16s mitochondrial  (Kapa Biosystems)


Bioz Verified Symbol Kapa Biosystems is a verified supplier
Bioz Manufacturer Symbol Kapa Biosystems manufactures this product  
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 85

    Structured Review

    Kapa Biosystems 16s mitochondrial
    Phylogenetic analysis of the concatenated <t>18S-16S</t> rRNA dataset. Indicated is the 50% majority consensus tree obtained with Bayesian as well as maximum parsimony analysis. Posterior probability and bootstrap support values are indicated above and below the nodes, respectively. Genbank accession numbers are indicated in brackets as 18S_16S.
    16s Mitochondrial, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 85/100, based on 134 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/16s mitochondrial/product/Kapa Biosystems
    Average 85 stars, based on 134 article reviews
    Price from $9.99 to $1999.99
    16s mitochondrial - by Bioz Stars, 2021-01
    85/100 stars

    Images

    1) Product Images from "Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks"

    Article Title: Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0023675

    Phylogenetic analysis of the concatenated 18S-16S rRNA dataset. Indicated is the 50% majority consensus tree obtained with Bayesian as well as maximum parsimony analysis. Posterior probability and bootstrap support values are indicated above and below the nodes, respectively. Genbank accession numbers are indicated in brackets as 18S_16S.
    Figure Legend Snippet: Phylogenetic analysis of the concatenated 18S-16S rRNA dataset. Indicated is the 50% majority consensus tree obtained with Bayesian as well as maximum parsimony analysis. Posterior probability and bootstrap support values are indicated above and below the nodes, respectively. Genbank accession numbers are indicated in brackets as 18S_16S.

    Techniques Used:

    2) Product Images from "Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation"

    Article Title: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

    Journal: Evolutionary Applications

    doi: 10.1111/eva.12274

    (A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table 1 ). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.
    Figure Legend Snippet: (A) STRUCTURE plots for Black-footed Albatross using RADseq data set 2 (see Table 1 ). Models with K = 3–5 were the most highly supported and consistently suggest two clusters corresponding to Hawaii and Japan, albeit differentiated in only a small portion of the genome. (B) Discriminant analysis of principal component (DAPC) plot based on data set 1 indicating that Hawaiian individuals from Tern and from Midway group together, but not with individuals from Izu-Torishima in Japan.

    Techniques Used:

    3) Product Images from "The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif"

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2014.00499

    pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.
    Figure Legend Snippet: pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Countercurrent Chromatography, Polymerase Chain Reaction, Positive Control

    Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).
    Figure Legend Snippet: Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).

    Techniques Used: Plasmid Preparation, Sequencing

    4) Product Images from "The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif"

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2014.00499

    pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.
    Figure Legend Snippet: pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Countercurrent Chromatography, Polymerase Chain Reaction, Positive Control

    5) Product Images from "SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum"

    Article Title: SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum

    Journal: Scientific Reports

    doi: 10.1038/srep09257

    CYP2D6*17 (1023C > T) TaqMan Assay Genotype Results. (Panels A and B) show the scatter plots for TaqMan assays C__2222771_40 (original assay) and C__2222771_A0 (alternative assay). Numbered subjects correspond to cases 1–9 and 21–23 ( Tables 1 and 2 ). Cases 1–9 were identified as 1023 T/T with the original assay (panel A), but genotyped accurately as 1023 C/T with the alternative assay (panel B). Additional samples of known genotypes were analyzed as references to allow cluster formation in the scatter plots; none of these controls carry a CYP2D6*4 .
    Figure Legend Snippet: CYP2D6*17 (1023C > T) TaqMan Assay Genotype Results. (Panels A and B) show the scatter plots for TaqMan assays C__2222771_40 (original assay) and C__2222771_A0 (alternative assay). Numbered subjects correspond to cases 1–9 and 21–23 ( Tables 1 and 2 ). Cases 1–9 were identified as 1023 T/T with the original assay (panel A), but genotyped accurately as 1023 C/T with the alternative assay (panel B). Additional samples of known genotypes were analyzed as references to allow cluster formation in the scatter plots; none of these controls carry a CYP2D6*4 .

    Techniques Used: TaqMan Assay

    CYP2D6*4 subvariants. The top panel provides details about the SNVs including rs numbers, positions relative to the numbering system on which the allele nomenclature is based (M33388) and the widely accepted CYP2D6*1 reference sequence AY545216, the nature of the SNV, and sequence context. The presence of the intron 1 conversion event is characterized by multiple SNPs (rs1080995, rs267608284, rs108996, rs74644586, rs75276289, rs28695233, rs149744965, rs56011157). The middle ‘checkerboard’ panel shows SNVs relative to the AY545216 reference. Variation is highlighted by colored boxes. Gray boxes denote sequence errors in M33388. For general information, sequence differences to Genome Build GRCh37 that harbors a CYP2D6*2 , is shown. Lines *4A through *4N depict a graphical representation of the P450 Nomenclature Database 20 for these alleles. Note that *4A-K lacks any annotations for intronic regions. Sequence variations found in cases 1 and 21 that match with CYP2D6*4A and *4D are highlighted in red and blue, respectively. Intronic SNPs in the cases are shown in light red and blue as these are not represented in the nomenclature-defined variants. Cases were sequenced between the SNPs shown in yellow. The bottom panels provide location of SNV regarding to exon and intron and consequence of SNV.
    Figure Legend Snippet: CYP2D6*4 subvariants. The top panel provides details about the SNVs including rs numbers, positions relative to the numbering system on which the allele nomenclature is based (M33388) and the widely accepted CYP2D6*1 reference sequence AY545216, the nature of the SNV, and sequence context. The presence of the intron 1 conversion event is characterized by multiple SNPs (rs1080995, rs267608284, rs108996, rs74644586, rs75276289, rs28695233, rs149744965, rs56011157). The middle ‘checkerboard’ panel shows SNVs relative to the AY545216 reference. Variation is highlighted by colored boxes. Gray boxes denote sequence errors in M33388. For general information, sequence differences to Genome Build GRCh37 that harbors a CYP2D6*2 , is shown. Lines *4A through *4N depict a graphical representation of the P450 Nomenclature Database 20 for these alleles. Note that *4A-K lacks any annotations for intronic regions. Sequence variations found in cases 1 and 21 that match with CYP2D6*4A and *4D are highlighted in red and blue, respectively. Intronic SNPs in the cases are shown in light red and blue as these are not represented in the nomenclature-defined variants. Cases were sequenced between the SNPs shown in yellow. The bottom panels provide location of SNV regarding to exon and intron and consequence of SNV.

    Techniques Used: Sequencing

    Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.
    Figure Legend Snippet: Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.

    Techniques Used: Sequencing, Variant Assay, Polymerase Chain Reaction, Binding Assay, TaqMan Assay

    Real-time amplification for the original and alternate CYP2D6*17 TaqMan assays. Fluorescent signals detected for individuals with CYP2D6*4/*4 and CYP2D6*1/*1 genotypes. (Panels A and C) represents the original TaqMan assay (C__222771_40), (panels B and D) the alternate assay C__2222771_A0). The green curves indicate amplification from the ‘C’ allele (wild-type/reference, 1023C or CYP2D6*17 ) while the green curve represents the ‘T’ allele (variant, 1023 T, CYP2D6*17 or other variant haplotype containing this SNP).
    Figure Legend Snippet: Real-time amplification for the original and alternate CYP2D6*17 TaqMan assays. Fluorescent signals detected for individuals with CYP2D6*4/*4 and CYP2D6*1/*1 genotypes. (Panels A and C) represents the original TaqMan assay (C__222771_40), (panels B and D) the alternate assay C__2222771_A0). The green curves indicate amplification from the ‘C’ allele (wild-type/reference, 1023C or CYP2D6*17 ) while the green curve represents the ‘T’ allele (variant, 1023 T, CYP2D6*17 or other variant haplotype containing this SNP).

    Techniques Used: Amplification, TaqMan Assay, Variant Assay

    6) Product Images from "Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks"

    Article Title: Nuttalliella namaqua: A Living Fossil and Closest Relative to the Ancestral Tick Lineage: Implications for the Evolution of Blood-Feeding in Ticks

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0023675

    Phylogenetic analysis of the concatenated 18S-16S rRNA dataset. Indicated is the 50% majority consensus tree obtained with Bayesian as well as maximum parsimony analysis. Posterior probability and bootstrap support values are indicated above and below the nodes, respectively. Genbank accession numbers are indicated in brackets as 18S_16S.
    Figure Legend Snippet: Phylogenetic analysis of the concatenated 18S-16S rRNA dataset. Indicated is the 50% majority consensus tree obtained with Bayesian as well as maximum parsimony analysis. Posterior probability and bootstrap support values are indicated above and below the nodes, respectively. Genbank accession numbers are indicated in brackets as 18S_16S.

    Techniques Used:

    Bayesian analysis of the 18S rRNA gene for the parasitiformes. Nodal support is indicated by posterior probability values. Genbank accession numbers are indicated in brackets.
    Figure Legend Snippet: Bayesian analysis of the 18S rRNA gene for the parasitiformes. Nodal support is indicated by posterior probability values. Genbank accession numbers are indicated in brackets.

    Techniques Used:

    7) Product Images from "Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study"

    Article Title: Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study

    Journal: BMC Medical Genetics

    doi: 10.1186/s12881-018-0681-y

    Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)
    Figure Legend Snippet: Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)

    Techniques Used: Real-time Polymerase Chain Reaction

    8) Product Images from "Evidence Suggesting that Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors"

    Article Title: Evidence Suggesting that Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors

    Journal: Cancer research

    doi: 10.1158/0008-5472.CAN-14-3437

    NPM-ALK up-regulation drives resistance-dependence. A, LI-WGS reads indicate NPM-ALK amplification in resistant-dependent subclone. B, copy-number assay confirms gain specifically of the fusion kinase-encoding regions of NPM and ALK
    Figure Legend Snippet: NPM-ALK up-regulation drives resistance-dependence. A, LI-WGS reads indicate NPM-ALK amplification in resistant-dependent subclone. B, copy-number assay confirms gain specifically of the fusion kinase-encoding regions of NPM and ALK

    Techniques Used: Amplification

    ALK up-regulation drives resistance-dependence in transformed pro-B cells. A, retroviral introduction of NPM-ALK in a GFP co-expressing vector transformed FL5.12 cells to cytokine independence with simultaneous ceritinib incubation. (*Cells did not survive.)
    Figure Legend Snippet: ALK up-regulation drives resistance-dependence in transformed pro-B cells. A, retroviral introduction of NPM-ALK in a GFP co-expressing vector transformed FL5.12 cells to cytokine independence with simultaneous ceritinib incubation. (*Cells did not survive.)

    Techniques Used: Transformation Assay, Expressing, Plasmid Preparation, Incubation

    9) Product Images from "SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum"

    Article Title: SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum

    Journal: Scientific Reports

    doi: 10.1038/srep09257

    Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.
    Figure Legend Snippet: Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.

    Techniques Used: Sequencing, Variant Assay, Polymerase Chain Reaction, Binding Assay, TaqMan Assay

    10) Product Images from "SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum"

    Article Title: SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum

    Journal: Scientific Reports

    doi: 10.1038/srep09257

    Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.
    Figure Legend Snippet: Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.

    Techniques Used: Sequencing, Variant Assay, Polymerase Chain Reaction, Binding Assay, TaqMan Assay

    11) Product Images from "Evidence Suggesting that Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors"

    Article Title: Evidence Suggesting that Discontinuous Dosing of ALK Kinase Inhibitors May Prolong Control of ALK+ Tumors

    Journal: Cancer research

    doi: 10.1158/0008-5472.CAN-14-3437

    NPM-ALK up-regulation drives resistance-dependence. A, LI-WGS reads indicate NPM-ALK amplification in resistant-dependent subclone. B, copy-number assay confirms gain specifically of the fusion kinase-encoding regions of NPM and ALK
    Figure Legend Snippet: NPM-ALK up-regulation drives resistance-dependence. A, LI-WGS reads indicate NPM-ALK amplification in resistant-dependent subclone. B, copy-number assay confirms gain specifically of the fusion kinase-encoding regions of NPM and ALK

    Techniques Used: Amplification

    ALK up-regulation drives resistance-dependence in transformed pro-B cells. A, retroviral introduction of NPM-ALK in a GFP co-expressing vector transformed FL5.12 cells to cytokine independence with simultaneous ceritinib incubation. (*Cells did not survive.)
    Figure Legend Snippet: ALK up-regulation drives resistance-dependence in transformed pro-B cells. A, retroviral introduction of NPM-ALK in a GFP co-expressing vector transformed FL5.12 cells to cytokine independence with simultaneous ceritinib incubation. (*Cells did not survive.)

    Techniques Used: Transformation Assay, Expressing, Plasmid Preparation, Incubation

    12) Product Images from "Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study"

    Article Title: Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study

    Journal: BMC Medical Genetics

    doi: 10.1186/s12881-018-0681-y

    Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)
    Figure Legend Snippet: Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)

    Techniques Used: Real-time Polymerase Chain Reaction

    13) Product Images from "The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif"

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2014.00499

    pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.
    Figure Legend Snippet: pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Countercurrent Chromatography, Polymerase Chain Reaction, Positive Control

    Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).
    Figure Legend Snippet: Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).

    Techniques Used: Plasmid Preparation, Sequencing

    Genetic crosses to visualize transfer and intramycelial plasmid spreading of pIJ303 and its derivatives . Dilutions of S. lividans TK54 containing derivatives of plasmid pIJ303 (thio R ) were streaked on a lawn (~10 6 spores) of plasmid free TK64::pSET152 (apra R ) on R5 plates, as schematically illustrated (A) . Pock structures associated with the conjugative plasmid transfer were visible after 2 days of incubation at 30°C (B) . After 7 days of incubation the fully sporulated plate (C) was replica plated on LB containing apramycin and thiostrepton to select for transconjugants (D) . Pock diameters and sizes of the transconjugant areas indicating efficiency of conjugative transfer and intramycelial plasmid spreading were approximately the same for all derivatives of pIJ303.
    Figure Legend Snippet: Genetic crosses to visualize transfer and intramycelial plasmid spreading of pIJ303 and its derivatives . Dilutions of S. lividans TK54 containing derivatives of plasmid pIJ303 (thio R ) were streaked on a lawn (~10 6 spores) of plasmid free TK64::pSET152 (apra R ) on R5 plates, as schematically illustrated (A) . Pock structures associated with the conjugative plasmid transfer were visible after 2 days of incubation at 30°C (B) . After 7 days of incubation the fully sporulated plate (C) was replica plated on LB containing apramycin and thiostrepton to select for transconjugants (D) . Pock diameters and sizes of the transconjugant areas indicating efficiency of conjugative transfer and intramycelial plasmid spreading were approximately the same for all derivatives of pIJ303.

    Techniques Used: Plasmid Preparation, Incubation

    14) Product Images from "AT-dinucleotide rich sequences drive fragile site formation"

    Article Title: AT-dinucleotide rich sequences drive fragile site formation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkz689

    Integration of FRA16C-derived AT-DRS using an HPRT gene targeting system. ( A ) The original pHPRThyg vector (left) and the newly cloned pHPRThyg_FRA16C vector (right) were designed to allow HR and construct integration within the HPRT locus. ( B ) A scheme of the HPRT locus after the integration of the pHPRThyg (upper panel) or pHPRThyg_FRA16C (lower panel) vector. The positions of primer sets 4 (4L-4R), 5 (5L-5R) and 6 (6L-6R) are illustrated. Light blue represents genomic regions that are not present in the vector. (i) Genomic DNA, isolated from HT1080 cells integrated with the pHPRThyg_FRA16C vector, was subjected to a long PCR across the AT-DRS at its ectopic integration site (HPRT locus), using two sets of chromosome X specific primers (4L-4R and 5L-5R). The same two sets of primers were also used to amplify genomic DNA isolated from HT1080 non-manipulated cells and cells integrated with the pHPRThyg vector. The red boxes mark the expected 10.6 kb PCR products harboring the 3.4 kb AT-DRS. (ii) The 10.6 kb DNA fragment, generated in the PCR of the pHPRThyg_FRA16C integrated cells, was subjected to nested PCR, using chromosome 16 specific primers (6L-6R), flanking the 3.4 kb AT-DRS. The red box marks the expected 3.8 kb PCR product harboring the 3.4 kb AT-DRS. (iii) The length of the AT-DRS at its endogenous site within FRA16C on chromosome 16 was determined by PCR on genomic DNA isolated from non-manipulated HT1080, using chromosome 16 specific primers (6L-6R). The red box marks a 3.2 kb PCR product suggesting that the AT-DRS in the endogenous FRA16C region is ∼2.8 kb. ( C ) Whole genome DNA replication rate analysis was performed by DNA combing, under normal or replication stress (0.1 μM aphidicolin) conditions. The distribution of replication fork rates in the non-manipulated and integrated HT1080 cells (pHPRThyg and pHPRThyg_FRA16C) is shown. The results are from three independent experiments. The median of each group is shown in red. The average fork rate of each group ±SE and the number of measurements (n) are indicated. Under normal growth conditions (-aphidicolin) the replication rate in the non-manipulated cells was not significantly different from the rate in the cells integrated with the pHPRThyg ( P = 0.89) or with pHPRT_FRA16C ( P = 0.72). There is also no significant difference between the replication rates in the pHPRThyg-integrated cells and the pHPRT_FRA16C-integrated cells ( P = 0.07). Aphidicolin treatment led to a significant reduction in the mean rate in all clones (**** P
    Figure Legend Snippet: Integration of FRA16C-derived AT-DRS using an HPRT gene targeting system. ( A ) The original pHPRThyg vector (left) and the newly cloned pHPRThyg_FRA16C vector (right) were designed to allow HR and construct integration within the HPRT locus. ( B ) A scheme of the HPRT locus after the integration of the pHPRThyg (upper panel) or pHPRThyg_FRA16C (lower panel) vector. The positions of primer sets 4 (4L-4R), 5 (5L-5R) and 6 (6L-6R) are illustrated. Light blue represents genomic regions that are not present in the vector. (i) Genomic DNA, isolated from HT1080 cells integrated with the pHPRThyg_FRA16C vector, was subjected to a long PCR across the AT-DRS at its ectopic integration site (HPRT locus), using two sets of chromosome X specific primers (4L-4R and 5L-5R). The same two sets of primers were also used to amplify genomic DNA isolated from HT1080 non-manipulated cells and cells integrated with the pHPRThyg vector. The red boxes mark the expected 10.6 kb PCR products harboring the 3.4 kb AT-DRS. (ii) The 10.6 kb DNA fragment, generated in the PCR of the pHPRThyg_FRA16C integrated cells, was subjected to nested PCR, using chromosome 16 specific primers (6L-6R), flanking the 3.4 kb AT-DRS. The red box marks the expected 3.8 kb PCR product harboring the 3.4 kb AT-DRS. (iii) The length of the AT-DRS at its endogenous site within FRA16C on chromosome 16 was determined by PCR on genomic DNA isolated from non-manipulated HT1080, using chromosome 16 specific primers (6L-6R). The red box marks a 3.2 kb PCR product suggesting that the AT-DRS in the endogenous FRA16C region is ∼2.8 kb. ( C ) Whole genome DNA replication rate analysis was performed by DNA combing, under normal or replication stress (0.1 μM aphidicolin) conditions. The distribution of replication fork rates in the non-manipulated and integrated HT1080 cells (pHPRThyg and pHPRThyg_FRA16C) is shown. The results are from three independent experiments. The median of each group is shown in red. The average fork rate of each group ±SE and the number of measurements (n) are indicated. Under normal growth conditions (-aphidicolin) the replication rate in the non-manipulated cells was not significantly different from the rate in the cells integrated with the pHPRThyg ( P = 0.89) or with pHPRT_FRA16C ( P = 0.72). There is also no significant difference between the replication rates in the pHPRThyg-integrated cells and the pHPRT_FRA16C-integrated cells ( P = 0.07). Aphidicolin treatment led to a significant reduction in the mean rate in all clones (**** P

    Techniques Used: Derivative Assay, Plasmid Preparation, Clone Assay, Construct, Isolation, Polymerase Chain Reaction, Generated, Nested PCR

    15) Product Images from "Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study"

    Article Title: Potential role for nectin-4 in the pathogenesis of pre-eclampsia: a molecular genetic study

    Journal: BMC Medical Genetics

    doi: 10.1186/s12881-018-0681-y

    Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)
    Figure Legend Snippet: Quantitative PCR analysis of NECTIN4 . Data were compared for uncomplicated normotensive pregnancy (open bars) versus severe pre-eclampsia (grey bars). The boxes indicate the 25th and 75th percentiles, whilst the bands near the middle indicate the median values. The bars indicate 1.5 interquartile ranges with the outliers specifically marked (x)

    Techniques Used: Real-time Polymerase Chain Reaction

    16) Product Images from "The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif"

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2014.00499

    Electrophoretic mobility shift assays demonstrating binding of SpdA2-His to the palindromic sequence motif sps . Different PCR fragments, as schematically illustrated, were incubated with ~2 pmol purified SpdA2-His protein (+) or without SpdA2-His (−), run on a 6% Tris-acetate polyacrylamide gel and stained with EtBr. The gray arrow indicates the band corresponding to a PCR fragment (FTraR pSVH1 ) added as a negative control for binding specificity. Black arrows mark retarded DNA fragments. Interaction of SpdA2-His with the FA2 fragment resulted in several retarded bands (A) . Whereas SpdA2-His did not interact with the FA2-sps fragment (B) , SpdA2-His shifted fragment F1sps, containing a single palindromic sps sequence (C) . SpdA2-His also bound to the PCR fragment FSpdA up , containing a T insertion within the palindromic sequence sps (D) , but did not recognize FSpdA, lacking sps (E) .
    Figure Legend Snippet: Electrophoretic mobility shift assays demonstrating binding of SpdA2-His to the palindromic sequence motif sps . Different PCR fragments, as schematically illustrated, were incubated with ~2 pmol purified SpdA2-His protein (+) or without SpdA2-His (−), run on a 6% Tris-acetate polyacrylamide gel and stained with EtBr. The gray arrow indicates the band corresponding to a PCR fragment (FTraR pSVH1 ) added as a negative control for binding specificity. Black arrows mark retarded DNA fragments. Interaction of SpdA2-His with the FA2 fragment resulted in several retarded bands (A) . Whereas SpdA2-His did not interact with the FA2-sps fragment (B) , SpdA2-His shifted fragment F1sps, containing a single palindromic sps sequence (C) . SpdA2-His also bound to the PCR fragment FSpdA up , containing a T insertion within the palindromic sequence sps (D) , but did not recognize FSpdA, lacking sps (E) .

    Techniques Used: Electrophoretic Mobility Shift Assay, Binding Assay, Sequencing, Polymerase Chain Reaction, Incubation, Purification, Staining, Negative Control

    pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.
    Figure Legend Snippet: pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Techniques Used: Plasmid Preparation, Agarose Gel Electrophoresis, Countercurrent Chromatography, Polymerase Chain Reaction, Positive Control

    17) Product Images from "Potential pitfalls of mass spectrometry to uncover mutations in childhood soft tissue sarcoma: A report from the Children’s Oncology Group"

    Article Title: Potential pitfalls of mass spectrometry to uncover mutations in childhood soft tissue sarcoma: A report from the Children’s Oncology Group

    Journal: Scientific Reports

    doi: 10.1038/srep33429

    ( A ) Schematic diagram shows DNA sequence variants in the human NRAS gene in either the RD or the Rh30 rhabdomyosarcoma cell lines. Forward and reverse primers used to amplify the genomic DNA for NGS are denoted by red and green arrows. ( B ) Photograph of ethidium bromide-stained 2% agarose gel shows semi-quantitative analysis of PCR amplification of one of the products noted in ( A ), confirming equal representation of each of the two sources of input DNA used for mixing experiment. ( C ) Graphs displaying the relative frequency of calls by NGS for each variant allele in DNA samples containing DNA from RD and Rh30 cells. The variant RD allele could be detected by NGS even when present 3.1% of the total DNA (arrow).
    Figure Legend Snippet: ( A ) Schematic diagram shows DNA sequence variants in the human NRAS gene in either the RD or the Rh30 rhabdomyosarcoma cell lines. Forward and reverse primers used to amplify the genomic DNA for NGS are denoted by red and green arrows. ( B ) Photograph of ethidium bromide-stained 2% agarose gel shows semi-quantitative analysis of PCR amplification of one of the products noted in ( A ), confirming equal representation of each of the two sources of input DNA used for mixing experiment. ( C ) Graphs displaying the relative frequency of calls by NGS for each variant allele in DNA samples containing DNA from RD and Rh30 cells. The variant RD allele could be detected by NGS even when present 3.1% of the total DNA (arrow).

    Techniques Used: Sequencing, Next-Generation Sequencing, Staining, Agarose Gel Electrophoresis, Real-time Polymerase Chain Reaction, Variant Assay

    18) Product Images from "The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif"

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    Journal: Frontiers in Microbiology

    doi: 10.3389/fmicb.2014.00499

    Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).
    Figure Legend Snippet: Schematic maps of pIJ303 derivatives used to elucidate the function of spdA2 . The spdA homolog spdA2 (black arrow) of plasmid pIJ303 lies downstream of rep . In pIJ303ΔspdA2, spdA2 was replaced (see Materials and Methods) by a linker sequence containing restriction sites (underlined). The NdeI site is coincident with the original spdA2 start codon. The complementing plasmid pIJ303spdA2c contains spdA2 with a C-terminal His-tag encoding sequence (hatched bar), while pIJ303-sps contains a synthetic spdA2-His gene, where the palindromic sequences (upper part, thin arrows) were removed by base substitutions (indicated by red color) that did not alter the amino acid sequence of SpdA2 (lower line).

    Techniques Used: Plasmid Preparation, Sequencing

    19) Product Images from "SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum"

    Article Title: SNP genotyping using TaqMan® technology: the CYP2D6*17 assay conundrum

    Journal: Scientific Reports

    doi: 10.1038/srep09257

    CYP2D6*17 (1023C > T) TaqMan Assay Genotype Results. (Panels A and B) show the scatter plots for TaqMan assays C__2222771_40 (original assay) and C__2222771_A0 (alternative assay). Numbered subjects correspond to cases 1–9 and 21–23 ( Tables 1 and 2 ). Cases 1–9 were identified as 1023 T/T with the original assay (panel A), but genotyped accurately as 1023 C/T with the alternative assay (panel B). Additional samples of known genotypes were analyzed as references to allow cluster formation in the scatter plots; none of these controls carry a CYP2D6*4 .
    Figure Legend Snippet: CYP2D6*17 (1023C > T) TaqMan Assay Genotype Results. (Panels A and B) show the scatter plots for TaqMan assays C__2222771_40 (original assay) and C__2222771_A0 (alternative assay). Numbered subjects correspond to cases 1–9 and 21–23 ( Tables 1 and 2 ). Cases 1–9 were identified as 1023 T/T with the original assay (panel A), but genotyped accurately as 1023 C/T with the alternative assay (panel B). Additional samples of known genotypes were analyzed as references to allow cluster formation in the scatter plots; none of these controls carry a CYP2D6*4 .

    Techniques Used: TaqMan Assay

    CYP2D6*4 subvariants. The top panel provides details about the SNVs including rs numbers, positions relative to the numbering system on which the allele nomenclature is based (M33388) and the widely accepted CYP2D6*1 reference sequence AY545216, the nature of the SNV, and sequence context. The presence of the intron 1 conversion event is characterized by multiple SNPs (rs1080995, rs267608284, rs108996, rs74644586, rs75276289, rs28695233, rs149744965, rs56011157). The middle ‘checkerboard’ panel shows SNVs relative to the AY545216 reference. Variation is highlighted by colored boxes. Gray boxes denote sequence errors in M33388. For general information, sequence differences to Genome Build GRCh37 that harbors a CYP2D6*2 , is shown. Lines *4A through *4N depict a graphical representation of the P450 Nomenclature Database 20 for these alleles. Note that *4A-K lacks any annotations for intronic regions. Sequence variations found in cases 1 and 21 that match with CYP2D6*4A and *4D are highlighted in red and blue, respectively. Intronic SNPs in the cases are shown in light red and blue as these are not represented in the nomenclature-defined variants. Cases were sequenced between the SNPs shown in yellow. The bottom panels provide location of SNV regarding to exon and intron and consequence of SNV.
    Figure Legend Snippet: CYP2D6*4 subvariants. The top panel provides details about the SNVs including rs numbers, positions relative to the numbering system on which the allele nomenclature is based (M33388) and the widely accepted CYP2D6*1 reference sequence AY545216, the nature of the SNV, and sequence context. The presence of the intron 1 conversion event is characterized by multiple SNPs (rs1080995, rs267608284, rs108996, rs74644586, rs75276289, rs28695233, rs149744965, rs56011157). The middle ‘checkerboard’ panel shows SNVs relative to the AY545216 reference. Variation is highlighted by colored boxes. Gray boxes denote sequence errors in M33388. For general information, sequence differences to Genome Build GRCh37 that harbors a CYP2D6*2 , is shown. Lines *4A through *4N depict a graphical representation of the P450 Nomenclature Database 20 for these alleles. Note that *4A-K lacks any annotations for intronic regions. Sequence variations found in cases 1 and 21 that match with CYP2D6*4A and *4D are highlighted in red and blue, respectively. Intronic SNPs in the cases are shown in light red and blue as these are not represented in the nomenclature-defined variants. Cases were sequenced between the SNPs shown in yellow. The bottom panels provide location of SNV regarding to exon and intron and consequence of SNV.

    Techniques Used: Sequencing

    Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.
    Figure Legend Snippet: Sequence Comparison of CYP2D6 variants, CYP2D7 and CYP2D8 . Each line represents the nucleotide sequence for a given gene or genetic variant. The key CYP2D6*17 SNP is highlighted by a black background and designated by an asterisk *. The tentatively interfering SNP trio is also indicated in the top panel by a black background; differing positions are highlighted ( CYP2D6*4A, B, C, F, G, H, J and M have the SNP trio, while *4C, D, E and K do not) *2E and *4L contain only the SNP at position 997. Light grey boxes emphasize differences between CYP2D6, 2D7 and 2D8 . Regions targeted for PCR primer and probe binding are shown in bold red type and plain green type, respectively. The red arrows above red letters denote the primer binding sites for the original (C__2222771_40) TaqMan assay while blue arrows indicate the primer sequences utilized for the CMH custom-made TaqMan assays. The probe binding site for the latter is shown by green letters.

    Techniques Used: Sequencing, Variant Assay, Polymerase Chain Reaction, Binding Assay, TaqMan Assay

    Real-time amplification for the original and alternate CYP2D6*17 TaqMan assays. Fluorescent signals detected for individuals with CYP2D6*4/*4 and CYP2D6*1/*1 genotypes. (Panels A and C) represents the original TaqMan assay (C__222771_40), (panels B and D) the alternate assay C__2222771_A0). The green curves indicate amplification from the ‘C’ allele (wild-type/reference, 1023C or CYP2D6*17 ) while the green curve represents the ‘T’ allele (variant, 1023 T, CYP2D6*17 or other variant haplotype containing this SNP).
    Figure Legend Snippet: Real-time amplification for the original and alternate CYP2D6*17 TaqMan assays. Fluorescent signals detected for individuals with CYP2D6*4/*4 and CYP2D6*1/*1 genotypes. (Panels A and C) represents the original TaqMan assay (C__222771_40), (panels B and D) the alternate assay C__2222771_A0). The green curves indicate amplification from the ‘C’ allele (wild-type/reference, 1023C or CYP2D6*17 ) while the green curve represents the ‘T’ allele (variant, 1023 T, CYP2D6*17 or other variant haplotype containing this SNP).

    Techniques Used: Amplification, TaqMan Assay, Variant Assay

    Related Articles

    Polymerase Chain Reaction:

    Article Title: A New Powerful Method for Site-Specific Transgene Stabilization Based on Chromosomal Double-Strand Break Repair
    Article Snippet: .. PCR analysis of DSB-repair products was carried out with different primer sets ( Suplementary ) using Kapa2G Robust HotStart Polymerase (for products < 2500 bp) or KAPA Long Range HotStart DNA Polymerase (for products > 2500 bp) under manufacturer's instructions (Kapa Biosystems). .. The presence of EGFP and I-SceI sites in flies of W+(G+)R+ derivatives of TS58A2xSce was confirmed by PCR and restriction analysis as described in legend for Supplementary .

    Similar Products

  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
  • 94
    Kapa Biosystems xl pcr
    Electrophoretic mobility shift assays demonstrating binding of <t>SpdA2-His</t> to the palindromic sequence motif sps . Different <t>PCR</t> fragments, as schematically illustrated, were incubated with ~2 pmol purified SpdA2-His protein (+) or without SpdA2-His (−), run on a 6% Tris-acetate polyacrylamide gel and stained with EtBr. The gray arrow indicates the band corresponding to a PCR fragment (FTraR pSVH1 ) added as a negative control for binding specificity. Black arrows mark retarded DNA fragments. Interaction of SpdA2-His with the FA2 fragment resulted in several retarded bands (A) . Whereas SpdA2-His did not interact with the FA2-sps fragment (B) , SpdA2-His shifted fragment F1sps, containing a single palindromic sps sequence (C) . SpdA2-His also bound to the PCR fragment FSpdA up , containing a T insertion within the palindromic sequence sps (D) , but did not recognize FSpdA, lacking sps (E) .
    Xl Pcr, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xl pcr/product/Kapa Biosystems
    Average 94 stars, based on 1 article reviews
    Price from $9.99 to $1999.99
    xl pcr - by Bioz Stars, 2021-01
    94/100 stars
      Buy from Supplier

    94
    Kapa Biosystems kapa long range hot start pcr kit
    Integration of FRA16C-derived AT-DRS using an HPRT gene targeting system. ( A ) The original pHPRThyg vector (left) and the newly cloned pHPRThyg_FRA16C vector (right) were designed to allow HR and construct integration within the HPRT locus. ( B ) A scheme of the HPRT locus after the integration of the pHPRThyg (upper panel) or pHPRThyg_FRA16C (lower panel) vector. The positions of primer sets 4 (4L-4R), 5 (5L-5R) and 6 (6L-6R) are illustrated. Light blue represents genomic regions that are not present in the vector. (i) Genomic <t>DNA,</t> isolated from HT1080 cells integrated with the pHPRThyg_FRA16C vector, was subjected to a long <t>PCR</t> across the AT-DRS at its ectopic integration site (HPRT locus), using two sets of chromosome X specific primers (4L-4R and 5L-5R). The same two sets of primers were also used to amplify genomic DNA isolated from HT1080 non-manipulated cells and cells integrated with the pHPRThyg vector. The red boxes mark the expected 10.6 kb PCR products harboring the 3.4 kb AT-DRS. (ii) The 10.6 kb DNA fragment, generated in the PCR of the pHPRThyg_FRA16C integrated cells, was subjected to nested PCR, using chromosome 16 specific primers (6L-6R), flanking the 3.4 kb AT-DRS. The red box marks the expected 3.8 kb PCR product harboring the 3.4 kb AT-DRS. (iii) The length of the AT-DRS at its endogenous site within FRA16C on chromosome 16 was determined by PCR on genomic DNA isolated from non-manipulated HT1080, using chromosome 16 specific primers (6L-6R). The red box marks a 3.2 kb PCR product suggesting that the AT-DRS in the endogenous FRA16C region is ∼2.8 kb. ( C ) Whole genome DNA replication rate analysis was performed by DNA combing, under normal or replication stress (0.1 μM aphidicolin) conditions. The distribution of replication fork rates in the non-manipulated and integrated HT1080 cells (pHPRThyg and pHPRThyg_FRA16C) is shown. The results are from three independent experiments. The median of each group is shown in red. The average fork rate of each group ±SE and the number of measurements (n) are indicated. Under normal growth conditions (-aphidicolin) the replication rate in the non-manipulated cells was not significantly different from the rate in the cells integrated with the pHPRThyg ( P = 0.89) or with pHPRT_FRA16C ( P = 0.72). There is also no significant difference between the replication rates in the pHPRThyg-integrated cells and the pHPRT_FRA16C-integrated cells ( P = 0.07). Aphidicolin treatment led to a significant reduction in the mean rate in all clones (**** P
    Kapa Long Range Hot Start Pcr Kit, supplied by Kapa Biosystems, used in various techniques. Bioz Stars score: 94/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/kapa long range hot start pcr kit/product/Kapa Biosystems
    Average 94 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    kapa long range hot start pcr kit - by Bioz Stars, 2021-01
    94/100 stars
      Buy from Supplier

    Image Search Results


    Electrophoretic mobility shift assays demonstrating binding of SpdA2-His to the palindromic sequence motif sps . Different PCR fragments, as schematically illustrated, were incubated with ~2 pmol purified SpdA2-His protein (+) or without SpdA2-His (−), run on a 6% Tris-acetate polyacrylamide gel and stained with EtBr. The gray arrow indicates the band corresponding to a PCR fragment (FTraR pSVH1 ) added as a negative control for binding specificity. Black arrows mark retarded DNA fragments. Interaction of SpdA2-His with the FA2 fragment resulted in several retarded bands (A) . Whereas SpdA2-His did not interact with the FA2-sps fragment (B) , SpdA2-His shifted fragment F1sps, containing a single palindromic sps sequence (C) . SpdA2-His also bound to the PCR fragment FSpdA up , containing a T insertion within the palindromic sequence sps (D) , but did not recognize FSpdA, lacking sps (E) .

    Journal: Frontiers in Microbiology

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    doi: 10.3389/fmicb.2014.00499

    Figure Lengend Snippet: Electrophoretic mobility shift assays demonstrating binding of SpdA2-His to the palindromic sequence motif sps . Different PCR fragments, as schematically illustrated, were incubated with ~2 pmol purified SpdA2-His protein (+) or without SpdA2-His (−), run on a 6% Tris-acetate polyacrylamide gel and stained with EtBr. The gray arrow indicates the band corresponding to a PCR fragment (FTraR pSVH1 ) added as a negative control for binding specificity. Black arrows mark retarded DNA fragments. Interaction of SpdA2-His with the FA2 fragment resulted in several retarded bands (A) . Whereas SpdA2-His did not interact with the FA2-sps fragment (B) , SpdA2-His shifted fragment F1sps, containing a single palindromic sps sequence (C) . SpdA2-His also bound to the PCR fragment FSpdA up , containing a T insertion within the palindromic sequence sps (D) , but did not recognize FSpdA, lacking sps (E) .

    Article Snippet: Construction of plasmids pIJ303ΔspdA2, pIJ303-sps, and pIJ303spdA2c To construct pIJ303Δ spdA2 we performed an XL-PCR (KAPA Long Range DNA Polymerase, Kapa Biosystems) with primers 303DelAl/303DelBu (Table ).

    Techniques: Electrophoretic Mobility Shift Assay, Binding Assay, Sequencing, Polymerase Chain Reaction, Incubation, Purification, Staining, Negative Control

    pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Journal: Frontiers in Microbiology

    Article Title: The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    doi: 10.3389/fmicb.2014.00499

    Figure Lengend Snippet: pIJ303 Δ spdA2 and pIJ303-sps do not accumulate single-stranded plasmid DNA . Approximately 10 6 protoplasts of S. lividans TK54 with respective plasmids were lysed in a 1% TA agarose gel containing 0.25% SDS (A) . Black arrows indicate chromosomal DNA, while the gray arrow marks ccc-DNA. The gel was either blotted in native state (B) to detect accumulation of single-stranded plasmid DNA, or denatured before blotting in order to detect also double-stranded plasmid DNA (C) . As a probe a 600 bp PCR-fragment corresponding to the dso of pIJ101 was used. Plasmid pIJ702, which lacks the sso , was used as a positive control for the accumulation of single-stranded plasmid DNA (white arrow). 1, pIJ303; 2, pIJ303-sps; 3, pIJ303Δ spdA2; 4, pIJ303spdA2c; 5, pIJ702; 6, plasmid free TK54.

    Article Snippet: Construction of plasmids pIJ303ΔspdA2, pIJ303-sps, and pIJ303spdA2c To construct pIJ303Δ spdA2 we performed an XL-PCR (KAPA Long Range DNA Polymerase, Kapa Biosystems) with primers 303DelAl/303DelBu (Table ).

    Techniques: Plasmid Preparation, Agarose Gel Electrophoresis, Countercurrent Chromatography, Polymerase Chain Reaction, Positive Control

    Integration of FRA16C-derived AT-DRS using an HPRT gene targeting system. ( A ) The original pHPRThyg vector (left) and the newly cloned pHPRThyg_FRA16C vector (right) were designed to allow HR and construct integration within the HPRT locus. ( B ) A scheme of the HPRT locus after the integration of the pHPRThyg (upper panel) or pHPRThyg_FRA16C (lower panel) vector. The positions of primer sets 4 (4L-4R), 5 (5L-5R) and 6 (6L-6R) are illustrated. Light blue represents genomic regions that are not present in the vector. (i) Genomic DNA, isolated from HT1080 cells integrated with the pHPRThyg_FRA16C vector, was subjected to a long PCR across the AT-DRS at its ectopic integration site (HPRT locus), using two sets of chromosome X specific primers (4L-4R and 5L-5R). The same two sets of primers were also used to amplify genomic DNA isolated from HT1080 non-manipulated cells and cells integrated with the pHPRThyg vector. The red boxes mark the expected 10.6 kb PCR products harboring the 3.4 kb AT-DRS. (ii) The 10.6 kb DNA fragment, generated in the PCR of the pHPRThyg_FRA16C integrated cells, was subjected to nested PCR, using chromosome 16 specific primers (6L-6R), flanking the 3.4 kb AT-DRS. The red box marks the expected 3.8 kb PCR product harboring the 3.4 kb AT-DRS. (iii) The length of the AT-DRS at its endogenous site within FRA16C on chromosome 16 was determined by PCR on genomic DNA isolated from non-manipulated HT1080, using chromosome 16 specific primers (6L-6R). The red box marks a 3.2 kb PCR product suggesting that the AT-DRS in the endogenous FRA16C region is ∼2.8 kb. ( C ) Whole genome DNA replication rate analysis was performed by DNA combing, under normal or replication stress (0.1 μM aphidicolin) conditions. The distribution of replication fork rates in the non-manipulated and integrated HT1080 cells (pHPRThyg and pHPRThyg_FRA16C) is shown. The results are from three independent experiments. The median of each group is shown in red. The average fork rate of each group ±SE and the number of measurements (n) are indicated. Under normal growth conditions (-aphidicolin) the replication rate in the non-manipulated cells was not significantly different from the rate in the cells integrated with the pHPRThyg ( P = 0.89) or with pHPRT_FRA16C ( P = 0.72). There is also no significant difference between the replication rates in the pHPRThyg-integrated cells and the pHPRT_FRA16C-integrated cells ( P = 0.07). Aphidicolin treatment led to a significant reduction in the mean rate in all clones (**** P

    Journal: Nucleic Acids Research

    Article Title: AT-dinucleotide rich sequences drive fragile site formation

    doi: 10.1093/nar/gkz689

    Figure Lengend Snippet: Integration of FRA16C-derived AT-DRS using an HPRT gene targeting system. ( A ) The original pHPRThyg vector (left) and the newly cloned pHPRThyg_FRA16C vector (right) were designed to allow HR and construct integration within the HPRT locus. ( B ) A scheme of the HPRT locus after the integration of the pHPRThyg (upper panel) or pHPRThyg_FRA16C (lower panel) vector. The positions of primer sets 4 (4L-4R), 5 (5L-5R) and 6 (6L-6R) are illustrated. Light blue represents genomic regions that are not present in the vector. (i) Genomic DNA, isolated from HT1080 cells integrated with the pHPRThyg_FRA16C vector, was subjected to a long PCR across the AT-DRS at its ectopic integration site (HPRT locus), using two sets of chromosome X specific primers (4L-4R and 5L-5R). The same two sets of primers were also used to amplify genomic DNA isolated from HT1080 non-manipulated cells and cells integrated with the pHPRThyg vector. The red boxes mark the expected 10.6 kb PCR products harboring the 3.4 kb AT-DRS. (ii) The 10.6 kb DNA fragment, generated in the PCR of the pHPRThyg_FRA16C integrated cells, was subjected to nested PCR, using chromosome 16 specific primers (6L-6R), flanking the 3.4 kb AT-DRS. The red box marks the expected 3.8 kb PCR product harboring the 3.4 kb AT-DRS. (iii) The length of the AT-DRS at its endogenous site within FRA16C on chromosome 16 was determined by PCR on genomic DNA isolated from non-manipulated HT1080, using chromosome 16 specific primers (6L-6R). The red box marks a 3.2 kb PCR product suggesting that the AT-DRS in the endogenous FRA16C region is ∼2.8 kb. ( C ) Whole genome DNA replication rate analysis was performed by DNA combing, under normal or replication stress (0.1 μM aphidicolin) conditions. The distribution of replication fork rates in the non-manipulated and integrated HT1080 cells (pHPRThyg and pHPRThyg_FRA16C) is shown. The results are from three independent experiments. The median of each group is shown in red. The average fork rate of each group ±SE and the number of measurements (n) are indicated. Under normal growth conditions (-aphidicolin) the replication rate in the non-manipulated cells was not significantly different from the rate in the cells integrated with the pHPRThyg ( P = 0.89) or with pHPRT_FRA16C ( P = 0.72). There is also no significant difference between the replication rates in the pHPRThyg-integrated cells and the pHPRT_FRA16C-integrated cells ( P = 0.07). Aphidicolin treatment led to a significant reduction in the mean rate in all clones (**** P

    Article Snippet: These PCRs were performed using the Kapa long range hot start PCR kit (Kapa Biosystems) with 10 ng genomic DNA.

    Techniques: Derivative Assay, Plasmid Preparation, Clone Assay, Construct, Isolation, Polymerase Chain Reaction, Generated, Nested PCR