diagnostic reindeer papillomavirus rtpv2 pcr  (Roche)


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    Structured Review

    Roche diagnostic reindeer papillomavirus rtpv2 pcr
    Genome organization and phylogenetic analysis of <t>RtPV2.</t> A. Genome organization of RtPV2 . The line indicates the complete genome with size indication. The boxes represent open reading frames encoding early (E) and late (L) proteins). B–C. Phylogenetic trees of the L1 ORF (B) and complete genome (C) nucleotide sequences of selected representative papillomaviruses were generated using MEGA5, with the Maximum Likelihood method with Kimura-2 parameter model and 1,000 bootstrap replicates. Significant bootstrap values are shown. The different <t>papillomavirus</t> genera are indicated. Human papillomavirus (HPV1, HPV4, HPV5, HPV32, HPV41), V01116, NC_001457, M17463, NC_001586, NC_001354;. Canis familiaris papillomavirus (CPV2, CPV3, CPV6), NC_006564, NC_008297, NC_013237; European elk papillomavirus (AaPV1), NC_001524; Sus scrofa papillomavirus (SsPV1), NC_011280; Francolinus leucoscepus papillomavirus 1 (FlPV1), NC_013117 ; Erinaceus europaeus papillomavirus 1 (EePV1), NC_011765; Equus caballus papillomavirus 1 (EcPV1), NC_003748; Equus caballus papillomavirus 2 (EcPV2), NC_012123; Felis domesticus papillomavirus 2 (FcaPV2), EU796884; Caretta caretta papillomavirus 1 (CcPV1), NC_011530; Bovine papillomavirus (BPV3, 4, 5, 6, 9, 10, 11, 12), NC_004197, . X05817, NC_004195, AJ620208, AB331650, AB331651, AB543507, JF834523; Fringilla coelebs papillomavirus (FcPV1), NC_004068; Mastomys natalensis papillomavirus (MnPV1), NC_001605; Cottontail rabbit papillomavirus (SfPV1), NC_001541; Ursus maritimus papillomavirus 1 (UmPV1), NC_010739; Capra hircus papillomavirus 1 (ChPV1), NC_008032; Phocoena spinipinnis papillomavirus (PsPV1), NC_003348; Hamster oral papillomavirus (MaPV1), E15111; Rousettus aegyptiacus papillomavirus 1 (RaPV1), NC_008298; Trichechus manatus papillomavirus 1 (TmPV1), NC_006563; Erethizon dorsatum papillomavirus 1 (EdPV1), NC_006951; Psittacus erithacus timneh papillomavirus (PePV1), NC_003973; Tursiops truncatus papillomavirus 1 (TtPV1), NC_011109; Odocoileus virginianus papillomavirus 1 (OvPV1), NC_001523; Rangifer tarandus papillomavirus (RtPV1, RtPV2), AF443292, KC810012.
    Diagnostic Reindeer Papillomavirus Rtpv2 Pcr, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1185 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer"

    Article Title: Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0069711

    Genome organization and phylogenetic analysis of RtPV2. A. Genome organization of RtPV2 . The line indicates the complete genome with size indication. The boxes represent open reading frames encoding early (E) and late (L) proteins). B–C. Phylogenetic trees of the L1 ORF (B) and complete genome (C) nucleotide sequences of selected representative papillomaviruses were generated using MEGA5, with the Maximum Likelihood method with Kimura-2 parameter model and 1,000 bootstrap replicates. Significant bootstrap values are shown. The different papillomavirus genera are indicated. Human papillomavirus (HPV1, HPV4, HPV5, HPV32, HPV41), V01116, NC_001457, M17463, NC_001586, NC_001354;. Canis familiaris papillomavirus (CPV2, CPV3, CPV6), NC_006564, NC_008297, NC_013237; European elk papillomavirus (AaPV1), NC_001524; Sus scrofa papillomavirus (SsPV1), NC_011280; Francolinus leucoscepus papillomavirus 1 (FlPV1), NC_013117 ; Erinaceus europaeus papillomavirus 1 (EePV1), NC_011765; Equus caballus papillomavirus 1 (EcPV1), NC_003748; Equus caballus papillomavirus 2 (EcPV2), NC_012123; Felis domesticus papillomavirus 2 (FcaPV2), EU796884; Caretta caretta papillomavirus 1 (CcPV1), NC_011530; Bovine papillomavirus (BPV3, 4, 5, 6, 9, 10, 11, 12), NC_004197, . X05817, NC_004195, AJ620208, AB331650, AB331651, AB543507, JF834523; Fringilla coelebs papillomavirus (FcPV1), NC_004068; Mastomys natalensis papillomavirus (MnPV1), NC_001605; Cottontail rabbit papillomavirus (SfPV1), NC_001541; Ursus maritimus papillomavirus 1 (UmPV1), NC_010739; Capra hircus papillomavirus 1 (ChPV1), NC_008032; Phocoena spinipinnis papillomavirus (PsPV1), NC_003348; Hamster oral papillomavirus (MaPV1), E15111; Rousettus aegyptiacus papillomavirus 1 (RaPV1), NC_008298; Trichechus manatus papillomavirus 1 (TmPV1), NC_006563; Erethizon dorsatum papillomavirus 1 (EdPV1), NC_006951; Psittacus erithacus timneh papillomavirus (PePV1), NC_003973; Tursiops truncatus papillomavirus 1 (TtPV1), NC_011109; Odocoileus virginianus papillomavirus 1 (OvPV1), NC_001523; Rangifer tarandus papillomavirus (RtPV1, RtPV2), AF443292, KC810012.
    Figure Legend Snippet: Genome organization and phylogenetic analysis of RtPV2. A. Genome organization of RtPV2 . The line indicates the complete genome with size indication. The boxes represent open reading frames encoding early (E) and late (L) proteins). B–C. Phylogenetic trees of the L1 ORF (B) and complete genome (C) nucleotide sequences of selected representative papillomaviruses were generated using MEGA5, with the Maximum Likelihood method with Kimura-2 parameter model and 1,000 bootstrap replicates. Significant bootstrap values are shown. The different papillomavirus genera are indicated. Human papillomavirus (HPV1, HPV4, HPV5, HPV32, HPV41), V01116, NC_001457, M17463, NC_001586, NC_001354;. Canis familiaris papillomavirus (CPV2, CPV3, CPV6), NC_006564, NC_008297, NC_013237; European elk papillomavirus (AaPV1), NC_001524; Sus scrofa papillomavirus (SsPV1), NC_011280; Francolinus leucoscepus papillomavirus 1 (FlPV1), NC_013117 ; Erinaceus europaeus papillomavirus 1 (EePV1), NC_011765; Equus caballus papillomavirus 1 (EcPV1), NC_003748; Equus caballus papillomavirus 2 (EcPV2), NC_012123; Felis domesticus papillomavirus 2 (FcaPV2), EU796884; Caretta caretta papillomavirus 1 (CcPV1), NC_011530; Bovine papillomavirus (BPV3, 4, 5, 6, 9, 10, 11, 12), NC_004197, . X05817, NC_004195, AJ620208, AB331650, AB331651, AB543507, JF834523; Fringilla coelebs papillomavirus (FcPV1), NC_004068; Mastomys natalensis papillomavirus (MnPV1), NC_001605; Cottontail rabbit papillomavirus (SfPV1), NC_001541; Ursus maritimus papillomavirus 1 (UmPV1), NC_010739; Capra hircus papillomavirus 1 (ChPV1), NC_008032; Phocoena spinipinnis papillomavirus (PsPV1), NC_003348; Hamster oral papillomavirus (MaPV1), E15111; Rousettus aegyptiacus papillomavirus 1 (RaPV1), NC_008298; Trichechus manatus papillomavirus 1 (TmPV1), NC_006563; Erethizon dorsatum papillomavirus 1 (EdPV1), NC_006951; Psittacus erithacus timneh papillomavirus (PePV1), NC_003973; Tursiops truncatus papillomavirus 1 (TtPV1), NC_011109; Odocoileus virginianus papillomavirus 1 (OvPV1), NC_001523; Rangifer tarandus papillomavirus (RtPV1, RtPV2), AF443292, KC810012.

    Techniques Used: Generated

    2) Product Images from "Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer"

    Article Title: Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0069711

    Phylogram of nucleotide sequence data for a ~400-bp genome fragment from cervid herpesvirus 3 (corresponding to nt 61499-61904 of human herpesvirus strain RK; GenBank AF037218) compared with data for the orthologous regions of selected representative mammalian herpesviruses. The phylogenetic tree was generated with MEGA5, with the neighbor joining method and the p-distance model. Bar, evolutionary distance of 0.05. Bootstrap values (1000 reiterations) are shown. The different herpesvirus genera are indicated. Human herpesvirus 5, NC_006273; Panine herpesvirus 2, AF480884; Aotine herpesvirus 1, FJ483970; Tupaia herpesvirus 2, AF281817; Murid herpesvirus 1, HE610456:. Caviid herpesvirus 2, AB592928; Human herpesvirus 6A, X83413; Human herpesvirus 6B, AF157706; Human herpesvirus 7, AF037218; Elephantid herpesvirus 1, AAF322977; Cervid herpesvirus 3, KC810014.
    Figure Legend Snippet: Phylogram of nucleotide sequence data for a ~400-bp genome fragment from cervid herpesvirus 3 (corresponding to nt 61499-61904 of human herpesvirus strain RK; GenBank AF037218) compared with data for the orthologous regions of selected representative mammalian herpesviruses. The phylogenetic tree was generated with MEGA5, with the neighbor joining method and the p-distance model. Bar, evolutionary distance of 0.05. Bootstrap values (1000 reiterations) are shown. The different herpesvirus genera are indicated. Human herpesvirus 5, NC_006273; Panine herpesvirus 2, AF480884; Aotine herpesvirus 1, FJ483970; Tupaia herpesvirus 2, AF281817; Murid herpesvirus 1, HE610456:. Caviid herpesvirus 2, AB592928; Human herpesvirus 6A, X83413; Human herpesvirus 6B, AF157706; Human herpesvirus 7, AF037218; Elephantid herpesvirus 1, AAF322977; Cervid herpesvirus 3, KC810014.

    Techniques Used: Sequencing, Generated

    3) Product Images from "Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR"

    Article Title: Detection of methylation in promoter sequences by melting curve analysis-based semiquantitative real time PCR

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-8-61

    MCA-MSP analysis in BLU and MGMT genes for the A172 and SIMA cell lines : The graphs show the unmethylated control peak (blood DNA) in red, the methylated control peak in green, the no template control in blue and the cell line peak, in brown. a) PCR for the unmethylated sequence, BLU gene, A172 cell line: only the blood DNA gives a peak, thus the cell line contains no unmethylated DNA. b) PCR for the methylated sequence, BLU gene, A172 cell line: the methylated DNA and the cell line give peak, thus the A172 cell line is methylated for the BLU gene. c) PCR for the unmethylated sequence, MGMT gene, SIMA cell line: the blood DNA and cell lines give peak, thus the cell line is unmethylated. d) PCR for the methylated sequence, MGMT gene, SIMA cell line: only the methylated DNA gives a peak, thus the cell line is not methylated.
    Figure Legend Snippet: MCA-MSP analysis in BLU and MGMT genes for the A172 and SIMA cell lines : The graphs show the unmethylated control peak (blood DNA) in red, the methylated control peak in green, the no template control in blue and the cell line peak, in brown. a) PCR for the unmethylated sequence, BLU gene, A172 cell line: only the blood DNA gives a peak, thus the cell line contains no unmethylated DNA. b) PCR for the methylated sequence, BLU gene, A172 cell line: the methylated DNA and the cell line give peak, thus the A172 cell line is methylated for the BLU gene. c) PCR for the unmethylated sequence, MGMT gene, SIMA cell line: the blood DNA and cell lines give peak, thus the cell line is unmethylated. d) PCR for the methylated sequence, MGMT gene, SIMA cell line: only the methylated DNA gives a peak, thus the cell line is not methylated.

    Techniques Used: Methylation, Polymerase Chain Reaction, Sequencing

    Hypermethylation analysis by bisulfite sequencing, MSP and MCA-Meth of MGMT gene in astrocytoma samples 26, 28 and in the U87MG cell line . a) Bisulfite sequencing results of the MGMT gene in astrocytoma samples 26 and 28 and in the U87MG cell line. Black squares indicate methylated CpG dinucleotides and white squares indicate unmethylated CpG dinucleotides in promoter sequences. Above the diagrams, the area of the promoter analyzed by MSP, MCA-Meth and bisulfite sequencing is indicated. The 5'- and 3'-priming sites of M- and U-primers are indicated as small black dots representing the CpG sites incorporated in the primer sequence. The position of CpGs in relation to the CpG-island as well as the number of CpGs analyzed are indicated in the brackets behind the respective techniques. On the right, the diagrams of peaks obtained with the sequencing software: it can be observed how after the bisulfite treatment, the cytosines remain unchanged in the methylated sample, while there is a shift to thymine in the unmethylated sample. b) MSP results of MGMT in astrocytoma samples 26, 28 and in the U87MG cell line. U: PCR with primers specific for the unmethylated sequence; M: PCR with primers specific for the methylated sequence. c) MCA-Meth results of MGMT in astrocytoma samples 26, 28 and in the U87MG cell line. The graphs show the unmethylated control peak (blood DNA) in red, the methylated control peak in green, the no template control in blue and the sample or cell line peak, in brown. It can be observed how in the case of the U87MG cell line, the amount of methylated cytosines in the area of the promoter analyzed by bisulfite sequencing is intermediate between the sample 26 (unmethylated) and sample 28 (fully methylated). Of note, MCA-Meth appreciates this inhomogeneous sequence methylation pattern of U87MG with a melting curve peak in an intermediate position as compared to the unmethylated (26) and the methylated sample (28).
    Figure Legend Snippet: Hypermethylation analysis by bisulfite sequencing, MSP and MCA-Meth of MGMT gene in astrocytoma samples 26, 28 and in the U87MG cell line . a) Bisulfite sequencing results of the MGMT gene in astrocytoma samples 26 and 28 and in the U87MG cell line. Black squares indicate methylated CpG dinucleotides and white squares indicate unmethylated CpG dinucleotides in promoter sequences. Above the diagrams, the area of the promoter analyzed by MSP, MCA-Meth and bisulfite sequencing is indicated. The 5'- and 3'-priming sites of M- and U-primers are indicated as small black dots representing the CpG sites incorporated in the primer sequence. The position of CpGs in relation to the CpG-island as well as the number of CpGs analyzed are indicated in the brackets behind the respective techniques. On the right, the diagrams of peaks obtained with the sequencing software: it can be observed how after the bisulfite treatment, the cytosines remain unchanged in the methylated sample, while there is a shift to thymine in the unmethylated sample. b) MSP results of MGMT in astrocytoma samples 26, 28 and in the U87MG cell line. U: PCR with primers specific for the unmethylated sequence; M: PCR with primers specific for the methylated sequence. c) MCA-Meth results of MGMT in astrocytoma samples 26, 28 and in the U87MG cell line. The graphs show the unmethylated control peak (blood DNA) in red, the methylated control peak in green, the no template control in blue and the sample or cell line peak, in brown. It can be observed how in the case of the U87MG cell line, the amount of methylated cytosines in the area of the promoter analyzed by bisulfite sequencing is intermediate between the sample 26 (unmethylated) and sample 28 (fully methylated). Of note, MCA-Meth appreciates this inhomogeneous sequence methylation pattern of U87MG with a melting curve peak in an intermediate position as compared to the unmethylated (26) and the methylated sample (28).

    Techniques Used: Methylation Sequencing, Methylation, Sequencing, Software, Polymerase Chain Reaction

    4) Product Images from "Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria"

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0007010

    Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.
    Figure Legend Snippet: Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.

    Techniques Used: Sequencing, Polymerase Chain Reaction

    Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”
    Figure Legend Snippet: Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”

    Techniques Used: Concentration Assay

    Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.
    Figure Legend Snippet: Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.

    Techniques Used:

    Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.
    Figure Legend Snippet: Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.

    Techniques Used:

    Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.
    Figure Legend Snippet: Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.

    Techniques Used: Labeling

    5) Product Images from "Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria"

    Article Title: Optimizing Taq Polymerase Concentration for Improved Signal-to-Noise in the Broad Range Detection of Low Abundance Bacteria

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0007010

    Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.
    Figure Legend Snippet: Sequences of contaminating bacterial DNA in three Taq polymerases. Sequence alignment of three contaminants from different commercial Taq polymerases showing the presence of different strains of the same Pseudomonas species. Roche FastStart, Platinum HiFi Platinum Taq polymerases contain similar strains of a Pseudomonas species with a single base difference in the region covered by the 16S350 PCR assay.

    Techniques Used: Sequencing, Polymerase Chain Reaction

    Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”
    Figure Legend Snippet: Approximating the copy number of 16S rDNA in commercial Taq polymerases. Six DNA polymerases were used with primers for 16S rDNA on 7 serial 10-fold dilutions of E. coli genomic DNA (10 ng to 10 fg) with no added DNA in the 8 th sample. The least squares fit equation for each dilution series was used to assign a value to the signal from the 8 th sample, which contains Taq-associated DNA only. The efficiency of the reaction was determined from the slope of the linear fit plotting the base10 log of the DNA concentration vs. the threshold cycle. A slope of −3.322 indicates an average doubling rate of “2,” which is approximately 100% efficiency (2̂3.322∼10). The rDNA values assigned are for “E. coli equivalents.”

    Techniques Used: Concentration Assay

    Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.
    Figure Legend Snippet: Detection of Pseudomonas fluorescens at high and low Taq polymerase concentrations. Bacterial detection with 0.5 Units (A) or 0.05 Units (B) Qiagen Taq DNA polymerase with 16S350B assay on samples containing 10 3 , 10 2 , 10 1 and zero Pseudomonas fluorescens bacteria. A composite of A and B is shown in C.

    Techniques Used:

    Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.
    Figure Legend Snippet: Detection of bacterial DNA in six Taq polymerases. Four dilutions of six DNA polymerase were tested with primers for 16S rDNA in the presence of 100 pg (∼10̂5 16S rDNA) E. coli genomic DNA (circled) or H 2 O.

    Techniques Used:

    Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.
    Figure Legend Snippet: Detection of the beta-lactamase gene in commercial Taq polymerase. Four dilutions of Amplitaq DNA polymerase were tested with primers for the beta-lactamase gene in the presence of 10 3 pUC19 plasmids (labeled 1000 pUC19 genomes) or H 2 O.

    Techniques Used: Labeling

    6) Product Images from "Toll-Like Receptor 4 Is Involved in Inflammatory and Joint Destructive Pathways in Collagen-Induced Arthritis in DBA1J Mice"

    Article Title: Toll-Like Receptor 4 Is Involved in Inflammatory and Joint Destructive Pathways in Collagen-Induced Arthritis in DBA1J Mice

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0023539

    Cytokines in sera and in vitro splenocyte cultures. Serum cytokine concentrations measured at days 34 (A) and 91 (B) in TLR4 negative and TLR4 positive groups of mice. Significantly higher IL-12p70, TNF alpha, MCP-1 and IL-10 concentrations in TLR4 negative groups of mice at day 34 after immunization, while at day 91 IL-12p40, TNF alpha and MCP-1 were higher in TLR4 positive mice. (C) Interleukin17 concentrations are reduced in TLR4 deficient in vitro spleen cell cultures after 48 hours in the presence of type II collagen (100 ug/ml) or anti-CD3 antibodies (1 ug/ml)(*p
    Figure Legend Snippet: Cytokines in sera and in vitro splenocyte cultures. Serum cytokine concentrations measured at days 34 (A) and 91 (B) in TLR4 negative and TLR4 positive groups of mice. Significantly higher IL-12p70, TNF alpha, MCP-1 and IL-10 concentrations in TLR4 negative groups of mice at day 34 after immunization, while at day 91 IL-12p40, TNF alpha and MCP-1 were higher in TLR4 positive mice. (C) Interleukin17 concentrations are reduced in TLR4 deficient in vitro spleen cell cultures after 48 hours in the presence of type II collagen (100 ug/ml) or anti-CD3 antibodies (1 ug/ml)(*p

    Techniques Used: In Vitro, Mouse Assay

    Incidence and severity of arthritis. Suppressed incidence (A) and severity (B) of collagen induced arthritis (incomplete Freund's adjuvant) in TLR4 defective DBA/1J (n = 17) compared to TLR4 pos/pos (n = 17) DBA1/J mice.
    Figure Legend Snippet: Incidence and severity of arthritis. Suppressed incidence (A) and severity (B) of collagen induced arthritis (incomplete Freund's adjuvant) in TLR4 defective DBA/1J (n = 17) compared to TLR4 pos/pos (n = 17) DBA1/J mice.

    Techniques Used: Mouse Assay

    Histological joint destruction in paw sections. Synovial inflammation is suppressed in CIA in DBA1J TLR4 negative mice (A, C) compared to wt mice (B, D). Representative front paw sections showing wrist and carpal joints and stained in H E, original magnification ×10 are shown in (A) and (B) and interphalangeal joints with extensive pannus formation and bone destruction stained with Nuclear Fast Rubine-Aniline Blue-Orange G in (C) and (D), original magnification ×100. Histological joint scores reflecting significantly suppressed inflammation and cartilage and bone destruction in TLR4 defective mice are shown in (E).
    Figure Legend Snippet: Histological joint destruction in paw sections. Synovial inflammation is suppressed in CIA in DBA1J TLR4 negative mice (A, C) compared to wt mice (B, D). Representative front paw sections showing wrist and carpal joints and stained in H E, original magnification ×10 are shown in (A) and (B) and interphalangeal joints with extensive pannus formation and bone destruction stained with Nuclear Fast Rubine-Aniline Blue-Orange G in (C) and (D), original magnification ×100. Histological joint scores reflecting significantly suppressed inflammation and cartilage and bone destruction in TLR4 defective mice are shown in (E).

    Techniques Used: Mouse Assay, Staining

    B and T cell responses. No significant difference in peripheral blood anti-collagen type II antibody concentrations of the IgG2a subclass at days 34 and 89 in TLR4 negative versus positive groups of mice (A). Anti-cyclic citrullinted peptide (CCP) antibody concentrations (anti-LXP) are significantly higher in TLR4 positive groups of mice at day 34 after immunization, while anti-non-citrullinated controle peptide antibody concentrations are comparable (B). T cell recall responses in TLR4 negative mice were significantly stronger than in wt mice at the lower tested antigen concentration (C). No influence on foxp3 positive Treg numbers was seen (D).
    Figure Legend Snippet: B and T cell responses. No significant difference in peripheral blood anti-collagen type II antibody concentrations of the IgG2a subclass at days 34 and 89 in TLR4 negative versus positive groups of mice (A). Anti-cyclic citrullinted peptide (CCP) antibody concentrations (anti-LXP) are significantly higher in TLR4 positive groups of mice at day 34 after immunization, while anti-non-citrullinated controle peptide antibody concentrations are comparable (B). T cell recall responses in TLR4 negative mice were significantly stronger than in wt mice at the lower tested antigen concentration (C). No influence on foxp3 positive Treg numbers was seen (D).

    Techniques Used: Mouse Assay, Concentration Assay

    7) Product Images from "A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5? UTR"

    Article Title: A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5? UTR

    Journal: Nucleic Acids Research

    doi:

    Delineation of the transcription initiation site. ( A ) The upper sequence (5′ UTR) corresponds to the HCV 5′ UTR sequence. The EGFP mRNA sequence corresponds to that obtained from capped mRNA transcripts derived from HCV 5′ UTR. Bold letters represent the RNA oligonucleotide used in the 5′ RACE method. The vertical arrowhead indicates the position of the initiation site for EGFP transcription. The horizontal arrow indicates the location (nucleotides 321–341) of the primer used for the reverse transcriptase reaction. ( B ) Position of the initiation site in the IRES structure proposed by Honda et al ).
    Figure Legend Snippet: Delineation of the transcription initiation site. ( A ) The upper sequence (5′ UTR) corresponds to the HCV 5′ UTR sequence. The EGFP mRNA sequence corresponds to that obtained from capped mRNA transcripts derived from HCV 5′ UTR. Bold letters represent the RNA oligonucleotide used in the 5′ RACE method. The vertical arrowhead indicates the position of the initiation site for EGFP transcription. The horizontal arrow indicates the location (nucleotides 321–341) of the primer used for the reverse transcriptase reaction. ( B ) Position of the initiation site in the IRES structure proposed by Honda et al ).

    Techniques Used: Sequencing, Derivative Assay

    8) Product Images from "Myofibroblast-Derived SFRP1 as Potential Inhibitor of Colorectal Carcinoma Field Effect"

    Article Title: Myofibroblast-Derived SFRP1 as Potential Inhibitor of Colorectal Carcinoma Field Effect

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0106143

    Promoter hypermethylation of SFRP1 gene in BS-PCR HRM. SFRP1 is hypermethylated in α-SMA positive myofibroblasts in CRC. A: Melting peaks of SFRP1 BS-PCR products. Melting temperature (Tm) of 0% methylated standard sample was 77.1°C, while Tm of 100% methylated standard was 79.6°C. B: There was only one unmethylated melting peak detectable for NAT samples (green curves). In CRC samples (red curves) an additional melting peak belonging to hypermethylated products appeared, suggesting that α-SMA positive myofibroblasts are heterogenous concerning SFRP1 promoter methylation.
    Figure Legend Snippet: Promoter hypermethylation of SFRP1 gene in BS-PCR HRM. SFRP1 is hypermethylated in α-SMA positive myofibroblasts in CRC. A: Melting peaks of SFRP1 BS-PCR products. Melting temperature (Tm) of 0% methylated standard sample was 77.1°C, while Tm of 100% methylated standard was 79.6°C. B: There was only one unmethylated melting peak detectable for NAT samples (green curves). In CRC samples (red curves) an additional melting peak belonging to hypermethylated products appeared, suggesting that α-SMA positive myofibroblasts are heterogenous concerning SFRP1 promoter methylation.

    Techniques Used: Polymerase Chain Reaction, Methylation

    9) Product Images from "Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi"

    Article Title: Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi

    Journal: BMC Microbiology

    doi: 10.1186/1471-2180-9-90

    Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.
    Figure Legend Snippet: Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.

    Techniques Used: Mass Spectrometry, Construct, Polymerase Chain Reaction, Clone Assay, Southern Blot, Labeling

    Disruption of dhfr-ts using a conventional KO construct pBSdh1f8Neo . A) Diagram of the expected genomic loci of dhfr-ts and 1f8Neo in dhfr-ts +/- / Neo parasites. B) PCR analysis with Neo specific primers of WT Tulahuen and both uncloned and selected clones of dhfr-ts +/- / Neo parasites. C) PCR analysis with gDNA from selected clones of dhfr-ts +/- / Neo and WT Tulahuen parasites confirming the expected gene disruption of one allele of the dhfr-ts gene by 1f8Neo . D) Southern Blot analysis of WT Tulahuen and two dhfr-ts +/- / Neo clones digested with SalI and probed with dhfr-ts probe. Diagram not to scale. Numbers are sizes (bp) of expected products.
    Figure Legend Snippet: Disruption of dhfr-ts using a conventional KO construct pBSdh1f8Neo . A) Diagram of the expected genomic loci of dhfr-ts and 1f8Neo in dhfr-ts +/- / Neo parasites. B) PCR analysis with Neo specific primers of WT Tulahuen and both uncloned and selected clones of dhfr-ts +/- / Neo parasites. C) PCR analysis with gDNA from selected clones of dhfr-ts +/- / Neo and WT Tulahuen parasites confirming the expected gene disruption of one allele of the dhfr-ts gene by 1f8Neo . D) Southern Blot analysis of WT Tulahuen and two dhfr-ts +/- / Neo clones digested with SalI and probed with dhfr-ts probe. Diagram not to scale. Numbers are sizes (bp) of expected products.

    Techniques Used: Construct, Polymerase Chain Reaction, Clone Assay, Southern Blot

    10) Product Images from "Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor"

    Article Title: Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor

    Journal:

    doi: 10.1182/blood-2008-03-141424

    Expression of RXR-α and RXR-β subunits before therapy and after relapse of disease. Western blot analysis of protein extracts from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy revealed marked down-regulation
    Figure Legend Snippet: Expression of RXR-α and RXR-β subunits before therapy and after relapse of disease. Western blot analysis of protein extracts from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy revealed marked down-regulation

    Techniques Used: Expressing, Western Blot

    11) Product Images from "Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor"

    Article Title: Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor

    Journal:

    doi: 10.1182/blood-2008-03-141424

    Transcription of RXR-α mRNA before therapy and after relapse of disease. Real-time PCR of RXR-α was performed from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy. No change in the relative mean fold
    Figure Legend Snippet: Transcription of RXR-α mRNA before therapy and after relapse of disease. Real-time PCR of RXR-α was performed from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy. No change in the relative mean fold

    Techniques Used: Real-time Polymerase Chain Reaction

    12) Product Images from "Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis"

    Article Title: Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0070942

    Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.
    Figure Legend Snippet: Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.

    Techniques Used: Real-time Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Serial Dilution, Plasmid Preparation, Negative Control

    13) Product Images from "Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi"

    Article Title: Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi

    Journal: BMC Microbiology

    doi: 10.1186/1471-2180-9-90

    Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.
    Figure Legend Snippet: Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.

    Techniques Used: Mass Spectrometry, Construct, Polymerase Chain Reaction, Clone Assay, Southern Blot, Labeling

    Timeline for constructing a KO plasmids using MS/GW strategy . The Multisite Gateway based method consists of three steps: 1) PCR with attB-containing primers to amplify 5' and 3' UTR from genomic DNA; 2) BP recombination of each PCR products with specific donor vectors to generate entry clones containing the UTRs; 3) LR recombination of the two entry clones made in step 2 and a third entry clone containing Neo/Hyg to create the final construct. (Kan, kanamycin-resistance gene; Amp, ampicillin-resistance gene; Ori, Origin of replication).
    Figure Legend Snippet: Timeline for constructing a KO plasmids using MS/GW strategy . The Multisite Gateway based method consists of three steps: 1) PCR with attB-containing primers to amplify 5' and 3' UTR from genomic DNA; 2) BP recombination of each PCR products with specific donor vectors to generate entry clones containing the UTRs; 3) LR recombination of the two entry clones made in step 2 and a third entry clone containing Neo/Hyg to create the final construct. (Kan, kanamycin-resistance gene; Amp, ampicillin-resistance gene; Ori, Origin of replication).

    Techniques Used: Mass Spectrometry, Polymerase Chain Reaction, Clone Assay, Construct

    14) Product Images from "Sensitive HPV detection in oropharyngeal cancers"

    Article Title: Sensitive HPV detection in oropharyngeal cancers

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-9-440

    Methodological flowchart of DNA analyses performed . DNA extracted from clinical samples was subjected to both Linear Array and PGMY09/11 PCR analysis. In the event of a positive Linear Array result, the HPV subtype was known immediately. In the case of a positive PGMY result, direct sequencing (using the GP5+ internal primer) enabled the subtype present to be determined. In the case of a PGMY negative result, a further nested PCR amplification step was performed using the GP5+/GP6+ primer set. Subsequent positive results were then directly sequenced using the GP5+ primer alone. Samples negative for both Linear Array and nested PCR were classified as free from infection.
    Figure Legend Snippet: Methodological flowchart of DNA analyses performed . DNA extracted from clinical samples was subjected to both Linear Array and PGMY09/11 PCR analysis. In the event of a positive Linear Array result, the HPV subtype was known immediately. In the case of a positive PGMY result, direct sequencing (using the GP5+ internal primer) enabled the subtype present to be determined. In the case of a PGMY negative result, a further nested PCR amplification step was performed using the GP5+/GP6+ primer set. Subsequent positive results were then directly sequenced using the GP5+ primer alone. Samples negative for both Linear Array and nested PCR were classified as free from infection.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Nested PCR, Amplification, Infection

    15) Product Images from "Characterisation of microbial communities within aggressive prostate cancer tissues"

    Article Title: Characterisation of microbial communities within aggressive prostate cancer tissues

    Journal: Infectious Agents and Cancer

    doi: 10.1186/s13027-016-0112-7

    Taxa summary of ‘core’ OTUs identified in 95% of samples ( n = 20) that underwent sequencing of the V2-V3 region of the 16S rRNA gene. The figure depicts the relative contribution of each member of the ‘core’ community to each sample in addition to its overall contribution to the core community over all samples combined. The contribution of taxa to the core community is expressed as a percentage. The letter A next to the patient ID denotes “adjacent” tissue and M denotes “malignant” tissue. The letters in the taxonomy column refer to k – kingdom, p – phylum, c –class, o –order, f – family, g – genus, s – species
    Figure Legend Snippet: Taxa summary of ‘core’ OTUs identified in 95% of samples ( n = 20) that underwent sequencing of the V2-V3 region of the 16S rRNA gene. The figure depicts the relative contribution of each member of the ‘core’ community to each sample in addition to its overall contribution to the core community over all samples combined. The contribution of taxa to the core community is expressed as a percentage. The letter A next to the patient ID denotes “adjacent” tissue and M denotes “malignant” tissue. The letters in the taxonomy column refer to k – kingdom, p – phylum, c –class, o –order, f – family, g – genus, s – species

    Techniques Used: Sequencing

    Taxa summary of ‘core’ OTUs identified in 95% of samples ( n = 20) that underwent sequencing of the V4 hypervariable region of the 16S rRNA gene. The figure depicts the relative contribution of each member of the ‘core’ community to each sample in addition to its overall contribution to the core community over all samples combined. The contribution of taxa to the core community is expressed as a percentage. The letter A next to the patient ID denotes “adjacent” tissue and M denotes “malignant” tissue. The letters in the taxonomy column refer to k – kingdom, p – phylum, c –class, o –order, f – family, g – genus, s – species
    Figure Legend Snippet: Taxa summary of ‘core’ OTUs identified in 95% of samples ( n = 20) that underwent sequencing of the V4 hypervariable region of the 16S rRNA gene. The figure depicts the relative contribution of each member of the ‘core’ community to each sample in addition to its overall contribution to the core community over all samples combined. The contribution of taxa to the core community is expressed as a percentage. The letter A next to the patient ID denotes “adjacent” tissue and M denotes “malignant” tissue. The letters in the taxonomy column refer to k – kingdom, p – phylum, c –class, o –order, f – family, g – genus, s – species

    Techniques Used: Sequencing

    16) Product Images from "Frequent detection of human polyomavirus 6 in keratoacanthomas"

    Article Title: Frequent detection of human polyomavirus 6 in keratoacanthomas

    Journal: Diagnostic Pathology

    doi: 10.1186/s13000-016-0509-z

    Photomicrographs of a representative example of the presence of HPyV6 detected by FISH in a keratoacanthoma: a DNA sequence nuclear hybridization signals in the keratinocytes of the lesion (red), located mainly in the middle and upper epidermis (scale bar 30 μm). b HE staining of keratoacanthoma used for HPyV6 FISH. c DNA sequence nuclear hybridization signals with dot-like specific positivity in the keratin layer of the lesion (red) (scale bar 30 μm). d overlay DAPI staining of nuclei of keratinocytes (blue) of the area of the lesion shown in C, showing no nuclei in the keratin layer with the positive FISH signals
    Figure Legend Snippet: Photomicrographs of a representative example of the presence of HPyV6 detected by FISH in a keratoacanthoma: a DNA sequence nuclear hybridization signals in the keratinocytes of the lesion (red), located mainly in the middle and upper epidermis (scale bar 30 μm). b HE staining of keratoacanthoma used for HPyV6 FISH. c DNA sequence nuclear hybridization signals with dot-like specific positivity in the keratin layer of the lesion (red) (scale bar 30 μm). d overlay DAPI staining of nuclei of keratinocytes (blue) of the area of the lesion shown in C, showing no nuclei in the keratin layer with the positive FISH signals

    Techniques Used: Fluorescence In Situ Hybridization, Sequencing, Hybridization, Staining

    Photomicrographs of a representative example of HPyV6 detected by FISH in BCC: a Nuclear HPyV6 DNA hybridization signals in the epithelial tumor cells of a BCC (red), DAPI staining the nuclei (scale bar 30 μm). b Magnification of the marked quadrangular area in a . c HE staining of BCC used for HPyV6 FISH detection (scale bar 30 μm)
    Figure Legend Snippet: Photomicrographs of a representative example of HPyV6 detected by FISH in BCC: a Nuclear HPyV6 DNA hybridization signals in the epithelial tumor cells of a BCC (red), DAPI staining the nuclei (scale bar 30 μm). b Magnification of the marked quadrangular area in a . c HE staining of BCC used for HPyV6 FISH detection (scale bar 30 μm)

    Techniques Used: Fluorescence In Situ Hybridization, DNA Hybridization, Staining

    2 % agarose gel showing the specimen control size (SCS) ladder HPyV6 DNA-PCR and SCS ladder for keratoacanthoma (KA), results HPyV6 DNA-PCR: a reveals adequate DNA quality of KA in order to proceed with HPyV6 testing. b HPyV6 DNA PCR results of selected KA, showing amplification of the 123 bp fragment of the VP1 gene (123 bp) while using the primers according to Schowalter et al. [ 12 ] with the 123 pb positive controle. c Summary of the HPyV6-DNA PCR results on (KA), trichoblastoma (TB), basal cell carcinoma (BCC) and squamous cell carcinoma (SCC)
    Figure Legend Snippet: 2 % agarose gel showing the specimen control size (SCS) ladder HPyV6 DNA-PCR and SCS ladder for keratoacanthoma (KA), results HPyV6 DNA-PCR: a reveals adequate DNA quality of KA in order to proceed with HPyV6 testing. b HPyV6 DNA PCR results of selected KA, showing amplification of the 123 bp fragment of the VP1 gene (123 bp) while using the primers according to Schowalter et al. [ 12 ] with the 123 pb positive controle. c Summary of the HPyV6-DNA PCR results on (KA), trichoblastoma (TB), basal cell carcinoma (BCC) and squamous cell carcinoma (SCC)

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

    17) Product Images from "Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay"

    Article Title: Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay

    Journal:

    doi: 10.1128/JCM.43.4.1851-1857.2005

    Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,
    Figure Legend Snippet: Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,

    Techniques Used: Amplification, Cell Culture

    18) Product Images from "Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay"

    Article Title: Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay

    Journal:

    doi: 10.1128/JCM.43.4.1851-1857.2005

    Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,
    Figure Legend Snippet: Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,

    Techniques Used: Amplification, Cell Culture

    19) Product Images from "Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor"

    Article Title: Clinical and in vitro resistance to bexarotene in adult T-cell leukemia: loss of RXR-? receptor

    Journal:

    doi: 10.1182/blood-2008-03-141424

    Transcription of RXR-α mRNA before therapy and after relapse of disease. Real-time PCR of RXR-α was performed from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy. No change in the relative mean fold
    Figure Legend Snippet: Transcription of RXR-α mRNA before therapy and after relapse of disease. Real-time PCR of RXR-α was performed from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy. No change in the relative mean fold

    Techniques Used: Real-time Polymerase Chain Reaction

    Expression of RXR-α and RXR-β subunits before therapy and after relapse of disease. Western blot analysis of protein extracts from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy revealed marked down-regulation
    Figure Legend Snippet: Expression of RXR-α and RXR-β subunits before therapy and after relapse of disease. Western blot analysis of protein extracts from patient PBMCs collected at day 0 before therapy and day 180 after initiating therapy revealed marked down-regulation

    Techniques Used: Expressing, Western Blot

    20) Product Images from "Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note"

    Article Title: Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-12-288

    Schematic of MSP-3α PCR-RFLP protocol for in silico digestion. Drawn approximately to scale, an example from each size class is shown.
    Figure Legend Snippet: Schematic of MSP-3α PCR-RFLP protocol for in silico digestion. Drawn approximately to scale, an example from each size class is shown.

    Techniques Used: Polymerase Chain Reaction, In Silico

    Alignment and recombination at select MSP-3α regions. The less frequent variants are outlined in colour for seven regions of the amino acid MSP-3α alignment (positions of the region in the full 880 residue alignment are shown above sequence blocks). Dashes represent alignment gaps due to indel events. Haplotypes are represented to the right, with the presence of a deletion (unfilled gray squares), the more common allele (filled gray square), or the rarer allele (orange or blue) marked for each of the 7 polymorphic regions. 27 of the 48 P. vivax sequences are shown here.
    Figure Legend Snippet: Alignment and recombination at select MSP-3α regions. The less frequent variants are outlined in colour for seven regions of the amino acid MSP-3α alignment (positions of the region in the full 880 residue alignment are shown above sequence blocks). Dashes represent alignment gaps due to indel events. Haplotypes are represented to the right, with the presence of a deletion (unfilled gray squares), the more common allele (filled gray square), or the rarer allele (orange or blue) marked for each of the 7 polymorphic regions. 27 of the 48 P. vivax sequences are shown here.

    Techniques Used: Sequencing

    Geographic origin of the P. vivax MSP-3α sequences in this study. Sampling locations of previously published studies using PCR-RFLP analysis of MSP-3α are marked in black. Sampling locations of the isolates with complete sequences used here are shown in colour.
    Figure Legend Snippet: Geographic origin of the P. vivax MSP-3α sequences in this study. Sampling locations of previously published studies using PCR-RFLP analysis of MSP-3α are marked in black. Sampling locations of the isolates with complete sequences used here are shown in colour.

    Techniques Used: Sampling, Polymerase Chain Reaction

    Phylogenetic tree of P. vivax and P. cynomolgi MSP-3α sequences. Trees constructed from Neighbor-joining (A) and Bayesian methods (B) are shown with nodes with greater than 50% bootstrap or 0.50 posterior probability support, respectively, noted. Sequences are labelled by species ( Pv or Pc ), country of isolate origin, and PCR-RFLP haplotype. Curved, gray lines connect recombination events between P. vivax sequences as detected by the RDP [ 53 ] algorithm.
    Figure Legend Snippet: Phylogenetic tree of P. vivax and P. cynomolgi MSP-3α sequences. Trees constructed from Neighbor-joining (A) and Bayesian methods (B) are shown with nodes with greater than 50% bootstrap or 0.50 posterior probability support, respectively, noted. Sequences are labelled by species ( Pv or Pc ), country of isolate origin, and PCR-RFLP haplotype. Curved, gray lines connect recombination events between P. vivax sequences as detected by the RDP [ 53 ] algorithm.

    Techniques Used: Construct, Polymerase Chain Reaction

    21) Product Images from "LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E"

    Article Title: LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E

    Journal: Nucleic Acids Research

    doi:

    Validation of the apoE microtiter plate assay on patient samples. The absorbance values at 450 nm are given on the x -axis, and patient samples and genotypes on the y -axis. Black bars indicate signals from wells containing the codon 112 TGC capture probe. Hatched bars indicate signals from wells containing the codon 112 CGC capture probe. Open bars indicate signals from wells containing the codon 158 CGC capture probe. Finally, gray bars indicate signals from wells containing the codon 158 TGC capture probe.
    Figure Legend Snippet: Validation of the apoE microtiter plate assay on patient samples. The absorbance values at 450 nm are given on the x -axis, and patient samples and genotypes on the y -axis. Black bars indicate signals from wells containing the codon 112 TGC capture probe. Hatched bars indicate signals from wells containing the codon 112 CGC capture probe. Open bars indicate signals from wells containing the codon 158 CGC capture probe. Finally, gray bars indicate signals from wells containing the codon 158 TGC capture probe.

    Techniques Used:

    22) Product Images from "Transformation of Anaplasma phagocytophilum"

    Article Title: Transformation of Anaplasma phagocytophilum

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-6-42

    Transposition insertion diagram and Southern blot. (A) This diagram represents eight Ap genomic locations and direction of the transposon (arrow under the line) as determined by rescue cloning from GFP/Ap genomic DNA and sequence mapping onto the Ap HZ genome. Four insertions were found in putative coding sequences and four were in intergenic sites. The band sizes on the left of the diagram correspond to bands in the BglII digest lane of the Southern blot. (B) Southern blot of restriction digested GFP/Ap genomic DNA probed with a GFPuv coding sequence probe. The labels indicate restriction enzyme used and the numbers on the right indicate the sizes of visible bands in the BglII lane.
    Figure Legend Snippet: Transposition insertion diagram and Southern blot. (A) This diagram represents eight Ap genomic locations and direction of the transposon (arrow under the line) as determined by rescue cloning from GFP/Ap genomic DNA and sequence mapping onto the Ap HZ genome. Four insertions were found in putative coding sequences and four were in intergenic sites. The band sizes on the left of the diagram correspond to bands in the BglII digest lane of the Southern blot. (B) Southern blot of restriction digested GFP/Ap genomic DNA probed with a GFPuv coding sequence probe. The labels indicate restriction enzyme used and the numbers on the right indicate the sizes of visible bands in the BglII lane.

    Techniques Used: Southern Blot, Clone Assay, Sequencing

    23) Product Images from "CpG Methylation of Human Papillomavirus Type 16 DNA in Cervical Cancer Cell Lines and in Clinical Specimens: Genomic Hypomethylation Correlates with Carcinogenic Progression"

    Article Title: CpG Methylation of Human Papillomavirus Type 16 DNA in Cervical Cancer Cell Lines and in Clinical Specimens: Genomic Hypomethylation Correlates with Carcinogenic Progression

    Journal: Journal of Virology

    doi: 10.1128/JVI.77.11.6227-6234.2003

    Hpa II/ Msp I cleavage identifies CpG methylation of SiHa and CaSki DNA as a likely source of transcriptional repression. (A) Distribution of CpGs in the LCR (positions 7154 to 7906 and 1 to 96) and in the E6 gene of HPV-16 (positions 97 to 559) and positions of two Hpa II/ Msp I sites, one (position 57) overlapping with elements of the E6 promoter P97 and the other located in the 3′ part of the E6 gene (position 502). (B) Reverse transcription-PCR confirms that similar amounts of E6 and E7 transcripts are generated by SiHa and CaSki cells. GAPDH, glyceraldehyde-3-phosphate dehydrogenase, served as the cellular control transcript. (C) Genomic PCR confirms the large excess of HPV-16 DNA in CaSki cells. (D) Chromosomal DNA of SiHa and CaSki cells was not cut (CT, control) or was cleaved with one of the two enzymes (H, Hpa II; M, Msp I) and PCR amplified to generate the amplicons P2, P5, and P11. None of the three amplicons could be generated after cleavage with either of the two enzymes in the case of SiHa cells, indicating lack of any methylated CCGG sequences. In the case of CaSki cells, most of the DNA was resistant to Hpa II digestion but was readily cleaved by Msp I, indicating methylation of these two sites in most of the 500 HPV-16 copies in CaSki cells.
    Figure Legend Snippet: Hpa II/ Msp I cleavage identifies CpG methylation of SiHa and CaSki DNA as a likely source of transcriptional repression. (A) Distribution of CpGs in the LCR (positions 7154 to 7906 and 1 to 96) and in the E6 gene of HPV-16 (positions 97 to 559) and positions of two Hpa II/ Msp I sites, one (position 57) overlapping with elements of the E6 promoter P97 and the other located in the 3′ part of the E6 gene (position 502). (B) Reverse transcription-PCR confirms that similar amounts of E6 and E7 transcripts are generated by SiHa and CaSki cells. GAPDH, glyceraldehyde-3-phosphate dehydrogenase, served as the cellular control transcript. (C) Genomic PCR confirms the large excess of HPV-16 DNA in CaSki cells. (D) Chromosomal DNA of SiHa and CaSki cells was not cut (CT, control) or was cleaved with one of the two enzymes (H, Hpa II; M, Msp I) and PCR amplified to generate the amplicons P2, P5, and P11. None of the three amplicons could be generated after cleavage with either of the two enzymes in the case of SiHa cells, indicating lack of any methylated CCGG sequences. In the case of CaSki cells, most of the DNA was resistant to Hpa II digestion but was readily cleaved by Msp I, indicating methylation of these two sites in most of the 500 HPV-16 copies in CaSki cells.

    Techniques Used: CpG Methylation Assay, Polymerase Chain Reaction, Generated, Amplification, Methylation

    24) Product Images from "A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5? UTR"

    Article Title: A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5? UTR

    Journal: Nucleic Acids Research

    doi:

    Analysis of the promoter activity of different DNA sequences. The EGFP expression in transient transfected HuH7 cells was analyzed by flow cytometry. The mean fluorescence was calculated from positive fluorescent cells. The results are the mean of four independent experiments.
    Figure Legend Snippet: Analysis of the promoter activity of different DNA sequences. The EGFP expression in transient transfected HuH7 cells was analyzed by flow cytometry. The mean fluorescence was calculated from positive fluorescent cells. The results are the mean of four independent experiments.

    Techniques Used: Activity Assay, Expressing, Transfection, Flow Cytometry, Cytometry, Fluorescence

    25) Product Images from "Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results"

    Article Title: Effect of the enzyme and PCR conditions on the quality of high-throughput DNA sequencing results

    Journal: Scientific Reports

    doi: 10.1038/srep08056

    Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .
    Figure Legend Snippet: Proportion of correct reads for the three genetic systems (simple: a single allele per individual, squares ; medium: two alleles, circles ; and complex: multiple alleles, triangles ) using standard PCR conditions ( open ) and modified PCR conditions to reduce chimera formation ( gray ). The size of the shape is indicative of the number of reads (see legend). All enzymes yielded at least 50% correct reads in the simplest system, mitochondrial DNA (Test 1; open squares). Some enzymes only worked for a given set of conditions (cycling conditions/genetic system). A group of enzymes consisting of Phusion, Gold and FastStart yielded a high proportion of correct reads cosistently accross all conditions. Others, such as Roche Taq, HotStar and Biotaq, yielded a low percent of correct reads for the more complex systems (MHC class I and MHC class II). Abbreviations as defined in Table 1 .

    Techniques Used: Polymerase Chain Reaction, Modification

    26) Product Images from "A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay"

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-40035-5

    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Figure Legend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Techniques Used: Polymerase Chain Reaction, Hot Start PCR

    27) Product Images from "Human Papillomavirus Type-Specific Prevalence in the Cervical Cancer Screening Population of Czech Women"

    Article Title: Human Papillomavirus Type-Specific Prevalence in the Cervical Cancer Screening Population of Czech Women

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0079156

    HPV prevalence by age and method of HPV DNA detection (PCR=BS-RLB, HPV6/11 and HPV 16/18 were detected by means of BS-RLB).
    Figure Legend Snippet: HPV prevalence by age and method of HPV DNA detection (PCR=BS-RLB, HPV6/11 and HPV 16/18 were detected by means of BS-RLB).

    Techniques Used: Polymerase Chain Reaction

    28) Product Images from "Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note"

    Article Title: Merozoite surface protein-3 alpha as a genetic marker for epidemiologic studies in Plasmodium vivax: a cautionary note

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-12-288

    Schematic of MSP-3α PCR-RFLP protocol for in silico digestion. Drawn approximately to scale, an example from each size class is shown.
    Figure Legend Snippet: Schematic of MSP-3α PCR-RFLP protocol for in silico digestion. Drawn approximately to scale, an example from each size class is shown.

    Techniques Used: Polymerase Chain Reaction, In Silico

    Alignment and recombination at select MSP-3α regions. The less frequent variants are outlined in colour for seven regions of the amino acid MSP-3α alignment (positions of the region in the full 880 residue alignment are shown above sequence blocks). Dashes represent alignment gaps due to indel events. Haplotypes are represented to the right, with the presence of a deletion (unfilled gray squares), the more common allele (filled gray square), or the rarer allele (orange or blue) marked for each of the 7 polymorphic regions. 27 of the 48 P. vivax sequences are shown here.
    Figure Legend Snippet: Alignment and recombination at select MSP-3α regions. The less frequent variants are outlined in colour for seven regions of the amino acid MSP-3α alignment (positions of the region in the full 880 residue alignment are shown above sequence blocks). Dashes represent alignment gaps due to indel events. Haplotypes are represented to the right, with the presence of a deletion (unfilled gray squares), the more common allele (filled gray square), or the rarer allele (orange or blue) marked for each of the 7 polymorphic regions. 27 of the 48 P. vivax sequences are shown here.

    Techniques Used: Sequencing

    Geographic origin of the P. vivax MSP-3α sequences in this study. Sampling locations of previously published studies using PCR-RFLP analysis of MSP-3α are marked in black. Sampling locations of the isolates with complete sequences used here are shown in colour.
    Figure Legend Snippet: Geographic origin of the P. vivax MSP-3α sequences in this study. Sampling locations of previously published studies using PCR-RFLP analysis of MSP-3α are marked in black. Sampling locations of the isolates with complete sequences used here are shown in colour.

    Techniques Used: Sampling, Polymerase Chain Reaction

    Phylogenetic tree of P. vivax and P. cynomolgi MSP-3α sequences. Trees constructed from Neighbor-joining (A) and Bayesian methods (B) are shown with nodes with greater than 50% bootstrap or 0.50 posterior probability support, respectively, noted. Sequences are labelled by species ( Pv or Pc ), country of isolate origin, and PCR-RFLP haplotype. Curved, gray lines connect recombination events between P. vivax sequences as detected by the RDP [ 53 ] algorithm.
    Figure Legend Snippet: Phylogenetic tree of P. vivax and P. cynomolgi MSP-3α sequences. Trees constructed from Neighbor-joining (A) and Bayesian methods (B) are shown with nodes with greater than 50% bootstrap or 0.50 posterior probability support, respectively, noted. Sequences are labelled by species ( Pv or Pc ), country of isolate origin, and PCR-RFLP haplotype. Curved, gray lines connect recombination events between P. vivax sequences as detected by the RDP [ 53 ] algorithm.

    Techniques Used: Construct, Polymerase Chain Reaction

    29) Product Images from "Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer"

    Article Title: Identification and Characterization of Two Novel Viruses in Ocular Infections in Reindeer

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0069711

    Genome organization and phylogenetic analysis of RtPV2. A. Genome organization of RtPV2 . The line indicates the complete genome with size indication. The boxes represent open reading frames encoding early (E) and late (L) proteins). B–C. Phylogenetic trees of the L1 ORF (B) and complete genome (C) nucleotide sequences of selected representative papillomaviruses were generated using MEGA5, with the Maximum Likelihood method with Kimura-2 parameter model and 1,000 bootstrap replicates. Significant bootstrap values are shown. The different papillomavirus genera are indicated. Human papillomavirus (HPV1, HPV4, HPV5, HPV32, HPV41), V01116, NC_001457, M17463, NC_001586, NC_001354;. Canis familiaris papillomavirus (CPV2, CPV3, CPV6), NC_006564, NC_008297, NC_013237; European elk papillomavirus (AaPV1), NC_001524; Sus scrofa papillomavirus (SsPV1), NC_011280; Francolinus leucoscepus papillomavirus 1 (FlPV1), NC_013117 ; Erinaceus europaeus papillomavirus 1 (EePV1), NC_011765; Equus caballus papillomavirus 1 (EcPV1), NC_003748; Equus caballus papillomavirus 2 (EcPV2), NC_012123; Felis domesticus papillomavirus 2 (FcaPV2), EU796884; Caretta caretta papillomavirus 1 (CcPV1), NC_011530; Bovine papillomavirus (BPV3, 4, 5, 6, 9, 10, 11, 12), NC_004197, . X05817, NC_004195, AJ620208, AB331650, AB331651, AB543507, JF834523; Fringilla coelebs papillomavirus (FcPV1), NC_004068; Mastomys natalensis papillomavirus (MnPV1), NC_001605; Cottontail rabbit papillomavirus (SfPV1), NC_001541; Ursus maritimus papillomavirus 1 (UmPV1), NC_010739; Capra hircus papillomavirus 1 (ChPV1), NC_008032; Phocoena spinipinnis papillomavirus (PsPV1), NC_003348; Hamster oral papillomavirus (MaPV1), E15111; Rousettus aegyptiacus papillomavirus 1 (RaPV1), NC_008298; Trichechus manatus papillomavirus 1 (TmPV1), NC_006563; Erethizon dorsatum papillomavirus 1 (EdPV1), NC_006951; Psittacus erithacus timneh papillomavirus (PePV1), NC_003973; Tursiops truncatus papillomavirus 1 (TtPV1), NC_011109; Odocoileus virginianus papillomavirus 1 (OvPV1), NC_001523; Rangifer tarandus papillomavirus (RtPV1, RtPV2), AF443292, KC810012.
    Figure Legend Snippet: Genome organization and phylogenetic analysis of RtPV2. A. Genome organization of RtPV2 . The line indicates the complete genome with size indication. The boxes represent open reading frames encoding early (E) and late (L) proteins). B–C. Phylogenetic trees of the L1 ORF (B) and complete genome (C) nucleotide sequences of selected representative papillomaviruses were generated using MEGA5, with the Maximum Likelihood method with Kimura-2 parameter model and 1,000 bootstrap replicates. Significant bootstrap values are shown. The different papillomavirus genera are indicated. Human papillomavirus (HPV1, HPV4, HPV5, HPV32, HPV41), V01116, NC_001457, M17463, NC_001586, NC_001354;. Canis familiaris papillomavirus (CPV2, CPV3, CPV6), NC_006564, NC_008297, NC_013237; European elk papillomavirus (AaPV1), NC_001524; Sus scrofa papillomavirus (SsPV1), NC_011280; Francolinus leucoscepus papillomavirus 1 (FlPV1), NC_013117 ; Erinaceus europaeus papillomavirus 1 (EePV1), NC_011765; Equus caballus papillomavirus 1 (EcPV1), NC_003748; Equus caballus papillomavirus 2 (EcPV2), NC_012123; Felis domesticus papillomavirus 2 (FcaPV2), EU796884; Caretta caretta papillomavirus 1 (CcPV1), NC_011530; Bovine papillomavirus (BPV3, 4, 5, 6, 9, 10, 11, 12), NC_004197, . X05817, NC_004195, AJ620208, AB331650, AB331651, AB543507, JF834523; Fringilla coelebs papillomavirus (FcPV1), NC_004068; Mastomys natalensis papillomavirus (MnPV1), NC_001605; Cottontail rabbit papillomavirus (SfPV1), NC_001541; Ursus maritimus papillomavirus 1 (UmPV1), NC_010739; Capra hircus papillomavirus 1 (ChPV1), NC_008032; Phocoena spinipinnis papillomavirus (PsPV1), NC_003348; Hamster oral papillomavirus (MaPV1), E15111; Rousettus aegyptiacus papillomavirus 1 (RaPV1), NC_008298; Trichechus manatus papillomavirus 1 (TmPV1), NC_006563; Erethizon dorsatum papillomavirus 1 (EdPV1), NC_006951; Psittacus erithacus timneh papillomavirus (PePV1), NC_003973; Tursiops truncatus papillomavirus 1 (TtPV1), NC_011109; Odocoileus virginianus papillomavirus 1 (OvPV1), NC_001523; Rangifer tarandus papillomavirus (RtPV1, RtPV2), AF443292, KC810012.

    Techniques Used: Generated

    30) Product Images from "Multiplex Assay Detection of Immunoglobulin G Antibodies That Recognize Giardia intestinalis and Cryptosporidium parvum Antigens ▿"

    Article Title: Multiplex Assay Detection of Immunoglobulin G Antibodies That Recognize Giardia intestinalis and Cryptosporidium parvum Antigens ▿

    Journal: Clinical and Vaccine Immunology : CVI

    doi: 10.1128/CVI.00160-10

    Clustal sequence alignment of Giardia VSP fragments. VSP fragment coding sequences were PCR amplified from isolated genomic DNA using the primer pairs given in Table . Clones were sequenced, and predicted amino acid sequences were aligned
    Figure Legend Snippet: Clustal sequence alignment of Giardia VSP fragments. VSP fragment coding sequences were PCR amplified from isolated genomic DNA using the primer pairs given in Table . Clones were sequenced, and predicted amino acid sequences were aligned

    Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification, Isolation, Clone Assay

    31) Product Images from "Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis"

    Article Title: Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0070942

    Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.
    Figure Legend Snippet: Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.

    Techniques Used: Real-time Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Serial Dilution, Plasmid Preparation, Negative Control

    32) Product Images from "An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications"

    Article Title: An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0013042

    Efficiency of hl-dsDNase treatment. 1.3 pg of λ DNA was incubated with various quantities of hl-dsDNase in 90% Taq DNA polymerase storage buffer for 30 minutes at 25°C and qPCR quantification of a 73 bp fragment was performed. The average of the percentage of remaining DNA is plotted as a function of the quantities of hl-dsDNase.
    Figure Legend Snippet: Efficiency of hl-dsDNase treatment. 1.3 pg of λ DNA was incubated with various quantities of hl-dsDNase in 90% Taq DNA polymerase storage buffer for 30 minutes at 25°C and qPCR quantification of a 73 bp fragment was performed. The average of the percentage of remaining DNA is plotted as a function of the quantities of hl-dsDNase.

    Techniques Used: Incubation, Real-time Polymerase Chain Reaction

    33) Product Images from "Single-nucleotide polymorphism genotyping on optical thin-film biosensor chips"

    Article Title: Single-nucleotide polymorphism genotyping on optical thin-film biosensor chips

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

    doi: 10.1073/pnas.1934783100

    Specificity and sensitivity of SNP genotyping on biosensor chips spotted with 40 nl ( A ) or 1 nl ( B ) of P-1 capture probe at the indicated concentrations. ( A ) Oligomers for three different HoxB gene SNPs were arrayed and hybridized with the indicated concentrations of the target DNA PCR products in the presence of a mixture of P-2 probes and Ampligase (see text for details). ( B ) An array of Msp T/C SNP P-1 oligomers hybridized with 100 fmol of target DNA from three individuals with AA, GG, and AG genotypes.
    Figure Legend Snippet: Specificity and sensitivity of SNP genotyping on biosensor chips spotted with 40 nl ( A ) or 1 nl ( B ) of P-1 capture probe at the indicated concentrations. ( A ) Oligomers for three different HoxB gene SNPs were arrayed and hybridized with the indicated concentrations of the target DNA PCR products in the presence of a mixture of P-2 probes and Ampligase (see text for details). ( B ) An array of Msp T/C SNP P-1 oligomers hybridized with 100 fmol of target DNA from three individuals with AA, GG, and AG genotypes.

    Techniques Used: Polymerase Chain Reaction

    Increased discrimination of G/A and C/T mismatches using a mutant T. thermophilus DNA ligase ( A ) or a nitropyrrole base (N*) or a second mismatched base 3 nt from the 3′ terminus of the P-1 probe ( B ). ( A ) P-1 probes for Factor V (FV), Factor II (FII), and MTHFR gene mutations (G-A, G-A, and C-T, respectively) hybridized to a mixture of PCR products in the presence of either the wild type (Wt) or the K294 mutant T. thermophilus ligase. ( B ) Relative signal intensity from Msp C/T SNP P-1 probes with or without a third base-mismatch (3rd mis) or nitropyrrole substitution.
    Figure Legend Snippet: Increased discrimination of G/A and C/T mismatches using a mutant T. thermophilus DNA ligase ( A ) or a nitropyrrole base (N*) or a second mismatched base 3 nt from the 3′ terminus of the P-1 probe ( B ). ( A ) P-1 probes for Factor V (FV), Factor II (FII), and MTHFR gene mutations (G-A, G-A, and C-T, respectively) hybridized to a mixture of PCR products in the presence of either the wild type (Wt) or the K294 mutant T. thermophilus ligase. ( B ) Relative signal intensity from Msp C/T SNP P-1 probes with or without a third base-mismatch (3rd mis) or nitropyrrole substitution.

    Techniques Used: Mutagenesis, Polymerase Chain Reaction

    Determination of allele discrimination specificity and target DNA-detection sensitivity on the biosensor chip. Chips were spotted manually with 200 nl of the HoxB6 gene Sac (G/C) SNP P-1 probes at the concentrations indicated and hybridized to target DNA (a 560-bp PCR product) at concentrations of 100, 10, 1, and 0.1 fmol in the presence of the biotinylated SAC P-2 probe with and without DNA ligase. The–Ampligase chips were assayed posthybridization with no 0.01 M NaOH wash step, whereas the +Ampligase chips were NaOH-treated before visualization.
    Figure Legend Snippet: Determination of allele discrimination specificity and target DNA-detection sensitivity on the biosensor chip. Chips were spotted manually with 200 nl of the HoxB6 gene Sac (G/C) SNP P-1 probes at the concentrations indicated and hybridized to target DNA (a 560-bp PCR product) at concentrations of 100, 10, 1, and 0.1 fmol in the presence of the biotinylated SAC P-2 probe with and without DNA ligase. The–Ampligase chips were assayed posthybridization with no 0.01 M NaOH wash step, whereas the +Ampligase chips were NaOH-treated before visualization.

    Techniques Used: Chromatin Immunoprecipitation, Polymerase Chain Reaction

    34) Product Images from "Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay"

    Article Title: Detection of Human Immunodeficiency Virus Type 1 DNA in Dried Blood Spots by a Duplex Real-Time PCR Assay

    Journal:

    doi: 10.1128/JCM.43.4.1851-1857.2005

    Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,
    Figure Legend Snippet: Amplifications of HIV-1 LTR and RNase P DNA with 8E5 cellular DNA. (A) Amplification profiles of HIV-1 LTR. Chromosomal DNA was extracted from cultured 8E5 cells and amplified using an HIV LTR primer and probe set. The HIV forward primer, reverse primer,

    Techniques Used: Amplification, Cell Culture

    35) Product Images from "The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture"

    Article Title: The human vascular endothelial cell line HUV-EC-C harbors the integrated HHV-6B genome which remains stable in long term culture

    Journal: Cytotechnology

    doi: 10.1007/s10616-017-0119-y

    Copy number of HHV-6 DNA after chemical treatment. The copy number was assessed by digital PCR. Sample DNA was collected after treatment with various combinations of 3 mM SB and different concentration of TPA for 24 h. The copy number was not increased under these conditions
    Figure Legend Snippet: Copy number of HHV-6 DNA after chemical treatment. The copy number was assessed by digital PCR. Sample DNA was collected after treatment with various combinations of 3 mM SB and different concentration of TPA for 24 h. The copy number was not increased under these conditions

    Techniques Used: Digital PCR, Concentration Assay

    Copy number of HHV-6 DNA in HUV-EC-C ( a ). The slash columns indicate the copy number of U66 ORF representing HHV-6. The stippled column is the copy number of EBV in RAJI cells ( b ). The black columns are the copy number of RNase P in their hosts as a reference
    Figure Legend Snippet: Copy number of HHV-6 DNA in HUV-EC-C ( a ). The slash columns indicate the copy number of U66 ORF representing HHV-6. The stippled column is the copy number of EBV in RAJI cells ( b ). The black columns are the copy number of RNase P in their hosts as a reference

    Techniques Used:

    In situ hybridization of HHV-6 probes on metaphases of HUV-EC-C ( a ). Three DNA probes of HHV-6B 5-10 kbp labeled with Cy3, DNP and Cy5 hybridized to one of chromosome 9 at the distal end of the long arm ( b ), and zoomed ( c )
    Figure Legend Snippet: In situ hybridization of HHV-6 probes on metaphases of HUV-EC-C ( a ). Three DNA probes of HHV-6B 5-10 kbp labeled with Cy3, DNP and Cy5 hybridized to one of chromosome 9 at the distal end of the long arm ( b ), and zoomed ( c )

    Techniques Used: In Situ Hybridization, Labeling

    36) Product Images from "Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi"

    Article Title: Evaluation of high efficiency gene knockout strategies for Trypanosoma cruzi

    Journal: BMC Microbiology

    doi: 10.1186/1471-2180-9-90

    Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.
    Figure Legend Snippet: Replacement of dhfr-ts gene with a MS/GW construct pDEST/dhfr-ts_1F8Hyg . A) Schematic of the expected genomic loci of dhfr-ts and 1f8Hyg in dhfr-ts +/- / Hyg parasites. B) PCR analysis with gDNA from cloned drug resistant parasites and WT Tulahuen parasites confirm the expected gene deletion of one allele of the dhfr-ts gene and correct insertion of 1f8Hyg . Primer H1 plus the R1, R2 or R3 downstream primers, yield the expected products of 1.8, 2.0 and 2.3 kb, respectively and the combination of H5 plus upstream primers F3, F2 and F1 give the predicted bands of 2.1, 2.4 and 2.8 kb for respectively. See additional file 3 : Table S5 for nucleotide sequences of primers. C) Genomic DNA Southern blot analysis of a dhfr-ts +/- / Hyg Tulahuen clone. gDNA digested with BsrGI and hybridized with labeled Hyg CDS probe. Diagram not to scale. Numbers are sizes (bp) of expected products.

    Techniques Used: Mass Spectrometry, Construct, Polymerase Chain Reaction, Clone Assay, Southern Blot, Labeling

    Disruption of dhfr-ts using a conventional KO construct pBSdh1f8Neo . A) Diagram of the expected genomic loci of dhfr-ts and 1f8Neo in dhfr-ts +/- / Neo parasites. B) PCR analysis with Neo specific primers of WT Tulahuen and both uncloned and selected clones of dhfr-ts +/- / Neo parasites. C) PCR analysis with gDNA from selected clones of dhfr-ts +/- / Neo and WT Tulahuen parasites confirming the expected gene disruption of one allele of the dhfr-ts gene by 1f8Neo . D) Southern Blot analysis of WT Tulahuen and two dhfr-ts +/- / Neo clones digested with SalI and probed with dhfr-ts probe. Diagram not to scale. Numbers are sizes (bp) of expected products.
    Figure Legend Snippet: Disruption of dhfr-ts using a conventional KO construct pBSdh1f8Neo . A) Diagram of the expected genomic loci of dhfr-ts and 1f8Neo in dhfr-ts +/- / Neo parasites. B) PCR analysis with Neo specific primers of WT Tulahuen and both uncloned and selected clones of dhfr-ts +/- / Neo parasites. C) PCR analysis with gDNA from selected clones of dhfr-ts +/- / Neo and WT Tulahuen parasites confirming the expected gene disruption of one allele of the dhfr-ts gene by 1f8Neo . D) Southern Blot analysis of WT Tulahuen and two dhfr-ts +/- / Neo clones digested with SalI and probed with dhfr-ts probe. Diagram not to scale. Numbers are sizes (bp) of expected products.

    Techniques Used: Construct, Polymerase Chain Reaction, Clone Assay, Southern Blot

    37) Product Images from "Novel Cyclovirus in Human Cerebrospinal Fluid, Malawi, 2010-2011"

    Article Title: Novel Cyclovirus in Human Cerebrospinal Fluid, Malawi, 2010-2011

    Journal: Emerging Infectious Diseases

    doi: 10.3201/eid1909.130404

    Cyclovirus genome organization and phylogenetic analysis of translated putative replication-associated protein (Rep) sequences. A) Size and predicted genome organization of human cyclovirus VS5700009, showing the 2 major open reading frames (ORFs) encoding Rep and the putative capsid protein (Cap, and other ORFs with a coding capacity > 100 aa (ORFs 3–5). B) Phylogenetic tree of the translated Rep sequence of human cyclovirus VS5700009 and representative human and animal cycloviruses, generated by using MEGA5 with the neighbor-joining method with p-distance and 1,000 bootstrap replicates. A chimpanzee circovirus was used as an outgroup. Significant bootstrap values are shown. Cycloviruses in the same species are defined as having > 85% aa identity in the Rep region and are labeled by vertical bars as described ( 11 ). The human (white), dragonfly (blue), bat (red), goat (pink), cattle (black), chicken (green), and chimpanzee (gray) cycloviruses are indicated, and VS5700009 is highlighted in red. Scale bar = 5% estimated phylogenetic divergence. C) Phylogenetic tree of the genomic area, corresponding to nt 392–733 in human cyclovirus VS5700009 and representative human and animal cycloviruses, generated by using MEGA5 with the neighbor-joining method with p-distance and 1,000 bootstrap replicates. Significant bootstrap values are shown. Cycloviruses isolated from the same species are labeled by vertical bars as described ( 11 ). Cycloviruses from humans (white), cattle (black), and chimpanzees (gray) are indicated, and VS5700009 is highlighted in red. Scale bar = 10% estimated phylogenetic divergence.
    Figure Legend Snippet: Cyclovirus genome organization and phylogenetic analysis of translated putative replication-associated protein (Rep) sequences. A) Size and predicted genome organization of human cyclovirus VS5700009, showing the 2 major open reading frames (ORFs) encoding Rep and the putative capsid protein (Cap, and other ORFs with a coding capacity > 100 aa (ORFs 3–5). B) Phylogenetic tree of the translated Rep sequence of human cyclovirus VS5700009 and representative human and animal cycloviruses, generated by using MEGA5 with the neighbor-joining method with p-distance and 1,000 bootstrap replicates. A chimpanzee circovirus was used as an outgroup. Significant bootstrap values are shown. Cycloviruses in the same species are defined as having > 85% aa identity in the Rep region and are labeled by vertical bars as described ( 11 ). The human (white), dragonfly (blue), bat (red), goat (pink), cattle (black), chicken (green), and chimpanzee (gray) cycloviruses are indicated, and VS5700009 is highlighted in red. Scale bar = 5% estimated phylogenetic divergence. C) Phylogenetic tree of the genomic area, corresponding to nt 392–733 in human cyclovirus VS5700009 and representative human and animal cycloviruses, generated by using MEGA5 with the neighbor-joining method with p-distance and 1,000 bootstrap replicates. Significant bootstrap values are shown. Cycloviruses isolated from the same species are labeled by vertical bars as described ( 11 ). Cycloviruses from humans (white), cattle (black), and chimpanzees (gray) are indicated, and VS5700009 is highlighted in red. Scale bar = 10% estimated phylogenetic divergence.

    Techniques Used: Sequencing, Generated, Labeling, Isolation

    38) Product Images from "Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis"

    Article Title: Eprobe Mediated Real-Time PCR Monitoring and Melting Curve Analysis

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0070942

    Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.
    Figure Legend Snippet: Use of exo+ and exo− Taq polymerase. Eprobe mediated real-time PCR experiments were performed by using an exo+ (Amplitaq) and exo− (Genotyping Master) Taq polymerase and Eprobes with different melting temperatures. Amplification curves (Random fluorescent units (RFU) plotted against PCR cycle number) using a 7 times serial dilution of the DNA template are shown on the left. The R-squared values of the PCR efficiency plots are indicated in the graphs. Differential melting curve analysis by plotting –dF/dT against temperature is shown on the right. Main peaks are indicated in the graph to show the different T M values for both Eprobes. EGFR wild-type plasmid DNA concentrations are indicated by colors: Red: 1.5×10 8 copies, Dark blue: 1.5×10 7 copies, Yellow: 1.5×10 6 copies, Green: 1.5×10 5 copies, Pink: 1.5×10 4 copies, Sky blue: 1.5×10 3 copies, Brown: 150 copies, Orange: TE negative control. A: Amplitaq and Eprobe 215-21 wt TO. B: Genotyping Mastermix and Eprobe 215-21 TO. C: Amplitaq and Eprobe 205-13 wt TO. D: Genotyping Master and Eprobe 205-13 wt TO.

    Techniques Used: Real-time Polymerase Chain Reaction, Amplification, Polymerase Chain Reaction, Serial Dilution, Plasmid Preparation, Negative Control

    39) Product Images from "Eprobe-mediated screening system for somatic mutations in the KRAS locus"

    Article Title: Eprobe-mediated screening system for somatic mutations in the KRAS locus

    Journal: Oncology Reports

    doi: 10.3892/or.2015.3883

    Mutant allele enrichment by Eprobe-PCR using primer competition. (A) Reduction of amplification of the wild-type (WT) template. The Eprobe is designed to match the WT allele sequence (WT Eprobe). WT Eprobe has greater stability to WT template than the reverse primer and reduces its amplification by competing with the reverse primer, resulting in limited amplification of the WT gene. (B) WT Eprobe has less stability to mutant type (MT) template and does not reduce its amplification. (A and B) These combinations enrich the reaction in MT amplicons.
    Figure Legend Snippet: Mutant allele enrichment by Eprobe-PCR using primer competition. (A) Reduction of amplification of the wild-type (WT) template. The Eprobe is designed to match the WT allele sequence (WT Eprobe). WT Eprobe has greater stability to WT template than the reverse primer and reduces its amplification by competing with the reverse primer, resulting in limited amplification of the WT gene. (B) WT Eprobe has less stability to mutant type (MT) template and does not reduce its amplification. (A and B) These combinations enrich the reaction in MT amplicons.

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

    40) Product Images from "Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing"

    Article Title: Senataxin Plays an Essential Role with DNA Damage Response Proteins in Meiotic Recombination and Gene Silencing

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1003435

    Targeted disruption of the mouse Setx gene. A. Diagram of the Setx wild type allele (WT), targeting vector, and mutant alleles (neo+ and KO). Primers used for PCR genotyping (In3F, In3R, LoxPR) and the length of the PCR fragments obtained for WT (In3F and In3R yielding a 600 bp product) and KO (In3F and LoxpR yielding a 339 bp product) are indicated. E, exon; I, intron. NeoR represents the neomycin cassette, and triangles the loxP sites. B. Representative image of PCR genotyping using In3F, In3R and LoxPR primers. Wild type (+/+), heterozygotes (+/−) and knockout (−/−) alleles generate PCR products of 600 bp, 600 bp and 339 bp, and 339 bp, respectively. A negative control for the PCR reaction (−ve) is also shown. M, 100 bp marker. C. RT-PCR of 35 day-old mice testes samples using primers specific to Setx cDNA indicates the absence of Setx expression in KO testes. GAPDH was used as an internal standard. D. Immunoprecipitation of senataxin using anti-human senataxin antibodies (Ab-1/Ab-3) from 35 day-old mouse testes extracts confirmed the absence of the protein in the Setx −/− . Immunoprecipitation of senataxin from human lymphoblastoid cell extracts from normal (C3ABR) and an AOA2 patient (SETX2RM) confirmed the similar size of senataxin in both species. A species-matched non-specific serum (NSIg) was used as a negative control in for the IP experiments. As expected, no senataxin protein was brought down from Setx +/+ testes following the IP with the non-specific serum (NSIg).
    Figure Legend Snippet: Targeted disruption of the mouse Setx gene. A. Diagram of the Setx wild type allele (WT), targeting vector, and mutant alleles (neo+ and KO). Primers used for PCR genotyping (In3F, In3R, LoxPR) and the length of the PCR fragments obtained for WT (In3F and In3R yielding a 600 bp product) and KO (In3F and LoxpR yielding a 339 bp product) are indicated. E, exon; I, intron. NeoR represents the neomycin cassette, and triangles the loxP sites. B. Representative image of PCR genotyping using In3F, In3R and LoxPR primers. Wild type (+/+), heterozygotes (+/−) and knockout (−/−) alleles generate PCR products of 600 bp, 600 bp and 339 bp, and 339 bp, respectively. A negative control for the PCR reaction (−ve) is also shown. M, 100 bp marker. C. RT-PCR of 35 day-old mice testes samples using primers specific to Setx cDNA indicates the absence of Setx expression in KO testes. GAPDH was used as an internal standard. D. Immunoprecipitation of senataxin using anti-human senataxin antibodies (Ab-1/Ab-3) from 35 day-old mouse testes extracts confirmed the absence of the protein in the Setx −/− . Immunoprecipitation of senataxin from human lymphoblastoid cell extracts from normal (C3ABR) and an AOA2 patient (SETX2RM) confirmed the similar size of senataxin in both species. A species-matched non-specific serum (NSIg) was used as a negative control in for the IP experiments. As expected, no senataxin protein was brought down from Setx +/+ testes following the IP with the non-specific serum (NSIg).

    Techniques Used: Plasmid Preparation, Mutagenesis, Polymerase Chain Reaction, Knock-Out, Negative Control, Marker, Reverse Transcription Polymerase Chain Reaction, Mouse Assay, Expressing, Immunoprecipitation

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  • 93
    Roche amplitaq gold dna polymerase
    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); <t>Amplitaq</t> = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq <t>DNA</t> Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Amplitaq Gold Dna Polymerase, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 64 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/amplitaq gold dna polymerase/product/Roche
    Average 93 stars, based on 64 article reviews
    Price from $9.99 to $1999.99
    amplitaq gold dna polymerase - by Bioz Stars, 2020-09
    93/100 stars
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    93
    Roche taq polymerase
    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); <t>Amplitaq</t> = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq <t>DNA</t> Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.
    Taq Polymerase, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 205 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq polymerase/product/Roche
    Average 93 stars, based on 205 article reviews
    Price from $9.99 to $1999.99
    taq polymerase - by Bioz Stars, 2020-09
    93/100 stars
      Buy from Supplier

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    Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Journal: Scientific Reports

    Article Title: A novel perspective on MOL-PCR optimization and MAGPIX analysis of in-house multiplex foodborne pathogens detection assay

    doi: 10.1038/s41598-019-40035-5

    Figure Lengend Snippet: Impact evaluation of Master Mix used in singleplex PCR. In graph: Elizyme = 2X EliZyme HS Robust MIX (Elisabeth Pharmacon, Czech Republic); Accustart II = AccuStart II PCR ToughMix (QuantaBio, Massachusetts, USA); Amplitaq = AmpliTaq Gold 360 Master Mix (Thermo Fisher Scientific, Massachusetts, USA); OneTaq = OneTaq Hot Start 2X Master Mix with GC Buffer (New England BioLabs, Massachusetts, USA); Platinum = Platinum Hot Start PCR 2X Master Mix (Invitrogen, California, USA); HotStarTaq = HotStarTaq DNA Polymerase (Qiagen, Germany). YE = Y . enterocolitica; TG = T . gondii ; plus sign in legend = positive sample; minus sign = NTC.

    Article Snippet: Optimization of the multiplex oligonucleotide ligation step In the very first paper dealing with MOL-PCR by Deshpande et al ., ligation and PCR were conducted in a single reaction using Ampligase (Epicentre, Wisconsin, USA) and Amplitaq Gold DNA polymerase (Roche, Switzerland).

    Techniques: Polymerase Chain Reaction, Hot Start PCR