acids of wild-type ADA Env are indicated as a square with a diagonal line.
Figure Legend Snippet: Soft randomization introduces a controlled number of amino-acid substitutions into a specific target region. ( A ) The distributions of the number of amino-acid substitutions in the Loop D and V5 regions are shown. Pie charts are generated based on the data from approximately 600,000 next generation sequence reads. ( B ) Amino acid substitutions in Loop D and V5 regions of the parental virus library are shown in 2-dimensional heat maps. The relative frequency of the substitutions of each residue is represented by a red gradient. The original amino acids of wild-type ADA Env are indicated as a square with a diagonal line.

Techniques Used: Generated, Sequencing

Alteration of Loop D residues is preferred to that of V5 residues for viral escape of CD4bs bNAbs. ( A ) The frequency of mutation at each amino acid position in the Loop D and V5 regions of the VRC07 selected passage 5 virus swarm. The top 150 sequences determined by their copy numbers detected through deep sequencing, was analyzed. Soft-randomized residues are shown on X-axis, and bold “N” indicates a putative N-glycosylation site. ‘Control passage 15’ virus is the library virus passaged in the absence of an antibody but the same number of times as the VRC07-selected viruses. The residue alterations in the control virus likely represent those advantageous for replication in GHOST-R3/X4/R5 cells. Mutations in Loop D appear to be more frequently selected than those in V5, and loss of glycosylation is one of the most frequently selected changes in both regions. ( B ) Amino acid substitutions in the Loop D and V5 regions of VRC07 selected passage 5 viruses are shown in 2-dimensional heat maps. The relative frequency of the substitutions of a residue is represented by a color gradient. ( C ) Three Loop D (N276, D279 and A281) and two V5 (N461 and S465) residues found most frequently substituted in escape variants are indicated in orange in a space-filling model of an Env trimer (PDB 5V8M). In this structure, Env is derived from a clade A isolate, BG505, and its residue 279 is N, and both 461 and 465 are T. Residues involved in the association of VRC07 are derived from the VRC07-bound Env monomer structure (PDB 4OLU) and are indicated in blue. One monomer of gp120 is shown in light green, 2 nd gp120 monomer in grey, and gp41 molecules in pink. N-glycans are represented as balls and sticks in dark green.
Figure Legend Snippet: Alteration of Loop D residues is preferred to that of V5 residues for viral escape of CD4bs bNAbs. ( A ) The frequency of mutation at each amino acid position in the Loop D and V5 regions of the VRC07 selected passage 5 virus swarm. The top 150 sequences determined by their copy numbers detected through deep sequencing, was analyzed. Soft-randomized residues are shown on X-axis, and bold “N” indicates a putative N-glycosylation site. ‘Control passage 15’ virus is the library virus passaged in the absence of an antibody but the same number of times as the VRC07-selected viruses. The residue alterations in the control virus likely represent those advantageous for replication in GHOST-R3/X4/R5 cells. Mutations in Loop D appear to be more frequently selected than those in V5, and loss of glycosylation is one of the most frequently selected changes in both regions. ( B ) Amino acid substitutions in the Loop D and V5 regions of VRC07 selected passage 5 viruses are shown in 2-dimensional heat maps. The relative frequency of the substitutions of a residue is represented by a color gradient. ( C ) Three Loop D (N276, D279 and A281) and two V5 (N461 and S465) residues found most frequently substituted in escape variants are indicated in orange in a space-filling model of an Env trimer (PDB 5V8M). In this structure, Env is derived from a clade A isolate, BG505, and its residue 279 is N, and both 461 and 465 are T. Residues involved in the association of VRC07 are derived from the VRC07-bound Env monomer structure (PDB 4OLU) and are indicated in blue. One monomer of gp120 is shown in light green, 2 nd gp120 monomer in grey, and gp41 molecules in pink. N-glycans are represented as balls and sticks in dark green.

Techniques Used: Mutagenesis, Sequencing, Derivative Assay

A subset of escape mutations selected from soft-randomized library are found in natural isolates and previously-identified in vivo escape variants. ( A ) Sequence analysis of the Loop D and V5 regions of our top 150 escape variants (top panel) and 5471 naturally-occurring HIV-1 isolates (bottom panel) was performed using the AnalizeAlign tool available at LANL ( www.hiv.lanl.gov ), and presented in logo plots. ( B ) Similar sequence analyses of these 150 escape variants (top panel) and the escape mutations detected in the clinical trials evaluating VRC01 or 3BNC117 is shown. Only four trials [ 6 , 7 , 11 , 12 ], from which complete sequence information is available, are included in the analyses. For clarity, parental sequences and insertion mutations have been excluded. Clinical trial IDs, antibodies, and references are indicated for each analysis. Amino-acid numbers are based on HXB2 numbering.
Figure Legend Snippet: A subset of escape mutations selected from soft-randomized library are found in natural isolates and previously-identified in vivo escape variants. ( A ) Sequence analysis of the Loop D and V5 regions of our top 150 escape variants (top panel) and 5471 naturally-occurring HIV-1 isolates (bottom panel) was performed using the AnalizeAlign tool available at LANL ( www.hiv.lanl.gov ), and presented in logo plots. ( B ) Similar sequence analyses of these 150 escape variants (top panel) and the escape mutations detected in the clinical trials evaluating VRC01 or 3BNC117 is shown. Only four trials [ 6 , 7 , 11 , 12 ], from which complete sequence information is available, are included in the analyses. For clarity, parental sequences and insertion mutations have been excluded. Clinical trial IDs, antibodies, and references are indicated for each analysis. Amino-acid numbers are based on HXB2 numbering.

Techniques Used: In Vivo, Sequencing

17) Product Images from "Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing"

Article Title: Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next generation sequencing

Journal: International Journal of Oncology

doi: 10.3892/ijo.2017.3935

Frequency and distribution of mutations. Plot of mutations of (A) pathologically diagnosed AdCa or strongly suspected AdCa according to all materials (n=411), and (B) by surgical material alone (n=186). ex19del, L858R, G719X, L861Q, T790M and ex20ins; mutations of EGFR , exons 2–4; mutation of KRAS, ALK and RET fusion genes.
Figure Legend Snippet: Frequency and distribution of mutations. Plot of mutations of (A) pathologically diagnosed AdCa or strongly suspected AdCa according to all materials (n=411), and (B) by surgical material alone (n=186). ex19del, L858R, G719X, L861Q, T790M and ex20ins; mutations of EGFR , exons 2–4; mutation of KRAS, ALK and RET fusion genes.

Techniques Used: Mutagenesis

Distribution of EGFR and KRAS mutations by smoking status. (A) Pathologically diagnosed AdCa or strongly suspected AdCa according to all materials. (B) AdCa diagnosed pathologically from surgical materials only. Numbers represent case numbers.
Figure Legend Snippet: Distribution of EGFR and KRAS mutations by smoking status. (A) Pathologically diagnosed AdCa or strongly suspected AdCa according to all materials. (B) AdCa diagnosed pathologically from surgical materials only. Numbers represent case numbers.

Techniques Used:

18) Product Images from "Responses of denitrifying bacterial communities to short-term waterlogging of soils"

Article Title: Responses of denitrifying bacterial communities to short-term waterlogging of soils

Journal: Scientific Reports

doi: 10.1038/s41598-017-00953-8

Quantification of the abundance of nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), nosZ in clade II ( d ), and the total quantity of nosZ ( nosZ in clades I and II) ( e ) in soil by qPCR. Error bars represent standard deviations ( n = 3). Different lowercase letters above columns represent significant differences among different soil depths at each sampling time.
Figure Legend Snippet: Quantification of the abundance of nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), nosZ in clade II ( d ), and the total quantity of nosZ ( nosZ in clades I and II) ( e ) in soil by qPCR. Error bars represent standard deviations ( n = 3). Different lowercase letters above columns represent significant differences among different soil depths at each sampling time.

Techniques Used: Real-time Polymerase Chain Reaction, Sampling

Average relative abundances of nirK in cluster II ( a ) and nirS in cluster I ( b ) sequences affiliated with taxonomic groups at the genus level. Each group is labeled with its genus name, with its phylum or subphylum name in parenthesis. Groups with
Figure Legend Snippet: Average relative abundances of nirK in cluster II ( a ) and nirS in cluster I ( b ) sequences affiliated with taxonomic groups at the genus level. Each group is labeled with its genus name, with its phylum or subphylum name in parenthesis. Groups with

Techniques Used: Labeling

Evaluation of the effect of environmental factors on microbial communities harboring nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), and nosZ in clade II ( d ) in −99-h soil cores by constrained correspondence analysis.
Figure Legend Snippet: Evaluation of the effect of environmental factors on microbial communities harboring nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), and nosZ in clade II ( d ) in −99-h soil cores by constrained correspondence analysis.

Techniques Used:

Nonmetric multidimensional scaling plot of Hellinger-transformed Bray-Curtis dissimilarity matrices describing microbial communities harboring nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), and nosZ in clade II ( d ) in −99-h soil cores. Overlapped symbols indicate equivalent values of data.
Figure Legend Snippet: Nonmetric multidimensional scaling plot of Hellinger-transformed Bray-Curtis dissimilarity matrices describing microbial communities harboring nirK in cluster II ( a ), nirS in cluster I ( b ), nosZ in clade I ( c ), and nosZ in clade II ( d ) in −99-h soil cores. Overlapped symbols indicate equivalent values of data.

Techniques Used: Transformation Assay

19) Product Images from "An Efficient Strategy for Broad-Range Detection of Low Abundance Bacteria without DNA Decontamination of PCR Reagents"

Article Title: An Efficient Strategy for Broad-Range Detection of Low Abundance Bacteria without DNA Decontamination of PCR Reagents

Journal: PLoS ONE

doi: 10.1371/journal.pone.0020303

HotStart and low-DNA Taq DNA polymerases are not sufficiently pure for sensitive and specific broad-range amplification of bacterial DNA. The genomic DNA (100 fg) of S. aureus was amplified by HotStart or low-DNA Taq DNA polymerases (Taq #1: Hot Start Taq DNA polymerase, Protech Inc.; Taq #2: Fast Hot Start Taq DNA polymerase, KAPA Biosystems; Taq #3: Taq DNA polymerase, TakaRa Inc.; Taq #4: ULTRATOOLS Taq DNA polymerase, Biotools Inc.) using the primer set p201 and p1370 (lanes 1, 3, 5, and 7). Significant amount of PCR product was present in the no template control reactions (lanes 2, 4, 6, and 8).
Figure Legend Snippet: HotStart and low-DNA Taq DNA polymerases are not sufficiently pure for sensitive and specific broad-range amplification of bacterial DNA. The genomic DNA (100 fg) of S. aureus was amplified by HotStart or low-DNA Taq DNA polymerases (Taq #1: Hot Start Taq DNA polymerase, Protech Inc.; Taq #2: Fast Hot Start Taq DNA polymerase, KAPA Biosystems; Taq #3: Taq DNA polymerase, TakaRa Inc.; Taq #4: ULTRATOOLS Taq DNA polymerase, Biotools Inc.) using the primer set p201 and p1370 (lanes 1, 3, 5, and 7). Significant amount of PCR product was present in the no template control reactions (lanes 2, 4, 6, and 8).

Techniques Used: Amplification, Polymerase Chain Reaction

20) Product Images from "Antioxidant Dietary Supplementation in Mice Exposed to Proton Radiation Attenuates Expression of Programmed Cell Death-Associated Genes"

Article Title: Antioxidant Dietary Supplementation in Mice Exposed to Proton Radiation Attenuates Expression of Programmed Cell Death-Associated Genes

Journal: Radiation Research

doi: 10.1667/RR2330.1

Proton radiation induces mRNA expression of the apoptosis-related genes BAX (panel A), NFκB1 (panel B), caspase-9 (panel C), TGFβ1 (panel D), caspase-8 (panel E), and BCL2 (panel F). Total bone marrow cells were collected 4 h after 1 Gy
Figure Legend Snippet: Proton radiation induces mRNA expression of the apoptosis-related genes BAX (panel A), NFκB1 (panel B), caspase-9 (panel C), TGFβ1 (panel D), caspase-8 (panel E), and BCL2 (panel F). Total bone marrow cells were collected 4 h after 1 Gy

Techniques Used: Expressing

21) Product Images from "miR-3664-5P suppresses the proliferation and metastasis of gastric cancer by attenuating the NF-κB signaling pathway through targeting MTDH"

Article Title: miR-3664-5P suppresses the proliferation and metastasis of gastric cancer by attenuating the NF-κB signaling pathway through targeting MTDH

Journal: International Journal of Oncology

doi: 10.3892/ijo.2019.4680

Overexpression of miR-3664-5P increases apoptosis and cell cycle arrest. Following treatment with miR-3664-5P inhibitors and mimics for 48 h, GC cells were stained and analyzed by flow cytometry. (A) The cell cycle distribution of MKN45 and MGC803 cells was detected using flow cytometry and the comparative analysis of cell numbers in the G1 and S + G2 phases are presented. (B) Total apoptosis of MKN45 and MGC803 cells was determined by flow cytometry and the comparative analysis of the number of apoptotic cells is presented. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P
Figure Legend Snippet: Overexpression of miR-3664-5P increases apoptosis and cell cycle arrest. Following treatment with miR-3664-5P inhibitors and mimics for 48 h, GC cells were stained and analyzed by flow cytometry. (A) The cell cycle distribution of MKN45 and MGC803 cells was detected using flow cytometry and the comparative analysis of cell numbers in the G1 and S + G2 phases are presented. (B) Total apoptosis of MKN45 and MGC803 cells was determined by flow cytometry and the comparative analysis of the number of apoptotic cells is presented. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P

Techniques Used: Over Expression, Staining, Flow Cytometry, Cytometry

MTDH mediates the antitumor function of miR-3664-5P through the NF-κB signaling pathway. (A-D) miR-3664-5P inhibition enhanced the proliferation, migration and invasion of GC cells as determined by (A) plate colony assays, (B) transwell migration assays, (C) transwell invasion assays and (D) Cell Counting Kit-8 assays, which was reversed following transfection with MTDH siRNA. Magnification, x200; scale bars, 200 µ m. (E) MKN45 transfected with miR-3664-5P inhibitors exhibited significant upregulation of MTDH and key molecules of the NF-κB signaling. Following transfection with MTDH siRNA, expression levels were restored to the original (untransfected) levels. (F) mRNA expression levels of the downstream targets of the NF-κB signaling pathway were upregulated in miR-3664-5P inhibited MKN45 cells and this effect was reversed following transfection with MTDH siRNA. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P
Figure Legend Snippet: MTDH mediates the antitumor function of miR-3664-5P through the NF-κB signaling pathway. (A-D) miR-3664-5P inhibition enhanced the proliferation, migration and invasion of GC cells as determined by (A) plate colony assays, (B) transwell migration assays, (C) transwell invasion assays and (D) Cell Counting Kit-8 assays, which was reversed following transfection with MTDH siRNA. Magnification, x200; scale bars, 200 µ m. (E) MKN45 transfected with miR-3664-5P inhibitors exhibited significant upregulation of MTDH and key molecules of the NF-κB signaling. Following transfection with MTDH siRNA, expression levels were restored to the original (untransfected) levels. (F) mRNA expression levels of the downstream targets of the NF-κB signaling pathway were upregulated in miR-3664-5P inhibited MKN45 cells and this effect was reversed following transfection with MTDH siRNA. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P

Techniques Used: Inhibition, Migration, Cell Counting, Transfection, Expressing

miR-3664-5P inhibits GC cell migration and invasion in vitro . Transwell assays were performed to evaluate the migration and invasion abilities of GC cells. (A and B) The inhibition of miR-3664-5P enhanced, while the overexpression of miR-3664-5P suppressed, the migration and invasion of (A) MKN45 and (B) MGC803 cells. Magnification, x200; scale bars, 200 µ m. Data are presented as the mean ± standard error of the mean, from three independent experiments. *** P
Figure Legend Snippet: miR-3664-5P inhibits GC cell migration and invasion in vitro . Transwell assays were performed to evaluate the migration and invasion abilities of GC cells. (A and B) The inhibition of miR-3664-5P enhanced, while the overexpression of miR-3664-5P suppressed, the migration and invasion of (A) MKN45 and (B) MGC803 cells. Magnification, x200; scale bars, 200 µ m. Data are presented as the mean ± standard error of the mean, from three independent experiments. *** P

Techniques Used: Migration, In Vitro, Inhibition, Over Expression

miR-3664-5P is significantly downregulated in GC and associated with favorable prognosis in patients with GC. (A) miR-3664-5P expression in 100 human GC and paired adjacent normal tissues was detected via RT-qPCR. (B) miR-3664-5P expression was downregulated in GC cell lines when compared with the human normal gastric cell line GES-1; miR-3664-5P expression was determined by RT-qPCR with GAPDH as control. (C) Kaplan-Meier analysis indicated that patients with high miR-3664-5P expression (n=50) had a better overall survival and cancer specific survival when compared with the low expression group (n=50). (D) miR-3664-5P expression was detected in preoperatively obtained plasma from patients with GC (n=60) and compared with tumor-free patients (n=40). ROC curve analysis of miR-3664-5P was utilized to detect the diagnostic efficiency of GC. Data are presented as mean ± standard error of the mean. *** P
Figure Legend Snippet: miR-3664-5P is significantly downregulated in GC and associated with favorable prognosis in patients with GC. (A) miR-3664-5P expression in 100 human GC and paired adjacent normal tissues was detected via RT-qPCR. (B) miR-3664-5P expression was downregulated in GC cell lines when compared with the human normal gastric cell line GES-1; miR-3664-5P expression was determined by RT-qPCR with GAPDH as control. (C) Kaplan-Meier analysis indicated that patients with high miR-3664-5P expression (n=50) had a better overall survival and cancer specific survival when compared with the low expression group (n=50). (D) miR-3664-5P expression was detected in preoperatively obtained plasma from patients with GC (n=60) and compared with tumor-free patients (n=40). ROC curve analysis of miR-3664-5P was utilized to detect the diagnostic efficiency of GC. Data are presented as mean ± standard error of the mean. *** P

Techniques Used: Expressing, Quantitative RT-PCR, Diagnostic Assay

MTDH is the functional target of miR-3664-5P. (A) MTDH levels were significantly increased in GC tissues when compared with the control. *** P
Figure Legend Snippet: MTDH is the functional target of miR-3664-5P. (A) MTDH levels were significantly increased in GC tissues when compared with the control. *** P

Techniques Used: Functional Assay

miR-3664-5P inhibits tumor growth in vivo . (A) BALB/c nude mice (age, 6 weeks) were subcutaneously transplanted with LV-miR-3664-5P MGC803 cells (1×10 7 ) in the left and LV-NC MGC803 cells (1×10 7 ) in the right groin (n=10). (B) Tumor volume was determined every 5 days following transplantation and mice were sacrificed following 30 days. Tumor volume was calculated using: (width 2 × length)/2. (C) Tumor weight was measured following sacrifice (D) A tail vein xenograft model was constructed to investigate metastasis. (E) Representative images of hematoxylin and eosin staining of tumor tissues from mice subcutaneously injected with miR-3664-5P overexpression cells or NC cells (magnification, x200). (F) The number of metastatic lesions was calculated in each group. Data are presented as the mean ± standard deviation (n=10). * P
Figure Legend Snippet: miR-3664-5P inhibits tumor growth in vivo . (A) BALB/c nude mice (age, 6 weeks) were subcutaneously transplanted with LV-miR-3664-5P MGC803 cells (1×10 7 ) in the left and LV-NC MGC803 cells (1×10 7 ) in the right groin (n=10). (B) Tumor volume was determined every 5 days following transplantation and mice were sacrificed following 30 days. Tumor volume was calculated using: (width 2 × length)/2. (C) Tumor weight was measured following sacrifice (D) A tail vein xenograft model was constructed to investigate metastasis. (E) Representative images of hematoxylin and eosin staining of tumor tissues from mice subcutaneously injected with miR-3664-5P overexpression cells or NC cells (magnification, x200). (F) The number of metastatic lesions was calculated in each group. Data are presented as the mean ± standard deviation (n=10). * P

Techniques Used: In Vivo, Mouse Assay, Transplantation Assay, Construct, Staining, Injection, Over Expression, Standard Deviation

miR-3664-5P inhibits GC cell proliferation in vitro . (A) Following transfection with miR-3664-5P mimics or inhibitors, the expression of miR-3664-5P was significantly upregulated or downregulated, respectively, in the MKN45 and MGC803 cell lines. MGC803 was transfected with miR-3664-5P overexpres-sion lentivirus for in vivo assays. miR-3664-5P levels were determined by reverse transcription-quantitative polymerase chain reaction. (B) EdU, (C) Cell Counting Kit-8 and (D) plate colony assays were performed to detect the viability of GC cell lines (magnification, x200). miR-3664-5P upregulation inhibited and miR-3664-5P downregulation promoted the proliferation of GC cells. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P
Figure Legend Snippet: miR-3664-5P inhibits GC cell proliferation in vitro . (A) Following transfection with miR-3664-5P mimics or inhibitors, the expression of miR-3664-5P was significantly upregulated or downregulated, respectively, in the MKN45 and MGC803 cell lines. MGC803 was transfected with miR-3664-5P overexpres-sion lentivirus for in vivo assays. miR-3664-5P levels were determined by reverse transcription-quantitative polymerase chain reaction. (B) EdU, (C) Cell Counting Kit-8 and (D) plate colony assays were performed to detect the viability of GC cell lines (magnification, x200). miR-3664-5P upregulation inhibited and miR-3664-5P downregulation promoted the proliferation of GC cells. Data are presented as the mean ± standard error of the mean, from three independent experiments. ** P

Techniques Used: In Vitro, Transfection, Expressing, In Vivo, Real-time Polymerase Chain Reaction, Cell Counting

22) Product Images from "DNA elements for constitutive androstane receptor- and pregnane X receptor-mediated regulation of bovine CYP3A28 gene"

Article Title: DNA elements for constitutive androstane receptor- and pregnane X receptor-mediated regulation of bovine CYP3A28 gene

Journal: PLoS ONE

doi: 10.1371/journal.pone.0214338

bCAR-mediated transactivation of the proximal promoter and the fragment 3 in CYP3A28 promoter. The transactivation by bCAR of the most responsive fragments PP and F3 was evaluated. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmids or PBREM-tk-luc (PBREM, 50 ng/well) and either bCAR expression plasmids or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as mean luciferase activities ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P
Figure Legend Snippet: bCAR-mediated transactivation of the proximal promoter and the fragment 3 in CYP3A28 promoter. The transactivation by bCAR of the most responsive fragments PP and F3 was evaluated. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmids or PBREM-tk-luc (PBREM, 50 ng/well) and either bCAR expression plasmids or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as mean luciferase activities ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P

Techniques Used: Transfection, Expressing, Plasmid Preparation, Luciferase

Induction of CYP3A28 mRNA in BFH12 cells exposed to increasing concentrations of RU486 for 6 hours. BFH12 cells were treated with different concentrations of RU486 (1, 2.5, 5, 10, 25, 50 and 100 μM) for 6 hours, as described in Materials and Methods. The expression of CYP3A28 was detected by qPCR in control (0.1% DMSO) and treated cells, using RPLP0 as internal control gene. The relative expression of DMSO-treated cells was set to 1 and its value was used for the normalization of the other groups. Data are expressed as the mean ± SD of three independent experiments (arbitrary units, AU). Statistical analysis: ANOVA + Tukey’s post test. Significance was defined as: P
Figure Legend Snippet: Induction of CYP3A28 mRNA in BFH12 cells exposed to increasing concentrations of RU486 for 6 hours. BFH12 cells were treated with different concentrations of RU486 (1, 2.5, 5, 10, 25, 50 and 100 μM) for 6 hours, as described in Materials and Methods. The expression of CYP3A28 was detected by qPCR in control (0.1% DMSO) and treated cells, using RPLP0 as internal control gene. The relative expression of DMSO-treated cells was set to 1 and its value was used for the normalization of the other groups. Data are expressed as the mean ± SD of three independent experiments (arbitrary units, AU). Statistical analysis: ANOVA + Tukey’s post test. Significance was defined as: P

Techniques Used: Expressing, Real-time Polymerase Chain Reaction

bPXR-mediated transactivation of the proximal promoter and the fragment 3 in CYP3A28 promoter. The transactivation by bPXR of the most responsive fragments PP and F3 was evaluated. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmids or CYP3A4-XREM-luc (XREM, 50 ng/well) and either bPXR expression plasmids or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as mean luciferase activities ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P
Figure Legend Snippet: bPXR-mediated transactivation of the proximal promoter and the fragment 3 in CYP3A28 promoter. The transactivation by bPXR of the most responsive fragments PP and F3 was evaluated. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmids or CYP3A4-XREM-luc (XREM, 50 ng/well) and either bPXR expression plasmids or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as mean luciferase activities ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P

Techniques Used: Transfection, Expressing, Plasmid Preparation, Luciferase

ChIP in control BFH12 cells to quantify the binding of CAR to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO for 6 hours. Chromatin was then isolated, subjected to ChIP using anti-human CAR antibody and quantified by qPCR as described in S1 File . Results for both ER6 and DR5 DNA regions are reported. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.
Figure Legend Snippet: ChIP in control BFH12 cells to quantify the binding of CAR to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO for 6 hours. Chromatin was then isolated, subjected to ChIP using anti-human CAR antibody and quantified by qPCR as described in S1 File . Results for both ER6 and DR5 DNA regions are reported. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Isolation, Real-time Polymerase Chain Reaction, Derivative Assay, Immunoprecipitation, Negative Control

ChIP in control and treated BFH12 cells to quantify the binding of RXRα to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO and 100 μM RU486 for 6 hours. Chromatin was isolated, subjected to ChIP using anti-human RXRα antibody and quantified by qPCR as described in S1 File . Results for ER6 and DR5 DNA regions are reported in panels A and B, respectively. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.
Figure Legend Snippet: ChIP in control and treated BFH12 cells to quantify the binding of RXRα to ER6 and DR5 binding sites. BFH12 cells were exposed to 0.1% DMSO and 100 μM RU486 for 6 hours. Chromatin was isolated, subjected to ChIP using anti-human RXRα antibody and quantified by qPCR as described in S1 File . Results for ER6 and DR5 DNA regions are reported in panels A and B, respectively. Data are normalized to input DNA and expressed as % ChIP/input. The experiment was performed four times independently, and similar results were obtained. The data shown derived from a representative experiment. Chromatin samples from control cells immunoprecipitated with or without Histone H3 antibody are shown as Histone H3 and beads, respectively. A further negative control (exon 13), representing a CYP3A28 DNA region without NR binding sites, is reported in the graph. In all experiments, negative and positive controls behaved as expected.

Techniques Used: Chromatin Immunoprecipitation, Binding Assay, Isolation, Real-time Polymerase Chain Reaction, Derivative Assay, Immunoprecipitation, Negative Control

Sequence comparison and distribution of regulatory elements in the human CYP3A4 and bovine CYP3A28 proximal promoters. Identical nucleotides are denoted by asterisks. The transcription start sites are indicated by arrows. The sequence is numbered relative to the transcription start site taken as +1. The binding sites previously characterized in human proximal promoter are boxed (modified from [ 45 ]), the newly identified bovine elements are bolded and underlined. For the elements identified through MatInspector analysis, the nucleotides matching the matrix core are highlighted in grey colour.
Figure Legend Snippet: Sequence comparison and distribution of regulatory elements in the human CYP3A4 and bovine CYP3A28 proximal promoters. Identical nucleotides are denoted by asterisks. The transcription start sites are indicated by arrows. The sequence is numbered relative to the transcription start site taken as +1. The binding sites previously characterized in human proximal promoter are boxed (modified from [ 45 ]), the newly identified bovine elements are bolded and underlined. For the elements identified through MatInspector analysis, the nucleotides matching the matrix core are highlighted in grey colour.

Techniques Used: Sequencing, Binding Assay, Modification

Screening for bPXR- and bCAR-responsive regions in CYP3A28 promoter. A series of CYP3A28 luciferase reporter gene constructs (PP, lnPP, PP+F1, PP+F2, PP+F3, PP+F4, PP+F5) was prepared as described in S1 File . Numbers indicate the positions relative to the transcriptional start site. HepG2 cells were transfected with the control reporter pCMVβ (600 ng/well), each reporter plasmids or PBREM-tk-luc (PBREM) and CYP3A4-XREM-luc (XREM) or with negative control reporter pGL4.10-luc (500 ng/well) and either bCAR and bPXR expression plasmids or pCI-neo empty vector (100 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as relative activities to those in pGL4.10 transfected cells (= 100) for each condition (pCI-neo, bCAR or bPXR co-transfection). Data are the mean ± SD (n = 3 or 4) and representative of one assay.
Figure Legend Snippet: Screening for bPXR- and bCAR-responsive regions in CYP3A28 promoter. A series of CYP3A28 luciferase reporter gene constructs (PP, lnPP, PP+F1, PP+F2, PP+F3, PP+F4, PP+F5) was prepared as described in S1 File . Numbers indicate the positions relative to the transcriptional start site. HepG2 cells were transfected with the control reporter pCMVβ (600 ng/well), each reporter plasmids or PBREM-tk-luc (PBREM) and CYP3A4-XREM-luc (XREM) or with negative control reporter pGL4.10-luc (500 ng/well) and either bCAR and bPXR expression plasmids or pCI-neo empty vector (100 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as relative activities to those in pGL4.10 transfected cells (= 100) for each condition (pCI-neo, bCAR or bPXR co-transfection). Data are the mean ± SD (n = 3 or 4) and representative of one assay.

Techniques Used: Luciferase, Construct, Transfection, Negative Control, Expressing, Plasmid Preparation, Cotransfection

Identification of bPXR-responsive elements in the proximal promoter and fragment 3 in CYP3A28 promoter. Several constructs were produced to study the binding elements identified in the CYP3A28 proximal promoter (PP) and the contribution of the binding motif DR5 identified in F3. The parental PP was deleted of the whole putative region containing several TF binding-sites resulting in the PP_del; through site-directed mutagenesis the ER6 (PP_mER6) and DR1 (PP_mDR1) motifs were inactivated. The parental PP+F3 was deleted of the whole putative region containing several TF binding-sites resulting in the PP_del+F3; through site-directed mutagenesis the ER6 (PP_mER6+F3), the DR5 motif (PP+F3_mDR5 and PP_del+F3_mDR5) or both (PP_mER6+F3_mDR5) were inactivated. Details are reported in S1 File . Numbers indicate the positions relative to the transcriptional start site. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmid or CYP3A4-XREM-luc (XREM, 50 ng/well) and either bPXR expression plasmid or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as relative activities to those in pGL4.10 transfected cells (= 100) for each condition (pCI-neo empty or bPXR co-transfection). Data are the mean ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P
Figure Legend Snippet: Identification of bPXR-responsive elements in the proximal promoter and fragment 3 in CYP3A28 promoter. Several constructs were produced to study the binding elements identified in the CYP3A28 proximal promoter (PP) and the contribution of the binding motif DR5 identified in F3. The parental PP was deleted of the whole putative region containing several TF binding-sites resulting in the PP_del; through site-directed mutagenesis the ER6 (PP_mER6) and DR1 (PP_mDR1) motifs were inactivated. The parental PP+F3 was deleted of the whole putative region containing several TF binding-sites resulting in the PP_del+F3; through site-directed mutagenesis the ER6 (PP_mER6+F3), the DR5 motif (PP+F3_mDR5 and PP_del+F3_mDR5) or both (PP_mER6+F3_mDR5) were inactivated. Details are reported in S1 File . Numbers indicate the positions relative to the transcriptional start site. C3A cells were transfected with the control reporter pCMVβ (150 ng/well), each reporter plasmid or CYP3A4-XREM-luc (XREM, 50 ng/well) and either bPXR expression plasmid or pCI-neo empty vector (25 ng/well). After transfection, cells were treated with vehicle (0.1% DMSO) or SR12813 (10 μM) for 24 hours, and reporter activities were measured. Firefly luciferase activities were normalized with β-galactosidase activities. Data are expressed as relative activities to those in pGL4.10 transfected cells (= 100) for each condition (pCI-neo empty or bPXR co-transfection). Data are the mean ± SD (n = 3 or 4). Results shown are representative of 3 independent assays. Statistical significance P

Techniques Used: Construct, Produced, Binding Assay, Mutagenesis, Transfection, Plasmid Preparation, Expressing, Luciferase, Cotransfection

Sequence comparison and distribution of distal regulatory elements in the bovine CYP3A28 F3 fragment and human CYP3A4 promoter region. Identical nucleotides are denoted by asterisks. The sequence is numbered relative to the transcription start site taken as +1. The newly identified bovine elements (C/EBPα) are bolded and underlined. The DR5 element, identified in both species through NUBIscan analysis, is highlighted in grey colour and boxed.
Figure Legend Snippet: Sequence comparison and distribution of distal regulatory elements in the bovine CYP3A28 F3 fragment and human CYP3A4 promoter region. Identical nucleotides are denoted by asterisks. The sequence is numbered relative to the transcription start site taken as +1. The newly identified bovine elements (C/EBPα) are bolded and underlined. The DR5 element, identified in both species through NUBIscan analysis, is highlighted in grey colour and boxed.

Techniques Used: Sequencing

23) Product Images from "A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis"

Article Title: A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0022900

Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.
Figure Legend Snippet: Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.

Techniques Used: Polymerase Chain Reaction, Amplification, Concentration Assay, Marker

24) Product Images from "Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR)"

Article Title: Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR)

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms14036436

Effects of Tth MutS on standard polymerase chain reaction (PCR) amplification of an 80-bp template. ( A ) Schema tic representation of the primers and templates used in ( B , C ). Perfectly matched, GT-mismatched or unpaired T-containing primers were used; ( B ) Perfectly matched (left), GT-mismatched (middle) or unpaired T-containing (right) primers were used to amplify the perfectly matched template; ( C ) The relative amounts of the products from perfectly matched (blue), GT-mismatched (red) or unpaired T-containing (purple) primers were plotted against the Tth MutS concentration for reactions using three polymerases: LA Taq (left), KOD polymerase (middle) and A. aeolicus DnaE (right). The amounts of the products were normalized by those at 0 μM Tth MutS.
Figure Legend Snippet: Effects of Tth MutS on standard polymerase chain reaction (PCR) amplification of an 80-bp template. ( A ) Schema tic representation of the primers and templates used in ( B , C ). Perfectly matched, GT-mismatched or unpaired T-containing primers were used; ( B ) Perfectly matched (left), GT-mismatched (middle) or unpaired T-containing (right) primers were used to amplify the perfectly matched template; ( C ) The relative amounts of the products from perfectly matched (blue), GT-mismatched (red) or unpaired T-containing (purple) primers were plotted against the Tth MutS concentration for reactions using three polymerases: LA Taq (left), KOD polymerase (middle) and A. aeolicus DnaE (right). The amounts of the products were normalized by those at 0 μM Tth MutS.

Techniques Used: Polymerase Chain Reaction, Amplification, Concentration Assay

25) Product Images from "Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA"

Article Title: Direct Assessment of Viral Diversity in Soils by Random PCR Amplification of Polymorphic DNA

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00268-13

RAPD-PCR of viral assemblages from a Delaware soil sample using four different decamer primers at four levels of viral template DNA. Lanes 4, 5, 6, and 7 indicate 10 4 , 10 5 , 10 6 , and 10 7 viruses per PCR, respectively. Lanes M, molecular size marker lanes;
Figure Legend Snippet: RAPD-PCR of viral assemblages from a Delaware soil sample using four different decamer primers at four levels of viral template DNA. Lanes 4, 5, 6, and 7 indicate 10 4 , 10 5 , 10 6 , and 10 7 viruses per PCR, respectively. Lanes M, molecular size marker lanes;

Techniques Used: Polymerase Chain Reaction, Marker

Reproducibility of RAPD-PCR fingerprints using the HCB-1 decamer against whole viral assemblages from a single Delaware soil sample. The scale at the upper top left is the percent similarity of RAPD-PCR fingerprints. Numbers at the nodes of the dendrogram
Figure Legend Snippet: Reproducibility of RAPD-PCR fingerprints using the HCB-1 decamer against whole viral assemblages from a single Delaware soil sample. The scale at the upper top left is the percent similarity of RAPD-PCR fingerprints. Numbers at the nodes of the dendrogram

Techniques Used: Polymerase Chain Reaction

RAPD-PCR fingerprints of viral communities in soils from Antarctica, Kellogg Biological Station (KBS), and Delaware. (A) RAPD-PCR fingerprints from Antarctic soils (ETP and SOB series). (B) RAPD-PCR fingerprints from KBS soils (T1, T4, T7, T8, and SF2)
Figure Legend Snippet: RAPD-PCR fingerprints of viral communities in soils from Antarctica, Kellogg Biological Station (KBS), and Delaware. (A) RAPD-PCR fingerprints from Antarctic soils (ETP and SOB series). (B) RAPD-PCR fingerprints from KBS soils (T1, T4, T7, T8, and SF2)

Techniques Used: Polymerase Chain Reaction

26) Product Images from "Long noncoding RNA ZEB1-AS1 acts as an oncogene in osteosarcoma by epigenetically activating ZEB1"

Article Title: Long noncoding RNA ZEB1-AS1 acts as an oncogene in osteosarcoma by epigenetically activating ZEB1

Journal: American Journal of Translational Research

doi:

ZEB1-AS1-induced proliferation and migration are dependent on ZEB1. A. After the transfection of ZEB1specific siRNAs or control siRNAs into ZEB1-AS1 stably overexpressed HOS cells, ZEB1-AS1 expression level was measured by qRT-PCR. B. Cell growth curves
Figure Legend Snippet: ZEB1-AS1-induced proliferation and migration are dependent on ZEB1. A. After the transfection of ZEB1specific siRNAs or control siRNAs into ZEB1-AS1 stably overexpressed HOS cells, ZEB1-AS1 expression level was measured by qRT-PCR. B. Cell growth curves

Techniques Used: Migration, Transfection, Stable Transfection, Expressing, Quantitative RT-PCR

ZEB1-AS1 and ZEB1 expression levels are significantly correlated in osteosarcoma. A. ZEB1 Expression level in 50 pairs of osteosarcoma tissues and adjacent normal tissues. The expression of ZEB1 was quantified by qRT-PCR. The horizontal lines in the box
Figure Legend Snippet: ZEB1-AS1 and ZEB1 expression levels are significantly correlated in osteosarcoma. A. ZEB1 Expression level in 50 pairs of osteosarcoma tissues and adjacent normal tissues. The expression of ZEB1 was quantified by qRT-PCR. The horizontal lines in the box

Techniques Used: Expressing, Quantitative RT-PCR

Overexpression of ZEB1-AS1 in osteosarcoma and its association with poor prognosis of osteosarcoma patients. A. ZEB1-AS1 Expression level in 50 pairs of osteosarcoma tissues and adjacent normal tissues. The expression of ZEB1-AS1 was quantified by qRT-PCR.
Figure Legend Snippet: Overexpression of ZEB1-AS1 in osteosarcoma and its association with poor prognosis of osteosarcoma patients. A. ZEB1-AS1 Expression level in 50 pairs of osteosarcoma tissues and adjacent normal tissues. The expression of ZEB1-AS1 was quantified by qRT-PCR.

Techniques Used: Over Expression, Expressing, Quantitative RT-PCR

ZEB1-AS1 induces epigenetic changes at the ZEB1 promoter. A. ChIP shows the euchromatic histone marks at the ZEB1 promoter in ZEB1-AS1 stably overexpressed and control HOS cells. Data were normalized to input values and are shown in reference to control
Figure Legend Snippet: ZEB1-AS1 induces epigenetic changes at the ZEB1 promoter. A. ChIP shows the euchromatic histone marks at the ZEB1 promoter in ZEB1-AS1 stably overexpressed and control HOS cells. Data were normalized to input values and are shown in reference to control

Techniques Used: Chromatin Immunoprecipitation, Stable Transfection

ZEB1-AS1 upregulates ZEB1 expression. A. Schematic of the human ZEB1-AS1 locus. Arrows mark transcription start sites. B. ZEB1 mRNA levels in ZEB1-AS1 stably overexpressed and control HOS cells. C. ZEB1 protein levels in ZEB1-AS1 stably overexpressed
Figure Legend Snippet: ZEB1-AS1 upregulates ZEB1 expression. A. Schematic of the human ZEB1-AS1 locus. Arrows mark transcription start sites. B. ZEB1 mRNA levels in ZEB1-AS1 stably overexpressed and control HOS cells. C. ZEB1 protein levels in ZEB1-AS1 stably overexpressed

Techniques Used: Expressing, Stable Transfection

Knockdown of ZEB1-AS1 inhibits osteosarcoma cell proliferation and migration. A. ZEB1-AS1 expression level in ZEB1-AS1 stably depleted and control Saos-2 cells. B. Knockdown of ZEB1-AS1 inhibits Saos-2 cells proliferation. Cell growth curves were determined
Figure Legend Snippet: Knockdown of ZEB1-AS1 inhibits osteosarcoma cell proliferation and migration. A. ZEB1-AS1 expression level in ZEB1-AS1 stably depleted and control Saos-2 cells. B. Knockdown of ZEB1-AS1 inhibits Saos-2 cells proliferation. Cell growth curves were determined

Techniques Used: Migration, Expressing, Stable Transfection

ZEB1-AS1 is overexpressed in osteosarcoma and indicates poor prognosis of osteosarcoma patients
Figure Legend Snippet: ZEB1-AS1 is overexpressed in osteosarcoma and indicates poor prognosis of osteosarcoma patients

Techniques Used:

Overexpression of ZEB1-AS1 promotes osteosarcoma cell proliferation and migration. A. ZEB1-AS1 expression level in ZEB1-AS1 stably overexpressed and control HOS cells. B. ZEB1-AS1 overexpression promotes HOS cells proliferation. Cell growth curves were
Figure Legend Snippet: Overexpression of ZEB1-AS1 promotes osteosarcoma cell proliferation and migration. A. ZEB1-AS1 expression level in ZEB1-AS1 stably overexpressed and control HOS cells. B. ZEB1-AS1 overexpression promotes HOS cells proliferation. Cell growth curves were

Techniques Used: Over Expression, Migration, Expressing, Stable Transfection

27) Product Images from "Serum Anti-BPAG1 Auto-Antibody Is a Novel Marker for Human Melanoma"

Article Title: Serum Anti-BPAG1 Auto-Antibody Is a Novel Marker for Human Melanoma

Journal: PLoS ONE

doi: 10.1371/journal.pone.0010566

Expression of BPAG1 in normal human melanocytes and human melanoma cell lines. (A) The expression of BPAG1 and BPAG2 mRNA was quantified by RT-PCR in normal human melanocytes (NHM) and human melanoma cell lines A375 and G361. Normal human keratinocyte (NHK) mRNA was used as a positive control. β-actin was amplified as a loading control for cDNA. NTC; no template control. (B) The expression of BPAG1 protein was detected by IP-western blotting in human melanoma cell lines A375 and G361. A431 was used as positive control for BPAG1. The arrow indicates BPAG1.
Figure Legend Snippet: Expression of BPAG1 in normal human melanocytes and human melanoma cell lines. (A) The expression of BPAG1 and BPAG2 mRNA was quantified by RT-PCR in normal human melanocytes (NHM) and human melanoma cell lines A375 and G361. Normal human keratinocyte (NHK) mRNA was used as a positive control. β-actin was amplified as a loading control for cDNA. NTC; no template control. (B) The expression of BPAG1 protein was detected by IP-western blotting in human melanoma cell lines A375 and G361. A431 was used as positive control for BPAG1. The arrow indicates BPAG1.

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Positive Control, Amplification, Western Blot

28) Product Images from "miR-532-5p promotes breast cancer proliferation and migration by targeting RERG"

Article Title: miR-532-5p promotes breast cancer proliferation and migration by targeting RERG

Journal: Experimental and Therapeutic Medicine

doi: 10.3892/etm.2019.8186

Expression of miR-532-5p is negatively correlated with RERG mRNA levels in breast tumor tissues. (A) Compared with normal tissues, expression level of RERG mRNA was significantly decreased in breast tumor tissues. (B) Pearson's correlation analysis showed that there was a significant negative correlation between miR-532-5p expression and RERG mRNA levels in breast tumor tissues from 20 patients with breast cancer. ***P
Figure Legend Snippet: Expression of miR-532-5p is negatively correlated with RERG mRNA levels in breast tumor tissues. (A) Compared with normal tissues, expression level of RERG mRNA was significantly decreased in breast tumor tissues. (B) Pearson's correlation analysis showed that there was a significant negative correlation between miR-532-5p expression and RERG mRNA levels in breast tumor tissues from 20 patients with breast cancer. ***P

Techniques Used: Expressing

RERG is a target gene of miR-532-5p in breast cancer cells. (A) Sequence alignment showed that there was a putative binding site for miR-532-5p within the 3′-UTR of RERG mRNA. Two point mutations were introduced in the 3′-UTR-WT of RERG to establish RERG 3′-UTR-Mut. (B) In a dual luciferase reporter assay, transfection of miR-532-5p mimic reduced luciferase activity of MDA-MB-231 cells transfected with RERG 3′-UTR-WT. (C) In a dual luciferase reporter assay, transfection of miR-532-5p mimic reduced luciferase activity of BT549 cells transfected with RERG 3′-UTR-WT. **P
Figure Legend Snippet: RERG is a target gene of miR-532-5p in breast cancer cells. (A) Sequence alignment showed that there was a putative binding site for miR-532-5p within the 3′-UTR of RERG mRNA. Two point mutations were introduced in the 3′-UTR-WT of RERG to establish RERG 3′-UTR-Mut. (B) In a dual luciferase reporter assay, transfection of miR-532-5p mimic reduced luciferase activity of MDA-MB-231 cells transfected with RERG 3′-UTR-WT. (C) In a dual luciferase reporter assay, transfection of miR-532-5p mimic reduced luciferase activity of BT549 cells transfected with RERG 3′-UTR-WT. **P

Techniques Used: Sequencing, Binding Assay, Luciferase, Reporter Assay, Transfection, Activity Assay, Multiple Displacement Amplification

RERG was negatively regulated by miR-532-5p in breast cancer cells. (A) Transfection with miR-532-5p inhibitor decreased miR-532-5p expression in MDA-MB-231 cells. (B) Downregulation of miR-532-5p increased RERG mRNA levels in MDA-MB-231 cells. (C) Downregulation of miR-532-5p increased RERG protein expression levels and decreased p-MET and p-ERK1/2 protein levels in MDA-MB-231 cells. (D) Western blotting results were analyzed quantitatively. (E) Transfection with miR-532-5p mimics successfully increased the expression of miR-532-5p. (F) Upregulation of miR-532-5p decreased RERG mRNA levels in MDA-MB-231 cells. (G) Upregulation of miR-532-5p decreased RERG protein levels and increased p-MET and p-ERK1/2 protein levels in MDA-MB-231 cells. (H) Western blotting results were analyzed quantitatively. **P
Figure Legend Snippet: RERG was negatively regulated by miR-532-5p in breast cancer cells. (A) Transfection with miR-532-5p inhibitor decreased miR-532-5p expression in MDA-MB-231 cells. (B) Downregulation of miR-532-5p increased RERG mRNA levels in MDA-MB-231 cells. (C) Downregulation of miR-532-5p increased RERG protein expression levels and decreased p-MET and p-ERK1/2 protein levels in MDA-MB-231 cells. (D) Western blotting results were analyzed quantitatively. (E) Transfection with miR-532-5p mimics successfully increased the expression of miR-532-5p. (F) Upregulation of miR-532-5p decreased RERG mRNA levels in MDA-MB-231 cells. (G) Upregulation of miR-532-5p decreased RERG protein levels and increased p-MET and p-ERK1/2 protein levels in MDA-MB-231 cells. (H) Western blotting results were analyzed quantitatively. **P

Techniques Used: Transfection, Expressing, Multiple Displacement Amplification, Western Blot

29) Product Images from "Human DJ-1-specific Transcriptional Activation of Tyrosine Hydroxylase Gene *"

Article Title: Human DJ-1-specific Transcriptional Activation of Tyrosine Hydroxylase Gene *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M110.137034

Sequestration of PSF from DNA by DJ-1. A , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human DJ-1. Forty-eight h after transfection, DNA extracted from chromatin was immunoprecipitated ( IP ) with an anti-FLAG antibody or IgG, and regions spanning −2909 to −2707 and −4000 to −3800 were amplified by PCR using specific primers. B , SH-SY5Y cells were transfected under the same conditions as described for A . After chromatin had been immunoprecipitated with an anti-SP1 antibody or IgG, regions spanning −1157 to −932 and −4000 to −3800 were amplified by PCR using specific primers. C , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human L166P DJ-1 and subjected to ChIP assays as described in A. D , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human L166P DJ-1 and subjected to ChIP assays as described in B .
Figure Legend Snippet: Sequestration of PSF from DNA by DJ-1. A , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human DJ-1. Forty-eight h after transfection, DNA extracted from chromatin was immunoprecipitated ( IP ) with an anti-FLAG antibody or IgG, and regions spanning −2909 to −2707 and −4000 to −3800 were amplified by PCR using specific primers. B , SH-SY5Y cells were transfected under the same conditions as described for A . After chromatin had been immunoprecipitated with an anti-SP1 antibody or IgG, regions spanning −1157 to −932 and −4000 to −3800 were amplified by PCR using specific primers. C , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human L166P DJ-1 and subjected to ChIP assays as described in A. D , SH-SY5Y cells were transfected with a constant amount of FLAG-human PSF and various amounts of HA-human L166P DJ-1 and subjected to ChIP assays as described in B .

Techniques Used: Transfection, Immunoprecipitation, Amplification, Polymerase Chain Reaction, Chromatin Immunoprecipitation

Association of DJ-1 and PSF with the TH promoter. A and B , chromatin solutions from SH-SY5Y ( A ) and Neuro-2a ( B ) cells were co-immunoprecipitated ( IP ) with anti-DJ-1 (α- DJ-1 ), anti-PSF (α- PSF ), and anti-SP1 (α- SP1 ) antibodies. Segments in DNA extracted from precipitated chromatin were amplified by PCR using specific primers as described under “Experimental Procedures.” C , regions to be amplified by PCR are schematically drawn.
Figure Legend Snippet: Association of DJ-1 and PSF with the TH promoter. A and B , chromatin solutions from SH-SY5Y ( A ) and Neuro-2a ( B ) cells were co-immunoprecipitated ( IP ) with anti-DJ-1 (α- DJ-1 ), anti-PSF (α- PSF ), and anti-SP1 (α- SP1 ) antibodies. Segments in DNA extracted from precipitated chromatin were amplified by PCR using specific primers as described under “Experimental Procedures.” C , regions to be amplified by PCR are schematically drawn.

Techniques Used: Immunoprecipitation, Amplification, Polymerase Chain Reaction

30) Product Images from "Delayed union of femoral fractures in older rats:decreased gene expression"

Article Title: Delayed union of femoral fractures in older rats:decreased gene expression

Journal: BMC Musculoskeletal Disorders

doi: 10.1186/1471-2474-2-2

Change in the mRNA expression of osteocalcin (top), type I collagen α1 (middle), and type II collagen (bottom) with time after mid-diaphyseal femoral fracture in rats at 6 weeks (younger) and 15 months (older) of age. The mRNA was extracted, reverse transcribed, and amplified by the polymerase chain reaction. The amplimers were separated by electrophoresis, blotted to nylon membranes and hybridized with 32 P-labeled internal oligonucleotides. The level of radioactivity of each sample was measured in units of photo stimulated luminescence (PSL). The data are shown as mean ± SEM for three to four samples per point except for 2 (n = 2) and 6 (n = 1) week older rats. SEM smaller than the radius of the point are not shown.
Figure Legend Snippet: Change in the mRNA expression of osteocalcin (top), type I collagen α1 (middle), and type II collagen (bottom) with time after mid-diaphyseal femoral fracture in rats at 6 weeks (younger) and 15 months (older) of age. The mRNA was extracted, reverse transcribed, and amplified by the polymerase chain reaction. The amplimers were separated by electrophoresis, blotted to nylon membranes and hybridized with 32 P-labeled internal oligonucleotides. The level of radioactivity of each sample was measured in units of photo stimulated luminescence (PSL). The data are shown as mean ± SEM for three to four samples per point except for 2 (n = 2) and 6 (n = 1) week older rats. SEM smaller than the radius of the point are not shown.

Techniques Used: Expressing, Amplification, Polymerase Chain Reaction, Electrophoresis, Labeling, Radioactivity

31) Product Images from "Long Noncoding RNA PVT1 as a Novel Diagnostic Biomarker and Therapeutic Target for Melanoma"

Article Title: Long Noncoding RNA PVT1 as a Novel Diagnostic Biomarker and Therapeutic Target for Melanoma

Journal: BioMed Research International

doi: 10.1155/2017/7038579

Overexpression of PVT1 enhances melanoma cells proliferation, cell cycle progression, and migration. (a) PVT1 expression levels in PVT1 stably overexpressed and control A375 cells were measured by qPCR. (b) The effect of PVT1 overexpression on A375 cells proliferation was measured by CCK-8 assays. (c) The effect of PVT1 overexpression on A375 cells proliferation was measured by EdU incorporation assays. Scale bars, 100 μ m. (d) The effect of PVT1 overexpression on A375 cell cycle distribution was measured by flow cytometry. (e) The effect of PVT1 overexpression on A375 cells migration was measured by transwell assays. Scale bars, 100 μ m. (f) Western blot analysis of MYC protein in PVT1 stably overexpressed and control A375 cells. Data are presented as mean ± SD. n = 3, ∗ P
Figure Legend Snippet: Overexpression of PVT1 enhances melanoma cells proliferation, cell cycle progression, and migration. (a) PVT1 expression levels in PVT1 stably overexpressed and control A375 cells were measured by qPCR. (b) The effect of PVT1 overexpression on A375 cells proliferation was measured by CCK-8 assays. (c) The effect of PVT1 overexpression on A375 cells proliferation was measured by EdU incorporation assays. Scale bars, 100 μ m. (d) The effect of PVT1 overexpression on A375 cell cycle distribution was measured by flow cytometry. (e) The effect of PVT1 overexpression on A375 cells migration was measured by transwell assays. Scale bars, 100 μ m. (f) Western blot analysis of MYC protein in PVT1 stably overexpressed and control A375 cells. Data are presented as mean ± SD. n = 3, ∗ P

Techniques Used: Over Expression, Migration, Expressing, Stable Transfection, Real-time Polymerase Chain Reaction, CCK-8 Assay, Flow Cytometry, Cytometry, Western Blot

Depletion of PVT1 inhibits melanoma cells proliferation, cell cycle progression, and migration. (a) PVT1 expression levels in PVT1 stably depleted and control A375 cells were measured by qPCR. (b) The effects of PVT1 depletion on A375 cells proliferation were measured by CCK-8 assays. (c) The effects of PVT1 depletion on A375 cells proliferation were measured by EdU incorporation assays. Scale bars, 100 μ m. (d) The effects of PVT1 depletion on A375 cell cycle distribution were measured by flow cytometry. (e) The effects of PVT1 depletion on A375 cells migration were measured by transwell assays. Scale bars, 100 μ m. (f) Western blot analysis of MYC protein in PVT1 stably depleted and control A375 cells. Data are presented as mean ± SD. n = 3, ∗ P
Figure Legend Snippet: Depletion of PVT1 inhibits melanoma cells proliferation, cell cycle progression, and migration. (a) PVT1 expression levels in PVT1 stably depleted and control A375 cells were measured by qPCR. (b) The effects of PVT1 depletion on A375 cells proliferation were measured by CCK-8 assays. (c) The effects of PVT1 depletion on A375 cells proliferation were measured by EdU incorporation assays. Scale bars, 100 μ m. (d) The effects of PVT1 depletion on A375 cell cycle distribution were measured by flow cytometry. (e) The effects of PVT1 depletion on A375 cells migration were measured by transwell assays. Scale bars, 100 μ m. (f) Western blot analysis of MYC protein in PVT1 stably depleted and control A375 cells. Data are presented as mean ± SD. n = 3, ∗ P

Techniques Used: Migration, Expressing, Stable Transfection, Real-time Polymerase Chain Reaction, CCK-8 Assay, Flow Cytometry, Cytometry, Western Blot

32) Product Images from "Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells"

Article Title: Regulation of Cathepsin E gene expression by the transcription factor Kaiso in MRL/lpr mice derived CD4+ T cells

Journal: Scientific Reports

doi: 10.1038/s41598-019-38809-y

Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p
Figure Legend Snippet: Kaiso binding to mCGCG motif located in Ctse intron 1 and HDAC3 (Histone deacetylase 3) in CD4+ T cells from MRL mice. ( A ) Methylation specific PCR analysis in EL4 cells treated with or without 1 μM of 5-azaC, and CD4+ T cells derived from B6 and MRL mice. Methylation-sensitive restriction enzyme Acc II digests unmethylated CGCG motifs, while methylated CGCG is resistant to Acc II. The genomic DNAs were digested with Acc II, amplified by PCR using primer sets; Primer F2/R2 and Primer F2/R3. The densitometry intensity ratios of PCR products (F2R2/F2R3) are shown. *p

Techniques Used: Binding Assay, Histone Deacetylase Assay, Mouse Assay, Methylation, Polymerase Chain Reaction, Derivative Assay, Amplification

33) Product Images from "Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products"

Article Title: Multiplex PCR: use of heat-stable Thermus thermophilus RecA protein to minimize non-specific PCR products

Journal: Nucleic Acids Research

doi: 10.1093/nar/gni111

PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.
Figure Legend Snippet: PCR of subdivided genomic sequences. Three regions of human genomic DNA (GenBank accession nos AC006454 , AC093734 and X91835 , with 5103, 5193 and 12 114 bp, respectively) were subdivided into nine 567, 577 and 1346 bp PCR sites, respectively. PCR was performed for each subdivided site using primer sets (20 bp each) corresponding to the terminal sequence of each site using the Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio). PCR was carried out in the absence and in the presence of Tth RecA protein and ATP. The products were electrophoresed and stained with ethidium bromide. ( a ) A diagrammatic representation of the subdivided region (5103 bp in GenBank accession no AC006454 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( b ) A diagrammatic representation of the subdivided region (5193 bp in GenBank accession no AC093734 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). ( c ) A diagrammatic representation of the subdivided region (12 114 bp in GenBank accession no X91835 ) (upper panel) and the electrophoretic patterns of the PCR products (lower panel). Throughout (a–c), nine subdivided sites for each region are indicated as a-1 to a-9, b-1 to b-9 and c-1 to c-9. Nucleotide (nt) numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

Techniques Used: Polymerase Chain Reaction, Genomic Sequencing, Sequencing, Staining

PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.
Figure Legend Snippet: PCR with primers carrying mismatched bases. PCR was performed at two human genomic sites with primers (20 bp), one of which (forward primer) carried one, two or three mismatched bases in the middle of the primer, in the absence (left) or presence (right) of Tth RecA protein and ATP using the Taq DNA polymerase ( rTaq DNA polymerase plus ‘hot start’ antibody). ( a ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 66 562 and nt 66 581 in GenBank accession no AC006454 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set a-1); lanes 2 and 6, PCR products using primers (primer set a-2 with one mismatched base at nt 66 566, T to C); lanes 3 and 7, PCR products using primers (primer set a-3 with two mismatched base at nt 66 566 and nt 66 571, both T to C); and lanes 4 and 8, PCR products using primers (primer set a-4 with three mismatched base at nt 66 566 and nt 66 571, T to C and nt 66 576, G to C). The oligonucleotide sequences used for the forward primers (mismatched bases are underlined) are as follows: primer set a-1, 5′-CATGGCACCTGCTCTGAGAC-3′; primer set a-2, 5′-CATGGCACC C GCTCTGAGAC-3′; primer set a-3, 5′-CATGGCACC C GCTC C GAGAC-3′; and primer set a-4, 5′-CATG C CACC C GCTC C GAGAC-3′. ( b ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 38 501 and nt 38 520 in GenBank accession no. AC0937734 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set b-1); lanes 2 and 6, PCR products using primers (primer set b-2 with one mismatched base at nt 38 505, G to A); lanes 3 and 7, PCR products using primers (primer set b-3 with two mismatched base at nt 38 505 and nt 38 510, both G to A); and lanes 4 and 8, PCR products using primers (primer set b-4 with three mismatched base at nt 38 505, nt 38 510 and nt 38 515, all G to A). The oligonucleotide sequences used for the forward primers are as follows: primer set b-1, 5′-ATCTGTGTGGTTCGGCTCTG-3′; primer set b-2, 5′-ATCTGTGTG A TTCGGCTCTG-3′; primer set b-3, 5′-ATCTGTGTG A TTCG A CTCTG-3′; and primer set b-4, 5′-ATCT A TGTG A TTCG A CTCTG-3′. ( c ) Upper panel: a diagrammatic representation of the location of the PCR site (20 bp between nt 63 957 and nt 63 976 in GenBank accession no. AC004975 ) and of the primers. Lower panel: lanes 1 and 5, PCR products using primers without mismatched bases (primer set c-1); lanes 2 and 6, PCR products using primers (primer set c-2 with one mismatched base at nt 63 961, A to T); lanes 3 and 7, PCR products using primers (primer set c-3 with two mismatched base at nt 63 961 and nt 63 966, A to T and C to T); and lanes 4 and 8, PCR products using primers (primer set c-4 with three mismatched base at nt 63 961, nt 63 966 and nt 63 971, A to T, C to T and G to T). The oligonucleotide sequences used for the forward primers are as follows: primer set c-1, 5′-GCAGGCACCAAGAACTACTG-3′; primer set c-2, 5′-GCAGGCACC T AGAACTACTG-3′; primer set c-3, 5′-GCAGGCACC T AGAA T TACTG-3′; and primer set c-4, 5′-GCAG T CACC T AGAA T TACTG-3′. The sequences for the backward primers are 5′-TCACCTCCCAGCCTGGCCCA-3′ for ( a ), 5′-AGGGAGATGTTCTCATAAAT-3′ and 5′-CTGTAAGTGGCAGACATTAC-3′ for ( b ). Nucleotide numbers correspond to registries in GenBank. Locations of the specific PCR products are indicated by arrows.

Techniques Used: Polymerase Chain Reaction

Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).
Figure Legend Snippet: Effect of T.thermophilus RecA protein on PCR. PCR with Taq DNA polymerase ( ExTaq DNA polymerase plus ‘hot start’ antibody; Takara-bio) for several randomly selected sequences (300–650 bp) in human genomic DNA was carried out in the absence or in the presence of the Tth RecA protein. ( a ) Control, PCR under the standard conditions described in Materials and Methods. ( b ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture). ( c ) Similar to (a), but with ATP (400 μM). ( d ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP (300 μM). ( e ) Similar to (a), but with Tth RecA protein (0.4 μg per 25 μl reaction mixture) and ATP-γS (300 μM). The products were electrophoresed and stained with ethidium bromide. Molecular weight markers are indicated on the right-hand side of these panels. The oligonucleotide sequences used for the primers were as follows: 5′-ACAATGGGCTCACTCACCCA-3′ and 5′-CTAAGACCAATGGATAGCTG-3′ for lane 1 (300 bp); 5′-GCTCAGCATGGTGGTGGCAT-3′ and 5′-CCTCATACCTTCCCCCCCAT-3′ for lane 2 (319 bp); 5′-GACTACTCTAGCGACTGTCC-3′ and 5′-GACAGCCACCAGATCCAATC-3′ for lane 3 (360 bp); 5′-AACCTCACAACCTTGGCTGA-3′ and 5′-TTCACAACTTAAGATTTGGC-3′ for lane 4 (400 bp); 5′-AGGCAACTAGGATGGTGTGG-3′ and 5′-CAGGGAGCGTGTCCATAGGG-3′ for lane 5 (450 bp); 5′-CTGCTGAAAGAGATGCGGTG-3′ and 5′-AGGAAAACAGCCCAAGGGAC-3′ for lane 6 (469 bp); and 5′-ACTTTGTTCTGAGCCTCACA-3′ and 5′-GTTGCCCAATCGCCCCTCTC-3′ for lane 7 (650 bp).

Techniques Used: Polymerase Chain Reaction, Staining, Molecular Weight

34) Product Images from "Distribution of Podoplanin-Expressing Cells in the Mouse Nervous Systems"

Article Title: Distribution of Podoplanin-Expressing Cells in the Mouse Nervous Systems

Journal: Acta Histochemica et Cytochemica

doi: 10.1267/ahc.13035

Gene analysis for the expression of podoplanin mRNA in the mouse brain. Total RNA extraction from tissue of the cerebral cortex (Ctx), hippocampus (Hi), thalamus (Th), caudate nucleus (CN), and fornix (Fo) were examined. ( A ) Real-time PCR analysis. Relative mRNA amounts are expressed in arbitrary units. Target gene cDNA units in each sample were normalized to β-actin cDNA units. The podoplanin mRNA amount in the fornix was significantly smaller than in other areas. There were no differences in the tested areas except for in the fornix. *Significantly different (p
Figure Legend Snippet: Gene analysis for the expression of podoplanin mRNA in the mouse brain. Total RNA extraction from tissue of the cerebral cortex (Ctx), hippocampus (Hi), thalamus (Th), caudate nucleus (CN), and fornix (Fo) were examined. ( A ) Real-time PCR analysis. Relative mRNA amounts are expressed in arbitrary units. Target gene cDNA units in each sample were normalized to β-actin cDNA units. The podoplanin mRNA amount in the fornix was significantly smaller than in other areas. There were no differences in the tested areas except for in the fornix. *Significantly different (p

Techniques Used: Expressing, RNA Extraction, Real-time Polymerase Chain Reaction

35) Product Images from "Selectively enhanced expression of prophenoloxidase activating enzyme 1 (PPAE1) at a bacteria clearance site in the white shrimp, Litopenaeus vannamei"

Article Title: Selectively enhanced expression of prophenoloxidase activating enzyme 1 (PPAE1) at a bacteria clearance site in the white shrimp, Litopenaeus vannamei

Journal: BMC Immunology

doi: 10.1186/1471-2172-12-70

Gene silencing of the prophenoloxidase-activating enzyme from white shrimp Litopenaeus vannamei (lvPPAE1) and related bioassays . (A) RNAi of lvPPAE1 using gene-specific dsRNA analyzed by qRT-PCR and normalized to β-actin. Five samples were mixed and analyzed 12 and 24 h after the first dsRNA injection and another 24 h after the second injection. (B) Phenoloxidase activity assay after gene silencing, analyzed by analysis of variance (ANOVA) followed by Duncan's multiple range test. Five individuals were taken as replicates. Bars with different letters are significantly different ( P
Figure Legend Snippet: Gene silencing of the prophenoloxidase-activating enzyme from white shrimp Litopenaeus vannamei (lvPPAE1) and related bioassays . (A) RNAi of lvPPAE1 using gene-specific dsRNA analyzed by qRT-PCR and normalized to β-actin. Five samples were mixed and analyzed 12 and 24 h after the first dsRNA injection and another 24 h after the second injection. (B) Phenoloxidase activity assay after gene silencing, analyzed by analysis of variance (ANOVA) followed by Duncan's multiple range test. Five individuals were taken as replicates. Bars with different letters are significantly different ( P

Techniques Used: Quantitative RT-PCR, Injection, Activity Assay

Tissue distribution of the prophenoloxidase-activating enzyme mRNA from white shrimp Litopenaeus vannamei (lvPPAE1) before and after Vibrio harveyi challenge . The transcription level was detected by Taqman qRT-PCR. Gene expression level was normalized to 18 s rRNA. Five samples were taken as replicates.
Figure Legend Snippet: Tissue distribution of the prophenoloxidase-activating enzyme mRNA from white shrimp Litopenaeus vannamei (lvPPAE1) before and after Vibrio harveyi challenge . The transcription level was detected by Taqman qRT-PCR. Gene expression level was normalized to 18 s rRNA. Five samples were taken as replicates.

Techniques Used: Quantitative RT-PCR, Expressing

Time-course mRNA expression of the prophenoloxidase-activating enzyme from white shrimp Litopenaeus vannamei (lvPPAE1) in fluid hemocytes after the shrimp was injected with saline or Vibrio harveyi . Sampling time points were 0, 1, 2, 4, 8, 16, 24 and 48 h post-injection. Transcript levels were detected by Taqman qRT-PCR. Two sets of data were obtained by normalized to different inferences separately. Five individuals were sampled as replicates. Data were analyzed with Dunnett's t -test and Tukey's range test. Significant differences from the control (0 h, P
Figure Legend Snippet: Time-course mRNA expression of the prophenoloxidase-activating enzyme from white shrimp Litopenaeus vannamei (lvPPAE1) in fluid hemocytes after the shrimp was injected with saline or Vibrio harveyi . Sampling time points were 0, 1, 2, 4, 8, 16, 24 and 48 h post-injection. Transcript levels were detected by Taqman qRT-PCR. Two sets of data were obtained by normalized to different inferences separately. Five individuals were sampled as replicates. Data were analyzed with Dunnett's t -test and Tukey's range test. Significant differences from the control (0 h, P

Techniques Used: Expressing, Injection, Sampling, Quantitative RT-PCR

Vibrio amounts in different water conditions and corresponding lvPPAE1 mRNA expression levels . Five samples were taken as replicates. (A) Log value of the Vibrio colony amount per milliliter biofloc water and filtered seawater. (B) qRT-PCR analysis of lvPPAE1 mRNA expression level in FHs of shrimp reared in biofloc or filtered seawater. Data were analyzed with the unpaired t -test. Different letters indicate significantly different means ( P
Figure Legend Snippet: Vibrio amounts in different water conditions and corresponding lvPPAE1 mRNA expression levels . Five samples were taken as replicates. (A) Log value of the Vibrio colony amount per milliliter biofloc water and filtered seawater. (B) qRT-PCR analysis of lvPPAE1 mRNA expression level in FHs of shrimp reared in biofloc or filtered seawater. Data were analyzed with the unpaired t -test. Different letters indicate significantly different means ( P

Techniques Used: Expressing, Quantitative RT-PCR

36) Product Images from "Pentraxin 3 (PTX3) promoter methylation associated with PTX3 plasma levels and neutrophil to lymphocyte ratio in coronary artery disease"

Article Title: Pentraxin 3 (PTX3) promoter methylation associated with PTX3 plasma levels and neutrophil to lymphocyte ratio in coronary artery disease

Journal: Journal of Geriatric Cardiology : JGC

doi: 10.11909/j.issn.1671-5411.2016.08.010

Association between the NLR and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with NLR in male patients ( r = −0.58, P = 0.002). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.
Figure Legend Snippet: Association between the NLR and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with NLR in male patients ( r = −0.58, P = 0.002). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.

Techniques Used: Methylation

Association between PTX3 levels and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with plasma PTX3 levels ( r = −0.29, P = 0.02). PTX3: Pentraxin 3.
Figure Legend Snippet: Association between PTX3 levels and levels of PTX3 promoter methylation. Levels of PTX3 promoter methylation are negatively correlated with plasma PTX3 levels ( r = −0.29, P = 0.02). PTX3: Pentraxin 3.

Techniques Used: Methylation

PTX3 levels and levels of PTX3 promoter methylation according to CAD occurrence. (A): PTX3 levels in the CAD-free group were 3.65 ± 2.14 ng/mL ( n = 25), lower than the CAD group ( n = 39); (B): the levels of PTX3 promoter methylation in the CAD-free group were 72.45% ± 11.84% ( n = 25), higher than the CAD group (62.69% ± 20.57%, n = 39). CAD: coronary artery disease; PTX3: Pentraxin 3.
Figure Legend Snippet: PTX3 levels and levels of PTX3 promoter methylation according to CAD occurrence. (A): PTX3 levels in the CAD-free group were 3.65 ± 2.14 ng/mL ( n = 25), lower than the CAD group ( n = 39); (B): the levels of PTX3 promoter methylation in the CAD-free group were 72.45% ± 11.84% ( n = 25), higher than the CAD group (62.69% ± 20.57%, n = 39). CAD: coronary artery disease; PTX3: Pentraxin 3.

Techniques Used: Methylation

Association between the NLR and PTX3 levels. NLR was not correlated with PTX3 levels ( r = 0.11, P = 0.48). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.
Figure Legend Snippet: Association between the NLR and PTX3 levels. NLR was not correlated with PTX3 levels ( r = 0.11, P = 0.48). NLR: neutrophil to lymphocyte ratio; PTX3: Pentraxin 3.

Techniques Used:

37) Product Images from "YY1 targets tubulin polymerisation-promoting protein to inhibit migration, invasion and angiogenesis in pancreatic cancer via p38/MAPK and PI3K/AKT pathways"

Article Title: YY1 targets tubulin polymerisation-promoting protein to inhibit migration, invasion and angiogenesis in pancreatic cancer via p38/MAPK and PI3K/AKT pathways

Journal: British Journal of Cancer

doi: 10.1038/s41416-019-0604-5

YY1 combined with the promoter region of TPPP regulates the expression of TPPP. a , b The TPPP expression in PANC-1-YY1 shRNA and BxPC-3-YY1 shRNA cells was measured by quantitative RT-PCR and western blot. c The cchematic diagram of the luciferase reporter construct containing the human TPPP promoter (pTPPP) and the mutant construct (pTPPP-YY1-M) containing the TPPP promoter in which the presumed YY1 binding site was mutated. d Luciferase assays demonstrating the luciferase activity of pTPPP (NC, WT or MUT) in PANC-1 (left) and BxPC-3 (right) cells transfected with YY1-overexpressing lentiviruses or control lentiviruses. Each error bar indicates the variation between the means of three independent experiments. e ChIP assays were performed in PANC-1-YY1 (left) and BxPC-3-YY1 (right) cells. Lane 1, DNA marker; lane 2, input DNA; lane 3, DNA from BxPC-3-YY1 cells immunoprecipitated with normal rabbit IgG; lane 4, DNA from BxPC-3-YY1 cells immunoprecipitated with an anti-YY1 antibody. (*represents p
Figure Legend Snippet: YY1 combined with the promoter region of TPPP regulates the expression of TPPP. a , b The TPPP expression in PANC-1-YY1 shRNA and BxPC-3-YY1 shRNA cells was measured by quantitative RT-PCR and western blot. c The cchematic diagram of the luciferase reporter construct containing the human TPPP promoter (pTPPP) and the mutant construct (pTPPP-YY1-M) containing the TPPP promoter in which the presumed YY1 binding site was mutated. d Luciferase assays demonstrating the luciferase activity of pTPPP (NC, WT or MUT) in PANC-1 (left) and BxPC-3 (right) cells transfected with YY1-overexpressing lentiviruses or control lentiviruses. Each error bar indicates the variation between the means of three independent experiments. e ChIP assays were performed in PANC-1-YY1 (left) and BxPC-3-YY1 (right) cells. Lane 1, DNA marker; lane 2, input DNA; lane 3, DNA from BxPC-3-YY1 cells immunoprecipitated with normal rabbit IgG; lane 4, DNA from BxPC-3-YY1 cells immunoprecipitated with an anti-YY1 antibody. (*represents p

Techniques Used: Expressing, shRNA, Quantitative RT-PCR, Western Blot, Luciferase, Construct, Mutagenesis, Binding Assay, Activity Assay, Transfection, Chromatin Immunoprecipitation, Marker, Immunoprecipitation

38) Product Images from "A novel method of identifying genetic mutations using an electrochemical DNA array"

Article Title: A novel method of identifying genetic mutations using an electrochemical DNA array

Journal: Nucleic Acids Research

doi: 10.1093/nar/gnh141

The process for the determination of mutations by the SMMD system using an ECA chip and FND. As the first step, asymmetric PCR (A-PCR) was performed with counter primer and special primer in the ratio of 1:4 and the first PCR product, as a template, from genomic DNA ( A ). The special primer contains the Tag sequence (cyan) at its 5′ end, which is a complement to the genomic region [yellow-colored region in ( B )] between the mutation point (red) and the special primer. Since the A-PCR product contains self-complemental sequences [cyan- and yellow-colored sequences in ( C )], it forms a self-loop ( D ). Before the hybridization and ligation reactions of the self-looped A-PCR product and a probe immobilized on the ECA chip, electric current ( I 0 , base line current response) was measured in a buffer containing FND ( E ). After the measurement of I 0 , the self-looped A-PCR product was hybridized with two types of probes, a wild type and a mutant type, fixed on individual electrodes of the ECA chip. If the 3′ end nucleotide of the probe is completely matched with the self-looped A-PCR product, indicated as a bar, denoting hydrogen bond between red (c, cytosine) and pink (g, guanine) nucleotides, the enzyme ligase glues the 3′ end nucleotide on the probe with the 5′ end of the self-looped A-PCR product [left panel of ( F )]. However, if the 3′ end nucleotide of the probe is mismatched with the 5′ end of the self-looped A-PCR product, the enzyme recognizes the gap, and it does not glue the probe and the A-PCR product [right panel of (F)]. After the ligation reaction, the ECA chip was denatured. When the A-PCR product is glued to the probe fixed on the electrode, the A-PCR product is not released from the probe [left panel of ( G )]. When the A-PCR product is not glued, it is released from the probe [right panel of (G)]. After washing out excess nucleotides, individual electrode was measured for its electrochemical current of FND molecule by an ECA chip reader. The electrode containing double-stranded DNA gives higher current [left panels of ( H) and ( I )] than the one containing only a single-stranded short DNA [(right panels of (H) and (I)].
Figure Legend Snippet: The process for the determination of mutations by the SMMD system using an ECA chip and FND. As the first step, asymmetric PCR (A-PCR) was performed with counter primer and special primer in the ratio of 1:4 and the first PCR product, as a template, from genomic DNA ( A ). The special primer contains the Tag sequence (cyan) at its 5′ end, which is a complement to the genomic region [yellow-colored region in ( B )] between the mutation point (red) and the special primer. Since the A-PCR product contains self-complemental sequences [cyan- and yellow-colored sequences in ( C )], it forms a self-loop ( D ). Before the hybridization and ligation reactions of the self-looped A-PCR product and a probe immobilized on the ECA chip, electric current ( I 0 , base line current response) was measured in a buffer containing FND ( E ). After the measurement of I 0 , the self-looped A-PCR product was hybridized with two types of probes, a wild type and a mutant type, fixed on individual electrodes of the ECA chip. If the 3′ end nucleotide of the probe is completely matched with the self-looped A-PCR product, indicated as a bar, denoting hydrogen bond between red (c, cytosine) and pink (g, guanine) nucleotides, the enzyme ligase glues the 3′ end nucleotide on the probe with the 5′ end of the self-looped A-PCR product [left panel of ( F )]. However, if the 3′ end nucleotide of the probe is mismatched with the 5′ end of the self-looped A-PCR product, the enzyme recognizes the gap, and it does not glue the probe and the A-PCR product [right panel of (F)]. After the ligation reaction, the ECA chip was denatured. When the A-PCR product is glued to the probe fixed on the electrode, the A-PCR product is not released from the probe [left panel of ( G )]. When the A-PCR product is not glued, it is released from the probe [right panel of (G)]. After washing out excess nucleotides, individual electrode was measured for its electrochemical current of FND molecule by an ECA chip reader. The electrode containing double-stranded DNA gives higher current [left panels of ( H) and ( I )] than the one containing only a single-stranded short DNA [(right panels of (H) and (I)].

Techniques Used: Chromatin Immunoprecipitation, Polymerase Chain Reaction, Sequencing, Mutagenesis, Hybridization, Ligation

39) Product Images from "Difference of two new LCMV strains in lethality and viral genome load in tissues"

Article Title: Difference of two new LCMV strains in lethality and viral genome load in tissues

Journal: Experimental Animals

doi: 10.1538/expanim.16-0097

Survival analysis of BALB/c (circles), DBA/1 (triangles) and C57BL/6 (squares) mice inoculated with 10 4 TCID 50 of LCMV strains BRC (A), OQ28 (B) and WE (ngs) (C). Survival analysis was statistically significant different between BALB/c and DBA/1 mice of OQ28 inoculation group ( P =0.0006) and of WE (ngs) inoculation group ( P =0.0005), and between C57BL/6 and DBA/1 mice of OQ28 inoculation group ( P =0.0014) and of WE (ngs) inoculation group ( P =0.0012).
Figure Legend Snippet: Survival analysis of BALB/c (circles), DBA/1 (triangles) and C57BL/6 (squares) mice inoculated with 10 4 TCID 50 of LCMV strains BRC (A), OQ28 (B) and WE (ngs) (C). Survival analysis was statistically significant different between BALB/c and DBA/1 mice of OQ28 inoculation group ( P =0.0006) and of WE (ngs) inoculation group ( P =0.0005), and between C57BL/6 and DBA/1 mice of OQ28 inoculation group ( P =0.0014) and of WE (ngs) inoculation group ( P =0.0012).

Techniques Used: Mouse Assay, Next-Generation Sequencing

The viral genome load in tissues of C57BL/6 mice infected with 10 4 TCID 50 of each virus strain at 4 and 28 dpi; BRC-4 dpi (A), BRC-28 dpi (B), OQ28-4 dpi (C), OQ28-28 dpi (D), WE (ngs)-4 dpi (E) and WE (ngs)-28 dpi (F). The viral genome copies/500 ng RNA of each mouse tissue was calculated with the Thermal Cycler Dice Real Time System Software based on the respective standard curves for each virus strain (circles). Dashed line indicates detection limits of synthesized RNA determined by standard curves. Viral genome load of several samples exceeded detection limits of synthesized RNA determined by standard curves, and non-quantifiable samples were not indicated.
Figure Legend Snippet: The viral genome load in tissues of C57BL/6 mice infected with 10 4 TCID 50 of each virus strain at 4 and 28 dpi; BRC-4 dpi (A), BRC-28 dpi (B), OQ28-4 dpi (C), OQ28-28 dpi (D), WE (ngs)-4 dpi (E) and WE (ngs)-28 dpi (F). The viral genome copies/500 ng RNA of each mouse tissue was calculated with the Thermal Cycler Dice Real Time System Software based on the respective standard curves for each virus strain (circles). Dashed line indicates detection limits of synthesized RNA determined by standard curves. Viral genome load of several samples exceeded detection limits of synthesized RNA determined by standard curves, and non-quantifiable samples were not indicated.

Techniques Used: Mouse Assay, Infection, Next-Generation Sequencing, Software, Synthesized

40) Product Images from "A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis"

Article Title: A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0022900

Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.
Figure Legend Snippet: Optimization of the UP-M-PCR. Lane A, B, C, D, E, amplicon fragments by UP (500 nmol L −1 ) and compound specific primer hpt-839, nptII-508, pat-262, bar-226 and sps-110 at a series concentrations of 500 nmol L −1 , 50 nmol L −1 , 25 nmol L −1 , 5 nmol L −1 , 0.5 nmol L −1 ; lane F1, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at 25 nmol L −1 ; lane F2, amplicon fragments by UP at 500 nmol L −1 and all compound specific primers at the optimized concentration; lane G1,G2,G3, amplicon fragments by all primers at the optimized concentration with TaKaRa Taq ™, Phire™ Hot Start DNA polymerase, iProof™ High-Fidelity DNA polymerase; lane H1, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the common amplification conditions; lane H2, amplicon fragments by all primers at the optimized concentration with Phire™ Hot Start DNA polymerase under the optimized amplification conditions; lane M, 100 bp DNA Marker.

Techniques Used: Polymerase Chain Reaction, Amplification, Concentration Assay, Marker

Related Articles

In Vivo:

Article Title: Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms
Article Snippet: .. In addition to these roles, RNase H has attracted increased interest regarding the two following issues ( ): (i) the presumed role of endogenous RNase H activity in the mechanisms of action of antisense oligonucleotides in vivo and (ii) the potential importance of the enzyme as an antiviral agent. .. Due to these concerns, the physiological functions and structure of this enzyme derived, in particular, from human immunodeficiency virus type 1 , E. coli ( , ), and Thermus thermophilus ( ) have been intensively studied in detail, and the enzyme is now commonly used in molecular biological research, such as in reverse transcription-PCR analyses and in in vitro studies involving the sequence-specific digestion of particular RNA strands ( ).

Selection:

Article Title: Selection of optimal antisense accessible sites of survivin and its application in treatment of gastric cancer
Article Snippet: .. In 1996, based on the fact that RNase H could specifically hydrolyze the phosphodiester backbone of the RNA strand in RNA-DNA duplex hybrid, Siew et al firstly brought forward a brand-new conception for the in vitro selection of antisense accessible sites by random oligonucleotide libraries/RNase H cleavage method. .. Firstly, a set of random oligonucleotide libraries, which were fixed in length and composed of possible sequences, were synthesized and incubated with targeted mRNA.

Article Title: Elucidation and characterization of oligonucleotide-accessible sites on HIV-2 leader region RNA
Article Snippet: .. The selection and identification of sites using this method relies on the recognition and cleavage of DNA:RNA heteroduplexes by RNase H, then using primer extension from an interior site on the RNA to detect the exact sites of cleavage. ..

Whole Genome Amplification:

Article Title: Rapid Genome Sequencing of RNA Viruses
Article Snippet: .. In accordance with the Invitrogen manual, cDNA was synthesized, by using random hexamers (Takara Bio Inc., Kyoto, Japan) and Superscript III (Invitrogen, Carlsbad, CA, USA) lacking RNase H activity, at 50°C for 1 h. Then 60 U of RNase H (Takara Bio Inc.) added before synthesis of second-strand cDNA at 50°C for 1 h. In accordance with the manual, a whole genome amplification system (WGA; Sigma-Aldrich, Saint Louis, MO, USA), which was developed for amplification of genomic DNA, was used to amplify viral double-stranded cDNA. .. Instead of the Taq polymerase recommended in the kit, we used 1.25 U of AmpliTaq Gold LD (Applied Biosystems, Foster City, CA, USA) to obtain a high yield of the PCR products.

In Vitro:

Article Title: Selection of optimal antisense accessible sites of survivin and its application in treatment of gastric cancer
Article Snippet: .. In 1996, based on the fact that RNase H could specifically hydrolyze the phosphodiester backbone of the RNA strand in RNA-DNA duplex hybrid, Siew et al firstly brought forward a brand-new conception for the in vitro selection of antisense accessible sites by random oligonucleotide libraries/RNase H cleavage method. .. Firstly, a set of random oligonucleotide libraries, which were fixed in length and composed of possible sequences, were synthesized and incubated with targeted mRNA.

Synthesized:

Article Title: Rapid Genome Sequencing of RNA Viruses
Article Snippet: .. In accordance with the Invitrogen manual, cDNA was synthesized, by using random hexamers (Takara Bio Inc., Kyoto, Japan) and Superscript III (Invitrogen, Carlsbad, CA, USA) lacking RNase H activity, at 50°C for 1 h. Then 60 U of RNase H (Takara Bio Inc.) added before synthesis of second-strand cDNA at 50°C for 1 h. In accordance with the manual, a whole genome amplification system (WGA; Sigma-Aldrich, Saint Louis, MO, USA), which was developed for amplification of genomic DNA, was used to amplify viral double-stranded cDNA. .. Instead of the Taq polymerase recommended in the kit, we used 1.25 U of AmpliTaq Gold LD (Applied Biosystems, Foster City, CA, USA) to obtain a high yield of the PCR products.

Incubation:

Article Title: PABP is not essential for microRNA-mediated translational repression and deadenylation in vitro
Article Snippet: .. The reaction was incubated at room temperature for 10 min, and then 0.1 U/ml RNase H (Takara Bio) was added. .. After incubation at 37 °C for 30 min, RNase H was quenched by 25 mM EDTA.

Amplification:

Article Title: Rapid Genome Sequencing of RNA Viruses
Article Snippet: .. In accordance with the Invitrogen manual, cDNA was synthesized, by using random hexamers (Takara Bio Inc., Kyoto, Japan) and Superscript III (Invitrogen, Carlsbad, CA, USA) lacking RNase H activity, at 50°C for 1 h. Then 60 U of RNase H (Takara Bio Inc.) added before synthesis of second-strand cDNA at 50°C for 1 h. In accordance with the manual, a whole genome amplification system (WGA; Sigma-Aldrich, Saint Louis, MO, USA), which was developed for amplification of genomic DNA, was used to amplify viral double-stranded cDNA. .. Instead of the Taq polymerase recommended in the kit, we used 1.25 U of AmpliTaq Gold LD (Applied Biosystems, Foster City, CA, USA) to obtain a high yield of the PCR products.

Activity Assay:

Article Title: Sequence-Specific Cleavage of Small-Subunit (SSU) rRNA with Oligonucleotides and RNase H: a Rapid and Simple Approach to SSU rRNA-Based Quantitative Detection of Microorganisms
Article Snippet: .. In addition to these roles, RNase H has attracted increased interest regarding the two following issues ( ): (i) the presumed role of endogenous RNase H activity in the mechanisms of action of antisense oligonucleotides in vivo and (ii) the potential importance of the enzyme as an antiviral agent. .. Due to these concerns, the physiological functions and structure of this enzyme derived, in particular, from human immunodeficiency virus type 1 , E. coli ( , ), and Thermus thermophilus ( ) have been intensively studied in detail, and the enzyme is now commonly used in molecular biological research, such as in reverse transcription-PCR analyses and in in vitro studies involving the sequence-specific digestion of particular RNA strands ( ).

Article Title: Rapid Genome Sequencing of RNA Viruses
Article Snippet: .. In accordance with the Invitrogen manual, cDNA was synthesized, by using random hexamers (Takara Bio Inc., Kyoto, Japan) and Superscript III (Invitrogen, Carlsbad, CA, USA) lacking RNase H activity, at 50°C for 1 h. Then 60 U of RNase H (Takara Bio Inc.) added before synthesis of second-strand cDNA at 50°C for 1 h. In accordance with the manual, a whole genome amplification system (WGA; Sigma-Aldrich, Saint Louis, MO, USA), which was developed for amplification of genomic DNA, was used to amplify viral double-stranded cDNA. .. Instead of the Taq polymerase recommended in the kit, we used 1.25 U of AmpliTaq Gold LD (Applied Biosystems, Foster City, CA, USA) to obtain a high yield of the PCR products.

other:

Article Title: Fabrication and characterization of RNA aptamer microarrays for the study of protein-aptamer interactions with SPR imaging
Article Snippet: RNase H specifically hydrolyzes the RNA in an RNA/DNA heteroduplex, whereas it does not attack ssRNA, ssDNA, dsRNA or dsDNA.

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  • 85
    TaKaRa start ex taq
    Start Ex Taq, supplied by TaKaRa, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/start ex taq/product/TaKaRa
    Average 85 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    start ex taq - by Bioz Stars, 2020-07
    85/100 stars
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    92
    TaKaRa ex taq hot start version
    Ex Taq Hot Start Version, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 208 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ex taq hot start version/product/TaKaRa
    Average 92 stars, based on 208 article reviews
    Price from $9.99 to $1999.99
    ex taq hot start version - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

    92
    TaKaRa la taq hot start version kit
    La Taq Hot Start Version Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/la taq hot start version kit/product/TaKaRa
    Average 92 stars, based on 2 article reviews
    Price from $9.99 to $1999.99
    la taq hot start version kit - by Bioz Stars, 2020-07
    92/100 stars
      Buy from Supplier

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