pcr buffer  (TaKaRa)

 
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    dNTP Mixture
    Description:
    Our dNTPs for PCR are 98 pure and are tested for quality control in a variety of applications Individual dNTPs are supplied at a concentration of 100 mM and can be diluted with water or buffer as needed The dNTP Set Cat 4025 provides one of each of the four deoxynucleotide triphosphates
    Catalog Number:
    4030
    Price:
    None
    Size:
    3 2 µmol Each 1 25 mL
    Category:
    dNTPs dNTPs Other PCR related products PCR
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    Structured Review

    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
    Our dNTPs for PCR are 98 pure and are tested for quality control in a variety of applications Individual dNTPs are supplied at a concentration of 100 mM and can be diluted with water or buffer as needed The dNTP Set Cat 4025 provides one of each of the four deoxynucleotide triphosphates
    https://www.bioz.com/result/pcr buffer/product/TaKaRa
    Average 99 stars, based on 1840 article reviews
    Price from $9.99 to $1999.99
    pcr buffer - by Bioz Stars, 2020-11
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    Images

    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 "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

    5) 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

    6) 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

    7) 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

    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 "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

    10) 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

    11) 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

    12) 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

    13) 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

    14) 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

    15) 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

    16) 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

    17) 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

    18) 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

    19) 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

    20) 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

    21) 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

    22) 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

    23) 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

    24) Product Images from "Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut"

    Article Title: Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut

    Journal: Scientific Reports

    doi: 10.1038/s41598-020-68431-2

    Alternative splicing of the FT gene. ( A ) Gene structure of two alternative splice transcripts of FT gene. ( B ) Detection of alternative splice of FT gene in 8 dwarf coconut and 11 tall coconut samples by cDNA PCR amplification and then sequence.
    Figure Legend Snippet: Alternative splicing of the FT gene. ( A ) Gene structure of two alternative splice transcripts of FT gene. ( B ) Detection of alternative splice of FT gene in 8 dwarf coconut and 11 tall coconut samples by cDNA PCR amplification and then sequence.

    Techniques Used: Polymerase Chain Reaction, Amplification, Sequencing

    25) 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

    26) 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

    27) 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

    28) 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

    29) Product Images from "The complex evolution of the HSP70 gene family"

    Article Title: The complex evolution of the HSP70 gene family

    Journal: bioRxiv

    doi: 10.1101/2020.09.21.307264

    Expression analyses of B. plicatilis HSP70 genes. (A) Heat stress-induced expression of HSP70 quantified by real-time PCR. Beta-actin gene was used as the internal control. Bars represent standard errors from three replications. One-way ANOVA detected significant effects of heat treatment (F = 3.281, df = 5, P = 0.0426). Dunnett’s multiple comparison was used to detect significant differences between the control and other groups. Difference between control and two hours group was statistically significant (t = 3.246, P = 0.028). (B) In situ hybridization for B. plicatilis HSP70 genes. Rotifers were fixed 4 h after the heat treatment.
    Figure Legend Snippet: Expression analyses of B. plicatilis HSP70 genes. (A) Heat stress-induced expression of HSP70 quantified by real-time PCR. Beta-actin gene was used as the internal control. Bars represent standard errors from three replications. One-way ANOVA detected significant effects of heat treatment (F = 3.281, df = 5, P = 0.0426). Dunnett’s multiple comparison was used to detect significant differences between the control and other groups. Difference between control and two hours group was statistically significant (t = 3.246, P = 0.028). (B) In situ hybridization for B. plicatilis HSP70 genes. Rotifers were fixed 4 h after the heat treatment.

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, In Situ Hybridization

    Semi-quantitative reverse transcription-PCR B. plicatilis HSP70 genes. A representative result is shown out of three independent experiments. (A) Location of primers rHSP70_gapF and rHSP70_gapR that amplify cDNA fragment of 112 and 124 bp from HSP70-1 and HSP70-2 cDNAs, respectively. (B) Polyacrylamide gel electrophoresis patterns of the RT-PCR product. Cycle numbers within a linear range of PCR amplification were determined to be 24 to 28 cycles for both cDNAs by preliminary experiments on the basis of signal intensities of amplified products by RT-PCR. (C) Signal intensities of HSP70-1 and HSP70-2 genes standardized to those of β-actin.
    Figure Legend Snippet: Semi-quantitative reverse transcription-PCR B. plicatilis HSP70 genes. A representative result is shown out of three independent experiments. (A) Location of primers rHSP70_gapF and rHSP70_gapR that amplify cDNA fragment of 112 and 124 bp from HSP70-1 and HSP70-2 cDNAs, respectively. (B) Polyacrylamide gel electrophoresis patterns of the RT-PCR product. Cycle numbers within a linear range of PCR amplification were determined to be 24 to 28 cycles for both cDNAs by preliminary experiments on the basis of signal intensities of amplified products by RT-PCR. (C) Signal intensities of HSP70-1 and HSP70-2 genes standardized to those of β-actin.

    Techniques Used: Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Amplification

    30) 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

    31) 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

    32) 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

    33) Product Images from "Prevalence and Characterization of Murine Leukemia Virus Contamination in Human Cell Lines"

    Article Title: Prevalence and Characterization of Murine Leukemia Virus Contamination in Human Cell Lines

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0125622

    Detection of RT activity in human and mouse (ELM-I-1 and PSI-2) cell culture supernatants by PERT assay. The assay was carried out applying two different buffers containing MgCl 2 or MnCl 2 , respectively. The Mn 2+ -buffer was more sensitive in most cases, indicating that the contaminating viruses presumably belong to the Mn 2+ -dependent C-type retroviruses. The CML-T1 cell line was MLV-PCR positive due to contamination of the genomic DNA with mouse derived DNA. The size of the MS2 PCR product is 112 bp.
    Figure Legend Snippet: Detection of RT activity in human and mouse (ELM-I-1 and PSI-2) cell culture supernatants by PERT assay. The assay was carried out applying two different buffers containing MgCl 2 or MnCl 2 , respectively. The Mn 2+ -buffer was more sensitive in most cases, indicating that the contaminating viruses presumably belong to the Mn 2+ -dependent C-type retroviruses. The CML-T1 cell line was MLV-PCR positive due to contamination of the genomic DNA with mouse derived DNA. The size of the MS2 PCR product is 112 bp.

    Techniques Used: Activity Assay, Cell Culture, Polymerase Chain Reaction, Derivative Assay

    Detection of RT activity in cell lines infected with MLV of contaminated cell lines by PERT assay. Cell culture supernatants of the infected cell lines NCI-H82 and VERO-B4 were harvested after 45 and 44 days after infection, respectively. MS2 phage RNA was reverse transcribed with an MS2-specific primer and the MLV derived RT of the samples in the presence of MnCl 2 . The cDNA was then amplified with a second MS2-specific primer applying PCR. The signals of the cell lines infected with LCL-HO supernatant may potentially be ascribed to the activity of SMRV derived RT. dpi: days post infection.
    Figure Legend Snippet: Detection of RT activity in cell lines infected with MLV of contaminated cell lines by PERT assay. Cell culture supernatants of the infected cell lines NCI-H82 and VERO-B4 were harvested after 45 and 44 days after infection, respectively. MS2 phage RNA was reverse transcribed with an MS2-specific primer and the MLV derived RT of the samples in the presence of MnCl 2 . The cDNA was then amplified with a second MS2-specific primer applying PCR. The signals of the cell lines infected with LCL-HO supernatant may potentially be ascribed to the activity of SMRV derived RT. dpi: days post infection.

    Techniques Used: Activity Assay, Infection, Cell Culture, Derivative Assay, Amplification, Polymerase Chain Reaction

    34) Product Images from "The complex evolution of the HSP70 gene family"

    Article Title: The complex evolution of the HSP70 gene family

    Journal: bioRxiv

    doi: 10.1101/2020.09.21.307264

    Semi-quantitative reverse transcription-PCR B. plicatilis HSP70 genes. A representative result is shown out of three independent experiments. (A) Location of primers rHSP70_gapF and rHSP70_gapR that amplify cDNA fragment of 112 and 124 bp from HSP70-1 and HSP70-2 cDNAs, respectively. (B) Polyacrylamide gel electrophoresis patterns of the RT-PCR product. Cycle numbers within a linear range of PCR amplification were determined to be 24 to 28 cycles for both cDNAs by preliminary experiments on the basis of signal intensities of amplified products by RT-PCR. (C) Signal intensities of HSP70-1 and HSP70-2 genes standardized to those of β-actin.
    Figure Legend Snippet: Semi-quantitative reverse transcription-PCR B. plicatilis HSP70 genes. A representative result is shown out of three independent experiments. (A) Location of primers rHSP70_gapF and rHSP70_gapR that amplify cDNA fragment of 112 and 124 bp from HSP70-1 and HSP70-2 cDNAs, respectively. (B) Polyacrylamide gel electrophoresis patterns of the RT-PCR product. Cycle numbers within a linear range of PCR amplification were determined to be 24 to 28 cycles for both cDNAs by preliminary experiments on the basis of signal intensities of amplified products by RT-PCR. (C) Signal intensities of HSP70-1 and HSP70-2 genes standardized to those of β-actin.

    Techniques Used: Polymerase Chain Reaction, Polyacrylamide Gel Electrophoresis, Reverse Transcription Polymerase Chain Reaction, Amplification

    35) Product Images from "Development of a DNA Microarray for Molecular Identification of All 46 Salmonella O Serogroups"

    Article Title: Development of a DNA Microarray for Molecular Identification of All 46 Salmonella O Serogroups

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.00225-13

    Agarose gel electrophoresis of multiplex PCR products for all 46 Salmonella serogroups. (a) Group A. Lanes 1 and 16, DL2000 DNA markers; lanes 2 to 15, DNA templates from Salmonella serogroups F, G, H, I, J, K, L, M, S, R, Q, P, O, and N, respectively. (b) Group B. Lanes 1 and 15, DL2000 DNA markers; lanes 2 to 14, DNA templates from Salmonella serogroups O57, O55, O54, O53, O52, O51, Z, Y, X, W, V, U, and T, respectively. (c) Group C. Lane 9, DL2000 DNA marker; lanes 1 to 8, DNA templates from Salmonella serogroups O66, O65, O63, O62, O61, O60, O59, and O58, respectively. (d) Group D. Lane 1, DL2000 DNA marker; lanes 2 to 9, DNA templates from Salmonella serogroups A, D1, D3, D2, B, O67, E1, and E4. (e) Group E. Lane 1, DL2000 DNA marker; lanes 2 to 6, the DNA templates from Salmonella serogroups C1, E1, E4, O56, and C2.
    Figure Legend Snippet: Agarose gel electrophoresis of multiplex PCR products for all 46 Salmonella serogroups. (a) Group A. Lanes 1 and 16, DL2000 DNA markers; lanes 2 to 15, DNA templates from Salmonella serogroups F, G, H, I, J, K, L, M, S, R, Q, P, O, and N, respectively. (b) Group B. Lanes 1 and 15, DL2000 DNA markers; lanes 2 to 14, DNA templates from Salmonella serogroups O57, O55, O54, O53, O52, O51, Z, Y, X, W, V, U, and T, respectively. (c) Group C. Lane 9, DL2000 DNA marker; lanes 1 to 8, DNA templates from Salmonella serogroups O66, O65, O63, O62, O61, O60, O59, and O58, respectively. (d) Group D. Lane 1, DL2000 DNA marker; lanes 2 to 9, DNA templates from Salmonella serogroups A, D1, D3, D2, B, O67, E1, and E4. (e) Group E. Lane 1, DL2000 DNA marker; lanes 2 to 6, the DNA templates from Salmonella serogroups C1, E1, E4, O56, and C2.

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

    36) Product Images from "Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis"

    Article Title: Human defects in STAT3 promote oral mucosal fungal and bacterial dysbiosis

    Journal: JCI Insight

    doi: 10.1172/jci.insight.122061

    Increase in oral streptococci and dental caries susceptibility in AD-HIES. ( A ) Differentially represented bacterial genera in actively infected (A_HIES, n = 9 for tongue and n = 8 for buccal samples) and uninfected (U_HIES, n = 9 for tongue and buccal samples) patients with AD-HIES, determined via LEfSe analysis. ( B ) Real-time PCR quantitation of the genus Streptococcus in tongue and buccal surfaces of HC and AD-HIES patients. The number of samples included in the tongue panel were HC n = 15, U_HIES n = 8, and A_HIES n = 8; for the buccal panel, number of samples were HC n = 15, U_HIES n = 7, and A_HIES n = 8. Streptococcus biomass values are expressed as log 10 of 16S rRNA gene copy number. * P
    Figure Legend Snippet: Increase in oral streptococci and dental caries susceptibility in AD-HIES. ( A ) Differentially represented bacterial genera in actively infected (A_HIES, n = 9 for tongue and n = 8 for buccal samples) and uninfected (U_HIES, n = 9 for tongue and buccal samples) patients with AD-HIES, determined via LEfSe analysis. ( B ) Real-time PCR quantitation of the genus Streptococcus in tongue and buccal surfaces of HC and AD-HIES patients. The number of samples included in the tongue panel were HC n = 15, U_HIES n = 8, and A_HIES n = 8; for the buccal panel, number of samples were HC n = 15, U_HIES n = 7, and A_HIES n = 8. Streptococcus biomass values are expressed as log 10 of 16S rRNA gene copy number. * P

    Techniques Used: Infection, Real-time Polymerase Chain Reaction, Quantitation Assay

    37) Product Images from "Sensitive Enzyme Immunoassay for Hepatitis B Virus Core-Related Antigens and Their Correlation to Virus Load"

    Article Title: Sensitive Enzyme Immunoassay for Hepatitis B Virus Core-Related Antigens and Their Correlation to Virus Load

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.2.439-445.2002

    Correlation between concentrations of HBcrAg and HBV-DNA in serum of hepatitis B patients. ⧫, HBeAg positive; ◊, anti-HBe positive; ▪, HBeAg and anti-HBe antibody negative. The HBV-DNA level was measured by TMA (detection limit, 3.7 to 8.7 LGE/ml) (A) or RTD-PCR (detection limit, 20 copies/ml) (B).
    Figure Legend Snippet: Correlation between concentrations of HBcrAg and HBV-DNA in serum of hepatitis B patients. ⧫, HBeAg positive; ◊, anti-HBe positive; ▪, HBeAg and anti-HBe antibody negative. The HBV-DNA level was measured by TMA (detection limit, 3.7 to 8.7 LGE/ml) (A) or RTD-PCR (detection limit, 20 copies/ml) (B).

    Techniques Used: Polymerase Chain Reaction

    HBcrAg and HBV-DNA patterns in seroconversion panels. The data on HBsAg, HBeAg, and anti-HBs, anti-HBe, and anti-HBc antibodies were obtained from the supplier's data sheet. Closed symbols, positive; open symbols, under the cutoff. (A) BBI PHM935B panel. ▪ and □ HBcrAg [log(units/milliliter)]; ⧫ and ◊, HBV-DNA detected by the Roche Amplicor HBV Monitor test (detection limit, 4 × 10 2 to 4 × 10 7 copies/ml); ▴ and ▵, in-house RTD-PCR (detection limit 20 copies/ml). (B) BCP HBV6281 panel. ▪ and □, HBcrAg [log (units/milliliter)]; ⧫ and ◊, HBV-DNA detected by BCP PCR (detection limit, 10 2 copies/ml).
    Figure Legend Snippet: HBcrAg and HBV-DNA patterns in seroconversion panels. The data on HBsAg, HBeAg, and anti-HBs, anti-HBe, and anti-HBc antibodies were obtained from the supplier's data sheet. Closed symbols, positive; open symbols, under the cutoff. (A) BBI PHM935B panel. ▪ and □ HBcrAg [log(units/milliliter)]; ⧫ and ◊, HBV-DNA detected by the Roche Amplicor HBV Monitor test (detection limit, 4 × 10 2 to 4 × 10 7 copies/ml); ▴ and ▵, in-house RTD-PCR (detection limit 20 copies/ml). (B) BCP HBV6281 panel. ▪ and □, HBcrAg [log (units/milliliter)]; ⧫ and ◊, HBV-DNA detected by BCP PCR (detection limit, 10 2 copies/ml).

    Techniques Used: Polymerase Chain Reaction

    38) Product Images from "Production of biallelic CMP-Neu5Ac hydroxylase knock-out pigs"

    Article Title: Production of biallelic CMP-Neu5Ac hydroxylase knock-out pigs

    Journal: Scientific Reports

    doi: 10.1038/srep01981

    Comparison of homology length of donor DNA to induce HR in ZFN mediated gene targeting. (a) Construction of donor vectors with 5 different homology lengths. (b) Quantitative PCR analysis for detection of ZFN/donor DNA mediated targeted cells. For donor DNA construct and PCR primer sets, see the Method. For PCR analysis of ZFN-assisted homologous recombination events, w e used the same methods for screening and analysis of knockout colony using Neo A and CMAH B primers located outside of the recombination region ( Supplementary table 1 ).
    Figure Legend Snippet: Comparison of homology length of donor DNA to induce HR in ZFN mediated gene targeting. (a) Construction of donor vectors with 5 different homology lengths. (b) Quantitative PCR analysis for detection of ZFN/donor DNA mediated targeted cells. For donor DNA construct and PCR primer sets, see the Method. For PCR analysis of ZFN-assisted homologous recombination events, w e used the same methods for screening and analysis of knockout colony using Neo A and CMAH B primers located outside of the recombination region ( Supplementary table 1 ).

    Techniques Used: Real-time Polymerase Chain Reaction, Construct, Polymerase Chain Reaction, Homologous Recombination, Knock-Out

    Selection of CMAH targeted cells using a selection-independent and -dependent zinc finger nucleases. ( a) Design of the donor DNA and primers used for this study. The locations of primers used for genotyping are shown in the figure. (b) SNP heterozygosity of the ZFN binding site on the CMAH gene. Sequencing PCR products include the ZFN cutting site show that there is a SNP within the ZFN binding site (arrow). Female show complete mismatch compared to the reference sequence of pig CMAH (NC_010449). The position of the DNA nucleotide mutation is indicated by the red box. (c) Screening of KO events by PCR. 1.2 kb PCR product using primers of Neo 3-1 and ScAS3 indicates a KO event. PCR products (1.2 kb) indicate the amplification of right HR junction using Neo3-1 and ScAS3 primer. M, size marker (λ/HindIII and 1 kb ladder); P, positive control; N, negative control; Number, G418-resistant colonies. (d) Mutagenesis generated by ZFN. Sequencing PCR products includes ZFN cutting site show that ZFN alone could generate mutations adjacent to ZFN cutting sites. An insertion of adenosine on the left side of the ZFN cutting site was observed. (e) Predicted amino acid sequence of CMAH from disrupted allele in KO pigs by NHEJ. Premature stop codon (*) is generated by NHEJ and series of amino acid sequence before the stop codon does not code for any known protein. Red letters indicate newly generated amino acids due to the frame shift.
    Figure Legend Snippet: Selection of CMAH targeted cells using a selection-independent and -dependent zinc finger nucleases. ( a) Design of the donor DNA and primers used for this study. The locations of primers used for genotyping are shown in the figure. (b) SNP heterozygosity of the ZFN binding site on the CMAH gene. Sequencing PCR products include the ZFN cutting site show that there is a SNP within the ZFN binding site (arrow). Female show complete mismatch compared to the reference sequence of pig CMAH (NC_010449). The position of the DNA nucleotide mutation is indicated by the red box. (c) Screening of KO events by PCR. 1.2 kb PCR product using primers of Neo 3-1 and ScAS3 indicates a KO event. PCR products (1.2 kb) indicate the amplification of right HR junction using Neo3-1 and ScAS3 primer. M, size marker (λ/HindIII and 1 kb ladder); P, positive control; N, negative control; Number, G418-resistant colonies. (d) Mutagenesis generated by ZFN. Sequencing PCR products includes ZFN cutting site show that ZFN alone could generate mutations adjacent to ZFN cutting sites. An insertion of adenosine on the left side of the ZFN cutting site was observed. (e) Predicted amino acid sequence of CMAH from disrupted allele in KO pigs by NHEJ. Premature stop codon (*) is generated by NHEJ and series of amino acid sequence before the stop codon does not code for any known protein. Red letters indicate newly generated amino acids due to the frame shift.

    Techniques Used: Selection, Zinc-Fingers, Binding Assay, Sequencing, Polymerase Chain Reaction, Mutagenesis, Amplification, Marker, Positive Control, Negative Control, Generated, Non-Homologous End Joining

    (a) Images of CMAH KO pigs. (b) Genotyping of CMAH KO pigs. For genotyping, three different PCRs were run to verify KO events. Right indicates the amplification of right HR junction using Neo3-1 and ScAS3 primers. Left shows the amplification of left HR junction (1.2 kb for endogenous and 3.2 kb for KO by HR). Long is the the amplification of entire HR junction (1.8 kb for endogenous and 3.7 kb for KO by HR). PCR products from biallelic KO pigs suggest that one allele has 1 bp insertion through complete HR and the other allele has an insertion of 500 bp on the locus: lane 1 and 3: pigs from female D1 (biallelic KO); lane 2: a pig from B2 (heterozygous); lane 4: negative control. HR (red arrow), NHEZ (white arrow), and Endo (green arrow) indicate amplified DNA by homologous recombination, non-homologous end joints, and endogenous DNA, respectively. (c) PCR amplification of FokI domain from genemic DNAs of CMAH KO pigs [41-1 and 47-1 are DNAs from male and female pigs shown in (a)]. HPRT gene was used as an internal control. (d) Upper) Cel-I digest of heteroduplex DNA revealed no additional off-target mutations at the 8 loci with highest homology to CMAH; lane 1, AGAP1; 2, TRPM7; 3, NJEJ1; 4, TLK2; 5, TMOD2; 6, ESR1; 7, AKAP13; 8, NME2, SM, size marker. Bottom) Genes, gene IDS, and sequence homologies of CMAH related sequence to exclude off-target mutations. Upper case: ZFN binding sites; lower case; ZFN cut site; homolog base pairs in red. SM indicates size markers. (e) Western blot analysis: expression of CMAH gene in the fibroblast cells from wild type, CMAH monoallelic (MKO) and biallelic (BKO) mutant minature pigs; Actin was used as a housekeeping protein. (f) Comparison of Neu5Ac and Neu5Gc contents between control and KO pigs. The Neu5Gc content was determined based on the signal intensities (peak areas from Supplementary Fig. 2 ) of each 1,2-diamino-4, 5-methylenedioxybenzene (DMB) fluorescence–labeled Neu5Gc and Neu5Ac. Each value is the mean ± SD of triplicate determinations and was confirmed by t-test.
    Figure Legend Snippet: (a) Images of CMAH KO pigs. (b) Genotyping of CMAH KO pigs. For genotyping, three different PCRs were run to verify KO events. Right indicates the amplification of right HR junction using Neo3-1 and ScAS3 primers. Left shows the amplification of left HR junction (1.2 kb for endogenous and 3.2 kb for KO by HR). Long is the the amplification of entire HR junction (1.8 kb for endogenous and 3.7 kb for KO by HR). PCR products from biallelic KO pigs suggest that one allele has 1 bp insertion through complete HR and the other allele has an insertion of 500 bp on the locus: lane 1 and 3: pigs from female D1 (biallelic KO); lane 2: a pig from B2 (heterozygous); lane 4: negative control. HR (red arrow), NHEZ (white arrow), and Endo (green arrow) indicate amplified DNA by homologous recombination, non-homologous end joints, and endogenous DNA, respectively. (c) PCR amplification of FokI domain from genemic DNAs of CMAH KO pigs [41-1 and 47-1 are DNAs from male and female pigs shown in (a)]. HPRT gene was used as an internal control. (d) Upper) Cel-I digest of heteroduplex DNA revealed no additional off-target mutations at the 8 loci with highest homology to CMAH; lane 1, AGAP1; 2, TRPM7; 3, NJEJ1; 4, TLK2; 5, TMOD2; 6, ESR1; 7, AKAP13; 8, NME2, SM, size marker. Bottom) Genes, gene IDS, and sequence homologies of CMAH related sequence to exclude off-target mutations. Upper case: ZFN binding sites; lower case; ZFN cut site; homolog base pairs in red. SM indicates size markers. (e) Western blot analysis: expression of CMAH gene in the fibroblast cells from wild type, CMAH monoallelic (MKO) and biallelic (BKO) mutant minature pigs; Actin was used as a housekeeping protein. (f) Comparison of Neu5Ac and Neu5Gc contents between control and KO pigs. The Neu5Gc content was determined based on the signal intensities (peak areas from Supplementary Fig. 2 ) of each 1,2-diamino-4, 5-methylenedioxybenzene (DMB) fluorescence–labeled Neu5Gc and Neu5Ac. Each value is the mean ± SD of triplicate determinations and was confirmed by t-test.

    Techniques Used: Amplification, Polymerase Chain Reaction, Negative Control, Homologous Recombination, Marker, Sequencing, Binding Assay, Western Blot, Expressing, Mutagenesis, Fluorescence, Labeling

    Sialyltransferase gene expression levels in control, monoallelic, and biallelic CMAH KO pigs. (a) Electrophoretic analysis of RT-PCR from control, monoallelic, and biallelic CMAH KO pig-derived fibroblast cells. (b) Comparison of sialyltransferase gene expression in control-, monoallelic-, and biallelic-derived pig fibroblast cells by real-time RT-PCR. (c) Quantification of real-time RT-PCR analysis in control-, monoallelic-, and biallelic-pig fibroblast cells. All RT-PCR reactions were conducted in triplicate and normalized with pig actin mRNA. Each of monoallelic- and biallelic-pig relative values is presented as an n-fold expression difference compared to the control pig, which was set as 1. *P
    Figure Legend Snippet: Sialyltransferase gene expression levels in control, monoallelic, and biallelic CMAH KO pigs. (a) Electrophoretic analysis of RT-PCR from control, monoallelic, and biallelic CMAH KO pig-derived fibroblast cells. (b) Comparison of sialyltransferase gene expression in control-, monoallelic-, and biallelic-derived pig fibroblast cells by real-time RT-PCR. (c) Quantification of real-time RT-PCR analysis in control-, monoallelic-, and biallelic-pig fibroblast cells. All RT-PCR reactions were conducted in triplicate and normalized with pig actin mRNA. Each of monoallelic- and biallelic-pig relative values is presented as an n-fold expression difference compared to the control pig, which was set as 1. *P

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Derivative Assay, Quantitative RT-PCR

    39) Product Images from "Use of the 2A Peptide for Generation of Multi-Transgenic Pigs through a Single Round of Nuclear Transfer"

    Article Title: Use of the 2A Peptide for Generation of Multi-Transgenic Pigs through a Single Round of Nuclear Transfer

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0019986

    Genotype identification of multi-transgenic piglets. (A) Positions of the two primer pairs for genotype identification. Genomic DNA from Piglet 2, 3, 4, 6, 7, 9, 10 was extracted, whereas ZC (B) and TG (C) bicistronic cassettes in the genome were detected by PCR using appropriate primers. Lane 1, DNA marker; lane 2, positive control; lane 3, negative control; lane 4–10, genomic DNA from Piglet 2, 3, 4, 6, 7, 9 and 10.
    Figure Legend Snippet: Genotype identification of multi-transgenic piglets. (A) Positions of the two primer pairs for genotype identification. Genomic DNA from Piglet 2, 3, 4, 6, 7, 9, 10 was extracted, whereas ZC (B) and TG (C) bicistronic cassettes in the genome were detected by PCR using appropriate primers. Lane 1, DNA marker; lane 2, positive control; lane 3, negative control; lane 4–10, genomic DNA from Piglet 2, 3, 4, 6, 7, 9 and 10.

    Techniques Used: Transgenic Assay, Polymerase Chain Reaction, Marker, Positive Control, Negative Control

    40) Product Images from "DNA Methylation Variation Trends during the Embryonic Development of Chicken"

    Article Title: DNA Methylation Variation Trends during the Embryonic Development of Chicken

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0159230

    DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) gene bodies in the muscles of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the muscle. (b) IGF2 detected in the muscle. (c) The methylation levels of the TNF-α and IGF2 gene bodies in the histogram.
    Figure Legend Snippet: DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) gene bodies in the muscles of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the muscle. (b) IGF2 detected in the muscle. (c) The methylation levels of the TNF-α and IGF2 gene bodies in the histogram.

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

    DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) gene bodies in the livers of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the liver. (b) IGF2 detected in the liver. (c) The methylation levels of the TNF-α and IGF2 gene bodies in the histogram.
    Figure Legend Snippet: DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) gene bodies in the livers of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the liver. (b) IGF2 detected in the liver. (c) The methylation levels of the TNF-α and IGF2 gene bodies in the histogram.

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

    DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) promoters in the muscles and livers of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the muscle. (b) TNF-α detected in the liver. (d) IGF2 detected in the muscle. (e) IGF2 detected in the liver. (c) and (f) The methylation levels of the TNF-α and IGF2 promoter regions in the histogram. The data are presented as the means with their standard errors (n = 6). Bars with different letters differed significantly ( P
    Figure Legend Snippet: DNA methylation patterns of the tumer necrosis factor-alpha ( TNF-α ) and insulin-like growth factor 2 ( IGF2 ) promoters in the muscles and livers of broilers. The analytic method was the bisulfite sequencing polymerase chain reaction. Each line represents an individual bacterial clone, and each circle represents a single CpG dinucleotide. Open circles indicate unmethylated CpGs, and black circles indicate methylated CpGs. (a) TNF-α detected in the muscle. (b) TNF-α detected in the liver. (d) IGF2 detected in the muscle. (e) IGF2 detected in the liver. (c) and (f) The methylation levels of the TNF-α and IGF2 promoter regions in the histogram. The data are presented as the means with their standard errors (n = 6). Bars with different letters differed significantly ( P

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

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine
    Article Snippet: .. PCR was performed in a 50-μl reaction mixture containing template DNA, 0.2 μM concentrations of each primer, 0.2 mM concentrations of each deoxynucleoside triphosphate (dNTP), PCR buffer, and 1.25 U of ExTaq DNA polymerase (TaKaRa Bio, Inc., Shiga, Japan) using 30 amplification cycles of 30 s at 95°C, 30 s at 60°C, and 1 min at 72°C. .. PCR amplification of genes encoding various virulence factors (VFs; LT, STa, STb, EAST1, Stx1, Stx2, F4, F5, and F18) was performed as described by Vu-Khac et al. ( ).

    Article Title: Agrobacterium tumefaciens-Mediated Transformation of Valsa mali: An Efficient Tool for Random Insertion Mutagenesis
    Article Snippet: .. PCR reaction was carried out using 50 ng of total DNA, 4 μ M of primer, 0.2 mM of each dNTP, 10 × PCR buffer, and 1.5 units of Taq DNA polymerase (Takara Co. Ltd. Dalian, China). .. The PCR program was as follows: 94°C, 3 min; 94°C, 45 s; 61°C, 45 s; 72°C, 1 min for 35 cycles; 72°C, 5 min.

    Article Title: Generation and Immunity Testing of a Recombinant Adenovirus Expressing NcSRS2-NcGRA7 Fusion Protein of Bovine Neospora caninum
    Article Snippet: .. PCR amplification was performed in a 25 µl reaction system containing 1 µl of each primer (10 µM each), 2 µl of extracted DNA, 2.5 µl of 10× PCR buffer, 2 µl of dNTP (2.5 mM each), and 0.25 µl of TaKaRa (Dalian, China) Taq (5 U/µl). .. The reactions were performed in a thermal cycler (Eppendof, Hamburg, Germany) with the following program: 1 pre-denaturing cycle for 5 min at 94℃; 10 denaturing cycles for 30 sec at 94℃; annealing for 45 sec at 58℃; extension for 60 sec at 72℃; and extension for 7 min at 72℃.

    Article Title: Phylogenetic and Expression Analysis of RNA-binding Proteins with Triple RNA Recognition Motifs in Plants
    Article Snippet: .. Primary RACE PCR was set up with 1 μl of cDNA, 2.5 μl 10× PCR Buffer, 2 μl dNTP mix, 1.5 μl MgCl2 , 1 μl 3′RACE Outer Primer (10 μM 5′-gcgagcacagaattaa tacgact-3′), 1 μl 3′ RACE gene specific primer (10 μM 5′- atattacggaggctactctggtggag-3′ (FL) and 5′-gtggattagatgcatctgtc acggatg-3′, 1 μl Takara Taq, and nuclease free water to a total volume of 25 μl in a microfuge tube. .. PCR was performed using the following parameters: initial denaturation for 5 min at 94℃, followed by 30 cycles of amplification (94℃ 30 s, 63℃ 30 s, 72℃ 30 s), and final extension at 72℃ for 7 min. A secondary PCR for the splice variant was performed using 1 μl of primary PCR reaction.

    Article Title: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
    Article Snippet: .. The Touchdown PCR was performed in a Veriti96 PCR thermal cycler system (ABI, USA) using a 10 μl reaction containing 2 μl template DNA (10–70 ng totally), with mixed concentrations of 10 × PCR buffer, 20 μM dNTP, 10 mM of each forward and reverse primer, and 5U Taq polymerase (Takara, China). ..

    Article Title: Transmission of Bartonella henselae by Ixodes ricinus
    Article Snippet: .. The PCR cycle was identical for both amplification reactions: an initial denaturation step for 8 min at 94°C; 35 cycles of denaturation for 1 min at 94°C, annealing for 1 min at 54°C, and extension for 1 min at 72°C; and a final extension step at 72°C for 10 min. Each reaction was conducted in a total volume of 25 μL with 0.5 μmol/μL of each primer, 2.5 mmol/L of each dNTP, 2.5 μL of 10× PCR buffer, and 1 U of Taq DNA polymerase (Takara Biomedical Group, Shiga, Japan). ..

    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 ▿ †
    Article Snippet: .. The total volume of each PCR mix was 20 μl and contained 1 μl of DNA template, 2 μl 10× PCR buffer (TaKaRa), 0.4 μl of deoxynucleoside triphosphate (dNTP) mix (10 mM [each dNTP]), 0.2 μl of each primer (20 μM), and 1 unit of Taq DNA polymerase. .. The PCR temperature profile was 94°C for 4 min; 32 cycles of 94°C for 30 s, 55°C for 30 s, and 72°C for 1 min; and final extension at 72°C for 6 min. RT-PCR detection of transcripts of virus-related homologs in the Arabidopsis genome was performed using RevertAid.

    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). ..

    Amplification:

    Article Title: Lineage-Specific Distribution of Insertion Sequence Excision Enhancer in Enterotoxigenic Escherichia coli Isolated from Swine
    Article Snippet: .. PCR was performed in a 50-μl reaction mixture containing template DNA, 0.2 μM concentrations of each primer, 0.2 mM concentrations of each deoxynucleoside triphosphate (dNTP), PCR buffer, and 1.25 U of ExTaq DNA polymerase (TaKaRa Bio, Inc., Shiga, Japan) using 30 amplification cycles of 30 s at 95°C, 30 s at 60°C, and 1 min at 72°C. .. PCR amplification of genes encoding various virulence factors (VFs; LT, STa, STb, EAST1, Stx1, Stx2, F4, F5, and F18) was performed as described by Vu-Khac et al. ( ).

    Article Title: Generation and Immunity Testing of a Recombinant Adenovirus Expressing NcSRS2-NcGRA7 Fusion Protein of Bovine Neospora caninum
    Article Snippet: .. PCR amplification was performed in a 25 µl reaction system containing 1 µl of each primer (10 µM each), 2 µl of extracted DNA, 2.5 µl of 10× PCR buffer, 2 µl of dNTP (2.5 mM each), and 0.25 µl of TaKaRa (Dalian, China) Taq (5 U/µl). .. The reactions were performed in a thermal cycler (Eppendof, Hamburg, Germany) with the following program: 1 pre-denaturing cycle for 5 min at 94℃; 10 denaturing cycles for 30 sec at 94℃; annealing for 45 sec at 58℃; extension for 60 sec at 72℃; and extension for 7 min at 72℃.

    Article Title: Transmission of Bartonella henselae by Ixodes ricinus
    Article Snippet: .. The PCR cycle was identical for both amplification reactions: an initial denaturation step for 8 min at 94°C; 35 cycles of denaturation for 1 min at 94°C, annealing for 1 min at 54°C, and extension for 1 min at 72°C; and a final extension step at 72°C for 10 min. Each reaction was conducted in a total volume of 25 μL with 0.5 μmol/μL of each primer, 2.5 mmol/L of each dNTP, 2.5 μL of 10× PCR buffer, and 1 U of Taq DNA polymerase (Takara Biomedical Group, Shiga, Japan). ..

    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). ..

    Touchdown PCR:

    Article Title: The first set of universal nuclear protein-coding loci markers for avian phylogenetic and population genetic studies
    Article Snippet: .. The Touchdown PCR was performed in a Veriti96 PCR thermal cycler system (ABI, USA) using a 10 μl reaction containing 2 μl template DNA (10–70 ng totally), with mixed concentrations of 10 × PCR buffer, 20 μM dNTP, 10 mM of each forward and reverse primer, and 5U Taq polymerase (Takara, China). ..

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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 1844 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    TaKaRa rna pcr buffer
    Influence of OCT treatment on TLR2 and TLR4 mRNA expression in THP-1 and U937 cells. THP-1 and U937 cells were cultured in the presence or absence of OCT (0.1 μM/ml) for 3 days. Total <t>RNA</t> was extracted from the cells and analyzed for TLR2, TLR4, and GAPDH by <t>RT-PCR</t> (top). Densities of the bands of TLR2 and TLR4 mRNA shown at the top were analyzed with NIH Image and expressed as mRNA expression relative to that of GADPH mRNA as an internal standard. The results are representative of three different experiments.
    Rna Pcr Buffer, supplied by TaKaRa, used in various techniques. Bioz Stars score: 88/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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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

    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

    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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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).

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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).

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

    Techniques: 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.

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0043370

    Figure Lengend 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.

    Article Snippet: Characterization of Strains by Multiplex PCR Multiplex PCR for the characterization of vacA s1, vacA s2, vacA m1, vacA m2 and cagA was carried out in 25 µl volume containing 2.5 pmol of primers VAG-F and VAG-R, 25 pmol of primers VA1-F and VA1-R, 10 pmol of primers cag5c-F and cag3c-R, 0.25 mM of each deoxynucleoside triphosphate (Takara), 0.9 U of Taq DNA polymerase (Genei, Bangalore, India), and 1.5 mM of MgCl2 in standard PCR buffer (Takara).

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

    Influence of OCT treatment on TLR2 and TLR4 mRNA expression in THP-1 and U937 cells. THP-1 and U937 cells were cultured in the presence or absence of OCT (0.1 μM/ml) for 3 days. Total RNA was extracted from the cells and analyzed for TLR2, TLR4, and GAPDH by RT-PCR (top). Densities of the bands of TLR2 and TLR4 mRNA shown at the top were analyzed with NIH Image and expressed as mRNA expression relative to that of GADPH mRNA as an internal standard. The results are representative of three different experiments.

    Journal: Infection and Immunity

    Article Title: Synergistic Effect of Muramyldipeptide with Lipopolysaccharide or Lipoteichoic Acid To Induce Inflammatory Cytokines in Human Monocytic Cells in Culture

    doi: 10.1128/IAI.69.4.2045-2053.2001

    Figure Lengend Snippet: Influence of OCT treatment on TLR2 and TLR4 mRNA expression in THP-1 and U937 cells. THP-1 and U937 cells were cultured in the presence or absence of OCT (0.1 μM/ml) for 3 days. Total RNA was extracted from the cells and analyzed for TLR2, TLR4, and GAPDH by RT-PCR (top). Densities of the bands of TLR2 and TLR4 mRNA shown at the top were analyzed with NIH Image and expressed as mRNA expression relative to that of GADPH mRNA as an internal standard. The results are representative of three different experiments.

    Article Snippet: For cDNA preparation, 1.0 μg of RNA, 50 pmol of random primer, 5 mM MgCl2 , 2 μl of 10× RNA PCR buffer (Takara), 1.0 mM each deoxynucleoside triphosphate (Takara), 5 U of avian myeloblastosis virus RT XL, and 20 U of RNase inhibitor (Takara) were added to a total volume of 20 μl.

    Techniques: Expressing, Cell Culture, Reverse Transcription Polymerase Chain Reaction