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Effect of <t>DNA</t> 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 <t>qRT-PCR.</t> Asterisk (*), statistically significant ( p
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1) 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

2) Product Images from "Heterogeneous Expression and Release of CD14 by Human Gingival Fibroblasts: Characterization and CD14-Mediated Interleukin-8 Secretion in Response to Lipopolysaccharide"

Article Title: Heterogeneous Expression and Release of CD14 by Human Gingival Fibroblasts: Characterization and CD14-Mediated Interleukin-8 Secretion in Response to Lipopolysaccharide

Journal: Infection and Immunity

doi:

Heterogeneous expression of CD14 mRNA by CD14 high and CD14 low HGF. CD14 high HGF (lane 1, donor MH; lane 2, donor SM) and CD14 low HGF (lane 3, donor KT; lane 4, donor NK) from confluent cultures were collected by trypsinization. RNA was extracted from the cells, and its cDNA was prepared and analyzed by RT-PCR. The results are representative of three different experiments.
Figure Legend Snippet: Heterogeneous expression of CD14 mRNA by CD14 high and CD14 low HGF. CD14 high HGF (lane 1, donor MH; lane 2, donor SM) and CD14 low HGF (lane 3, donor KT; lane 4, donor NK) from confluent cultures were collected by trypsinization. RNA was extracted from the cells, and its cDNA was prepared and analyzed by RT-PCR. The results are representative of three different experiments.

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction

3) Product Images from "Generation and Immunity Testing of a Recombinant Adenovirus Expressing NcSRS2-NcGRA7 Fusion Protein of Bovine Neospora caninum"

Article Title: Generation and Immunity Testing of a Recombinant Adenovirus Expressing NcSRS2-NcGRA7 Fusion Protein of Bovine Neospora caninum

Journal: The Korean Journal of Parasitology

doi: 10.3347/kjp.2013.51.2.247

Results of PCR and SOE-PCR amplification. Lane M, DNA marker DL2,000; Lane 1, PCR products of the NcSRS2 gene; Lane 2, PCR products of the NcGRA7 gene; Lane 3, PCR products of the NcSRS2-NcGRA7 fusion gene; Lane 4, water control.
Figure Legend Snippet: Results of PCR and SOE-PCR amplification. Lane M, DNA marker DL2,000; Lane 1, PCR products of the NcSRS2 gene; Lane 2, PCR products of the NcGRA7 gene; Lane 3, PCR products of the NcSRS2-NcGRA7 fusion gene; Lane 4, water control.

Techniques Used: Polymerase Chain Reaction, Overlap Extension Polymerase Chain Reaction, Amplification, Marker

PCR identification of Ad5-NcSRS2-NcGRA7. Lane M, DNA marker is DL10,000; Lane 1, PCR products of Ad5-NcSRS2-NcGRA7; Lane 2, empty plasmid control.
Figure Legend Snippet: PCR identification of Ad5-NcSRS2-NcGRA7. Lane M, DNA marker is DL10,000; Lane 1, PCR products of Ad5-NcSRS2-NcGRA7; Lane 2, empty plasmid control.

Techniques Used: Polymerase Chain Reaction, Marker, Plasmid Preparation

4) Product Images from "Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India"

Article Title: Multiple Infection and Microdiversity among Helicobacter pylori Isolates in a Single Host in India

Journal: PLoS ONE

doi: 10.1371/journal.pone.0043370

Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus PCR. M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.
Figure Legend Snippet: Multiple strain colonization detected on the basis of HP0527 gene in cag PAI. Lanes 1 to 10, single colonies isolated from the patient; C, Control strain 26695. (a) Three types of colonies were identified in PG93. Lane 1 and 6 gave a higher amplicon than that of 26695; lanes 3, 4, 7 and 8 yielded same amplicon while lanes 2, 5, 9, 10 produced lower amplicon than that of 26695. (b) Mixed infections detected on the basis of vapD genetic locus PCR. M, 100 bp marker; lanes 1–10, single colonies isolated from PG137; 11, positive control (PCR225); 12, Negative control ( E. coli DNA). All the colonies are positive for vapD except colony numbers 1, 6, 9 and 10.

Techniques Used: Isolation, Amplification, Produced, Polymerase Chain Reaction, Marker, Positive Control, Negative Control

PG207 showed evidence of mixed infections on the basis of obtaining either iceA1 or iceA2 alleles. M, 100 bp marker; lanes 1–10, single colonies isolated from PG207; C, positive control; N, Negative control ( E. coli DNA). (a) All the single colonies were negative for iceA1 except for lane 8. (b) All these single colonies were positive for iceA2 except for lane 8. Three different amplicon sizes were obtained in this iceA2 PCR (lanes 1, 9; lanes 2, 3, 6, 7, 10 and lanes 4, 5).
Figure Legend Snippet: PG207 showed evidence of mixed infections on the basis of obtaining either iceA1 or iceA2 alleles. M, 100 bp marker; lanes 1–10, single colonies isolated from PG207; C, positive control; N, Negative control ( E. coli DNA). (a) All the single colonies were negative for iceA1 except for lane 8. (b) All these single colonies were positive for iceA2 except for lane 8. Three different amplicon sizes were obtained in this iceA2 PCR (lanes 1, 9; lanes 2, 3, 6, 7, 10 and lanes 4, 5).

Techniques Used: Marker, Isolation, Positive Control, Negative Control, Amplification, Polymerase Chain Reaction

Multiplex PCR for vacA subtypes and cagA gene for PG218. M, 100 bp marker; lanes 1–10, single colonies isolated from PG218 and “P” denotes pooled DNA sample; C, Positive control (26695); N, Negative control ( E. coli DNA). All the colonies isolated from this individual were cagA + and carried vacA s1 allele. Evidence of mixed infection was detected in the vacA middle region only. Lanes 1–3 and 10 yielded amplicon specific for m1, lanes 5–9 produced amplicon specific for m2 while in lane 4, no amplicon was obtained for vacA mid-region using this specific primer set.
Figure Legend Snippet: Multiplex PCR for vacA subtypes and cagA gene for PG218. M, 100 bp marker; lanes 1–10, single colonies isolated from PG218 and “P” denotes pooled DNA sample; C, Positive control (26695); N, Negative control ( E. coli DNA). All the colonies isolated from this individual were cagA + and carried vacA s1 allele. Evidence of mixed infection was detected in the vacA middle region only. Lanes 1–3 and 10 yielded amplicon specific for m1, lanes 5–9 produced amplicon specific for m2 while in lane 4, no amplicon was obtained for vacA mid-region using this specific primer set.

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Infection, Amplification, Produced

Analysis of vacA alleles by PCR and also the RFLP analysis of ∼ 3 kb fragment of vacA . M, marker; lanes 1 to 10; single colonies isolated from PG142; C, Positive control (26695); N, Negative control ( E. coli DNA). (A) Amplification of vacA s1 and m1 alleles, Lane M, 100 bp marker; all the colonies were positive for vacA s1m1. (B) Amplification of the vacA region with primer vas1F and vas GR. Lane M; 1 kb marker (Gibco BRL), Lanes 1, 3, 6, 8 and 10 failed to amplify. (C) Restriction fragment length polymorphism (RFLP) analysis of ∼3 kb fragment of vacA region using HaeIII restriction enzyme depicted microdiversity among the isolates as lane 5 showed a different digestion pattern than the rest of the colonies. Lane M, 100 bp marker.
Figure Legend Snippet: Analysis of vacA alleles by PCR and also the RFLP analysis of ∼ 3 kb fragment of vacA . M, marker; lanes 1 to 10; single colonies isolated from PG142; C, Positive control (26695); N, Negative control ( E. coli DNA). (A) Amplification of vacA s1 and m1 alleles, Lane M, 100 bp marker; all the colonies were positive for vacA s1m1. (B) Amplification of the vacA region with primer vas1F and vas GR. Lane M; 1 kb marker (Gibco BRL), Lanes 1, 3, 6, 8 and 10 failed to amplify. (C) Restriction fragment length polymorphism (RFLP) analysis of ∼3 kb fragment of vacA region using HaeIII restriction enzyme depicted microdiversity among the isolates as lane 5 showed a different digestion pattern than the rest of the colonies. Lane M, 100 bp marker.

Techniques Used: Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Amplification

Combination of genotype and RAPD analysis for PG157 indicated multiple infections and microdiversity in a single host. M, 100 bp marker; lanes 1–10, single colonies isolated from PG157; P, pooled DNA. (a) RAPD patterns using primer 1281 showed two distinct patterns (lanes 1–8 and lanes 9–10) (b) RAPD patterns using primer 1283 also yielded two distinct patterns (lanes 1–8 and lanes 9–10) (c) Multiplex PCR for vacA alleles and cagA showed existence of s1m1 cagA + strains in lanes 1–8 and s2m2 cagA − strains in lanes 9–10. (d) Variant cagA subtypes detected on the basis of PCR for 3′ end of cagA using primers CAG1 and CAG2. This PCR assay showed existence of type A strains in lanes 4, 6–8 and existence of type B/D strains in lanes 1–3 and 5. Lanes 9–10, which were detected as cagA − , did not produce any amplicon and the pooled sample yielded amplicons for type A and type B/D strains.
Figure Legend Snippet: Combination of genotype and RAPD analysis for PG157 indicated multiple infections and microdiversity in a single host. M, 100 bp marker; lanes 1–10, single colonies isolated from PG157; P, pooled DNA. (a) RAPD patterns using primer 1281 showed two distinct patterns (lanes 1–8 and lanes 9–10) (b) RAPD patterns using primer 1283 also yielded two distinct patterns (lanes 1–8 and lanes 9–10) (c) Multiplex PCR for vacA alleles and cagA showed existence of s1m1 cagA + strains in lanes 1–8 and s2m2 cagA − strains in lanes 9–10. (d) Variant cagA subtypes detected on the basis of PCR for 3′ end of cagA using primers CAG1 and CAG2. This PCR assay showed existence of type A strains in lanes 4, 6–8 and existence of type B/D strains in lanes 1–3 and 5. Lanes 9–10, which were detected as cagA − , did not produce any amplicon and the pooled sample yielded amplicons for type A and type B/D strains.

Techniques Used: Marker, Isolation, Multiplex Assay, Polymerase Chain Reaction, Variant Assay, Amplification

Multiplex PCR for vacA subtypes, cagA and cag PAI empty site for the absence of cag PAI. M, 100 bp marker (New England Biolabs); lanes 1–10, single colonies isolated from PG207; C, 26695 for the first set (a) and AM1 ( cag PAI negative strain) for the second set (b); N, Negative control ( E. coli DNA). (a) Multiplex PCR showed this particular patient was infected by at least three different strains. Lanes 1–6 and lanes 9–10 showed existence of s2m2 cagA − strains, lane 7 showed existence of s1m1 cagA − strain and lane 8 showed existence of s1m1 cagA + strain. (b) All the single colonies, which failed to give amplicon for cagA gene, yielded ∼550 bp product for cag PAI empty site. The colony (Lane 8) that produced amplicon for cagA did not show any amplicon with primers for cag PAI empty site.
Figure Legend Snippet: Multiplex PCR for vacA subtypes, cagA and cag PAI empty site for the absence of cag PAI. M, 100 bp marker (New England Biolabs); lanes 1–10, single colonies isolated from PG207; C, 26695 for the first set (a) and AM1 ( cag PAI negative strain) for the second set (b); N, Negative control ( E. coli DNA). (a) Multiplex PCR showed this particular patient was infected by at least three different strains. Lanes 1–6 and lanes 9–10 showed existence of s2m2 cagA − strains, lane 7 showed existence of s1m1 cagA − strain and lane 8 showed existence of s1m1 cagA + strain. (b) All the single colonies, which failed to give amplicon for cagA gene, yielded ∼550 bp product for cag PAI empty site. The colony (Lane 8) that produced amplicon for cagA did not show any amplicon with primers for cag PAI empty site.

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Marker, Isolation, Negative Control, Infection, Amplification, Produced

Variant cagA subtypes detected on the basis of PCR with primers CAG1 and CAG2 amplifying the 3′ end of the gene. M, 100 bp marker; lane 1–10, single colonies isolated from individual patient and “P” denotes pooled DNA sample; C, positive control for type A cagA (cagA types were named according to the types described by Yamaoka et al. , (1998); N, Negative control ( E. coli DNA). (a) Mixed H. pylori populations were detected by obtaining amplicons for type A and type C in PG218. (b) For PG93, mixed H. pylori populations were detected by obtaining amplicons for type A and a shorter amplicon of ∼500 bp, which could not be typed by the methodology developed by Yamaoka et al. , (1998). (c) For PG144, mixed H. p ylori populations were detected by obtaining amplicons for type A and type B/D.
Figure Legend Snippet: Variant cagA subtypes detected on the basis of PCR with primers CAG1 and CAG2 amplifying the 3′ end of the gene. M, 100 bp marker; lane 1–10, single colonies isolated from individual patient and “P” denotes pooled DNA sample; C, positive control for type A cagA (cagA types were named according to the types described by Yamaoka et al. , (1998); N, Negative control ( E. coli DNA). (a) Mixed H. pylori populations were detected by obtaining amplicons for type A and type C in PG218. (b) For PG93, mixed H. pylori populations were detected by obtaining amplicons for type A and a shorter amplicon of ∼500 bp, which could not be typed by the methodology developed by Yamaoka et al. , (1998). (c) For PG144, mixed H. p ylori populations were detected by obtaining amplicons for type A and type B/D.

Techniques Used: Variant Assay, Polymerase Chain Reaction, Marker, Isolation, Positive Control, Negative Control, Amplification

5) Product Images from "Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿ †"

Article Title: Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿Widespread Horizontal Gene Transfer from Double-Stranded RNA Viruses to Eukaryotic Nuclear Genomes ▿ †

Journal: Journal of Virology

doi: 10.1128/JVI.00955-10

PCR amplification of total DNA of Arabidopsis
Figure Legend Snippet: PCR amplification of total DNA of Arabidopsis

Techniques Used: Polymerase Chain Reaction, Amplification

6) Product Images from "Agrobacterium tumefaciens-Mediated Transformation of Valsa mali: An Efficient Tool for Random Insertion Mutagenesis"

Article Title: Agrobacterium tumefaciens-Mediated Transformation of Valsa mali: An Efficient Tool for Random Insertion Mutagenesis

Journal: The Scientific World Journal

doi: 10.1155/2013/968432

Molecular analysis of T-DNA integration into the genome of randomly chosen transformants resistant to hygromycin B. (a) Polymerase chain reaction assay with primers specific for the amplification of an internal 987 bp fragment of the hph gene. Lane P positive control with vector pBIG3C, W wild-type Valsa mali LXS240101 genomic DNA, Lanes 1–10 genomic DNA isolated from putative transformants PFL1–PFL10, and M DNA molecular weight markers with bases indicated on the left. (b) Southern blot analysis of transformants with DIG-labeled hph gene probe. P positive control with vector pBIG3C linearized with Apa I, W wild-type Valsa mali LXS240101 genomic DNA digested with Hin dIII, 1–6 genomic DNA isolated from putative transformants PFL1-PFL6 digested with Hin dIII, and M DNA molecular weight markers with bases indicated on the left. These six transformants show single copy inserts and the insertion sites are different.
Figure Legend Snippet: Molecular analysis of T-DNA integration into the genome of randomly chosen transformants resistant to hygromycin B. (a) Polymerase chain reaction assay with primers specific for the amplification of an internal 987 bp fragment of the hph gene. Lane P positive control with vector pBIG3C, W wild-type Valsa mali LXS240101 genomic DNA, Lanes 1–10 genomic DNA isolated from putative transformants PFL1–PFL10, and M DNA molecular weight markers with bases indicated on the left. (b) Southern blot analysis of transformants with DIG-labeled hph gene probe. P positive control with vector pBIG3C linearized with Apa I, W wild-type Valsa mali LXS240101 genomic DNA digested with Hin dIII, 1–6 genomic DNA isolated from putative transformants PFL1-PFL6 digested with Hin dIII, and M DNA molecular weight markers with bases indicated on the left. These six transformants show single copy inserts and the insertion sites are different.

Techniques Used: Polymerase Chain Reaction, Amplification, Positive Control, Plasmid Preparation, Isolation, Molecular Weight, Southern Blot, Labeling

7) Product Images from "Transformation of tobacco plants by Yali PPO-GFP fusion gene and observation of subcellular localization"

Article Title: Transformation of tobacco plants by Yali PPO-GFP fusion gene and observation of subcellular localization

Journal: American Journal of Translational Research

doi:

PCR implification of PPO and identification of cloning vector by endonuclease digest. Note: (A) PCR amplification products of PPO ; Lane M: 1 Kb DNA marker (2000 bp, 1000 bp, 750 bp, 500 bp, 250 bp, 100 bp); Lane 1: Product of PCR implification. (B) Product cut by EcoR I/ BamH I. Lane M, DNA marker; Lane 2: Product by endonuclease digest.
Figure Legend Snippet: PCR implification of PPO and identification of cloning vector by endonuclease digest. Note: (A) PCR amplification products of PPO ; Lane M: 1 Kb DNA marker (2000 bp, 1000 bp, 750 bp, 500 bp, 250 bp, 100 bp); Lane 1: Product of PCR implification. (B) Product cut by EcoR I/ BamH I. Lane M, DNA marker; Lane 2: Product by endonuclease digest.

Techniques Used: Polymerase Chain Reaction, Clone Assay, Plasmid Preparation, Amplification, Marker

8) Product Images from "Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine"

Article Title: Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03696-13

Genotyping and phylogenetic analysis of E. coli strains. A dendrogram obtained by PFGE of XbaI-digested DNA from 73 E. coli O139 and O149 strains is shown on the left side. Information about each strain, the results of the PCR screening for genes encoding
Figure Legend Snippet: Genotyping and phylogenetic analysis of E. coli strains. A dendrogram obtained by PFGE of XbaI-digested DNA from 73 E. coli O139 and O149 strains is shown on the left side. Information about each strain, the results of the PCR screening for genes encoding

Techniques Used: Polymerase Chain Reaction

9) Product Images from "Identification of TNIP1 Polymorphisms by High Resolution Melting Analysis with Unlabelled Probe: Association with Systemic Lupus Erythematosus"

Article Title: Identification of TNIP1 Polymorphisms by High Resolution Melting Analysis with Unlabelled Probe: Association with Systemic Lupus Erythematosus

Journal: Autoimmune Diseases

doi: 10.1155/2012/265823

SNP genotyping by HRM with unlabeled probe. (a) Derivative melting curves of unlabeled probe and amplicon for genotyping of SNP rs7708392. (b) Normalized difference curves of unlabeled probe region. (c) Normalized melting curves of unlabeled probe region. Unlike the classical SNP genotyping (wildtype, heterozygote, and homozygote), six types of curves were observed implying a new SNP also presented in probe region. (d) DNA sequencing result of SNP rs7708392. The sequencing was performed by using reverse primer of the PCR amplicon. The blue box indicates the SNP rs7708392 harbors G/C mutation by reverse sequencing. The red box shows that the polymorphism on the new SNP is C/T by reverse sequencing.
Figure Legend Snippet: SNP genotyping by HRM with unlabeled probe. (a) Derivative melting curves of unlabeled probe and amplicon for genotyping of SNP rs7708392. (b) Normalized difference curves of unlabeled probe region. (c) Normalized melting curves of unlabeled probe region. Unlike the classical SNP genotyping (wildtype, heterozygote, and homozygote), six types of curves were observed implying a new SNP also presented in probe region. (d) DNA sequencing result of SNP rs7708392. The sequencing was performed by using reverse primer of the PCR amplicon. The blue box indicates the SNP rs7708392 harbors G/C mutation by reverse sequencing. The red box shows that the polymorphism on the new SNP is C/T by reverse sequencing.

Techniques Used: Amplification, DNA Sequencing, Sequencing, Polymerase Chain Reaction, Mutagenesis

10) Product Images from "Simultaneous detection of Plasmodium vivax and Plasmodium falciparum gametocytes in clinical isolates by multiplex-nested RT-PCR"

Article Title: Simultaneous detection of Plasmodium vivax and Plasmodium falciparum gametocytes in clinical isolates by multiplex-nested RT-PCR

Journal: Malaria Journal

doi: 10.1186/1475-2875-11-190

Multiplex nested RT-PCR targeting Pfs25 and Pvs25 . Representative 2% agarose gel electrophoresis showing specific amplifications generated from secondary PCR. Lane M, 50-bp ladder marker; lanes 1–6, P. falciparum genomic DNA, P. vivax genomic DNA, water as negative control, P. falciparum cDNA , P. vivax cDNA and mixed P. falciparum and P. vivax cDNA, respectively. Molecular size in base pairs is shown on the left and right of the gel.
Figure Legend Snippet: Multiplex nested RT-PCR targeting Pfs25 and Pvs25 . Representative 2% agarose gel electrophoresis showing specific amplifications generated from secondary PCR. Lane M, 50-bp ladder marker; lanes 1–6, P. falciparum genomic DNA, P. vivax genomic DNA, water as negative control, P. falciparum cDNA , P. vivax cDNA and mixed P. falciparum and P. vivax cDNA, respectively. Molecular size in base pairs is shown on the left and right of the gel.

Techniques Used: Multiplex Assay, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated, Polymerase Chain Reaction, Marker, Negative Control

11) Product Images from "Patients with systemic lupus erythematosus have abnormally elevated Epstein-Barr virus load in blood"

Article Title: Patients with systemic lupus erythematosus have abnormally elevated Epstein-Barr virus load in blood

Journal: Arthritis Research & Therapy

doi: 10.1186/ar1181

Epstein–Barr virus (EBV) typing of normal individuals and patients with systemic lupus erythematosus (SLE) in mouthwash samples. (a) PCR/Southern blot of the EBV nuclear antigen (EBNA)-3C encoding region for the cell lines carrying type 1 (ES-1, B95-8, LCL2, and Namalwa) and type 2 (SNU-99 and AG876) EBV. DNA extracted from each EBV infected cell line (5 ng) was subjected to EBNA-3C-specific PCR/Southern blot. PCR amplified products were transferred to a membrane and hybridized with an EBNA-3C probe common to both type 1 and type 2 EBV. The expected PCR product sizes were 153 bp for type 1 EBV and 246 bp for type 2 EBV. The EBV negative cell line BJAB and distilled water served as negative controls. (b,c) PCR/Southern blot of the EBNA-3C encoding region for the DNA from mouthwash samples. One 20th of the DNA isolated from mouthwash samples was used for each PCR reaction. Representative results obtained from normal controls (panel b) and SLE patients (panel c) are shown. Namalwa and AG876 were used as positive controls for type 1 and type 2 EBV, respectively. Distilled water (dH 2 0) and DNA isolated from BJAB were used as negative controls.
Figure Legend Snippet: Epstein–Barr virus (EBV) typing of normal individuals and patients with systemic lupus erythematosus (SLE) in mouthwash samples. (a) PCR/Southern blot of the EBV nuclear antigen (EBNA)-3C encoding region for the cell lines carrying type 1 (ES-1, B95-8, LCL2, and Namalwa) and type 2 (SNU-99 and AG876) EBV. DNA extracted from each EBV infected cell line (5 ng) was subjected to EBNA-3C-specific PCR/Southern blot. PCR amplified products were transferred to a membrane and hybridized with an EBNA-3C probe common to both type 1 and type 2 EBV. The expected PCR product sizes were 153 bp for type 1 EBV and 246 bp for type 2 EBV. The EBV negative cell line BJAB and distilled water served as negative controls. (b,c) PCR/Southern blot of the EBNA-3C encoding region for the DNA from mouthwash samples. One 20th of the DNA isolated from mouthwash samples was used for each PCR reaction. Representative results obtained from normal controls (panel b) and SLE patients (panel c) are shown. Namalwa and AG876 were used as positive controls for type 1 and type 2 EBV, respectively. Distilled water (dH 2 0) and DNA isolated from BJAB were used as negative controls.

Techniques Used: Polymerase Chain Reaction, Southern Blot, Infection, Amplification, Isolation

Epstein–Barr virus (EBV) loads in peripheral blood mononuclear cells (PBMCs) from 29 normal individuals and 24 patients with systemic lupus erythematosus (SLE). (a) Sensitivity of PCR/Southern blot for the EBV nuclear antigen (EBNA)-3C sequence. DNA was purified from serial 10-fold dilutions of Namalwa cells (corresponding to 1 to 1 × 10 7 cells) were mixed with BJAB cells to yield a total cell number of 1 × 10 7 . PCR was performed using a 100th of the purified DNA (corresponding to DNA of 10 5 cells). The PCR products were separated in an agarose gel, transferred to a membrane, and probed with an EBNA-3C-specific oligonucleotide. (b) EBV loads of normal individuals and SLE patients. The mean EBV load of each group is presented as a heavy horizontal line.
Figure Legend Snippet: Epstein–Barr virus (EBV) loads in peripheral blood mononuclear cells (PBMCs) from 29 normal individuals and 24 patients with systemic lupus erythematosus (SLE). (a) Sensitivity of PCR/Southern blot for the EBV nuclear antigen (EBNA)-3C sequence. DNA was purified from serial 10-fold dilutions of Namalwa cells (corresponding to 1 to 1 × 10 7 cells) were mixed with BJAB cells to yield a total cell number of 1 × 10 7 . PCR was performed using a 100th of the purified DNA (corresponding to DNA of 10 5 cells). The PCR products were separated in an agarose gel, transferred to a membrane, and probed with an EBNA-3C-specific oligonucleotide. (b) EBV loads of normal individuals and SLE patients. The mean EBV load of each group is presented as a heavy horizontal line.

Techniques Used: Polymerase Chain Reaction, Southern Blot, Sequencing, Purification, Agarose Gel Electrophoresis

12) Product Images from "Transmission of Bartonella henselae by Ixodes ricinus "

Article Title: Transmission of Bartonella henselae by Ixodes ricinus

Journal: Emerging Infectious Diseases

doi: 10.3201/eid1407.071110

Seminested PCR detection of Bartonella spp. DNA in Ixodes ricinus ticks fed on B. henselae –infected ovine blood at preceding stage. Lane M, 100-bp DNA molecular mass marker; lane Ags, salivary glands of a female adult fed on infected blood as a nymph; lane A, carcass of a female adult fed on infected blood as a nymph; lane Ngs, salivary glands of a nymph fed on infected blood as a larva; lane N, carcass of a nymph fed on infected blood as a larva; lane E, eggs laid by female adult fed on infected blood; lane L, larvae hatched from female adult fed on infected blood; lane T+, B. bacilliformis DNA; lane T–, nymph fed on uninfected ovine blood.
Figure Legend Snippet: Seminested PCR detection of Bartonella spp. DNA in Ixodes ricinus ticks fed on B. henselae –infected ovine blood at preceding stage. Lane M, 100-bp DNA molecular mass marker; lane Ags, salivary glands of a female adult fed on infected blood as a nymph; lane A, carcass of a female adult fed on infected blood as a nymph; lane Ngs, salivary glands of a nymph fed on infected blood as a larva; lane N, carcass of a nymph fed on infected blood as a larva; lane E, eggs laid by female adult fed on infected blood; lane L, larvae hatched from female adult fed on infected blood; lane T+, B. bacilliformis DNA; lane T–, nymph fed on uninfected ovine blood.

Techniques Used: Polymerase Chain Reaction, Infection, Marker, Next-Generation Sequencing

Experimental framework of Ixodes ricinus tick infection by Bartonella henselae –infected blood. Ticks (200 larvae, 178 nymphs, and 55 female adults) were engorged by feeding through artificial skin on B. henselae –infected blood for 5 days for larvae, 12 days for nymphs, and 21 days for adults. Larvae and nymphs were allowed to molt and engorged females were allowed to lay eggs. To evaluate transtadial and transovarial transmission, Bartonella spp. DNA was detected by PCR in salivary glands (SGs) and carcasses of 9 nymphs, 6 female adults, 9 pools of eggs, and resulting pools of larvae. Eighteen nymphs and 13 adult females fed on infected blood at preceding stages were refed for 84 h on noninfected blood. Bartonella spp. DNA was detected by PCR in SGs of 7 engorged nymphs and 3 engorged female adults. B. henselae colonies were isolated from SGs of 3 nymphs and 4 adults and from blood removed from feeders. Infectivity of B. henselae in SGs was tested by infecting 2 cats with 1 pair of SGs from a potentially infected nymph and 1 pair of SGs from a potentially infected adult, respectively.
Figure Legend Snippet: Experimental framework of Ixodes ricinus tick infection by Bartonella henselae –infected blood. Ticks (200 larvae, 178 nymphs, and 55 female adults) were engorged by feeding through artificial skin on B. henselae –infected blood for 5 days for larvae, 12 days for nymphs, and 21 days for adults. Larvae and nymphs were allowed to molt and engorged females were allowed to lay eggs. To evaluate transtadial and transovarial transmission, Bartonella spp. DNA was detected by PCR in salivary glands (SGs) and carcasses of 9 nymphs, 6 female adults, 9 pools of eggs, and resulting pools of larvae. Eighteen nymphs and 13 adult females fed on infected blood at preceding stages were refed for 84 h on noninfected blood. Bartonella spp. DNA was detected by PCR in SGs of 7 engorged nymphs and 3 engorged female adults. B. henselae colonies were isolated from SGs of 3 nymphs and 4 adults and from blood removed from feeders. Infectivity of B. henselae in SGs was tested by infecting 2 cats with 1 pair of SGs from a potentially infected nymph and 1 pair of SGs from a potentially infected adult, respectively.

Techniques Used: Infection, Transmission Assay, Polymerase Chain Reaction, Isolation

Seminested PCR detection of Bartonella spp. DNA after partial refeeding of infected ticks. A) Bartonella spp. DNA detection in Ixodes ricinus ticks fed on B. henselae –infected blood at previous development stages and refed for 84 h on uninfected blood. Lane M, 100-bp DNA molecular mass; lane A, carcass of female adult; lane Ags, salivary glands of female adult, lane N, carcass of nymph; lane Ngs, salivary glands of nymph; lane T+, B. bacilliformis DNA; lane T–, nymph fed on uninfected ovine blood. B) Bartonella spp. DNA detection in blood isolated from feeders. Lane M, 100-bp DNA molecular mass marker; lane 48, ovine blood after 48 h of tick attachment on skin; lane 60, ovine blood after 60 h of tick attachment on skin; lane 72, ovine blood after 72 h of tick attachment on skin; lane 84, ovine blood after 84 h of tick attachment on skin; lane T+, B. bacilliformis DNA.
Figure Legend Snippet: Seminested PCR detection of Bartonella spp. DNA after partial refeeding of infected ticks. A) Bartonella spp. DNA detection in Ixodes ricinus ticks fed on B. henselae –infected blood at previous development stages and refed for 84 h on uninfected blood. Lane M, 100-bp DNA molecular mass; lane A, carcass of female adult; lane Ags, salivary glands of female adult, lane N, carcass of nymph; lane Ngs, salivary glands of nymph; lane T+, B. bacilliformis DNA; lane T–, nymph fed on uninfected ovine blood. B) Bartonella spp. DNA detection in blood isolated from feeders. Lane M, 100-bp DNA molecular mass marker; lane 48, ovine blood after 48 h of tick attachment on skin; lane 60, ovine blood after 60 h of tick attachment on skin; lane 72, ovine blood after 72 h of tick attachment on skin; lane 84, ovine blood after 84 h of tick attachment on skin; lane T+, B. bacilliformis DNA.

Techniques Used: Polymerase Chain Reaction, Infection, Next-Generation Sequencing, Isolation, Marker

13) Product Images from "Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy"

Article Title: Limited DNA methylation variation and the transcription of MET1 and DDM1 in the genus Chrysanthemum (Asteraceae): following the track of polyploidy

Journal: Frontiers in Plant Science

doi: 10.3389/fpls.2015.00668

Nuclear DNA content obtained by flow cytometry and MET1 / DDM1 transcription analysis. (A) Nuclear DNA content of Chrysanthemum nankingense (2x), C. indicum (4x), C. morifolium (6x), Ajania shiwogiku (8x) and C. crassum (10x); (B) The Ct value and melting temperature of each reference genes; the X axis represents the PCR cycle number. The red line represents the threshold fluorescence at which the Ct was determined. None of the reference genes were uniformly transcribed (Ct) in five ploidy levels and species. Melting curve analyses showed that each primer pair amplified a single PCR product. (C) Model of reference gene(s) used in five ploidy levels and species; (D) Transcript abundance was correlated with ploidy level for both MET1 and DDM1 . PP2A was selected as inter-run calibrators (IRCs) for EF1 α, TUB , and ACTIN , and the coefficient of variation (transcript abundance normalized using EF1 α 4x-6x -TUB 6x-8x -ACTIN 8x-10x vs. using PP2A 4x-8x-10x )
Figure Legend Snippet: Nuclear DNA content obtained by flow cytometry and MET1 / DDM1 transcription analysis. (A) Nuclear DNA content of Chrysanthemum nankingense (2x), C. indicum (4x), C. morifolium (6x), Ajania shiwogiku (8x) and C. crassum (10x); (B) The Ct value and melting temperature of each reference genes; the X axis represents the PCR cycle number. The red line represents the threshold fluorescence at which the Ct was determined. None of the reference genes were uniformly transcribed (Ct) in five ploidy levels and species. Melting curve analyses showed that each primer pair amplified a single PCR product. (C) Model of reference gene(s) used in five ploidy levels and species; (D) Transcript abundance was correlated with ploidy level for both MET1 and DDM1 . PP2A was selected as inter-run calibrators (IRCs) for EF1 α, TUB , and ACTIN , and the coefficient of variation (transcript abundance normalized using EF1 α 4x-6x -TUB 6x-8x -ACTIN 8x-10x vs. using PP2A 4x-8x-10x )

Techniques Used: Flow Cytometry, Cytometry, Polymerase Chain Reaction, Fluorescence, Amplification

14) Product Images from "Phylogenetic and Expression Analysis of RNA-binding Proteins with Triple RNA Recognition Motifs in Plants"

Article Title: Phylogenetic and Expression Analysis of RNA-binding Proteins with Triple RNA Recognition Motifs in Plants

Journal: Molecules and Cells

doi: 10.1007/s10059-011-0001-2

RT-PCR analysis of AtRBP45b full-length gene and the two splice variants in response to abiotic and biotic stresses. Top panel shows amplification products with 3 μl of cDNA and 30 cycles of PCR. Arrows indicate AtRBP45b full length (FL) and the two splice variant forms (SV1 and SV2). Middle panels labeled as FL’ are amplification products of full-length AtRBP45b with 1 μl of cDNA and 20 cycles of PCR. The bottom panel represents the amplification of constitutively expressed actin gene showing the quality of the cDNA. (A) Xanthine/Xanthine oxidase (X/XO) treatment. Lane 1, 1 h X, lane 2, 1 h X/XO; lane 3, 8 h X; lane 4, 8 h X/XO; lane 5, 24 h X; lane 6, 24 h X/XO. (B) Hydrogen peroxide treatment. Lane 1, 1 h water; lane 2, 1 h H 2 O 2 ; lane 3, 8 h water; lane 4, 8 h H 2 O 2 . Lane 5, 24 h water; lane 6, 24 h H 2 O 2 . (C) Glucose/Glucose oxidase (G/GO) treatment. Lane 1, 1 h G; lane 2, 1 h G/GO; lane 3, 8 h G; lane 4, 8 h G/GO; lane 5, 24 h G; lane 6, 24 h G/GO. (D) Bacterial pathogen treatment. Virulent strain P. syringae DC3000 and avirulent strain P. syringae DC3000 AvrRpt2. Lane 1, 1 h MgCl 2 ; lane 2, 1 h DC3000; lane 3, 1h AvrRpt2; lane 4, 2 h MgCl 2 ; lane 5, 2 h DC3000; lane 6, 2 h AvrRpt2; lane 7, 4 h MgCl 2 ; lane 8, 4 h DC3000; lane 9, 4 h AvrRpt2; lane 10, 6 h MgCl 2 ; lane 11, 6 h DC3000; lane 12, 6 h AvrRpt2. (E) Salt stress treatment. Lane 1, 1 h water; lane 2, 1 h NaCl; lane 3, 8 h water; lane 4, 8 h NaCl; lane 5, 24 h water; lane 6, 24 h NaCl. (F) Temperature stress treatment. lane 1, 1 h Control; lane 2, 1 h Heat; lane 3, 1 h Cold; lane 4, 8 h Control; lane 5, 8 h Heat; lane 6, 8 h Cold; lane 7, 24 h Control; lane 8, 24 h Heat; lane 9, 24 h Cold.
Figure Legend Snippet: RT-PCR analysis of AtRBP45b full-length gene and the two splice variants in response to abiotic and biotic stresses. Top panel shows amplification products with 3 μl of cDNA and 30 cycles of PCR. Arrows indicate AtRBP45b full length (FL) and the two splice variant forms (SV1 and SV2). Middle panels labeled as FL’ are amplification products of full-length AtRBP45b with 1 μl of cDNA and 20 cycles of PCR. The bottom panel represents the amplification of constitutively expressed actin gene showing the quality of the cDNA. (A) Xanthine/Xanthine oxidase (X/XO) treatment. Lane 1, 1 h X, lane 2, 1 h X/XO; lane 3, 8 h X; lane 4, 8 h X/XO; lane 5, 24 h X; lane 6, 24 h X/XO. (B) Hydrogen peroxide treatment. Lane 1, 1 h water; lane 2, 1 h H 2 O 2 ; lane 3, 8 h water; lane 4, 8 h H 2 O 2 . Lane 5, 24 h water; lane 6, 24 h H 2 O 2 . (C) Glucose/Glucose oxidase (G/GO) treatment. Lane 1, 1 h G; lane 2, 1 h G/GO; lane 3, 8 h G; lane 4, 8 h G/GO; lane 5, 24 h G; lane 6, 24 h G/GO. (D) Bacterial pathogen treatment. Virulent strain P. syringae DC3000 and avirulent strain P. syringae DC3000 AvrRpt2. Lane 1, 1 h MgCl 2 ; lane 2, 1 h DC3000; lane 3, 1h AvrRpt2; lane 4, 2 h MgCl 2 ; lane 5, 2 h DC3000; lane 6, 2 h AvrRpt2; lane 7, 4 h MgCl 2 ; lane 8, 4 h DC3000; lane 9, 4 h AvrRpt2; lane 10, 6 h MgCl 2 ; lane 11, 6 h DC3000; lane 12, 6 h AvrRpt2. (E) Salt stress treatment. Lane 1, 1 h water; lane 2, 1 h NaCl; lane 3, 8 h water; lane 4, 8 h NaCl; lane 5, 24 h water; lane 6, 24 h NaCl. (F) Temperature stress treatment. lane 1, 1 h Control; lane 2, 1 h Heat; lane 3, 1 h Cold; lane 4, 8 h Control; lane 5, 8 h Heat; lane 6, 8 h Cold; lane 7, 24 h Control; lane 8, 24 h Heat; lane 9, 24 h Cold.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Variant Assay, Labeling

15) Product Images from "Stable knockdown of PASG enhances DNA demethylation but does not accelerate cellular senescence in TIG-7 human fibroblasts"

Article Title: Stable knockdown of PASG enhances DNA demethylation but does not accelerate cellular senescence in TIG-7 human fibroblasts

Journal: Epigenetics : official journal of the DNA Methylation Society

doi:

mRNA expression levels of p16 , p21 and p53 gene in TIG-7/shPASG and TIG-7/shGFP control cells. (A and B), quantification of p16 , p21 and p53 gene expression was performed by real-time PCR as described in Materials and Methods. (A), RNA samples from the cells at 34 PDLs were analyzed and the mRNA levels of p16 , p21 and p53 were expressed relative to that of TIG-7/shGFP control cells cultured under 3% oxygen. (B), changes in mRNA levels of p16 , p21 and p53 during the passage of TIG-7/shPASG and TIG-7/shGFP control cells. mRNA levels at indicated PDLs were expressed relative to that at 34 PDLs. Values are the mean ± S.D. of triplicates. (C), Northern blot hybridization. Indicated RNA samples were separated on agarose electrophoresis and probed with p16 , p21 and p53 cDNA. GAPDH signals and ethidium bromide-staining pattern of rRNA were used as loading controls.
Figure Legend Snippet: mRNA expression levels of p16 , p21 and p53 gene in TIG-7/shPASG and TIG-7/shGFP control cells. (A and B), quantification of p16 , p21 and p53 gene expression was performed by real-time PCR as described in Materials and Methods. (A), RNA samples from the cells at 34 PDLs were analyzed and the mRNA levels of p16 , p21 and p53 were expressed relative to that of TIG-7/shGFP control cells cultured under 3% oxygen. (B), changes in mRNA levels of p16 , p21 and p53 during the passage of TIG-7/shPASG and TIG-7/shGFP control cells. mRNA levels at indicated PDLs were expressed relative to that at 34 PDLs. Values are the mean ± S.D. of triplicates. (C), Northern blot hybridization. Indicated RNA samples were separated on agarose electrophoresis and probed with p16 , p21 and p53 cDNA. GAPDH signals and ethidium bromide-staining pattern of rRNA were used as loading controls.

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Cell Culture, Northern Blot, Hybridization, Electrophoresis, Staining

16) Product Images from "The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies"

Article Title: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

Journal: Scientific Reports

doi: 10.1038/s41598-018-33646-x

PCR performance for the 136 NPCL marker candidates in 23 avian orders. ( A ) Genetic relationships among our experimental samples. 41 species are highlighted in different colors representing 23 avian orders widely distributed in the avian phylogenetic tree. ( B ) PCR performance for 136 NPCL marker candidates. Each square represents a PCR result. Success is shown in black and failure in white. 430 of 5146 reactions that could not be produced due to a paucity of DNA are shown in grey. The gene name and PCR success rate of each NPCL marker are indicated to the left. The success rate of each avian order is indicated at the bottom of the matrix of 63 universal NPCL markers.
Figure Legend Snippet: PCR performance for the 136 NPCL marker candidates in 23 avian orders. ( A ) Genetic relationships among our experimental samples. 41 species are highlighted in different colors representing 23 avian orders widely distributed in the avian phylogenetic tree. ( B ) PCR performance for 136 NPCL marker candidates. Each square represents a PCR result. Success is shown in black and failure in white. 430 of 5146 reactions that could not be produced due to a paucity of DNA are shown in grey. The gene name and PCR success rate of each NPCL marker are indicated to the left. The success rate of each avian order is indicated at the bottom of the matrix of 63 universal NPCL markers.

Techniques Used: Polymerase Chain Reaction, Marker, Produced

17) Product Images from "Self-compatibility in 'Zaohong' Japanese apricot is associated with the loss of function of pollen S genes"

Article Title: Self-compatibility in 'Zaohong' Japanese apricot is associated with the loss of function of pollen S genes

Journal: Molecular Biology Reports

doi: 10.1007/s11033-013-2765-2

PCR amplification of S - RNase and SFB alleles from ‘Zaohong’ and expression analysis for PmS - RNase ( a ), PmSFB ( b ), PmF - box genes ( c ) and Actin genes ( d ) in pollen ( P ), styles ( S ), and leaves ( L ). M is DNA marker, Z is Zaohong and G is genomic DNA. a RT-PCR of S - RNase alleles. b RT-PCR of SFB alleles. c RT-PCR of PmF - box alleles. d RT-PCR of Actin genes
Figure Legend Snippet: PCR amplification of S - RNase and SFB alleles from ‘Zaohong’ and expression analysis for PmS - RNase ( a ), PmSFB ( b ), PmF - box genes ( c ) and Actin genes ( d ) in pollen ( P ), styles ( S ), and leaves ( L ). M is DNA marker, Z is Zaohong and G is genomic DNA. a RT-PCR of S - RNase alleles. b RT-PCR of SFB alleles. c RT-PCR of PmF - box alleles. d RT-PCR of Actin genes

Techniques Used: Polymerase Chain Reaction, Amplification, Expressing, Peptide Mass Fingerprinting, Marker, Reverse Transcription Polymerase Chain Reaction

18) Product Images from "Antibiotic Resistance, Virulence Gene, and Molecular Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Diverse Sources in Calcutta, India"

Article Title: Antibiotic Resistance, Virulence Gene, and Molecular Profiles of Shiga Toxin-Producing Escherichia coli Isolates from Diverse Sources in Calcutta, India

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.40.6.2009-2015.2002

RAPD-PCR results for STEC strains that exhibited identical DNA banding patterns. In panel I, lanes 2 and 3 contain strains SD2 and SD5; lanes 4 to 6 contain strains SD8, SD10, and SD12, respectively. In panel II, lanes 2 and 3 contain SD4 and SD7; lanes 4 and 5 contain SD1 and SD3, respectively. In panel III, lanes 2 and 3 contain AK33 and AK36, respectively. In panel IV, lanes 2 and 3 contain AK48 and AK54, respectively. Lane 1 in each panel contains a 1-kb DNA ladder marker.
Figure Legend Snippet: RAPD-PCR results for STEC strains that exhibited identical DNA banding patterns. In panel I, lanes 2 and 3 contain strains SD2 and SD5; lanes 4 to 6 contain strains SD8, SD10, and SD12, respectively. In panel II, lanes 2 and 3 contain SD4 and SD7; lanes 4 and 5 contain SD1 and SD3, respectively. In panel III, lanes 2 and 3 contain AK33 and AK36, respectively. In panel IV, lanes 2 and 3 contain AK48 and AK54, respectively. Lane 1 in each panel contains a 1-kb DNA ladder marker.

Techniques Used: Polymerase Chain Reaction, Marker

19) Product Images from "Nuclease-resistant double-stranded DNA controls or standards for hepatitis B virus nucleic acid amplification assays"

Article Title: Nuclease-resistant double-stranded DNA controls or standards for hepatitis B virus nucleic acid amplification assays

Journal: Virology Journal

doi: 10.1186/1743-422X-6-226

Identification of Armored DNA by PCR Amplification . The PCR amplification products of the DNA extracted from lambda phages were analysed using ethidium-bromide stained 1% agarose gel. Lane 1: negative control with no template; Lane 2, 3, 4, 5, and 6: PCR products from positive chimeric phages.
Figure Legend Snippet: Identification of Armored DNA by PCR Amplification . The PCR amplification products of the DNA extracted from lambda phages were analysed using ethidium-bromide stained 1% agarose gel. Lane 1: negative control with no template; Lane 2, 3, 4, 5, and 6: PCR products from positive chimeric phages.

Techniques Used: Polymerase Chain Reaction, Amplification, Staining, Agarose Gel Electrophoresis, Negative Control

Durability of Armored DNA . Equal amounts of armored DNA and plasmid DNA (extracted from the armored DNA) were incubated with DNase I (0.1 units/μl) at 37°C for 60 min. After digestion, the samples were analysed by real-time PCR. The armored DNA was completely resistant to DNase I digestion, whereas plasmid DNA was degraded completely. Armored DNA and plasmid DNA indicate samples without DNase I digestion.
Figure Legend Snippet: Durability of Armored DNA . Equal amounts of armored DNA and plasmid DNA (extracted from the armored DNA) were incubated with DNase I (0.1 units/μl) at 37°C for 60 min. After digestion, the samples were analysed by real-time PCR. The armored DNA was completely resistant to DNase I digestion, whereas plasmid DNA was degraded completely. Armored DNA and plasmid DNA indicate samples without DNase I digestion.

Techniques Used: Plasmid Preparation, Incubation, Real-time Polymerase Chain Reaction

20) Product Images from "Rapid Detection of Lily mottle virus and Arabis mosaic virus Infecting Lily (Lilium spp.) Using Reverse Transcription Loop-Mediated Isothermal Amplification"

Article Title: Rapid Detection of Lily mottle virus and Arabis mosaic virus Infecting Lily (Lilium spp.) Using Reverse Transcription Loop-Mediated Isothermal Amplification

Journal: The Plant Pathology Journal

doi: 10.5423/PPJ.OA.04.2019.0096

Sensitivity of reverse transcription (RT) polymerase chain reaction (PCR) for (A) Lily mottle virus (LMoV) and (B) Arabis mosaic virus (ArMV). cDNA products were produced using total RNA extracted from lily leaves that were each infected with LMoV or ArMV, which were respectively diluted 10-fold and assayed by PCR. Amplified products from RT-PCR were visualized by agarose gel electrophoresis. (A) LMoV. Lane M, DL600 marker; lane 1, negative control; lane 2, initial cDNA; lane 3, 10 -1 ; lane 4, 10 -3 ; lane 5, 10 -5 ; lane 6, 10 -7 ; lane 7, 10 -8 ; lane 8, 10 -9 . (B) ArMV. Lane M, DL600 marker; lane 1, negative control; lane 2, initial cDNA; lane 3, 10 -1 ; e 7, 10 6; lane 8, 10 -7 .
Figure Legend Snippet: Sensitivity of reverse transcription (RT) polymerase chain reaction (PCR) for (A) Lily mottle virus (LMoV) and (B) Arabis mosaic virus (ArMV). cDNA products were produced using total RNA extracted from lily leaves that were each infected with LMoV or ArMV, which were respectively diluted 10-fold and assayed by PCR. Amplified products from RT-PCR were visualized by agarose gel electrophoresis. (A) LMoV. Lane M, DL600 marker; lane 1, negative control; lane 2, initial cDNA; lane 3, 10 -1 ; lane 4, 10 -3 ; lane 5, 10 -5 ; lane 6, 10 -7 ; lane 7, 10 -8 ; lane 8, 10 -9 . (B) ArMV. Lane M, DL600 marker; lane 1, negative control; lane 2, initial cDNA; lane 3, 10 -1 ; e 7, 10 6; lane 8, 10 -7 .

Techniques Used: Polymerase Chain Reaction, Produced, Infection, Amplification, Reverse Transcription Polymerase Chain Reaction, Agarose Gel Electrophoresis, Marker, Negative Control

21) Product Images from "Expression of matrix metalloproteinase-12 in aortic dissection"

Article Title: Expression of matrix metalloproteinase-12 in aortic dissection

Journal: BMC Cardiovascular Disorders

doi: 10.1186/1471-2261-13-34

Agarose gel electrophoresis analysis of PCR fragment obtained from human aorta. MMP-12 gene fragments were amplified from human aorta wall by RT-PCR. PCR amplifications were then analyzed by electrophoresis using 1% agarose gel stained with Gelview. The gel was viewed on a Tanon 3500R Gel Documentation System and recorded. ( A ) cDNA corresponding to MMP-12 in human aorta was PCR-amplified using primers for MMP-12. ( B ) cDNA corresponding to GAPDH in human aorta was PCR-amplified using primers for GAPDH. Lanes 1–2: Aorta wall of coronary heart disease patient; Lanes 3–10: AD; Lane M: DNA ladder; Lane 11: negative control.
Figure Legend Snippet: Agarose gel electrophoresis analysis of PCR fragment obtained from human aorta. MMP-12 gene fragments were amplified from human aorta wall by RT-PCR. PCR amplifications were then analyzed by electrophoresis using 1% agarose gel stained with Gelview. The gel was viewed on a Tanon 3500R Gel Documentation System and recorded. ( A ) cDNA corresponding to MMP-12 in human aorta was PCR-amplified using primers for MMP-12. ( B ) cDNA corresponding to GAPDH in human aorta was PCR-amplified using primers for GAPDH. Lanes 1–2: Aorta wall of coronary heart disease patient; Lanes 3–10: AD; Lane M: DNA ladder; Lane 11: negative control.

Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Reverse Transcription Polymerase Chain Reaction, Electrophoresis, Staining, Negative Control

22) Product Images from "ARAG1, an ABA-responsive DREB gene, plays a role in seed germination and drought tolerance of rice"

Article Title: ARAG1, an ABA-responsive DREB gene, plays a role in seed germination and drought tolerance of rice

Journal: Annals of Botany

doi: 10.1093/aob/mcp303

mRNA accumulation pattern of ARAG1 in different tissues or at different development stages examined by semi-quantitative RT-PCR in triplicate. The statistical data presented are the mean ± s.d. Tubulin A ( Tub. A ) transcripts were used as constitutive
Figure Legend Snippet: mRNA accumulation pattern of ARAG1 in different tissues or at different development stages examined by semi-quantitative RT-PCR in triplicate. The statistical data presented are the mean ± s.d. Tubulin A ( Tub. A ) transcripts were used as constitutive

Techniques Used: Quantitative RT-PCR

23) Product Images from "The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies"

Article Title: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies

Journal: Scientific Reports

doi: 10.1038/s41598-018-33646-x

PCR performance for the 136 NPCL marker candidates in 23 avian orders. ( A ) Genetic relationships among our experimental samples. 41 species are highlighted in different colors representing 23 avian orders widely distributed in the avian phylogenetic tree. ( B ) PCR performance for 136 NPCL marker candidates. Each square represents a PCR result. Success is shown in black and failure in white. 430 of 5146 reactions that could not be produced due to a paucity of DNA are shown in grey. The gene name and PCR success rate of each NPCL marker are indicated to the left. The success rate of each avian order is indicated at the bottom of the matrix of 63 universal NPCL markers.
Figure Legend Snippet: PCR performance for the 136 NPCL marker candidates in 23 avian orders. ( A ) Genetic relationships among our experimental samples. 41 species are highlighted in different colors representing 23 avian orders widely distributed in the avian phylogenetic tree. ( B ) PCR performance for 136 NPCL marker candidates. Each square represents a PCR result. Success is shown in black and failure in white. 430 of 5146 reactions that could not be produced due to a paucity of DNA are shown in grey. The gene name and PCR success rate of each NPCL marker are indicated to the left. The success rate of each avian order is indicated at the bottom of the matrix of 63 universal NPCL markers.

Techniques Used: Polymerase Chain Reaction, Marker, Produced

24) Product Images from "Phylogenetic Analysis and Pathogenicity Assessment of the Emerging Recombinant Subgroup K of Avian Leukosis Virus in South China"

Article Title: Phylogenetic Analysis and Pathogenicity Assessment of the Emerging Recombinant Subgroup K of Avian Leukosis Virus in South China

Journal: Viruses

doi: 10.3390/v10040194

PCR amplification of the complete genomes of 3 isolates. M: DNA marker 3; 1–3: GD150509, GD160403, and GD160607; A, B, C, D: 4 DNA fragments of the complete genome.
Figure Legend Snippet: PCR amplification of the complete genomes of 3 isolates. M: DNA marker 3; 1–3: GD150509, GD160403, and GD160607; A, B, C, D: 4 DNA fragments of the complete genome.

Techniques Used: Polymerase Chain Reaction, Amplification, Marker

PCR amplification of the complete genomes of 3 isolates. M: DNA marker DL5000; 1–3: GDFX0601, GDFX0602, and GDFX0603; A, B, C, D: 4 DNA fragments of the complete genome.
Figure Legend Snippet: PCR amplification of the complete genomes of 3 isolates. M: DNA marker DL5000; 1–3: GDFX0601, GDFX0602, and GDFX0603; A, B, C, D: 4 DNA fragments of the complete genome.

Techniques Used: Polymerase Chain Reaction, Amplification, Marker

25) Product Images from "Rapid detection of intestinal pathogens in fecal samples by an improved reverse dot blot method"

Article Title: Rapid detection of intestinal pathogens in fecal samples by an improved reverse dot blot method

Journal: World Journal of Gastroenterology : WJG

doi: 10.3748/wjg.15.2537

Partial dual PCR amplification results for intestinal pathogens from fecal samples. M: DNA marker 2000; B: Blank control.
Figure Legend Snippet: Partial dual PCR amplification results for intestinal pathogens from fecal samples. M: DNA marker 2000; B: Blank control.

Techniques Used: Polymerase Chain Reaction, Amplification, Marker

26) Product Images from "Phylogenetic Analysis and Pathogenicity Assessment of the Emerging Recombinant Subgroup K of Avian Leukosis Virus in South China"

Article Title: Phylogenetic Analysis and Pathogenicity Assessment of the Emerging Recombinant Subgroup K of Avian Leukosis Virus in South China

Journal: Viruses

doi: 10.3390/v10040194

PCR amplification of the complete genomes of 3 isolates. M: DNA marker 3; 1–3: GD150509, GD160403, and GD160607; A, B, C, D: 4 DNA fragments of the complete genome.
Figure Legend Snippet: PCR amplification of the complete genomes of 3 isolates. M: DNA marker 3; 1–3: GD150509, GD160403, and GD160607; A, B, C, D: 4 DNA fragments of the complete genome.

Techniques Used: Polymerase Chain Reaction, Amplification, Marker

PCR amplification of the complete genomes of 3 isolates. M: DNA marker DL5000; 1–3: GDFX0601, GDFX0602, and GDFX0603; A, B, C, D: 4 DNA fragments of the complete genome.
Figure Legend Snippet: PCR amplification of the complete genomes of 3 isolates. M: DNA marker DL5000; 1–3: GDFX0601, GDFX0602, and GDFX0603; A, B, C, D: 4 DNA fragments of the complete genome.

Techniques Used: Polymerase Chain Reaction, Amplification, Marker

27) Product Images from "Reduction of lung metastasis, cell invasion, and adhesion in mouse melanoma by statin-induced blockade of the Rho/Rho-associated coiled-coil-containing protein kinase pathway"

Article Title: Reduction of lung metastasis, cell invasion, and adhesion in mouse melanoma by statin-induced blockade of the Rho/Rho-associated coiled-coil-containing protein kinase pathway

Journal: Journal of Experimental & Clinical Cancer Research : CR

doi: 10.1186/1756-9966-29-127

Effect of statins on B16BL6 cell adhesion to ECM components . B16BL6 cells, which had been treated with 0.05 μM fluvastatin or 0.1 μM simvastatin for 3 d, were incubated with (A) type I collagen-, (B) type IV collagen-, (C) fibronectin-, or (D) laminin-coated plates for 30 min at 37°C in an atmosphere containing 5% CO 2 . The results are representative of 5 independent experiments. (E) Image showing the results of RT-PCR analysis of integrins mRNA. B16BL6 cells were treated with 0.05 μM fluvastatin or 0.1 μM simvastatin. After 3 d, equal amounts of RNA were reverse-transcribed to generate cDNA, which was used for PCR analysis of integrins mRNA expression in B16BL6 cells. (E) Image showing western blot of the integrin α 2 , integrin α 4 , and integrin α 5 proteins. Whole-cell lysates were generated and immunoblotted with antibodies against integrin α 2 , integrin α 4 , integrin α 5 , and β-actin (internal standard).
Figure Legend Snippet: Effect of statins on B16BL6 cell adhesion to ECM components . B16BL6 cells, which had been treated with 0.05 μM fluvastatin or 0.1 μM simvastatin for 3 d, were incubated with (A) type I collagen-, (B) type IV collagen-, (C) fibronectin-, or (D) laminin-coated plates for 30 min at 37°C in an atmosphere containing 5% CO 2 . The results are representative of 5 independent experiments. (E) Image showing the results of RT-PCR analysis of integrins mRNA. B16BL6 cells were treated with 0.05 μM fluvastatin or 0.1 μM simvastatin. After 3 d, equal amounts of RNA were reverse-transcribed to generate cDNA, which was used for PCR analysis of integrins mRNA expression in B16BL6 cells. (E) Image showing western blot of the integrin α 2 , integrin α 4 , and integrin α 5 proteins. Whole-cell lysates were generated and immunoblotted with antibodies against integrin α 2 , integrin α 4 , integrin α 5 , and β-actin (internal standard).

Techniques Used: Incubation, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Expressing, Western Blot, Generated

28) Product Images from "Molecular Characterization and Identification of Calnexin 1 As a Radiation Biomarker from Tradescantia BNL4430"

Article Title: Molecular Characterization and Identification of Calnexin 1 As a Radiation Biomarker from Tradescantia BNL4430

Journal: Plants

doi: 10.3390/plants9030387

Isolation and identification of the TrCNX1 gene in Tradescantia . ( a ) PCR amplification of TrCNX1 from genomic DNA. ( b ) PCR amplification of TrCNX1 ORF from cDNA of Tradescantia . Target-specific amplicons indicated by an arrow. ( c ) Structural analysis of the TrCNX1 gene. In TrCNX1 , the start (ATG) and stop (TGA) codons are shown in the gene coding region. The numbers above the TrCNX1 gene represent the DNA base pair (bp). Corresponding positions of introns (I)/exons (E) are indicated by arrows with the bp position. Numbers of introns (I1–I5) and exons (E1–E6) are denoted by white and gray boxes, respectively. ( d ) General structural features of the TrCNX1 protein. The putative conserved domains are shown according to previous reports [ 27 ]. The gray box indicates the conserved central domain of the endoplasmic reticulum (ER) lumen and those numbered 1 and 2 represent Ca 2+ -binding regions (motif 1) and oligosaccharide-binding domains (motif 2), respectively. The dark gray box represents the transmembrane (TM) domain in the cytosol. The size of each domain is denoted in closed brackets with amino acid (aa) residue lengths.
Figure Legend Snippet: Isolation and identification of the TrCNX1 gene in Tradescantia . ( a ) PCR amplification of TrCNX1 from genomic DNA. ( b ) PCR amplification of TrCNX1 ORF from cDNA of Tradescantia . Target-specific amplicons indicated by an arrow. ( c ) Structural analysis of the TrCNX1 gene. In TrCNX1 , the start (ATG) and stop (TGA) codons are shown in the gene coding region. The numbers above the TrCNX1 gene represent the DNA base pair (bp). Corresponding positions of introns (I)/exons (E) are indicated by arrows with the bp position. Numbers of introns (I1–I5) and exons (E1–E6) are denoted by white and gray boxes, respectively. ( d ) General structural features of the TrCNX1 protein. The putative conserved domains are shown according to previous reports [ 27 ]. The gray box indicates the conserved central domain of the endoplasmic reticulum (ER) lumen and those numbered 1 and 2 represent Ca 2+ -binding regions (motif 1) and oligosaccharide-binding domains (motif 2), respectively. The dark gray box represents the transmembrane (TM) domain in the cytosol. The size of each domain is denoted in closed brackets with amino acid (aa) residue lengths.

Techniques Used: Isolation, Polymerase Chain Reaction, Amplification, Binding Assay

29) Product Images from "TFPI-2 is a putative tumor suppressor gene frequently inactivated by promoter hypermethylation in nasopharyngeal carcinoma"

Article Title: TFPI-2 is a putative tumor suppressor gene frequently inactivated by promoter hypermethylation in nasopharyngeal carcinoma

Journal: BMC Cancer

doi: 10.1186/1471-2407-10-617

Methylation status of the TFPI-2 promoter region in NPC cell lines and normal nasopharyngeal epithelia (NNE) . The data are representative of 2 independent experiments. In vitro -methylated DNA was used as a methylation-positive control and DNA from normal lymphocytes was used as an unmethylated-positive control. Water was included as a blank control. MSP: methylation-specific PCR; U: unmethylated alleles; M: methylated alleles. PC: positive control.
Figure Legend Snippet: Methylation status of the TFPI-2 promoter region in NPC cell lines and normal nasopharyngeal epithelia (NNE) . The data are representative of 2 independent experiments. In vitro -methylated DNA was used as a methylation-positive control and DNA from normal lymphocytes was used as an unmethylated-positive control. Water was included as a blank control. MSP: methylation-specific PCR; U: unmethylated alleles; M: methylated alleles. PC: positive control.

Techniques Used: Methylation, In Vitro, Positive Control, Polymerase Chain Reaction

30) Product Images from "Cloning and transcriptional expression of a novel gene during sex inversion of the rice field eel (Monopterus albus)"

Article Title: Cloning and transcriptional expression of a novel gene during sex inversion of the rice field eel (Monopterus albus)

Journal: SpringerPlus

doi: 10.1186/s40064-015-1544-z

The results of ACP DDRT-PCR obtained from the stage IV ovary (O) and ovotestis (T). O stage IV ovary, T ovotestis. The ACP DDRT-PCR products were separated on 2 % agarose gel and stained with ethidium bromide. ACP1-20 indicates the arbitrary primers that were used in the ACP DDRT-PCR technique. The arrow indicates the differentially expressed genes (G1-14) identified between the stage IV ovary and the ovotestis
Figure Legend Snippet: The results of ACP DDRT-PCR obtained from the stage IV ovary (O) and ovotestis (T). O stage IV ovary, T ovotestis. The ACP DDRT-PCR products were separated on 2 % agarose gel and stained with ethidium bromide. ACP1-20 indicates the arbitrary primers that were used in the ACP DDRT-PCR technique. The arrow indicates the differentially expressed genes (G1-14) identified between the stage IV ovary and the ovotestis

Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Staining

31) Product Images from "Biocontrol Agents Increase the Specific Rate of Patulin Production by Penicillium expansum but Decrease the Disease and Total Patulin Contamination of Apples"

Article Title: Biocontrol Agents Increase the Specific Rate of Patulin Production by Penicillium expansum but Decrease the Disease and Total Patulin Contamination of Apples

Journal: Frontiers in Microbiology

doi: 10.3389/fmicb.2017.01240

Agarose gel electrophoresis showing the assessment of specificity of the primer pair patF-F/patF-R used for the quantification of fungi ( Penicillium expansum ) DNA. Lane 1 in (A,B) : DNA 100-2000 Marker, Lanes 2–6 in (A,B) : DNA templates. (A) The primer pair used in the PCR reactions was patF-F/patF-R. DNA from PCR reactions in which different genomic DNAs were used as the templates were: lane 2: genomic DNA from P. expansum strain FS7; lane 3: genomic DNA from P. expansum strain PY; lane 4: genomic DNA from R. kratochvilovae strain LS11; lane 5: genomic DNA from R. mucilaginosa 3617, lane 6: genomic DNA from apple fruits cv. Fuji. (B) The primer pair used in the PCR reactions was ACTIN-F/ACTIN-R. Lanes 2–6 were loaded with DNA samples from PCR reactions in which the same genomic DNA templates as in (A) were used.
Figure Legend Snippet: Agarose gel electrophoresis showing the assessment of specificity of the primer pair patF-F/patF-R used for the quantification of fungi ( Penicillium expansum ) DNA. Lane 1 in (A,B) : DNA 100-2000 Marker, Lanes 2–6 in (A,B) : DNA templates. (A) The primer pair used in the PCR reactions was patF-F/patF-R. DNA from PCR reactions in which different genomic DNAs were used as the templates were: lane 2: genomic DNA from P. expansum strain FS7; lane 3: genomic DNA from P. expansum strain PY; lane 4: genomic DNA from R. kratochvilovae strain LS11; lane 5: genomic DNA from R. mucilaginosa 3617, lane 6: genomic DNA from apple fruits cv. Fuji. (B) The primer pair used in the PCR reactions was ACTIN-F/ACTIN-R. Lanes 2–6 were loaded with DNA samples from PCR reactions in which the same genomic DNA templates as in (A) were used.

Techniques Used: Agarose Gel Electrophoresis, Marker, Polymerase Chain Reaction

Assessment of the method for the quantification of P. expansum genomic DNA through qPCR based on the primers pair patF-F/patF-R. (A,B) Amplification curves of a set of six 10-fold serial dilutions of genomic DNA from strains PY and FS7 of P. expansum showing the fluorescence signal plotted versus log of PCR cycle number (blank controls were also performed but fluorescence signal was observed). (C,D) Dissociation curve of the PCR product. (E,F) Standard curve generated by qPCR assay using 10-fold serial dilutions of pure genomic DNA from strains PY and FS7 of P. expansum ; Ct values were obtained for each dilution and plotted versus known quantities of genomic DNA used in the analyses.
Figure Legend Snippet: Assessment of the method for the quantification of P. expansum genomic DNA through qPCR based on the primers pair patF-F/patF-R. (A,B) Amplification curves of a set of six 10-fold serial dilutions of genomic DNA from strains PY and FS7 of P. expansum showing the fluorescence signal plotted versus log of PCR cycle number (blank controls were also performed but fluorescence signal was observed). (C,D) Dissociation curve of the PCR product. (E,F) Standard curve generated by qPCR assay using 10-fold serial dilutions of pure genomic DNA from strains PY and FS7 of P. expansum ; Ct values were obtained for each dilution and plotted versus known quantities of genomic DNA used in the analyses.

Techniques Used: Real-time Polymerase Chain Reaction, Amplification, Fluorescence, Polymerase Chain Reaction, Generated

32) Product Images from "A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation"

Article Title: A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation

Journal: BMC Genomics

doi: 10.1186/1471-2164-13-135

Discovery of a Gaijin -like MITE in the 4th intron of PLRRP gene . (a) Expression profile of PLRRP gene in different organs of two rice cultivars, Zhonghua 11 and Xiushui 11. RNA samples were extracted from callus (lane 1), root (lane 2), stem (lane 3), leaf (lane 4) and embryo (lane 5) and amplified by the AS primer pair. The size of the lower molecular weight RT-PCR amplicons of Zhonghua 11 (Z1) and Xiushui 11 (X1) were similar. However, the size of the higher molecular weight amplicons in Xiushui 11 ( X 2) was bigger than Zhonghua 11 (Z2). (b) DNA polymorphism of PLRRP gene. gDNAs were extracted from rice cultivars and amplified by the AS primer pair. The molecular weight of PCR amplicon from Zhonghua 11 (Zg) was smaller than Xiushui 11 (Xg). (c) PLRRP gene and its spliced mRNA transcripts. PLRRP gene (Zg, thick black lines) was composed of 9 exons (white and grey boxes) and 8 introns (thin black lines). The additional fragment at the 4th intron was indicated with vertical strip lines and the two additional fragments, 8 bp ATTAATAT fragment and a 146 bp fragment ( mGing ) were illustrated in the pictograph. Amplicons of Zhonghua 11 (Z1, Z2 and Zg) and Xiushui 11 (X1, X 2 and Xg) from part (a) and part (b) were indicated. (d) Sequence analysis of PLRRP gene in Xiushui 11. Underlines showed the AS primer pair sequences. Double-underlines and arrows indicated the ATA duplication and the TIRs, respectively. The position of ATTAATAT sequence was boxed. Capital letters revealed the 146 bp fragment. (e) Sequence alignment of mGing against Gaijin . The Gaijin sequence was obtained from Repbase. The alignment was made using the online ClustalW program with the different residue at each position highlighted. The arrows indicated the mGing TD primers.
Figure Legend Snippet: Discovery of a Gaijin -like MITE in the 4th intron of PLRRP gene . (a) Expression profile of PLRRP gene in different organs of two rice cultivars, Zhonghua 11 and Xiushui 11. RNA samples were extracted from callus (lane 1), root (lane 2), stem (lane 3), leaf (lane 4) and embryo (lane 5) and amplified by the AS primer pair. The size of the lower molecular weight RT-PCR amplicons of Zhonghua 11 (Z1) and Xiushui 11 (X1) were similar. However, the size of the higher molecular weight amplicons in Xiushui 11 ( X 2) was bigger than Zhonghua 11 (Z2). (b) DNA polymorphism of PLRRP gene. gDNAs were extracted from rice cultivars and amplified by the AS primer pair. The molecular weight of PCR amplicon from Zhonghua 11 (Zg) was smaller than Xiushui 11 (Xg). (c) PLRRP gene and its spliced mRNA transcripts. PLRRP gene (Zg, thick black lines) was composed of 9 exons (white and grey boxes) and 8 introns (thin black lines). The additional fragment at the 4th intron was indicated with vertical strip lines and the two additional fragments, 8 bp ATTAATAT fragment and a 146 bp fragment ( mGing ) were illustrated in the pictograph. Amplicons of Zhonghua 11 (Z1, Z2 and Zg) and Xiushui 11 (X1, X 2 and Xg) from part (a) and part (b) were indicated. (d) Sequence analysis of PLRRP gene in Xiushui 11. Underlines showed the AS primer pair sequences. Double-underlines and arrows indicated the ATA duplication and the TIRs, respectively. The position of ATTAATAT sequence was boxed. Capital letters revealed the 146 bp fragment. (e) Sequence alignment of mGing against Gaijin . The Gaijin sequence was obtained from Repbase. The alignment was made using the online ClustalW program with the different residue at each position highlighted. The arrows indicated the mGing TD primers.

Techniques Used: Expressing, Amplification, Molecular Weight, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Stripping Membranes, Sequencing

33) Product Images from "The role of host DNA ligases in hepadnavirus covalently closed circular DNA formation"

Article Title: The role of host DNA ligases in hepadnavirus covalently closed circular DNA formation

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1006784

Ligase inhibitor treatment blocked cccDNA formation in nuclear extract. (A) Demonstration of the in vitro cccDNA formation assay. The indicated amount of purified DHBV rcDNA were incubated with HepG2 nuclear extract as described in Materials and Methods. After the in vitro cccDNA formation reaction, total DNA were extracted and subjected to DHBV Southern blot analysis (top panel) and cccDNA-specific PCR assay (bottom panel). The EcoRI-linearized DHBV unit-length DNA was used as marker in Southern blot and as PCR positive template in cccDNA PCR assay (lane 2). 1 ng of rcDNA alone (lane 3) and nuclear extract alone (lane 8) served as PCR negative controls. (B) The in vitro DHBV cccDNA formation reaction was treated with DNA ligases inhibitor L1 (20 μM), L25 (20 μM), or L189 (50 μM), or DMSO solvent, and cccDNA was detected by PCR (lanes 3–6). DHBV cccDNA purified from Dstet5 cells was used as PCR positive control (lane 1). 1 ng of rcDNA without incubation with nuclear extract (lane 7) or without PCR reaction (lane 8) served as negative controls.
Figure Legend Snippet: Ligase inhibitor treatment blocked cccDNA formation in nuclear extract. (A) Demonstration of the in vitro cccDNA formation assay. The indicated amount of purified DHBV rcDNA were incubated with HepG2 nuclear extract as described in Materials and Methods. After the in vitro cccDNA formation reaction, total DNA were extracted and subjected to DHBV Southern blot analysis (top panel) and cccDNA-specific PCR assay (bottom panel). The EcoRI-linearized DHBV unit-length DNA was used as marker in Southern blot and as PCR positive template in cccDNA PCR assay (lane 2). 1 ng of rcDNA alone (lane 3) and nuclear extract alone (lane 8) served as PCR negative controls. (B) The in vitro DHBV cccDNA formation reaction was treated with DNA ligases inhibitor L1 (20 μM), L25 (20 μM), or L189 (50 μM), or DMSO solvent, and cccDNA was detected by PCR (lanes 3–6). DHBV cccDNA purified from Dstet5 cells was used as PCR positive control (lane 1). 1 ng of rcDNA without incubation with nuclear extract (lane 7) or without PCR reaction (lane 8) served as negative controls.

Techniques Used: In Vitro, Tube Formation Assay, Purification, Incubation, Southern Blot, Polymerase Chain Reaction, Marker, Positive Control

34) Product Images from "A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cyprinid Herpesvirus 2 in Gibel Carp (Carassius auratus gibelio)"

Article Title: A Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cyprinid Herpesvirus 2 in Gibel Carp (Carassius auratus gibelio)

Journal: The Scientific World Journal

doi: 10.1155/2014/716413

Sensitivity of the nested PCR assay. 1–5: the first PCR products; 6–10: the second PCR products. 1, 6: negative control; 2, 7: 10 −4 dilution; 3, 8: 10 −3 dilution. 4, 9: 10 −2 dilution; 5, 10: 10 −1 dilution; M: DL2000 DNA marker.
Figure Legend Snippet: Sensitivity of the nested PCR assay. 1–5: the first PCR products; 6–10: the second PCR products. 1, 6: negative control; 2, 7: 10 −4 dilution; 3, 8: 10 −3 dilution. 4, 9: 10 −2 dilution; 5, 10: 10 −1 dilution; M: DL2000 DNA marker.

Techniques Used: Nested PCR, Polymerase Chain Reaction, Negative Control, Marker

35) Product Images from "Self-compatibility in 'Zaohong' Japanese apricot is associated with the loss of function of pollen S genes"

Article Title: Self-compatibility in 'Zaohong' Japanese apricot is associated with the loss of function of pollen S genes

Journal: Molecular Biology Reports

doi: 10.1007/s11033-013-2765-2

PCR amplification of S - RNase and SFB alleles from ‘Zaohong’ and expression analysis for PmS - RNase ( a ), PmSFB ( b ), PmF - box genes ( c ) and Actin genes ( d ) in pollen ( P ), styles ( S ), and leaves ( L ). M is DNA marker, Z is Zaohong and G is genomic DNA. a RT-PCR of S - RNase alleles. b RT-PCR of SFB alleles. c RT-PCR of PmF - box alleles. d RT-PCR of Actin genes
Figure Legend Snippet: PCR amplification of S - RNase and SFB alleles from ‘Zaohong’ and expression analysis for PmS - RNase ( a ), PmSFB ( b ), PmF - box genes ( c ) and Actin genes ( d ) in pollen ( P ), styles ( S ), and leaves ( L ). M is DNA marker, Z is Zaohong and G is genomic DNA. a RT-PCR of S - RNase alleles. b RT-PCR of SFB alleles. c RT-PCR of PmF - box alleles. d RT-PCR of Actin genes

Techniques Used: Polymerase Chain Reaction, Amplification, Expressing, Peptide Mass Fingerprinting, Marker, Reverse Transcription Polymerase Chain Reaction

36) Product Images from "Analysis of SLC4A11, ZEB1, LOXHD1, COL8A2 and TCF4 gene sequences in a multi-generational family with late-onset Fuchs corneal dystrophy"

Article Title: Analysis of SLC4A11, ZEB1, LOXHD1, COL8A2 and TCF4 gene sequences in a multi-generational family with late-onset Fuchs corneal dystrophy

Journal: International Journal of Molecular Medicine

doi: 10.3892/ijmm.2016.2570

Sequencing analysis of the ZEB1 gene. (A) Sequence electropherograms of PCR products encompassing the 5′-UTR region and exon 1 of the ZEB1 genomic DNA. Sequences and sequencing chromatograms of PCR products encompassing 5′-UTR region and exon 1 of the ZEB1 genomic DNA from H4 (healthy control), II-9 (proband), II-3 (FCD case), and II-1 (FCD case) are shown from top to bottom (homozygous is shown in only one sequence, heterozygous is shown in both sequences). ZEB1 genomic DNA sequence (GenBank reference ID: NC_000010.11) was show above (exon and 5′-UTR seqences are depicted by upper and lower case letters, respectively) The breakpoint is indicated by the red arrow. Three indels detected in the present study are indicated in different colors: green for Indel 1, 34 bp indel containing 23 bp of the 5′-UTR region and 11 bp 5′ end of exon 1 (NM_030751.5: c.-86_-53delinsgggaggggtggaggcggaggggtGGGGGGGAAGG); red for Indel 2, 7 bp (NM_030751.5:c.-52_-46delinsGGGAGGG); blue for Indel 3, 4 bp indel (NM_030751.5:c.-45_-42delinsAGGG). Transcription start site (TSS) is indicated by a horizontal green arrow underneath ATG. The numbering system used for sequence variations is based on cDNA sequence with +1 corresponding to the A of the ATG TSS (GenBank Reference ID: NM_030751.5). FCD, Fuchs corneal dystrophy. Sequencing analysis of ZEB1 gene. (B) DNA sequencing results of the four haplotypes subcloned into pZeroBack/blunt vector. Three indels were underlined in different colors: green for Indel 1; red for Indel 2; and blue for Indel 3. Sequencing chromatograms of 4 haplotypes (ordered as Indel 1/Indel 2/Indel 3), I/I/I, D/I/I, D/D/I, D/D/D, are shown from top to bottom. The 5′ and 3′ boundaries of indel are shown by a vertical red and a blue arrow, respectively. TSS is indicated by a horizontal green arrow underneath ATG. (C) Schematic illustration of the ZEB1 genomic DNA and distribution of 3 continuous Indels (Indel 1, 2 and 3) relative to exon 1. The numbering system used for sequence variations is based on cDNA sequence with +1 corresponding to the A of the ATG TSS (GenBank Reference ID: NM_030751.5). FCD, Fuchs corneal dystrophy.
Figure Legend Snippet: Sequencing analysis of the ZEB1 gene. (A) Sequence electropherograms of PCR products encompassing the 5′-UTR region and exon 1 of the ZEB1 genomic DNA. Sequences and sequencing chromatograms of PCR products encompassing 5′-UTR region and exon 1 of the ZEB1 genomic DNA from H4 (healthy control), II-9 (proband), II-3 (FCD case), and II-1 (FCD case) are shown from top to bottom (homozygous is shown in only one sequence, heterozygous is shown in both sequences). ZEB1 genomic DNA sequence (GenBank reference ID: NC_000010.11) was show above (exon and 5′-UTR seqences are depicted by upper and lower case letters, respectively) The breakpoint is indicated by the red arrow. Three indels detected in the present study are indicated in different colors: green for Indel 1, 34 bp indel containing 23 bp of the 5′-UTR region and 11 bp 5′ end of exon 1 (NM_030751.5: c.-86_-53delinsgggaggggtggaggcggaggggtGGGGGGGAAGG); red for Indel 2, 7 bp (NM_030751.5:c.-52_-46delinsGGGAGGG); blue for Indel 3, 4 bp indel (NM_030751.5:c.-45_-42delinsAGGG). Transcription start site (TSS) is indicated by a horizontal green arrow underneath ATG. The numbering system used for sequence variations is based on cDNA sequence with +1 corresponding to the A of the ATG TSS (GenBank Reference ID: NM_030751.5). FCD, Fuchs corneal dystrophy. Sequencing analysis of ZEB1 gene. (B) DNA sequencing results of the four haplotypes subcloned into pZeroBack/blunt vector. Three indels were underlined in different colors: green for Indel 1; red for Indel 2; and blue for Indel 3. Sequencing chromatograms of 4 haplotypes (ordered as Indel 1/Indel 2/Indel 3), I/I/I, D/I/I, D/D/I, D/D/D, are shown from top to bottom. The 5′ and 3′ boundaries of indel are shown by a vertical red and a blue arrow, respectively. TSS is indicated by a horizontal green arrow underneath ATG. (C) Schematic illustration of the ZEB1 genomic DNA and distribution of 3 continuous Indels (Indel 1, 2 and 3) relative to exon 1. The numbering system used for sequence variations is based on cDNA sequence with +1 corresponding to the A of the ATG TSS (GenBank Reference ID: NM_030751.5). FCD, Fuchs corneal dystrophy.

Techniques Used: Sequencing, Polymerase Chain Reaction, DNA Sequencing, Plasmid Preparation

Analysis of TGC trinucleotide repeat expansion (rs193922902) of TCF4 .(A)Sanger DNA sequencing of DNA samples of proband showed heterozygous for allele (TGC) 11 and (TGC) 12 . (B) STR analysis of PCR amplicons of proband verified heterozygous for allele (TGC) 11 and (TGC) 12 .
Figure Legend Snippet: Analysis of TGC trinucleotide repeat expansion (rs193922902) of TCF4 .(A)Sanger DNA sequencing of DNA samples of proband showed heterozygous for allele (TGC) 11 and (TGC) 12 . (B) STR analysis of PCR amplicons of proband verified heterozygous for allele (TGC) 11 and (TGC) 12 .

Techniques Used: DNA Sequencing, Polymerase Chain Reaction

37) Product Images from "Development of Selectable Marker-Free Transgenic Rice Plants with Enhanced Seed Tocopherol Content through FLP/FRT-Mediated Spontaneous Auto-Excision"

Article Title: Development of Selectable Marker-Free Transgenic Rice Plants with Enhanced Seed Tocopherol Content through FLP/FRT-Mediated Spontaneous Auto-Excision

Journal: PLoS ONE

doi: 10.1371/journal.pone.0132667

Identification of the T-DNA in transgenic rice plants to select marker-free transgenic rice lines. (a) PCR analysis of T 1 transgenic rice plants for marker excision. (b) RT-PCR analysis of NtTC and hpt from leaves of T 1 transgenic rice plants. The rice tubulin ( tub ) gene was used for normalization.
Figure Legend Snippet: Identification of the T-DNA in transgenic rice plants to select marker-free transgenic rice lines. (a) PCR analysis of T 1 transgenic rice plants for marker excision. (b) RT-PCR analysis of NtTC and hpt from leaves of T 1 transgenic rice plants. The rice tubulin ( tub ) gene was used for normalization.

Techniques Used: Transgenic Assay, Marker, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction

Schematic diagram of the T-DNA region of binary vectors for marker elimination and an DNA excised product. Restriction sites within the MCS were unique digestion sites in the vector. The structure of pCMF was the same to as of pHWMF except that the modified FLP gene was replaced with the native FLP gene. pCMF-TC was derived from inserting the NtTC gene, which is a tocopherol cyclase ortholog isolated from tobacco, into multiple cloning sites of pCMF. After gene excision, the CaMV 35S promoter was inserted adjacent to the NtTC coding region. P35SF, HPTR, and TCR primers were designed to detect the DNA excision. The PCR product amplified with P35SF/TCR would be 1.5 kb if DNA excision occurred and 5.7 kb otherwise. P35S, CaMV 35S gene promoter; hpt , hygromycin phosphotransferase gene; T35S, 35S CaMV gene terminator; Ppod, stress-inducible peroxidase gene promoter; FLP ; recombinase gene from Saccharomyces cerevisiae ; Tnos: Agrobacterium nopaline synthase gene terminator; MCS, multiple cloning site; LB, left border; RB, right border; NtTC , tocopherol cyclase gene isolated from tobacco; FRT , FLP recognition site.
Figure Legend Snippet: Schematic diagram of the T-DNA region of binary vectors for marker elimination and an DNA excised product. Restriction sites within the MCS were unique digestion sites in the vector. The structure of pCMF was the same to as of pHWMF except that the modified FLP gene was replaced with the native FLP gene. pCMF-TC was derived from inserting the NtTC gene, which is a tocopherol cyclase ortholog isolated from tobacco, into multiple cloning sites of pCMF. After gene excision, the CaMV 35S promoter was inserted adjacent to the NtTC coding region. P35SF, HPTR, and TCR primers were designed to detect the DNA excision. The PCR product amplified with P35SF/TCR would be 1.5 kb if DNA excision occurred and 5.7 kb otherwise. P35S, CaMV 35S gene promoter; hpt , hygromycin phosphotransferase gene; T35S, 35S CaMV gene terminator; Ppod, stress-inducible peroxidase gene promoter; FLP ; recombinase gene from Saccharomyces cerevisiae ; Tnos: Agrobacterium nopaline synthase gene terminator; MCS, multiple cloning site; LB, left border; RB, right border; NtTC , tocopherol cyclase gene isolated from tobacco; FRT , FLP recognition site.

Techniques Used: Marker, Plasmid Preparation, Modification, Derivative Assay, Isolation, Clone Assay, Polymerase Chain Reaction, Amplification

38) Product Images from "Analysis of DNA Methylation in Plasma for Monitoring Hepatocarcinogenesis"

Article Title: Analysis of DNA Methylation in Plasma for Monitoring Hepatocarcinogenesis

Journal: Genetic Testing and Molecular Biomarkers

doi: 10.1089/gtmb.2014.0292

MSP analysis of ELF , RASSF1A , p16 , and GSTP1 in liver tissue and plasma samples of hepatocellular carcinoma (HCC) and liver cirrhosis (LC) patients. (A) Representative examples of tumor, nontumor tissue, and corresponding plasma samples from two HCC patients. (B) Methylation status in cirrhosis and corresponding plasma from two LC patients and one normal liver tissue and one plasma sample from patients without liver disease. Bisulfite-treated DNA was amplified with primers specific to the methylated (m) or the unmethylated (u) CpG islands of each gene. MSP products were stained with ethidium bromide after 2.0% agarose gel electrophoresis. C, cirrhosis; M, molecular weight standard; MSP, methylation-specific PCR; m, methylated; W, water contamination control; Pos, MSP product from positive plasma or cell line DNA used as positive control ( ELF pro m for ELF , Huh-7 for RASSF1A , T47D for p 16, and MCF-7 for GSTP1 ); Neg, unmethylated product of normal liver DNA as negative control; Non, nontumor; N, normal cases; P, plasma samples; PCR, polymerase chain reaction; T, tumor; Tis, tissue; u, unmethylated.
Figure Legend Snippet: MSP analysis of ELF , RASSF1A , p16 , and GSTP1 in liver tissue and plasma samples of hepatocellular carcinoma (HCC) and liver cirrhosis (LC) patients. (A) Representative examples of tumor, nontumor tissue, and corresponding plasma samples from two HCC patients. (B) Methylation status in cirrhosis and corresponding plasma from two LC patients and one normal liver tissue and one plasma sample from patients without liver disease. Bisulfite-treated DNA was amplified with primers specific to the methylated (m) or the unmethylated (u) CpG islands of each gene. MSP products were stained with ethidium bromide after 2.0% agarose gel electrophoresis. C, cirrhosis; M, molecular weight standard; MSP, methylation-specific PCR; m, methylated; W, water contamination control; Pos, MSP product from positive plasma or cell line DNA used as positive control ( ELF pro m for ELF , Huh-7 for RASSF1A , T47D for p 16, and MCF-7 for GSTP1 ); Neg, unmethylated product of normal liver DNA as negative control; Non, nontumor; N, normal cases; P, plasma samples; PCR, polymerase chain reaction; T, tumor; Tis, tissue; u, unmethylated.

Techniques Used: Methylation, Amplification, Staining, Agarose Gel Electrophoresis, Molecular Weight, Polymerase Chain Reaction, Positive Control, Negative Control

39) Product Images from "Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays"

Article Title: Screening insertion libraries for mutations in many genes simultaneously using DNA microarrays

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.121189598

Screening for insertions in many different genes. DNA pools prepared from 100 uncharacterized Ds lines were TAIL-PCR-amplified in the presence of Cy3- Ds 5′2 primer and degenerate primer AD7 ( a ) or AD8 ( b ) and hybridized to a 1,200-EST Arabidopsis “stress” gene microarray (see Materials and Methods ).
Figure Legend Snippet: Screening for insertions in many different genes. DNA pools prepared from 100 uncharacterized Ds lines were TAIL-PCR-amplified in the presence of Cy3- Ds 5′2 primer and degenerate primer AD7 ( a ) or AD8 ( b ) and hybridized to a 1,200-EST Arabidopsis “stress” gene microarray (see Materials and Methods ).

Techniques Used: Polymerase Chain Reaction, Amplification, Microarray

( a ) Cross-hybridization between Ds -flanking sequences and homologs. DNA fragments of genes with decreasing homology to the genes disrupted in lines 326–8 (cytochrome p450, ♦) and 301–7 (subtilisin-type protease, ●) were spotted and hybridized to end-labeled PCR fragments amplified from genomic DNA of the two lines. ( b ) Detecting insertions inside and outside ORFs. Ds -flanking fragments were amplified and both terminally and internally labeled from lines with insertions 24, 48, 259, 387, 473, and 576 bp from the ORF by using Ds - and gene-specific primers (♦) or Ds -specific and degenerate primers under TAIL-PCR conditions (●).
Figure Legend Snippet: ( a ) Cross-hybridization between Ds -flanking sequences and homologs. DNA fragments of genes with decreasing homology to the genes disrupted in lines 326–8 (cytochrome p450, ♦) and 301–7 (subtilisin-type protease, ●) were spotted and hybridized to end-labeled PCR fragments amplified from genomic DNA of the two lines. ( b ) Detecting insertions inside and outside ORFs. Ds -flanking fragments were amplified and both terminally and internally labeled from lines with insertions 24, 48, 259, 387, 473, and 576 bp from the ORF by using Ds - and gene-specific primers (♦) or Ds -specific and degenerate primers under TAIL-PCR conditions (●).

Techniques Used: Hybridization, Labeling, Polymerase Chain Reaction, Amplification

40) Product Images from "Arg-Gingipain A DNA Vaccine Induces Protective Immunity against Infection by Porphyromonas gingivalis in a Murine Model"

Article Title: Arg-Gingipain A DNA Vaccine Induces Protective Immunity against Infection by Porphyromonas gingivalis in a Murine Model

Journal: Infection and Immunity

doi: 10.1128/IAI.69.5.2858-2864.2001

Expression of rgpA -specific mRNA around the immunized regions of mice. RNA was purified from transfected cells of mice and amplified by RT-PCR using rgpA -specific primers. Lanes: 1, plasmid pVAX1 containing rgpA gene (positive control); 2, rgpA DNA vaccine plasmid-transfected cells without RT reaction (negative control); 3, rgpA DNA vaccine plasmid-transfected cells.
Figure Legend Snippet: Expression of rgpA -specific mRNA around the immunized regions of mice. RNA was purified from transfected cells of mice and amplified by RT-PCR using rgpA -specific primers. Lanes: 1, plasmid pVAX1 containing rgpA gene (positive control); 2, rgpA DNA vaccine plasmid-transfected cells without RT reaction (negative control); 3, rgpA DNA vaccine plasmid-transfected cells.

Techniques Used: Expressing, Mouse Assay, Purification, Transfection, Amplification, Reverse Transcription Polymerase Chain Reaction, Plasmid Preparation, Positive Control, Negative Control

Related Articles

Amplification:

Article Title: Essential Domains for Ribonucleoprotein Complex Formation Required for Retrotransposition of Telomere-Specific Non-Long Terminal Repeat Retrotransposon SART1 †
Article Snippet: .. After heat inactivation at 80°C for 20 min, 1 μl of the reaction mixture was amplified by PCR for 35 cycles of 98°C for 20 s, 60°C for 30 s, and 72°C for 30 s, with an initial denaturation at 96°C for 2 min and a final extension at 72°C for 5 min. PCR mixtures contained 200 μM concentrations of each dNTP, 2 mM MgCl2 , 50 mM KCl, 0.5 U of Ex- Taq (TaKaRa), and 0.5 μM concentrations of each primer (see Table S1 in the supplemental material). .. Purified SART1 complex was overlaid onto 3.3 ml of 10 to 40% glycerol gradient in the HG500 buffer.

Article Title: Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification
Article Snippet: .. The amplification reactions were carried out with 2720 thermal cycler (Applied Biosystems, Foster City, CA) in 20 μl volume containing 20 ng of genomic DNA, 0.2 mM of each dNTP, 0.4 μM of each primer, 10 × PCR buffer (Mg2+ free), 2.5 mM Mg2+ , 1 unit of Taq DNA polymerase (Takara, Dalian, China) with the following conditions: initial denaturation at 95 °C for 5 min, followed by 35 cycles of 94 °C, 30 s; 50 to 55 °C, 60 s; 72 °C, 45 s and a final extension of 72 °C for 8 min. ..

DNA Synthesis:

Article Title: Chemical Incorporation of Chain-Terminating Nucleoside Analogs as 3′-Blocking DNA Damage and Their Removal by Human ERCC1-XPF Endonuclease
Article Snippet: .. Resumption of DNA Synthesis by DNA Polymerase after the Removal of CTNAs The hybridized oligonucleotides (400 fmol) were first treated with ERCC1-XPF (230 fmol) in 10 µL of 50 mM Tris-HCl buffer (pH 8.0), containing 2 mM MgCl2 , 0.5 mM DTT and 0.1 mg·mL−1 BSA, at 25 °C for 16 h. To the reaction mixture was added 5 µL of 30 mM Tris-HCl buffer (pH 7.9), containing 150 mM NaCl, 30 mM MgCl2 , 30 mM DTT, 300 µM dNTPs and the Klenow fragment of Escherichia coli DNA polymerase I, lacking the 3′–5′ exonuclease activity (KF− , 0.1 unit, Takara Bio). ..

Marker:

Article Title: Small Molecular Contaminant and Microorganism Can Be Simultaneously Detected Based on Nanobody-Phage: Using Carcinogen Aflatoxin and Its Main Fungal Aspergillus Section Flavi spp. in Stored Maize for Demonstration
Article Snippet: .. DNA polymerase (iTaq), Mg2+ , dNTPs, 6× loading buffer, and DNA marker were bought from Takara Bio (Beijing, China). .. The anti-aflatoxins monoclonal antibody 1C11 (mAb 1C11) and V2–5 phage displaying nanobody specific for 1C11 were produced by our team ( ; ).

Activity Assay:

Article Title: Chemical Incorporation of Chain-Terminating Nucleoside Analogs as 3′-Blocking DNA Damage and Their Removal by Human ERCC1-XPF Endonuclease
Article Snippet: .. Resumption of DNA Synthesis by DNA Polymerase after the Removal of CTNAs The hybridized oligonucleotides (400 fmol) were first treated with ERCC1-XPF (230 fmol) in 10 µL of 50 mM Tris-HCl buffer (pH 8.0), containing 2 mM MgCl2 , 0.5 mM DTT and 0.1 mg·mL−1 BSA, at 25 °C for 16 h. To the reaction mixture was added 5 µL of 30 mM Tris-HCl buffer (pH 7.9), containing 150 mM NaCl, 30 mM MgCl2 , 30 mM DTT, 300 µM dNTPs and the Klenow fragment of Escherichia coli DNA polymerase I, lacking the 3′–5′ exonuclease activity (KF− , 0.1 unit, Takara Bio). ..

Polymerase Chain Reaction:

Article Title: Essential Domains for Ribonucleoprotein Complex Formation Required for Retrotransposition of Telomere-Specific Non-Long Terminal Repeat Retrotransposon SART1 †
Article Snippet: .. After heat inactivation at 80°C for 20 min, 1 μl of the reaction mixture was amplified by PCR for 35 cycles of 98°C for 20 s, 60°C for 30 s, and 72°C for 30 s, with an initial denaturation at 96°C for 2 min and a final extension at 72°C for 5 min. PCR mixtures contained 200 μM concentrations of each dNTP, 2 mM MgCl2 , 50 mM KCl, 0.5 U of Ex- Taq (TaKaRa), and 0.5 μM concentrations of each primer (see Table S1 in the supplemental material). .. Purified SART1 complex was overlaid onto 3.3 ml of 10 to 40% glycerol gradient in the HG500 buffer.

Article Title: Source identification of airborne Escherichia coli of swine house surroundings using ERIC-PCR and REP-PCR
Article Snippet: .. 2.5 ERIC-PCR and REP-PCR The PCR reaction mixture (25 μL) contained 1.5 U Taq DNA polymerase (TaKaRa), 300 ng μL−1 of each primer, 0.875 mM of each dNTP, 1× reaction buffer and 1.5 mM MgCl2 (TaKaRa). .. Amplification was performed in a thermocycler (Eppendorf, Germany) as follows: an initial denaturation (94 °C, 5 min) followed by 35 cycles of denaturation (94 °C, 1 min), annealing (1 min at 42 °C), and extension (65 °C, 8 min) with a single final extension (65 °C, 16 min).

Article Title: Development and characterization of 16 novel microsatellite markers by Transcriptome sequencing for Angelica dahurica and test for cross-species amplification
Article Snippet: .. The amplification reactions were carried out with 2720 thermal cycler (Applied Biosystems, Foster City, CA) in 20 μl volume containing 20 ng of genomic DNA, 0.2 mM of each dNTP, 0.4 μM of each primer, 10 × PCR buffer (Mg2+ free), 2.5 mM Mg2+ , 1 unit of Taq DNA polymerase (Takara, Dalian, China) with the following conditions: initial denaturation at 95 °C for 5 min, followed by 35 cycles of 94 °C, 30 s; 50 to 55 °C, 60 s; 72 °C, 45 s and a final extension of 72 °C for 8 min. ..

Plasmid Preparation:

Article Title: A transcription and translation-coupled DNA replication system using rolling-circle replication
Article Snippet: .. Assay of the TTcDR reaction The optimized composition of the TTcDR system was as follows: template plasmid DNA (1 ng/μl), dNTPs (0.3 mM each, Takara), [32 -P] dCTP (3.3 μM, PerkinElmer), magnesium acetate (7.9 mM, Wako), potassium glutamate (70 mM, Wako), spermidine (0.375 mM, Nakarai), dithiothreitol (6 mM, Nakarai), ATP (0.375 mM, GE Healthcare), GTP (0.25 mM, GE Healthcare), CTP (0.125 mM, GE Healthcare), UTP (0.125 mM, GE Healthcare), creatine phosphate (25 mM, Nakarai), E. coli tRNA mixture (0.518 μg/μl, Roche), 10-formyl-5,6,7,8-tetrahydrofolic acid (10 ng/μl), Cys (0.3 mM, Wako), Tyr (0.3 mM, Wako), the other 18 amino acids except for Cys and Tyr (0.36 mM, Wako), 2-[4-(2-hydroxyethyl)-1-piperazinyl]ethanesulfonic acid (100 mM, pH 7.6, Sigma), ribosomes (1 μM), IF1 (25 μM), IF2 (1 μM), IF3 (4.9 μM), EF-G (1.1 μM), EF-Tu (80 μM), EF-Ts (3.3 μM), RF1 (0.05 μM), RF2 (0.05 μM), RF3 (0.17 μM), RRF (3.9 μM), AlaRS (730 nM), ArgRS (30 nM), AsnRS (420 nM), AspRS (120 nM), CysRS (20 nM), GlnRS (60 nM), GluRS (230 nM), GlyRS (90 nM), HisRS (90 nM), IleRS (370 nM), LeuRS (40 nM), LysRS (120 nM), MetRS (110 nM), PheRS (130 nM), ProRS (170 nM), SerRS (80 nM), ThrRS (80 nM), TrpRS (30 nM), TyrRS (150 nM), ValRS (20 nM), MTF (590 nM), creatine kinase (0.25 μM), myokinase (1.4 μM), nucleoside-diphosphate kinase (20 nM), pyrophosphatase (40 nM), yeast inorganic pyrophosphatase (0.2 mU/μl, New England BioLabs (NEB)), ribonuclease inhibitor (0.1 U/μl; Promega), and T7 RNA polymerase (0.42 U/μl; Takara). .. Most of the proteins described above were purified according to a previously described method except for yeast inorganic pyrophosphatase, ribonuclease inhibitor, and T7 RNA polymerase.

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  • 95
    TaKaRa pcr buffer
    Effect of <t>DNA</t> 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 <t>qRT-PCR.</t> Asterisk (*), statistically significant ( p
    Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 95/100, based on 1840 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa pcr reaction buffer
    Ct values and copy number of <t>HBV</t> serum samples originated from three standard curves corresponding to the S (A), C (B) and X (C) regions respectively. Each real-time <t>PCR</t> reaction was performed in triplicate.
    Pcr Reaction Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 94/100, based on 89 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    88
    TaKaRa step rt pcr buffer
    Specificity of the multiplex <t>rRT-PCR</t> assay for pandemic (H1N1) 2009, H3N2, and reassortant avian H7N9 viruses. Signals from the <t>RNA</t> samples extracted from human pandemic (H1N1) 2009, seasonal H3N2, reassortant avian H7N9 virus (A/Zhejiang/DTID-ZJU01/2013), the clinical samples with negative FluA virus, and RP gene
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    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

    Journal: PLoS ONE

    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

    doi: 10.1371/journal.pone.0123133

    Figure Lengend 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

    Article Snippet: Briefly, a 20 μL reaction volume containing 25 ng bisulfite modified DNA, 1× PCR buffer, 1.5 mM MgCl2 , 0.25 mM dNTPs, 0.5 μM specific primer mix and 1 unit Ex-Taq Hot Start enzyme (Takara BioInc) was used.

    Techniques: 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.

    Journal: PLoS ONE

    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

    doi: 10.1371/journal.pone.0123133

    Figure Lengend 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.

    Article Snippet: Briefly, a 20 μL reaction volume containing 25 ng bisulfite modified DNA, 1× PCR buffer, 1.5 mM MgCl2 , 0.25 mM dNTPs, 0.5 μM specific primer mix and 1 unit Ex-Taq Hot Start enzyme (Takara BioInc) was used.

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

    Heterogeneous expression of CD14 mRNA by CD14 high and CD14 low HGF. CD14 high HGF (lane 1, donor MH; lane 2, donor SM) and CD14 low HGF (lane 3, donor KT; lane 4, donor NK) from confluent cultures were collected by trypsinization. RNA was extracted from the cells, and its cDNA was prepared and analyzed by RT-PCR. The results are representative of three different experiments.

    Journal: Infection and Immunity

    Article Title: Heterogeneous Expression and Release of CD14 by Human Gingival Fibroblasts: Characterization and CD14-Mediated Interleukin-8 Secretion in Response to Lipopolysaccharide

    doi:

    Figure Lengend Snippet: Heterogeneous expression of CD14 mRNA by CD14 high and CD14 low HGF. CD14 high HGF (lane 1, donor MH; lane 2, donor SM) and CD14 low HGF (lane 3, donor KT; lane 4, donor NK) from confluent cultures were collected by trypsinization. RNA was extracted from the cells, and its cDNA was prepared and analyzed by RT-PCR. The results are representative of three different experiments.

    Article Snippet: The PCR mixture contained 5 μl of the cDNA mixture, 2 μl of 10× PCR buffer, 0.2 mM deoxynucleoside triphosphates, 50 pmol of each primer, and 0.1 μl of Ex Taq DNA polymerase (Takara, Tokyo, Japan) in a total volume of 20 μl.

    Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction

    Ct values and copy number of HBV serum samples originated from three standard curves corresponding to the S (A), C (B) and X (C) regions respectively. Each real-time PCR reaction was performed in triplicate.

    Journal: World Journal of Gastroenterology : WJG

    Article Title: Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

    doi: 10.3748/wjg.v12.i45.7365

    Figure Lengend Snippet: Ct values and copy number of HBV serum samples originated from three standard curves corresponding to the S (A), C (B) and X (C) regions respectively. Each real-time PCR reaction was performed in triplicate.

    Article Snippet: Real-time PCR amplification was performed in 20 μL reaction mixture containing 1 μL standard DNA or 2 μL isolated serum HBV DNA, 2 × PCR reaction buffer [100 mmol/L Tris-HCl (pH8.3), 100 mmol/L KCl, 7.0 mmol/L MgCl2 , 400 μmol/L each of the deoxynucleotide triphosphates (dNTP), 1U hot star DNA polymerase Takara, Japan], 5pmol of each pair of primers and 2.5 pmol of corresponding TaqMan probe.

    Techniques: Real-time Polymerase Chain Reaction

    Quantitation of HBV viral DNA in sera by real-time PCR

    Journal: World Journal of Gastroenterology : WJG

    Article Title: Rapid quantification of hepatitis B virus DNA by real-time PCR using efficient TaqMan probe and extraction of virus DNA

    doi: 10.3748/wjg.v12.i45.7365

    Figure Lengend Snippet: Quantitation of HBV viral DNA in sera by real-time PCR

    Article Snippet: Real-time PCR amplification was performed in 20 μL reaction mixture containing 1 μL standard DNA or 2 μL isolated serum HBV DNA, 2 × PCR reaction buffer [100 mmol/L Tris-HCl (pH8.3), 100 mmol/L KCl, 7.0 mmol/L MgCl2 , 400 μmol/L each of the deoxynucleotide triphosphates (dNTP), 1U hot star DNA polymerase Takara, Japan], 5pmol of each pair of primers and 2.5 pmol of corresponding TaqMan probe.

    Techniques: Quantitation Assay, Real-time Polymerase Chain Reaction

    Specificity of the multiplex rRT-PCR assay for pandemic (H1N1) 2009, H3N2, and reassortant avian H7N9 viruses. Signals from the RNA samples extracted from human pandemic (H1N1) 2009, seasonal H3N2, reassortant avian H7N9 virus (A/Zhejiang/DTID-ZJU01/2013), the clinical samples with negative FluA virus, and RP gene

    Journal: SpringerPlus

    Article Title: Simultaneous detection of influenza A subtypes of H3N2 virus, pandemic (H1N1) 2009 virus and reassortant avian H7N9 virus in humans by multiplex one-step real-time RT-PCR assay

    doi: 10.1186/s40064-016-3733-9

    Figure Lengend Snippet: Specificity of the multiplex rRT-PCR assay for pandemic (H1N1) 2009, H3N2, and reassortant avian H7N9 viruses. Signals from the RNA samples extracted from human pandemic (H1N1) 2009, seasonal H3N2, reassortant avian H7N9 virus (A/Zhejiang/DTID-ZJU01/2013), the clinical samples with negative FluA virus, and RP gene

    Article Snippet: The final optimised 50 μl reaction mixture consisted of 5 μl of RNA, 25 μl of 2× One Step RT-PCR Buffer, 1 μl of TaKaRa EX Taq HS (5 U/μl), 1 μl of PrimeScript RT Enzyme Mix, 1 μl of forward primer (40 μM), 1 μl of reverse primer (40 μM), 0.5 μl of probe (20 μM) for each virus, 0.8 μl of RP forward primer (40 μM), 0.8 μl of RP reverse primer (40 μM), 0.4 μl of RP probe (20 μM), and 6 μl of RNase-free water.

    Techniques: Multiplex Assay, Quantitative RT-PCR