scaffold 6  (TaKaRa)

 
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    Msp I
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    C | CG GG GC | C
    Catalog Number:
    1150a
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    MspI HpaII HapII Restriction enzymes Cloning
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    Structured Review

    TaKaRa scaffold 6
    Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of <t>scaffold</t> 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
    C | CG GG GC | C
    https://www.bioz.com/result/scaffold 6/product/TaKaRa
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    Images

    1) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

    Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0116192

    Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
    Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

    Techniques Used: Polymerase Chain Reaction, Sequencing

    2) Product Images from "Polymorphisms in programmed death-1 gene are not associated with chronic HBV infection in Chinese patients"

    Article Title: Polymorphisms in programmed death-1 gene are not associated with chronic HBV infection in Chinese patients

    Journal: World Journal of Hepatology

    doi: 10.4254/wjh.v3.i3.72

    Gel electrophoresis patterns of PD-1.1 and PD-1.2. A: The amplified fragments of PD-1.1 were digested with MspI: the polymerase chain reaction (PCR) product size was 265 base pairs (bp) which was digested to 180 and 85 bp, the genotype was identified
    Figure Legend Snippet: Gel electrophoresis patterns of PD-1.1 and PD-1.2. A: The amplified fragments of PD-1.1 were digested with MspI: the polymerase chain reaction (PCR) product size was 265 base pairs (bp) which was digested to 180 and 85 bp, the genotype was identified

    Techniques Used: Nucleic Acid Electrophoresis, Amplification, Polymerase Chain Reaction

    3) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

    Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1432-5

    Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
    Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

    Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

    4) Product Images from "Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells *Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells * S⃞"

    Article Title: Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells *Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells * S⃞

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M808992200

    Analysis of the FGFR2 promoter. A , mapping the transcription start site of FGFR2 in C3H10T1/2. The experimentally determined transcription initiation site of the mouse FGFR2 promoter by 5′-RLM-RACE is denoted as +1. The cDNA sequences of KGFR and bek begin at position +17 and +37, respectively. B , DNase I hypersensitive site analysis of the FGFR2 promoter region. Top panel , nuclei from C3H10T1/2, C2C12, MC3T3, and primary osteoblasts were treated with increasing amounts of DNase I ( left to right , shown by triangles ). After DNA extraction and digestion with EcoR, they were hybridized with the probe shown in V. Bottom panel , the arrowhead shows bands (about 6.3 kb) due to DNase I cleavage. C , DNase accessibility of FGFR2 gene in C3H10T1/2 cells. Top panel , nuclei from C3H10T1/2 were harvested and treated with 50 units of DNase for 10 min at 25 °C. Then the genomic DNA was purified and quantitated relative to DNA I from undigested nuclei using the primers described in the bottom panel by quantitative PCR and listed as percent protected. Each bar represents the means ± S.D. of three independent experiments.
    Figure Legend Snippet: Analysis of the FGFR2 promoter. A , mapping the transcription start site of FGFR2 in C3H10T1/2. The experimentally determined transcription initiation site of the mouse FGFR2 promoter by 5′-RLM-RACE is denoted as +1. The cDNA sequences of KGFR and bek begin at position +17 and +37, respectively. B , DNase I hypersensitive site analysis of the FGFR2 promoter region. Top panel , nuclei from C3H10T1/2, C2C12, MC3T3, and primary osteoblasts were treated with increasing amounts of DNase I ( left to right , shown by triangles ). After DNA extraction and digestion with EcoR, they were hybridized with the probe shown in V. Bottom panel , the arrowhead shows bands (about 6.3 kb) due to DNase I cleavage. C , DNase accessibility of FGFR2 gene in C3H10T1/2 cells. Top panel , nuclei from C3H10T1/2 were harvested and treated with 50 units of DNase for 10 min at 25 °C. Then the genomic DNA was purified and quantitated relative to DNA I from undigested nuclei using the primers described in the bottom panel by quantitative PCR and listed as percent protected. Each bar represents the means ± S.D. of three independent experiments.

    Techniques Used: DNA Extraction, Purification, Real-time Polymerase Chain Reaction

    5) Product Images from "Loss of MYC and E-box3 binding contributes to defective MYC-mediated transcriptional suppression of human MC-let-7a-1~let-7d in glioblastoma"

    Article Title: Loss of MYC and E-box3 binding contributes to defective MYC-mediated transcriptional suppression of human MC-let-7a-1~let-7d in glioblastoma

    Journal: Oncotarget

    doi: 10.18632/oncotarget.10517

    MC-let-7a-1~let-7d promoter characterization in GBM as compared to that in HCC ( A ) primers used for 5′RACE. Gene-specific primers (GSPs) GSP1-1 was used to synthesize the first strand cDNA. Primary amplification was carried out with abridged anchor primer (AAP) and GSP2-1 primer. Nested PCR was performed with abridged universal amplification primer (AUAP) and GSP2-2.( B ) 5′RACE results. The ~700-bp products were amplified in U87 cells and U251 cells by using GSP2-2 and AUAP. ( C ) sequence analysis of 20 products from each cell lines revealed that variable TSSs were used. The major TSSs of MC-let-7a-1~let-7d in U87 is located about 28 bp, while in U251 is located about 40 bp downstream of the TSSs used in HepG2 cells. ( D ) schematic diagram of the reporter construct (left panel). Truncation of the downstream region to +1 dramatically improved the promoter activity, whereas truncation of the upstream region to −227 resulted in progressive loss of activity in both U87 cells and L02 cells.
    Figure Legend Snippet: MC-let-7a-1~let-7d promoter characterization in GBM as compared to that in HCC ( A ) primers used for 5′RACE. Gene-specific primers (GSPs) GSP1-1 was used to synthesize the first strand cDNA. Primary amplification was carried out with abridged anchor primer (AAP) and GSP2-1 primer. Nested PCR was performed with abridged universal amplification primer (AUAP) and GSP2-2.( B ) 5′RACE results. The ~700-bp products were amplified in U87 cells and U251 cells by using GSP2-2 and AUAP. ( C ) sequence analysis of 20 products from each cell lines revealed that variable TSSs were used. The major TSSs of MC-let-7a-1~let-7d in U87 is located about 28 bp, while in U251 is located about 40 bp downstream of the TSSs used in HepG2 cells. ( D ) schematic diagram of the reporter construct (left panel). Truncation of the downstream region to +1 dramatically improved the promoter activity, whereas truncation of the upstream region to −227 resulted in progressive loss of activity in both U87 cells and L02 cells.

    Techniques Used: Amplification, Nested PCR, Sequencing, Construct, Activity Assay

    6) Product Images from "The Early Intestinal Microbiota of Healthy Korean Newborns"

    Article Title: The Early Intestinal Microbiota of Healthy Korean Newborns

    Journal: Iranian Journal of Pediatrics

    doi: 10.5812/ijp.2079

    T-RFLP Analysis With HhaI and Clustering Analysis A, T-RFLP patterns of 16S rDNAs from stools digested with HhaI . The 16S rDNAs were extracted from samples and amplified with the universal primers 27F and 1492R. Each peak represents a terminal restriction fragment of a specific length that corresponds to a bacterial phylotype. The meconium sample numbers were 4, 5, 25, and 29. Out of 30 samples, the T-RFLP patterns of 26 samples were similar. B, Hierarchical clustering analysis of microbiota of meconium based on T-RFLP pattern derived from HhaI and MspI digestion. The figure shows the phylogenetic relationships among 30 meconium samples. The x-axis shows the % of similarity and 1 - 30, indicates the sample number.
    Figure Legend Snippet: T-RFLP Analysis With HhaI and Clustering Analysis A, T-RFLP patterns of 16S rDNAs from stools digested with HhaI . The 16S rDNAs were extracted from samples and amplified with the universal primers 27F and 1492R. Each peak represents a terminal restriction fragment of a specific length that corresponds to a bacterial phylotype. The meconium sample numbers were 4, 5, 25, and 29. Out of 30 samples, the T-RFLP patterns of 26 samples were similar. B, Hierarchical clustering analysis of microbiota of meconium based on T-RFLP pattern derived from HhaI and MspI digestion. The figure shows the phylogenetic relationships among 30 meconium samples. The x-axis shows the % of similarity and 1 - 30, indicates the sample number.

    Techniques Used: Amplification, Derivative Assay

    7) Product Images from "Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum"

    Article Title: Development and application of loop-mediated isothermal amplification for detection of the F167Y mutation of carbendazim-resistant isolates in Fusarium graminearum

    Journal: Scientific Reports

    doi: 10.1038/srep07094

    LAMP detection of the F167Y mutation in F. graminearum and digestion of positive LAMP products. (A) LAMP for detection of the F167Y mutation using HNB as a visual indicator. The reaction becomes sky blue if the β 2 -tubulin gene has a point mutation at codon F167Y but remains violet if the β 2 -tubulin gene has no mutation or other mutation at codon F167Y. 1, ddH 2 O; 2, 2021; 3, R9. (B) Agarose gel electrophoresis of LAMP products. The positive reaction is manifested as a ladder-like pattern on the 3.0% agarose gel. M, 100-bp ladder; 1, ddH 2 O; 2, 2021; 3, R9. (C), LAMP products were digested with Pvu I, and two fragments (119 bp, 88 bp) were observed by 3.0% agarose gel. M, 100-bp ladder, 1, LAMP products without digestion; 2, LAMP products digested by Pvu I.
    Figure Legend Snippet: LAMP detection of the F167Y mutation in F. graminearum and digestion of positive LAMP products. (A) LAMP for detection of the F167Y mutation using HNB as a visual indicator. The reaction becomes sky blue if the β 2 -tubulin gene has a point mutation at codon F167Y but remains violet if the β 2 -tubulin gene has no mutation or other mutation at codon F167Y. 1, ddH 2 O; 2, 2021; 3, R9. (B) Agarose gel electrophoresis of LAMP products. The positive reaction is manifested as a ladder-like pattern on the 3.0% agarose gel. M, 100-bp ladder; 1, ddH 2 O; 2, 2021; 3, R9. (C), LAMP products were digested with Pvu I, and two fragments (119 bp, 88 bp) were observed by 3.0% agarose gel. M, 100-bp ladder, 1, LAMP products without digestion; 2, LAMP products digested by Pvu I.

    Techniques Used: Mutagenesis, Agarose Gel Electrophoresis

    LAMP detection of the F167Y mutation in F. graminearum and digestion of positive LAMP products. (A) LAMP for detection of the F167Y mutation using HNB as a visual indicator. The reaction becomes sky blue if the β 2 -tubulin gene has a point mutation at codon F167Y but remains violet if the β 2 -tubulin gene has no mutation or other mutation at codon F167Y. 1, ddH 2 O; 2, 2021; 3, R9. (B) Agarose gel electrophoresis of LAMP products. The positive reaction is manifested as a ladder-like pattern on the 3.0% agarose gel. M, 100-bp ladder; 1, ddH 2 O; 2, 2021; 3, R9. (C), LAMP products were digested with Pvu I, and two fragments (119 bp, 88 bp) were observed by 3.0% agarose gel. M, 100-bp ladder, 1, LAMP products without digestion; 2, LAMP products digested by Pvu I.
    Figure Legend Snippet: LAMP detection of the F167Y mutation in F. graminearum and digestion of positive LAMP products. (A) LAMP for detection of the F167Y mutation using HNB as a visual indicator. The reaction becomes sky blue if the β 2 -tubulin gene has a point mutation at codon F167Y but remains violet if the β 2 -tubulin gene has no mutation or other mutation at codon F167Y. 1, ddH 2 O; 2, 2021; 3, R9. (B) Agarose gel electrophoresis of LAMP products. The positive reaction is manifested as a ladder-like pattern on the 3.0% agarose gel. M, 100-bp ladder; 1, ddH 2 O; 2, 2021; 3, R9. (C), LAMP products were digested with Pvu I, and two fragments (119 bp, 88 bp) were observed by 3.0% agarose gel. M, 100-bp ladder, 1, LAMP products without digestion; 2, LAMP products digested by Pvu I.

    Techniques Used: Mutagenesis, Agarose Gel Electrophoresis

    8) Product Images from "i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases"

    Article Title: i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases

    Journal: Genome Biology

    doi: 10.1186/s13059-018-1400-x

    Creating gene-inactivated animal models using the GONAD method. a Schematic of the targeting strategy to inactivate Foxe3 gene and the primer set used for genotyping. b Direct sequencing results of polymerase chain reaction (PCR) products amplified from the founder (G0) mice with the primer set shown in a . The red arrows below the electropherogram show the region with indel mutations. c Mutated Foxe3 alleles in the G0 mice. The changes in the nucleotide sequence are shown in red , and the type of changes (insertions +Xnt, or deletions Δ) is indicated on the right side of the sequences. d and e Cataract phenotypes in the G1 mice. f Efficiencies of Foxe3 gene editing. CRISPR components used were either Cas9 mRNA/sgRNA or Cas9 protein/CRISPR RNA (crRNA)/trans-activating crRNA (tracrRNA) (see Additional file 1 : Table S1 for details)
    Figure Legend Snippet: Creating gene-inactivated animal models using the GONAD method. a Schematic of the targeting strategy to inactivate Foxe3 gene and the primer set used for genotyping. b Direct sequencing results of polymerase chain reaction (PCR) products amplified from the founder (G0) mice with the primer set shown in a . The red arrows below the electropherogram show the region with indel mutations. c Mutated Foxe3 alleles in the G0 mice. The changes in the nucleotide sequence are shown in red , and the type of changes (insertions +Xnt, or deletions Δ) is indicated on the right side of the sequences. d and e Cataract phenotypes in the G1 mice. f Efficiencies of Foxe3 gene editing. CRISPR components used were either Cas9 mRNA/sgRNA or Cas9 protein/CRISPR RNA (crRNA)/trans-activating crRNA (tracrRNA) (see Additional file 1 : Table S1 for details)

    Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification, Mouse Assay, CRISPR

    9) Product Images from "Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice"

    Article Title: Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice

    Journal: Plant Biotechnology Journal

    doi: 10.1111/pbi.12544

    Quantitative real‐time PCR analyses of salt tolerance‐related marker genes. Three‐week‐old seedlings treated with 150 m m NaCl for 12 h or 0 h (Control) were harvested for total RNA extraction, transverse transcription and real‐time PCR analyses. WT , wild type; Z33 and Z38, independent transgenic lines. Values are means ± SD of three biological replicates from the WT or the transgenic lines. Asterisks indicate statistically significant difference in comparison with the WT (Student's t ‐test, *, P
    Figure Legend Snippet: Quantitative real‐time PCR analyses of salt tolerance‐related marker genes. Three‐week‐old seedlings treated with 150 m m NaCl for 12 h or 0 h (Control) were harvested for total RNA extraction, transverse transcription and real‐time PCR analyses. WT , wild type; Z33 and Z38, independent transgenic lines. Values are means ± SD of three biological replicates from the WT or the transgenic lines. Asterisks indicate statistically significant difference in comparison with the WT (Student's t ‐test, *, P

    Techniques Used: Real-time Polymerase Chain Reaction, Marker, RNA Extraction, Transgenic Assay

    10) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

    Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0116192

    Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
    Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

    Techniques Used: Polymerase Chain Reaction, Sequencing

    Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
    Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

    Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

    11) Product Images from "Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells *Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells * S⃞"

    Article Title: Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells *Nuclear Factor Y Is Required for Basal Activation and Chromatin Accessibility of Fibroblast Growth Factor Receptor 2 Promoter in Osteoblast-like Cells * S⃞

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M808992200

    Analysis of the FGFR2 promoter. A , mapping the transcription start site of FGFR2 in C3H10T1/2. The experimentally determined transcription initiation site of the mouse FGFR2 promoter by 5′-RLM-RACE is denoted as +1. The cDNA sequences of KGFR and bek begin at position +17 and +37, respectively. B , DNase I hypersensitive site analysis of the FGFR2 promoter region. Top panel , nuclei from C3H10T1/2, C2C12, MC3T3, and primary osteoblasts were treated with increasing amounts of DNase I ( left to right , shown by triangles ). After DNA extraction and digestion with EcoR, they were hybridized with the probe shown in V. Bottom panel , the arrowhead shows bands (about 6.3 kb) due to DNase I cleavage. C , DNase accessibility of FGFR2 gene in C3H10T1/2 cells. Top panel , nuclei from C3H10T1/2 were harvested and treated with 50 units of DNase for 10 min at 25 °C. Then the genomic DNA was purified and quantitated relative to DNA I from undigested nuclei using the primers described in the bottom panel by quantitative PCR and listed as percent protected. Each bar represents the means ± S.D. of three independent experiments.
    Figure Legend Snippet: Analysis of the FGFR2 promoter. A , mapping the transcription start site of FGFR2 in C3H10T1/2. The experimentally determined transcription initiation site of the mouse FGFR2 promoter by 5′-RLM-RACE is denoted as +1. The cDNA sequences of KGFR and bek begin at position +17 and +37, respectively. B , DNase I hypersensitive site analysis of the FGFR2 promoter region. Top panel , nuclei from C3H10T1/2, C2C12, MC3T3, and primary osteoblasts were treated with increasing amounts of DNase I ( left to right , shown by triangles ). After DNA extraction and digestion with EcoR, they were hybridized with the probe shown in V. Bottom panel , the arrowhead shows bands (about 6.3 kb) due to DNase I cleavage. C , DNase accessibility of FGFR2 gene in C3H10T1/2 cells. Top panel , nuclei from C3H10T1/2 were harvested and treated with 50 units of DNase for 10 min at 25 °C. Then the genomic DNA was purified and quantitated relative to DNA I from undigested nuclei using the primers described in the bottom panel by quantitative PCR and listed as percent protected. Each bar represents the means ± S.D. of three independent experiments.

    Techniques Used: DNA Extraction, Purification, Real-time Polymerase Chain Reaction

    12) Product Images from "Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR"

    Article Title: Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR

    Journal: Journal of Nucleic Acids

    doi: 10.1155/2013/823730

    The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.
    Figure Legend Snippet: The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.

    Techniques Used: Polymerase Chain Reaction, Generated, Amplification, Software

    Various target sequences were amplified in the presence of ttRecA and ttMutS. (a) A 611 bp region of the ttha0122 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. The amounts of amplified fragments were quantified and are shown as bar graphs in the lower panel. Gray and blue bars indicate nonspecific and desired amplifications, respectively. (b) A 423 bp region of the ttha1806 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. (c) A 466 bp region of the ttha1300 gene was amplified from T. thermophilus HB8 genomic DNA in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttMutS were used here. (d) A 1,278 bp region of the ttha1548 gene was amplified in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttRecA were used here.
    Figure Legend Snippet: Various target sequences were amplified in the presence of ttRecA and ttMutS. (a) A 611 bp region of the ttha0122 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. The amounts of amplified fragments were quantified and are shown as bar graphs in the lower panel. Gray and blue bars indicate nonspecific and desired amplifications, respectively. (b) A 423 bp region of the ttha1806 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. (c) A 466 bp region of the ttha1300 gene was amplified from T. thermophilus HB8 genomic DNA in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttMutS were used here. (d) A 1,278 bp region of the ttha1548 gene was amplified in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttRecA were used here.

    Techniques Used: Amplification

    13) Product Images from "Potential Spermatogenesis Recovery with Bone Marrow Mesenchymal Stem Cells in an Azoospermic Rat Model"

    Article Title: Potential Spermatogenesis Recovery with Bone Marrow Mesenchymal Stem Cells in an Azoospermic Rat Model

    Journal: International Journal of Molecular Sciences

    doi: 10.3390/ijms150813151

    Relative level of spermatogenic specific genes expression in recipient rat testicular tissue after BMSCs transplantation detected by real time PCR. Vasa, dazl, smad1 and stella expression were detected 2 weeks post-transplantation and increased to a relatively high level at 4 to 8 weeks. C-kit and GCNF were expressed at relatively high levels immediately after injection, and expression levels decreased to almost zero within 2 weeks. GCNF expression increased gradually at 4 weeks post-transplantation, while expression of c-kit remained at a relatively low level.
    Figure Legend Snippet: Relative level of spermatogenic specific genes expression in recipient rat testicular tissue after BMSCs transplantation detected by real time PCR. Vasa, dazl, smad1 and stella expression were detected 2 weeks post-transplantation and increased to a relatively high level at 4 to 8 weeks. C-kit and GCNF were expressed at relatively high levels immediately after injection, and expression levels decreased to almost zero within 2 weeks. GCNF expression increased gradually at 4 weeks post-transplantation, while expression of c-kit remained at a relatively low level.

    Techniques Used: Expressing, Transplantation Assay, Real-time Polymerase Chain Reaction, Injection

    14) Product Images from "Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome"

    Article Title: Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0165499

    Methylation profiling analysis of CRISPR cut clonal lines derived from somatic hybrid CHO cells and iPS cells. DNA methylation profiling analysis was performed using Infinium HumanMethylation450 BeadChip. Data analysis was focused on the 8 probe positions at the promoter region of FMR1 gene. Silent clonal lines were shown in red, and expressing clonal lines were shown in blue. (A) Methylation states of CRISPR cut somatic hybrid CHO cells. (B) Methylation states of CRISPR cut iPS cells.
    Figure Legend Snippet: Methylation profiling analysis of CRISPR cut clonal lines derived from somatic hybrid CHO cells and iPS cells. DNA methylation profiling analysis was performed using Infinium HumanMethylation450 BeadChip. Data analysis was focused on the 8 probe positions at the promoter region of FMR1 gene. Silent clonal lines were shown in red, and expressing clonal lines were shown in blue. (A) Methylation states of CRISPR cut somatic hybrid CHO cells. (B) Methylation states of CRISPR cut iPS cells.

    Techniques Used: Methylation, CRISPR, Derivative Assay, DNA Methylation Assay, Expressing

    15) Product Images from "Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways"

    Article Title: Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways

    Journal: Antonie Van Leeuwenhoek

    doi: 10.1007/s10482-009-9400-1

    Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5
    Figure Legend Snippet: Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5

    Techniques Used: Agarose Gel Electrophoresis, Marker

    16) Product Images from "Detection of Amantadine-Resistant Influenza A Virus Strains in Nursing Homes by PCR-Restriction Fragment Length Polymorphism Analysis with Nasopharyngeal Swabs"

    Article Title: Detection of Amantadine-Resistant Influenza A Virus Strains in Nursing Homes by PCR-Restriction Fragment Length Polymorphism Analysis with Nasopharyngeal Swabs

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.1.84-88.2002

    PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and Hha I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the M2 protein, respectively; M, 50-bp molecular size marker.
    Figure Legend Snippet: PCR-RFLP analysis of amantadine-resistant reference viruses. Each aliquot of 5 μl of reverse transcription-PCR product, amplified by specific nested primer sets, was treated with 5 U of Bsp Lu11I (A) at 48°C for 2 h and Hha I (B) or Sca I (C) at 37°C for 2 h, respectively, and then electrophoresed in 4% agarose X gels. Lanes: S, amantadine-sensitive virus without substitution; 27, 30, and 31, and strains having amantadine resistance substitutions at amino acids 27, 30, and 31 of the M2 protein, respectively; M, 50-bp molecular size marker.

    Techniques Used: Polymerase Chain Reaction, Amplification, Marker

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

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

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2015.00668

    Representative fragments in methylation sensitive amplification polymorphism (MSAP) profiles (A,B) and the relationship between U- values and ploidy level (C–E). (A) Hpa II and Msp I sensitivities to 5-CCGG methylation status (“+”: enzyme cuts; “-”: enzyme does not cut): three types of fragment generated. Type I: non-methylated, appearing in both the H and M lanes; Type II: fully methylated, present in the M but not the H lanes; Type III: hemi-methylated, present in the H but not the M lanes; (B) Examples of MSAP electrophoresis patterns in ABI3730xl; The relationship between U- values and ploidy level (C-E) . U- values associated with (C) total methylation, (D) full methylation, (E) hemi-methylation. A higher U -value implies a larger difference between different samples, but only U -values > 1.96 were statistically significant.
    Figure Legend Snippet: Representative fragments in methylation sensitive amplification polymorphism (MSAP) profiles (A,B) and the relationship between U- values and ploidy level (C–E). (A) Hpa II and Msp I sensitivities to 5-CCGG methylation status (“+”: enzyme cuts; “-”: enzyme does not cut): three types of fragment generated. Type I: non-methylated, appearing in both the H and M lanes; Type II: fully methylated, present in the M but not the H lanes; Type III: hemi-methylated, present in the H but not the M lanes; (B) Examples of MSAP electrophoresis patterns in ABI3730xl; The relationship between U- values and ploidy level (C-E) . U- values associated with (C) total methylation, (D) full methylation, (E) hemi-methylation. A higher U -value implies a larger difference between different samples, but only U -values > 1.96 were statistically significant.

    Techniques Used: Methylation, Amplification, Generated, Electrophoresis

    18) Product Images from "Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways"

    Article Title: Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways

    Journal: Antonie Van Leeuwenhoek

    doi: 10.1007/s10482-009-9400-1

    Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5
    Figure Legend Snippet: Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5

    Techniques Used: Agarose Gel Electrophoresis, Marker

    19) Product Images from "i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases"

    Article Title: i-GONAD: a robust method for in situ germline genome engineering using CRISPR nucleases

    Journal: Genome Biology

    doi: 10.1186/s13059-018-1400-x

    Generation of reporter knock-in mice using the i -GONAD method. a Schematic diagram showing insertion of T2A-mCitrine cassette into Pitx3 locus. The target sequence and the genotyping primer sets are shown. A 925-base-long ssDNA synthesized by iv TRT method was used as the donor DNA. b mCitrine fluorescence in fetus collected at E12.5. The eye of the fetus is enlarged as an inset . c Example of genotyping analysis of knock-in G0 fetuses. Expected fragment sizes: M1035/M390 = 948 bp, M389/M1036 = 956 bp, M389/PP226 = 809 bp. N negative control, M size marker. d Representative sequencing chromatogram showing 5′ and 3′ junctional regions of the inserted cassette. The junctional sequences showing insertion derived from G0-#1 in c are shown. Red arrows indicate junctions between the arms and the genomic sequences. e Genome editing efficiency of the Pitx3 locus by the i -GONAD method
    Figure Legend Snippet: Generation of reporter knock-in mice using the i -GONAD method. a Schematic diagram showing insertion of T2A-mCitrine cassette into Pitx3 locus. The target sequence and the genotyping primer sets are shown. A 925-base-long ssDNA synthesized by iv TRT method was used as the donor DNA. b mCitrine fluorescence in fetus collected at E12.5. The eye of the fetus is enlarged as an inset . c Example of genotyping analysis of knock-in G0 fetuses. Expected fragment sizes: M1035/M390 = 948 bp, M389/M1036 = 956 bp, M389/PP226 = 809 bp. N negative control, M size marker. d Representative sequencing chromatogram showing 5′ and 3′ junctional regions of the inserted cassette. The junctional sequences showing insertion derived from G0-#1 in c are shown. Red arrows indicate junctions between the arms and the genomic sequences. e Genome editing efficiency of the Pitx3 locus by the i -GONAD method

    Techniques Used: Knock-In, Mouse Assay, Sequencing, Synthesized, Fluorescence, Negative Control, Marker, Derivative Assay, Genomic Sequencing

    20) Product Images from "Methylation analysis of the glypican 3 gene in embryonal tumours"

    Article Title: Methylation analysis of the glypican 3 gene in embryonal tumours

    Journal: British Journal of Cancer

    doi: 10.1038/sj.bjc.6601716

    Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, Amplification, Expressing

    Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, DNA Methylation Assay

    21) Product Images from "Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.)"

    Article Title: Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.)

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-2084-1

    Nucleotide polymorphisms from an alignment of EPSPS cDNA sequences of allohexaploid wheat and wheat progenitors. Vertical lines in the diagram indicate the position of nucleotide polymorphisms identified in a ClustalW multiple sequence alignment of the 1190-bp cDNA clones from T. aestivum ‘Louise’ (T.a_cDNA#), with our 1190-bp cDNA consensus sequences for T. turgidum (AB progenitor) (T.t_cDNA), Ae. tauschii (D progenitor) (Ae.t_cDNA), T. monococcum (A-relative) (T.m_cDNA), and Ae. speltoides (B-relative) (Ae.s_cDNA). The equivalent 1190-bp sequence of the genomic DNA consensus sequences of “TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1” are shown with intron sequences removed. Only the TaEPSPS-7A1 and TaEPSPS-7D1 cDNAs were recovered by F3-R1 PCR amplification. The corresponding 1190-bp TaEPSPS-4A1 cDNA sequence (T.a_cDNA13) was derived from an independent experiment
    Figure Legend Snippet: Nucleotide polymorphisms from an alignment of EPSPS cDNA sequences of allohexaploid wheat and wheat progenitors. Vertical lines in the diagram indicate the position of nucleotide polymorphisms identified in a ClustalW multiple sequence alignment of the 1190-bp cDNA clones from T. aestivum ‘Louise’ (T.a_cDNA#), with our 1190-bp cDNA consensus sequences for T. turgidum (AB progenitor) (T.t_cDNA), Ae. tauschii (D progenitor) (Ae.t_cDNA), T. monococcum (A-relative) (T.m_cDNA), and Ae. speltoides (B-relative) (Ae.s_cDNA). The equivalent 1190-bp sequence of the genomic DNA consensus sequences of “TaEPSPS-7A1, TaEPSPS-7D1, and TaEPSPS-4A1” are shown with intron sequences removed. Only the TaEPSPS-7A1 and TaEPSPS-7D1 cDNAs were recovered by F3-R1 PCR amplification. The corresponding 1190-bp TaEPSPS-4A1 cDNA sequence (T.a_cDNA13) was derived from an independent experiment

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

    Optimization of the GC-rich TaEPSPS-7A1 PCR amplification. Louise genomic DNA was amplified using the F1.2-R1 primer pair with the indicated buffers designed for amplification of difficult templates (GCI, GCII, D, E, F, G, H, and I), and the indicated concentrations of DMSO (0 %, 2.5 %, 5 %, and 7.5 %). ‘M’ stands for the 1 kb DNA ladder (Thermo Scientific)
    Figure Legend Snippet: Optimization of the GC-rich TaEPSPS-7A1 PCR amplification. Louise genomic DNA was amplified using the F1.2-R1 primer pair with the indicated buffers designed for amplification of difficult templates (GCI, GCII, D, E, F, G, H, and I), and the indicated concentrations of DMSO (0 %, 2.5 %, 5 %, and 7.5 %). ‘M’ stands for the 1 kb DNA ladder (Thermo Scientific)

    Techniques Used: Polymerase Chain Reaction, Amplification

    22) Product Images from "Methylation analysis of the glypican 3 gene in embryonal tumours"

    Article Title: Methylation analysis of the glypican 3 gene in embryonal tumours

    Journal: British Journal of Cancer

    doi: 10.1038/sj.bjc.6601716

    Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, Amplification, Expressing

    Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, DNA Methylation Assay

    23) Product Images from "Epidemiologic Study of Malassezia Yeasts in Seborrheic Dermatitis Patients by the Analysis of 26S rDNA PCR-RFLP"

    Article Title: Epidemiologic Study of Malassezia Yeasts in Seborrheic Dermatitis Patients by the Analysis of 26S rDNA PCR-RFLP

    Journal: Annals of Dermatology

    doi: 10.5021/ad.2010.22.2.149

    PCR-RFLP patterns of 26S rDNA PCR digested with Hha I (A), BtsC I (B) of 11 Malassezia standard strains. Lanes: M: molecular marker, 1: M. furfur (KCTC 7743), 2: M. sympodialis (KCTC 7985), 3: M. globosa (CBS 7966), 4: M. restricta (KCTC 7848), 5: M. slooffiae (KCTC 17431), 6: M. pachydermatis (KCTC 17008), 7: M. japonica (CBS 9432), 8: M. nana (JCM 12085), 9: M. dermatis (JCM 11348), 10: M. obtusa (KCTC 7847), 11: M. yamatoensis (CBS 9725).
    Figure Legend Snippet: PCR-RFLP patterns of 26S rDNA PCR digested with Hha I (A), BtsC I (B) of 11 Malassezia standard strains. Lanes: M: molecular marker, 1: M. furfur (KCTC 7743), 2: M. sympodialis (KCTC 7985), 3: M. globosa (CBS 7966), 4: M. restricta (KCTC 7848), 5: M. slooffiae (KCTC 17431), 6: M. pachydermatis (KCTC 17008), 7: M. japonica (CBS 9432), 8: M. nana (JCM 12085), 9: M. dermatis (JCM 11348), 10: M. obtusa (KCTC 7847), 11: M. yamatoensis (CBS 9725).

    Techniques Used: Polymerase Chain Reaction, Marker

    24) Product Images from "Differential Identification of Mycobacterium tuberculosis Complex and Nontuberculous Mycobacteria by Duplex PCR Assay Using the RNA Polymerase Gene (rpoB)"

    Article Title: Differential Identification of Mycobacterium tuberculosis Complex and Nontuberculous Mycobacteria by Duplex PCR Assay Using the RNA Polymerase Gene (rpoB)

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.42.3.1308-1312.2004

    Algorithm for species identification by DPCR-RFLP (136-bp amplicons) with Msp I and Hae III.
    Figure Legend Snippet: Algorithm for species identification by DPCR-RFLP (136-bp amplicons) with Msp I and Hae III.

    Techniques Used: Digital PCR

    25) Product Images from "Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR"

    Article Title: Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR

    Journal: Journal of Nucleic Acids

    doi: 10.1155/2013/823730

    The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.
    Figure Legend Snippet: The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.

    Techniques Used: Polymerase Chain Reaction, Generated, Amplification, Software

    26) Product Images from "Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes"

    Article Title: Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes

    Journal: Genetics

    doi: 10.1534/genetics.108.094672

    An Idaten transposon was trapped in the invA locus in mutant InvA4. (A–D) Young adults of four strains of V. carteri : (A) CRH22, the wild-type progenitor of all the mutants in this study; (B) strain InvA4; (C) strain InvA4R, a revertant derived
    Figure Legend Snippet: An Idaten transposon was trapped in the invA locus in mutant InvA4. (A–D) Young adults of four strains of V. carteri : (A) CRH22, the wild-type progenitor of all the mutants in this study; (B) strain InvA4; (C) strain InvA4R, a revertant derived

    Techniques Used: Mutagenesis, Derivative Assay

    27) Product Images from "Epidemiologic Study of Malassezia Yeasts in Acne Patients by Analysis of 26S rDNA PCR-RFLP"

    Article Title: Epidemiologic Study of Malassezia Yeasts in Acne Patients by Analysis of 26S rDNA PCR-RFLP

    Journal: Annals of Dermatology

    doi: 10.5021/ad.2011.23.3.321

    PCR-RFLP patterns of 26S rDNA PCR digested with Hha I (A), and Bst F51 (B) of 11 Malassezia standard strains. Lanes: M, molecular marker; 1. M. furfur (KCTC 7743); 2. M. sympodialis (KCTC 7985); 3. M. globosa (CBS 7966); 4. M. restricta (KCTC 7848); 5. M. slooffiae (KCTC 17431); 6. M. pachydermatis (KCTC 17008); 7. M. japonica (CBS 9432); 8. M. nana (JCM 12085); 9. M. dermatis (JCM 11348); 10. M. obtusa (KCTC 7847); 11. M. yamatoensis (CBS 9725).
    Figure Legend Snippet: PCR-RFLP patterns of 26S rDNA PCR digested with Hha I (A), and Bst F51 (B) of 11 Malassezia standard strains. Lanes: M, molecular marker; 1. M. furfur (KCTC 7743); 2. M. sympodialis (KCTC 7985); 3. M. globosa (CBS 7966); 4. M. restricta (KCTC 7848); 5. M. slooffiae (KCTC 17431); 6. M. pachydermatis (KCTC 17008); 7. M. japonica (CBS 9432); 8. M. nana (JCM 12085); 9. M. dermatis (JCM 11348); 10. M. obtusa (KCTC 7847); 11. M. yamatoensis (CBS 9725).

    Techniques Used: Polymerase Chain Reaction, Marker

    28) Product Images from "Skeletal Muscle-specific Calpain Is an Intracellular Na+-dependent Protease *"

    Article Title: Skeletal Muscle-specific Calpain Is an Intracellular Na+-dependent Protease *

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M110.126946

    Scheme for the differential proteome analysis to determine p94 substrates specific for the activating ions. A , total extracts from the GC muscles of WT and p94CS-KI mice were incubated in the presence of NaCl or CsCl and EDTA or of CaCl 2 or MgCl 2 and calpastatin. The samples were spun to obtain the Sup and Ppt fractions, digested by trypsin, and labeled with iTRAQ TM 8-plex reagent. The labeled samples were mixed and analyzed by two-dimensional/tandem mass spectometry, and peptides/proteins were identified by ProteinPilot TM . Candidates for substrates were selected as those showing a significant decrease after incubation with NaCl or CaCl 2 compared with the negative control (CsCl or MgCl 2 , respectively) only for WT but not for p94CS-KI, as indicated in the equations. B , shown is a Western blot analysis of the above samples using anti-pIS2. The above samples (total extracts before centrifugation) before ( lanes 1–4 ) or after ( lanes 5–12 ) incubation with CsCl ( lanes 5 and 7 ), NaCl ( lanes 6 and 8 ), MgCl 2 ( lanes 9 and 11 ), or CaCl 2 ( lanes 10 and 12 ) were examined by Western blot analysis using the anti-IS2 antibody. The upper and middle panels show 30-s and 3-min exposures. Asterisks denote nonspecific signals. The lowest panel , the 210-kDa myosin heavy chain stained by Coomassie Brilliant Blue ( BBC ), shows that each sample had a different protein concentration before the incubation (the second WT sample was especially skewed). The amounts of p94 in the WT and p94CS-KI mouse muscle were roughly equal (see Fig. 2 A ). C , theoretical signal patterns for p94 substrates that were recognized in a Na + -specific ( 1 ), Ca 2+ -specific ( 2 ), or Na + /Ca 2+ ( 3 ) manner (for a list of substrates, see Fig. 6 as indicated). If substrates were constitutively proteolyzed in vivo , their amounts should be lower in WT than in p94CS-KI muscle without in vitro p94 activation. Therefore, they should be lower in WT-CsCl than in p94CS-KI-CsCl ( 4 ∼ 6 ). For candidate in vivo substrates, those identified by only a single kind of peptide were eliminated to avoid false positives (for a list, see Fig. 7 ). The numbers in the right-hand column indicate the number of proteins in each fraction (Sup or Ppt) that showed the corresponding patterns.
    Figure Legend Snippet: Scheme for the differential proteome analysis to determine p94 substrates specific for the activating ions. A , total extracts from the GC muscles of WT and p94CS-KI mice were incubated in the presence of NaCl or CsCl and EDTA or of CaCl 2 or MgCl 2 and calpastatin. The samples were spun to obtain the Sup and Ppt fractions, digested by trypsin, and labeled with iTRAQ TM 8-plex reagent. The labeled samples were mixed and analyzed by two-dimensional/tandem mass spectometry, and peptides/proteins were identified by ProteinPilot TM . Candidates for substrates were selected as those showing a significant decrease after incubation with NaCl or CaCl 2 compared with the negative control (CsCl or MgCl 2 , respectively) only for WT but not for p94CS-KI, as indicated in the equations. B , shown is a Western blot analysis of the above samples using anti-pIS2. The above samples (total extracts before centrifugation) before ( lanes 1–4 ) or after ( lanes 5–12 ) incubation with CsCl ( lanes 5 and 7 ), NaCl ( lanes 6 and 8 ), MgCl 2 ( lanes 9 and 11 ), or CaCl 2 ( lanes 10 and 12 ) were examined by Western blot analysis using the anti-IS2 antibody. The upper and middle panels show 30-s and 3-min exposures. Asterisks denote nonspecific signals. The lowest panel , the 210-kDa myosin heavy chain stained by Coomassie Brilliant Blue ( BBC ), shows that each sample had a different protein concentration before the incubation (the second WT sample was especially skewed). The amounts of p94 in the WT and p94CS-KI mouse muscle were roughly equal (see Fig. 2 A ). C , theoretical signal patterns for p94 substrates that were recognized in a Na + -specific ( 1 ), Ca 2+ -specific ( 2 ), or Na + /Ca 2+ ( 3 ) manner (for a list of substrates, see Fig. 6 as indicated). If substrates were constitutively proteolyzed in vivo , their amounts should be lower in WT than in p94CS-KI muscle without in vitro p94 activation. Therefore, they should be lower in WT-CsCl than in p94CS-KI-CsCl ( 4 ∼ 6 ). For candidate in vivo substrates, those identified by only a single kind of peptide were eliminated to avoid false positives (for a list, see Fig. 7 ). The numbers in the right-hand column indicate the number of proteins in each fraction (Sup or Ppt) that showed the corresponding patterns.

    Techniques Used: Mouse Assay, Incubation, Labeling, Negative Control, Western Blot, Centrifugation, Staining, Protein Concentration, In Vivo, In Vitro, Activation Assay

    29) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

    Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1432-5

    Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
    Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

    Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

    30) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

    Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-1432-5

    Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
    Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

    Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

    31) Product Images from "Duplex fluorescence melting curve analysis as a new tool for rapid detection and differentiation of genotype I, II and Bartha-K61 vaccine strains of pseudorabies virus"

    Article Title: Duplex fluorescence melting curve analysis as a new tool for rapid detection and differentiation of genotype I, II and Bartha-K61 vaccine strains of pseudorabies virus

    Journal: BMC Veterinary Research

    doi: 10.1186/s12917-018-1697-4

    Schematic illustration of the duplex FMCA method. ( a ) Relative binding positions of primers and probes along the gC gene of PRV. Melting peak calculation by derivative plotting -dF/dT versus temperature in the FAM channel ( b ) and the HEX channel ( c ). Red, blue, and green lines represent Bartha-K61 vaccine, European/American (Genotype I), and Chinese (Genotype II) strains, respectively
    Figure Legend Snippet: Schematic illustration of the duplex FMCA method. ( a ) Relative binding positions of primers and probes along the gC gene of PRV. Melting peak calculation by derivative plotting -dF/dT versus temperature in the FAM channel ( b ) and the HEX channel ( c ). Red, blue, and green lines represent Bartha-K61 vaccine, European/American (Genotype I), and Chinese (Genotype II) strains, respectively

    Techniques Used: Binding Assay

    32) Product Images from "Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice"

    Article Title: Ectopic expression of a cytochrome P450 monooxygenase gene PtCYP714A3 from Populus trichocarpa reduces shoot growth and improves tolerance to salt stress in transgenic rice

    Journal: Plant Biotechnology Journal

    doi: 10.1111/pbi.12544

    Quantitative real‐time PCR analyses of salt tolerance‐related marker genes. Three‐week‐old seedlings treated with 150 m m NaCl for 12 h or 0 h (Control) were harvested for total RNA extraction, transverse transcription and real‐time PCR analyses. WT , wild type; Z33 and Z38, independent transgenic lines. Values are means ± SD of three biological replicates from the WT or the transgenic lines. Asterisks indicate statistically significant difference in comparison with the WT (Student's t ‐test, *, P
    Figure Legend Snippet: Quantitative real‐time PCR analyses of salt tolerance‐related marker genes. Three‐week‐old seedlings treated with 150 m m NaCl for 12 h or 0 h (Control) were harvested for total RNA extraction, transverse transcription and real‐time PCR analyses. WT , wild type; Z33 and Z38, independent transgenic lines. Values are means ± SD of three biological replicates from the WT or the transgenic lines. Asterisks indicate statistically significant difference in comparison with the WT (Student's t ‐test, *, P

    Techniques Used: Real-time Polymerase Chain Reaction, Marker, RNA Extraction, Transgenic Assay

    33) Product Images from "Visual detection of the human metapneumovirus using reverse transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye"

    Article Title: Visual detection of the human metapneumovirus using reverse transcription loop-mediated isothermal amplification with hydroxynaphthol blue dye

    Journal: Virology Journal

    doi: 10.1186/1743-422X-9-138

    hMPV RT-LAMP amplification and digestion of positive RT-LAMP products. (A ) RT-LAMP products were examined by agarose gel electrophoresis (upper panel) and visually amplification for color change (lower panel). Lane M, DNA marker DL2000 (Biomed, China, with bands of 2000, 1000, 750, 500, 250 and 100 bp); 1–2, positive hMPV RNA; 3, DEPC-treated H 2 O. (B) RT-LAMP products were digested with Msp I, and two fragments (103 bp, 116 bp) were observed by polyacrylamide gel electrophoresis attained with ethidium bromide and photographed under a UV transilluminator. 1, RT-LAMP products without digestion; 2, RT-LAMP products digested by Msp I; M, DNA marker DL500 (Biomed, China, with bands of 500, 400, 300, 250, 200, 150, 100 and 50 bp).
    Figure Legend Snippet: hMPV RT-LAMP amplification and digestion of positive RT-LAMP products. (A ) RT-LAMP products were examined by agarose gel electrophoresis (upper panel) and visually amplification for color change (lower panel). Lane M, DNA marker DL2000 (Biomed, China, with bands of 2000, 1000, 750, 500, 250 and 100 bp); 1–2, positive hMPV RNA; 3, DEPC-treated H 2 O. (B) RT-LAMP products were digested with Msp I, and two fragments (103 bp, 116 bp) were observed by polyacrylamide gel electrophoresis attained with ethidium bromide and photographed under a UV transilluminator. 1, RT-LAMP products without digestion; 2, RT-LAMP products digested by Msp I; M, DNA marker DL500 (Biomed, China, with bands of 500, 400, 300, 250, 200, 150, 100 and 50 bp).

    Techniques Used: Amplification, Agarose Gel Electrophoresis, Marker, Polyacrylamide Gel Electrophoresis

    hMPV RT-LAMP amplification and digestion of positive RT-LAMP products. (A ) RT-LAMP products were examined by agarose gel electrophoresis (upper panel) and visually amplification for color change (lower panel). Lane M, DNA marker DL2000 (Biomed, China, with bands of 2000, 1000, 750, 500, 250 and 100 bp); 1–2, positive hMPV RNA; 3, DEPC-treated H 2 O. (B) RT-LAMP products were digested with Msp I, and two fragments (103 bp, 116 bp) were observed by polyacrylamide gel electrophoresis attained with ethidium bromide and photographed under a UV transilluminator. 1, RT-LAMP products without digestion; 2, RT-LAMP products digested by Msp I; M, DNA marker DL500 (Biomed, China, with bands of 500, 400, 300, 250, 200, 150, 100 and 50 bp).
    Figure Legend Snippet: hMPV RT-LAMP amplification and digestion of positive RT-LAMP products. (A ) RT-LAMP products were examined by agarose gel electrophoresis (upper panel) and visually amplification for color change (lower panel). Lane M, DNA marker DL2000 (Biomed, China, with bands of 2000, 1000, 750, 500, 250 and 100 bp); 1–2, positive hMPV RNA; 3, DEPC-treated H 2 O. (B) RT-LAMP products were digested with Msp I, and two fragments (103 bp, 116 bp) were observed by polyacrylamide gel electrophoresis attained with ethidium bromide and photographed under a UV transilluminator. 1, RT-LAMP products without digestion; 2, RT-LAMP products digested by Msp I; M, DNA marker DL500 (Biomed, China, with bands of 500, 400, 300, 250, 200, 150, 100 and 50 bp).

    Techniques Used: Amplification, Agarose Gel Electrophoresis, Marker, Polyacrylamide Gel Electrophoresis

    34) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

    Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0116192

    Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
    Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

    Techniques Used: Polymerase Chain Reaction, Sequencing

    35) Product Images from "Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.)"

    Article Title: Molecular and phylogenetic characterization of the homoeologous EPSP Synthase genes of allohexaploid wheat, Triticum aestivum (L.)

    Journal: BMC Genomics

    doi: 10.1186/s12864-015-2084-1

    Exon-intron structure of the wheat EPSPS genes compared to OsEPSPS . The boxes and solid lines represent exons (E#) and introns (I#), respectively. Numbers indicate exon and intron size in bp. The cleavage site of the chloroplastic transit signal peptide (cTP) predicted by PredSL is shown. The positions of the primers F1.2, F3, and R1 (arrows) used for initial genomic and cDNA cloning are labeled
    Figure Legend Snippet: Exon-intron structure of the wheat EPSPS genes compared to OsEPSPS . The boxes and solid lines represent exons (E#) and introns (I#), respectively. Numbers indicate exon and intron size in bp. The cleavage site of the chloroplastic transit signal peptide (cTP) predicted by PredSL is shown. The positions of the primers F1.2, F3, and R1 (arrows) used for initial genomic and cDNA cloning are labeled

    Techniques Used: Clone Assay, Labeling

    Optimization of the GC-rich TaEPSPS-7A1 PCR amplification. Louise genomic DNA was amplified using the F1.2-R1 primer pair with the indicated buffers designed for amplification of difficult templates (GCI, GCII, D, E, F, G, H, and I), and the indicated concentrations of DMSO (0 %, 2.5 %, 5 %, and 7.5 %). ‘M’ stands for the 1 kb DNA ladder (Thermo Scientific)
    Figure Legend Snippet: Optimization of the GC-rich TaEPSPS-7A1 PCR amplification. Louise genomic DNA was amplified using the F1.2-R1 primer pair with the indicated buffers designed for amplification of difficult templates (GCI, GCII, D, E, F, G, H, and I), and the indicated concentrations of DMSO (0 %, 2.5 %, 5 %, and 7.5 %). ‘M’ stands for the 1 kb DNA ladder (Thermo Scientific)

    Techniques Used: Polymerase Chain Reaction, Amplification

    36) Product Images from "Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes"

    Article Title: Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes

    Journal: Genetics

    doi: 10.1534/genetics.108.094672

    Transposon tagging with Idaten-2 . (A) A young adult of the “fully inversionless” mutant, InvC1; note gonidia that are exposed on the outside. Bar, 100 μm. (B) A young adult of InvC1R, a revertant strain derived from InvC; note
    Figure Legend Snippet: Transposon tagging with Idaten-2 . (A) A young adult of the “fully inversionless” mutant, InvC1; note gonidia that are exposed on the outside. Bar, 100 μm. (B) A young adult of InvC1R, a revertant strain derived from InvC; note

    Techniques Used: Mutagenesis, Derivative Assay

    Structure of Idaten . (A) Schematic maps of Idaten and Idaten-2 . The pair of solid triangles at opposite ends represent the terminal inverted repeats (TIRs). Both elements contain repetitive regions (striped boxes). Repetitive region I is enriched in C
    Figure Legend Snippet: Structure of Idaten . (A) Schematic maps of Idaten and Idaten-2 . The pair of solid triangles at opposite ends represent the terminal inverted repeats (TIRs). Both elements contain repetitive regions (striped boxes). Repetitive region I is enriched in C

    Techniques Used:

    Modifications of target-site sequences that are associated with insertion and excision of Idaten and Idaten-2 . The 3-bp TSDs are shown in boldface type. Open rectangles with closed triangles at their ends represent Idaten or Idaten-2 inserts. In the revertants,
    Figure Legend Snippet: Modifications of target-site sequences that are associated with insertion and excision of Idaten and Idaten-2 . The 3-bp TSDs are shown in boldface type. Open rectangles with closed triangles at their ends represent Idaten or Idaten-2 inserts. In the revertants,

    Techniques Used:

    37) Product Images from "Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China"

    Article Title: Combination of Single Nucleotide Polymorphism and Variable-Number Tandem Repeats for Genotyping a Homogenous Population of Mycobacterium tuberculosis Beijing Strains in China

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.05539-11

    VNTR-15-based dendrogram and 3-hypervariable-VNTR-locus profiles of the five clusters with mixed sublineages. The boxes in the sublineage section indicate the five clusters (numbered as in ); boxes in hypervariable locus section indicate clustered
    Figure Legend Snippet: VNTR-15-based dendrogram and 3-hypervariable-VNTR-locus profiles of the five clusters with mixed sublineages. The boxes in the sublineage section indicate the five clusters (numbered as in ); boxes in hypervariable locus section indicate clustered

    Techniques Used:

    38) Product Images from "Methylation analysis of the glypican 3 gene in embryonal tumours"

    Article Title: Methylation analysis of the glypican 3 gene in embryonal tumours

    Journal: British Journal of Cancer

    doi: 10.1038/sj.bjc.6601716

    Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in nontumoural samples. ( A ) CpG dinucleotides positions in the GPC3 promoter region. The methylation status of 11 of these CpG sites was determined either by the PCR-based methylation assay (#) or by the Southern blot-based methylation assay (+) using methyl-sensitive restriction endonucleases Hpa II (H), Sac II (S), Eag I (E), and Bss HII (B). Hpa II contains one CpG site, whereas Sac II, Eag I and Bss HII contain two CpG sites each. The distal and proximal sites were amplified in distinct PCRs. ( B and C ) Representative results of the methylation analysis in normal peripheral blood and placental DNA samples obtained by the PCR-based ( B ) and Southern blot-based ( C ) methylation assays. See Table 1 for details concerning the samples. ( D ) PCR-based methylation assay performed on DNA samples from two individuals (AC-1 and DC) affected by the Turner syndrome. Digestions: ( B and D ) H, Hpa II; M, Msp I; U, undigested; ( C ) H, Hind III; B, Bss HII; S, Sac II and E, Eag I. GPC3+, expression of GPC3; GPC3−, no expression of GPC3.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, Amplification, Expressing

    Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.
    Figure Legend Snippet: Methylation analysis of the GPC3 promoter in tumour cell DNA samples. PCR- ( A ) and Southern blot- ( B ) based methylation assays were performed on tumour cell DNA samples from NB cell lines (SK-N-AS, SK-N-SH), primary NBs (N4, N5) and primary WTs (WT51, WT116, WT158, WT177). Only results for samples with abnormal DNA methylation patterns are shown. Digestions: ( A ) H: Hpa II; M: Msp I; U: undigested; ( B ) H: Hind III; B: Bss HII; S: Sac II and E: Eag I.

    Techniques Used: Methylation, Polymerase Chain Reaction, Southern Blot, DNA Methylation Assay

    Related Articles

    Clone Assay:

    Article Title: Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage ▿Spatial and Temporal Analysis of the Microbial Community in the Tailings of a Pb-Zn Mine Generating Acidic Drainage ▿ †
    Article Snippet: .. Randomly selected clones from each library were screened by restriction fragment length polymorphism (RFLP) analysis with separate enzymatic digestions by the MspI and RsaI endonucleases (Takara). .. Representative clones from each unique RFLP pattern were examined for their rRNA gene insert orientation and then sequenced in a forward direction using the M13/pUC universal primers on ABI 3730 xl capillary sequencers (Applied Biosystems).

    Agarose Gel Electrophoresis:

    Article Title: Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken
    Article Snippet: .. Thereafter, 3 µ L of each PCR product was separately digested with Taq I (New England Biolabs, Ipswich, MA, USA) and Msp I (TaKaRa Bio) incubated at 65°C or 37°C, respectively for 4 to 8 h, and then electrophoresed on a 2% agarose gel stained with ethidium bromide to visualize the DNA. .. Sequencing of PIT-1 Intron 5 After PCR-RFLP, amplified DNA that showed diverse digestion patterns for PIT-1/Msp I was selected for direct sequencing.

    Purification:

    Article Title: The Early Intestinal Microbiota of Healthy Korean Newborns
    Article Snippet: .. Restriction enzymes, HhaI (TaKara, 2,000 U) and MspI (TaKara, 3,000 U), were used to cut the purified PCR product. .. HhaI (2.0 µL) was mixed and incubated with 10X M-buffer (1.0 µL).

    Article Title: Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing
    Article Snippet: .. The PCR products were purified with MinElute® PCR Purification Kit (QIAGEN), then independently digested with restriction enzymes: Hha I (Takara Bio) and Msp I (Takara Bio). .. The digested fragments were separated by capillary electrophoresis (ABI Prism 3100 Genetic Analyzer, Applied Biosystems) as described in Noguchi et al. ( ).

    Article Title: Genetic Diversity and Phylogeny of Antagonistic Bacteria against Phytophthora nicotianae Isolated from Tobacco Rhizosphere
    Article Snippet: .. Purified PCR products were digested with four enzymes; Alu I, Hae III, Hinf I and Msp I (TaKaRa Biotechnology (Dalian) Co., Ltd.) in separate digestion reactions. .. The selection of the four restriction enzymes was based on the studies of Laguerre et al .

    Electrophoresis:

    Article Title: Polymorphisms in programmed death-1 gene are not associated with chronic HBV infection in Chinese patients
    Article Snippet: .. The polymerase chain reaction (PCR) product 265 bp was digested with MspI (TaKaRa Biotechnology, Co., Ltd. Dalian, China) according to the manufacturer’s instructions [total reaction volume 20 μL, including PCR product 10 μL, 10× T buffer 2 μL, 0.1% BSA 2 μL, restriction enzyme (10 U/μL) 1μL, H2 O 5 μL] and separated by electrophoresis on 3% agarose gels. ..

    Incubation:

    Article Title: Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken
    Article Snippet: .. Thereafter, 3 µ L of each PCR product was separately digested with Taq I (New England Biolabs, Ipswich, MA, USA) and Msp I (TaKaRa Bio) incubated at 65°C or 37°C, respectively for 4 to 8 h, and then electrophoresed on a 2% agarose gel stained with ethidium bromide to visualize the DNA. .. Sequencing of PIT-1 Intron 5 After PCR-RFLP, amplified DNA that showed diverse digestion patterns for PIT-1/Msp I was selected for direct sequencing.

    Article Title: DNA methylation in diploid inbred lines of potatoes and its possible role in the regulation of heterosis
    Article Snippet: .. Approximately 8 μg of DNA was digested completely by overnight incubation at 37°C with 25 units of Msp I (Takara Bio Inc., Japan) or 12 units of Hpa II (Toyobo Co., Ltd., Japan). .. Restriction enzymes Hpa II and Msp I recognize the same four-base sequence (CCGG) and cut DNA depending on the methylation status of internal cytosine.

    Polymerase Chain Reaction:

    Article Title: The Early Intestinal Microbiota of Healthy Korean Newborns
    Article Snippet: .. Restriction enzymes, HhaI (TaKara, 2,000 U) and MspI (TaKara, 3,000 U), were used to cut the purified PCR product. .. HhaI (2.0 µL) was mixed and incubated with 10X M-buffer (1.0 µL).

    Article Title: Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken
    Article Snippet: .. Thereafter, 3 µ L of each PCR product was separately digested with Taq I (New England Biolabs, Ipswich, MA, USA) and Msp I (TaKaRa Bio) incubated at 65°C or 37°C, respectively for 4 to 8 h, and then electrophoresed on a 2% agarose gel stained with ethidium bromide to visualize the DNA. .. Sequencing of PIT-1 Intron 5 After PCR-RFLP, amplified DNA that showed diverse digestion patterns for PIT-1/Msp I was selected for direct sequencing.

    Article Title: Development of a 16S rRNA Gene Primer and PCR-Restriction Fragment Length Polymorphism Method for Rapid Detection of Members of the Genus Megasphaera and Species-Level Identification ▿ and Species-Level Identification ▿ †
    Article Snippet: .. For restriction enzyme digestion, 10 μl of the PCR product was mixed with 20 U of HaeIII and MspI (Takara), according to the manufacturer's instructions. .. The restriction fragments were electrophoresed on a 4% agarose gel.

    Article Title: Polymorphisms in programmed death-1 gene are not associated with chronic HBV infection in Chinese patients
    Article Snippet: .. The polymerase chain reaction (PCR) product 265 bp was digested with MspI (TaKaRa Biotechnology, Co., Ltd. Dalian, China) according to the manufacturer’s instructions [total reaction volume 20 μL, including PCR product 10 μL, 10× T buffer 2 μL, 0.1% BSA 2 μL, restriction enzyme (10 U/μL) 1μL, H2 O 5 μL] and separated by electrophoresis on 3% agarose gels. ..

    Article Title: Bacterial Degraders of Coexisting Dichloromethane, Benzene, and Toluene, Identified by Stable-Isotope Probing
    Article Snippet: .. The PCR products were purified with MinElute® PCR Purification Kit (QIAGEN), then independently digested with restriction enzymes: Hha I (Takara Bio) and Msp I (Takara Bio). .. The digested fragments were separated by capillary electrophoresis (ABI Prism 3100 Genetic Analyzer, Applied Biosystems) as described in Noguchi et al. ( ).

    Article Title: Genetic Diversity and Phylogeny of Antagonistic Bacteria against Phytophthora nicotianae Isolated from Tobacco Rhizosphere
    Article Snippet: .. Purified PCR products were digested with four enzymes; Alu I, Hae III, Hinf I and Msp I (TaKaRa Biotechnology (Dalian) Co., Ltd.) in separate digestion reactions. .. The selection of the four restriction enzymes was based on the studies of Laguerre et al .

    Staining:

    Article Title: Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken
    Article Snippet: .. Thereafter, 3 µ L of each PCR product was separately digested with Taq I (New England Biolabs, Ipswich, MA, USA) and Msp I (TaKaRa Bio) incubated at 65°C or 37°C, respectively for 4 to 8 h, and then electrophoresed on a 2% agarose gel stained with ethidium bromide to visualize the DNA. .. Sequencing of PIT-1 Intron 5 After PCR-RFLP, amplified DNA that showed diverse digestion patterns for PIT-1/Msp I was selected for direct sequencing.

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