taq i  (New England Biolabs)


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    Name:
    Taq I Methyltransferase
    Description:
    Taq I Methyltransferase 1 000 units
    Catalog Number:
    m0219s
    Price:
    76
    Size:
    1 000 units
    Category:
    DNA Methylases
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    Structured Review

    New England Biolabs taq i
    Taq I Methyltransferase
    Taq I Methyltransferase 1 000 units
    https://www.bioz.com/result/taq i/product/New England Biolabs
    Average 95 stars, based on 9 article reviews
    Price from $9.99 to $1999.99
    taq i - by Bioz Stars, 2020-08
    95/100 stars

    Images

    1) Product Images from "Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat"

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.10.4414-4425.2001

    Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.
    Figure Legend Snippet: Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Techniques Used: Amplification, Positive Control

    2) Product Images from "HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer"

    Article Title: HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer

    Journal: OMICS : a Journal of Integrative Biology

    doi: 10.1089/omi.2017.0016

    COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.
    Figure Legend Snippet: COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.

    Techniques Used: Combined Bisulfite Restriction Analysis Assay, Marker, Amplification

    3) Product Images from "Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study"

    Article Title: Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0205841

    Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .
    Figure Legend Snippet: Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .

    Techniques Used: Agarose Gel Electrophoresis

    4) Product Images from "Patterns and Possible Roles of LINE-1 Methylation Changes in Smoke-Exposed Epithelia"

    Article Title: Patterns and Possible Roles of LINE-1 Methylation Changes in Smoke-Exposed Epithelia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0045292

    Methylation patterns of COBRALINE-1. (A) The LINE-1 amplicons were 160 bp and had 2 CpG dinucleotides. Four patterns of methylated CpGs were detected, including hypermethylation ( m C m C), hypomethylation ( u C u C), and two forms of partial methylation ( m C u C and u C m C). The Tas I enzyme targets unmethylated cytosine site 1, and Taq I targets methylated cytosine site 2. (B) After restriction digestion with Tas I and Taq I, four sizes of products (160, 98, 80, and 62 bp) were identified, depending on the methylation status of both CpG loci. (C) Examples of bisulfite sequencing. Left side represents sequences of the two CpG dinucleotides at Tas I and Taq I cut site whereas the right side represents the CpG dinucleotides in the amplified PCR products. Each circle exemplifies the methylation status of each selected clone. Black and white circles are methylated and unmethylated CpG dinucleotides, respectively. x is mutated sequence and – is deleted sequence.
    Figure Legend Snippet: Methylation patterns of COBRALINE-1. (A) The LINE-1 amplicons were 160 bp and had 2 CpG dinucleotides. Four patterns of methylated CpGs were detected, including hypermethylation ( m C m C), hypomethylation ( u C u C), and two forms of partial methylation ( m C u C and u C m C). The Tas I enzyme targets unmethylated cytosine site 1, and Taq I targets methylated cytosine site 2. (B) After restriction digestion with Tas I and Taq I, four sizes of products (160, 98, 80, and 62 bp) were identified, depending on the methylation status of both CpG loci. (C) Examples of bisulfite sequencing. Left side represents sequences of the two CpG dinucleotides at Tas I and Taq I cut site whereas the right side represents the CpG dinucleotides in the amplified PCR products. Each circle exemplifies the methylation status of each selected clone. Black and white circles are methylated and unmethylated CpG dinucleotides, respectively. x is mutated sequence and – is deleted sequence.

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

    5) Product Images from "Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study"

    Article Title: Serum 25-hydroxyvitamin D, serum calcium and vitamin D receptor (VDR) polymorphisms in a selected population with lumbar disc herniation—A case control study

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0205841

    Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .
    Figure Legend Snippet: Agarose gel electrophoresis for restriction fragment length polymorphism of VDR Taq I .

    Techniques Used: Agarose Gel Electrophoresis

    6) Product Images from "Protein genes in repetitive sequence--antifreeze glycoproteins in Atlantic cod genome"

    Article Title: Protein genes in repetitive sequence--antifreeze glycoproteins in Atlantic cod genome

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-13-293

    Southern blot analysis of Atlantic cod genomic DNA showing presence of AFGP coding sequences. Taq I digested genomic DNA (~10–15 μg) from Atlantic cod (lanes 1–14) and polar cod (lanes 15–17) hybridized strongly to a polar cod B. saida AFGP coding sequence probe. Atlantic cod individuals include Norwegian coastal cod (NCC) and North East Arctic cod (NEAC) from the Finnmark coast and marginal Barents Sea sites: (lanes 1–3) N69° 26.91′ E19° 37.56′; (lanes 4–5) N69° 58.34′ E30° 2.37′; (lanes 6–8) N70° 7.24′ E30° 48.47′; (lanes 9–13) N71° 11.93′ E27° 59.29′, and one individual (lane 14) from Øresund, Denmark. NEAC and NCC are distinguished by their Pan I genotype, BB and AA respectively as indicated, while AB can either be NEAC or NCC. For comparison, the related freshwater cod Lota lota (lane 18) that does not have AFGP shows no hybridization.
    Figure Legend Snippet: Southern blot analysis of Atlantic cod genomic DNA showing presence of AFGP coding sequences. Taq I digested genomic DNA (~10–15 μg) from Atlantic cod (lanes 1–14) and polar cod (lanes 15–17) hybridized strongly to a polar cod B. saida AFGP coding sequence probe. Atlantic cod individuals include Norwegian coastal cod (NCC) and North East Arctic cod (NEAC) from the Finnmark coast and marginal Barents Sea sites: (lanes 1–3) N69° 26.91′ E19° 37.56′; (lanes 4–5) N69° 58.34′ E30° 2.37′; (lanes 6–8) N70° 7.24′ E30° 48.47′; (lanes 9–13) N71° 11.93′ E27° 59.29′, and one individual (lane 14) from Øresund, Denmark. NEAC and NCC are distinguished by their Pan I genotype, BB and AA respectively as indicated, while AB can either be NEAC or NCC. For comparison, the related freshwater cod Lota lota (lane 18) that does not have AFGP shows no hybridization.

    Techniques Used: Southern Blot, Sequencing, Hybridization

    7) Product Images from "DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients"

    Article Title: DNA Methylation of the ABO Promoter Underlies Loss of ABO Allelic Expression in a Significant Proportion of Leukemic Patients

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0004788

    Loss of A expression by RT-PCR and restriction enzyme digestion. (A) Schematic representation of ABO allelic expression analysis. Kpn I digestion results in a 130 bp band if the O allele is present and no digestion of the A or B allele. BstE II digestion results in a 130 bp band if the A or B allele is present and no digestion of the O allele. (B) Lane M is the pUC19/ Hpa II marker while lane 1 is the uncut ABO RT-PCR product. Lanes 2, 4, 6 and 8 are digested with Kpn I while lanes 3, 5, 7 and 9 are digested with BstE II. Lanes 2 and 3 are from cDNA of patient F7, lanes 4 and 5 from F11, lanes 6 and 7 from F15 and lanes 8 and 9 from F17. F7 and F11 are AO patients with loss of the A allele, F17 is an AO patient with no loss of ABO allelic expression. Patient F15 has an A 1 A 2 genotype, hence no cutting with Kpn I was expected. (C) Lanes 1, 3 and 5 are ABO RT-PCR product digested with Kpn I while lanes 2, 4 and 6 are digests with BstE II. Lanes 1 and 2 are from cDNA of patient F23, an A 2 B genotype, hence no cutting with Kpn I was expected. Lanes 3 and 4 are F53, an A 1 O 1 patient with loss of A at the mRNA level. Lanes 5 and 6 are S8, which is a patient with an A 1 O 1 genotype with loss of A allelic expression. (D) The ABO CpG island promoter region assessed for methylation. The methylated and bisulfite modified sequence is shown and the primer sequences are double underlined. The capital Ts identify thymines that are a result of bisulfite modification of cytosines and the CpGs are shown in bold. The start of transcription is marked with +1. The different restriction enzymes used for assessing methylation by digestion are as follows: eight BstU I sites ( cg/cg ), two Taq I ( T/cga ) sites (however one is found in the primer and hence will cut regardless of methylation status), one Hinf I ( g/aTTc ) site. Regions 161–173 and 198–210 harbor Sp1 sites [55] .
    Figure Legend Snippet: Loss of A expression by RT-PCR and restriction enzyme digestion. (A) Schematic representation of ABO allelic expression analysis. Kpn I digestion results in a 130 bp band if the O allele is present and no digestion of the A or B allele. BstE II digestion results in a 130 bp band if the A or B allele is present and no digestion of the O allele. (B) Lane M is the pUC19/ Hpa II marker while lane 1 is the uncut ABO RT-PCR product. Lanes 2, 4, 6 and 8 are digested with Kpn I while lanes 3, 5, 7 and 9 are digested with BstE II. Lanes 2 and 3 are from cDNA of patient F7, lanes 4 and 5 from F11, lanes 6 and 7 from F15 and lanes 8 and 9 from F17. F7 and F11 are AO patients with loss of the A allele, F17 is an AO patient with no loss of ABO allelic expression. Patient F15 has an A 1 A 2 genotype, hence no cutting with Kpn I was expected. (C) Lanes 1, 3 and 5 are ABO RT-PCR product digested with Kpn I while lanes 2, 4 and 6 are digests with BstE II. Lanes 1 and 2 are from cDNA of patient F23, an A 2 B genotype, hence no cutting with Kpn I was expected. Lanes 3 and 4 are F53, an A 1 O 1 patient with loss of A at the mRNA level. Lanes 5 and 6 are S8, which is a patient with an A 1 O 1 genotype with loss of A allelic expression. (D) The ABO CpG island promoter region assessed for methylation. The methylated and bisulfite modified sequence is shown and the primer sequences are double underlined. The capital Ts identify thymines that are a result of bisulfite modification of cytosines and the CpGs are shown in bold. The start of transcription is marked with +1. The different restriction enzymes used for assessing methylation by digestion are as follows: eight BstU I sites ( cg/cg ), two Taq I ( T/cga ) sites (however one is found in the primer and hence will cut regardless of methylation status), one Hinf I ( g/aTTc ) site. Regions 161–173 and 198–210 harbor Sp1 sites [55] .

    Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Marker, Methylation, Modification, Sequencing

    ABO promoter methylation in leukemic cell lines. (A) MS-SSCA analysis of the ABO BIS PCR products. PBMNC refers to peripheral blood mononuclear cells and PBSC to peripheral blood stem cells. These were used as unmethylated controls. It is clear from the SSCA gel that only the K-562 leukemic cell line is unmethylated as it has the same banding pattern as the PBMNC and PBSC. The other cell lines all have varying amounts of methylation as seen by the various banding patterns. The JURKAT and RAJI cell lines were hypermethylated, as seen by the dramatic shift of the bottom doublet of bands. (B) Restriction enzyme digests of the ABO BIS PCR products. Digestion with any of the restriction enzymes is indicative of methylation at that CpG site within the restriction enzyme recognition sequence. All the products will cut with Taq I since there is a Taq I site in the reverse primer. (C) ABO re-expression in the JURKAT cell line after 24 h treatment with 5-aza-2′-deoxycytidine treatment. On the gel, the NEGATIVE was an RT control (RNA only), the VEHICLE lane was JURKAT cells treated with ultra pure water, the following lanes are JURKAT cells treated with 1 µM or 2 µM of 5-aza-2′-deoxycytidine respectively showing ABO re-expression. PBGD is the reference gene. (D) The ABO promoter is demethylated in JURKAT cells after 5-aza-2′-deoxycytidine treatment. In the VEHICLE treated JURKAT cells there is no evidence of unmethylated ABO promoter which would be a band at the same size as the UNCUT sample. However, after treatment with 1 or 2 µM of 5-aza-2′-deoxycytidine the ABO promoter is unmethylated as evidenced by a band at the same size as the UNCUT sample.
    Figure Legend Snippet: ABO promoter methylation in leukemic cell lines. (A) MS-SSCA analysis of the ABO BIS PCR products. PBMNC refers to peripheral blood mononuclear cells and PBSC to peripheral blood stem cells. These were used as unmethylated controls. It is clear from the SSCA gel that only the K-562 leukemic cell line is unmethylated as it has the same banding pattern as the PBMNC and PBSC. The other cell lines all have varying amounts of methylation as seen by the various banding patterns. The JURKAT and RAJI cell lines were hypermethylated, as seen by the dramatic shift of the bottom doublet of bands. (B) Restriction enzyme digests of the ABO BIS PCR products. Digestion with any of the restriction enzymes is indicative of methylation at that CpG site within the restriction enzyme recognition sequence. All the products will cut with Taq I since there is a Taq I site in the reverse primer. (C) ABO re-expression in the JURKAT cell line after 24 h treatment with 5-aza-2′-deoxycytidine treatment. On the gel, the NEGATIVE was an RT control (RNA only), the VEHICLE lane was JURKAT cells treated with ultra pure water, the following lanes are JURKAT cells treated with 1 µM or 2 µM of 5-aza-2′-deoxycytidine respectively showing ABO re-expression. PBGD is the reference gene. (D) The ABO promoter is demethylated in JURKAT cells after 5-aza-2′-deoxycytidine treatment. In the VEHICLE treated JURKAT cells there is no evidence of unmethylated ABO promoter which would be a band at the same size as the UNCUT sample. However, after treatment with 1 or 2 µM of 5-aza-2′-deoxycytidine the ABO promoter is unmethylated as evidenced by a band at the same size as the UNCUT sample.

    Techniques Used: Methylation, Mass Spectrometry, Polymerase Chain Reaction, Sequencing, Expressing

    8) Product Images from "Genotyping of Epidemic Methicillin-Resistant Staphylococcus aureus Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis"

    Article Title: Genotyping of Epidemic Methicillin-Resistant Staphylococcus aureus Phage Type 15 Isolates by Fluorescent Amplified-Fragment Length Polymorphism Analysis

    Journal: Journal of Clinical Microbiology

    doi:

    GeneScan version 2.1 software-derived electropherograms of the predominant EMRSA-15 FAFLP profile for Apa I+0 and Taq I+G (a) and for Eco RI+0 and Mse I+C (b). The solid arrowheads and peaks indicate fragments that are present in the predominant profile but absent in other EMRSA-15 isolates (sizes are indicated in base pairs). The open arrowheads indicate the absence from the predominant profile of a polymorphic fragment that is present in another EMRSA-15 isolate.
    Figure Legend Snippet: GeneScan version 2.1 software-derived electropherograms of the predominant EMRSA-15 FAFLP profile for Apa I+0 and Taq I+G (a) and for Eco RI+0 and Mse I+C (b). The solid arrowheads and peaks indicate fragments that are present in the predominant profile but absent in other EMRSA-15 isolates (sizes are indicated in base pairs). The open arrowheads indicate the absence from the predominant profile of a polymorphic fragment that is present in another EMRSA-15 isolate.

    Techniques Used: Software, Derivative Assay

    UPGMA dendrograms derived from FAFLP data. (a) Apa I+0 and Taq I+G; (b) Eco RI+0 and Mse I+C; (c) combined data from both primer pairs. The d ). The horizontal scale bars represent 5% divergence.
    Figure Legend Snippet: UPGMA dendrograms derived from FAFLP data. (a) Apa I+0 and Taq I+G; (b) Eco RI+0 and Mse I+C; (c) combined data from both primer pairs. The d ). The horizontal scale bars represent 5% divergence.

    Techniques Used: Derivative Assay

    9) Product Images from "A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia"

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0000436

    The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).
    Figure Legend Snippet: The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).

    Techniques Used: Mutagenesis, Derivative Assay, Reverse Transcription Polymerase Chain Reaction

    SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.
    Figure Legend Snippet: SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.

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

    Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.
    Figure Legend Snippet: Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.

    Techniques Used: Mutagenesis, Sequencing, Reverse Transcription Polymerase Chain Reaction, Labeling, Nucleic Acid Electrophoresis, Molecular Weight, Marker, Agarose Gel Electrophoresis, Purification

    10) Product Images from "A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia"

    Article Title: A Recurrent Stop-Codon Mutation in Succinate Dehydrogenase Subunit B Gene in Normal Peripheral Blood and Childhood T-Cell Acute Leukemia

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0000436

    The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).
    Figure Legend Snippet: The steady-state fraction of mutant SDHB cDNAs resistant to Taq I RE digestion. Each circle represents a sample from a different subject (total indicated by n) except for those in the PHA stimulated PBMCs which were obtained from two normal donors, stimulated by 2.5 µg/ml and 5.0 µg/ml concentrations of PHA and tested at days 2, 5 and 8 for a total of 12 samples. The value corresponding to each circle was derived from three RT-PCR reactions. Two outlier PBMC values were shown at the top with their mutant transcript fractions in parentheses. Boxes and the vertical lines denote the means and their 95% confidence intervals of samples sets. “PBMC mutation carrier” group contains 5 SDHC and 24 SDHD mutation carriers. The leukemic cell lines were derived from B cells (n = 3), T cells (n = 9), NK cells (n = 1) and monocytes (n = 2).

    Techniques Used: Mutagenesis, Derivative Assay, Reverse Transcription Polymerase Chain Reaction

    SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.
    Figure Legend Snippet: SDHB mutations in genomic DNAs (gDNAs). A. Taq I RE digestion of PCR-amplified exon 2 shows no evidence of undigested mutant DNAs at 260 bp size (pointed by an arrow head). Taq I RE digestion products of the wild-type DNA co-migrate at sizes of 128 and 132 bps (denoted by a star). B. Gel electrophoresis of Taq I RE-digested (mutation) enrichment PCR ( e PCR) products shows variable amounts of mutant gDNAs at 233 bp size (pointed by an arrow head), which are confirmed to be primarily composed of c.136C > T by sequencing ( Table 1 ). Taq I digestion of wild-type e PCR products gives two bands at sizes, 101 and 132 bp (shown by a star). C. e PCR analyses of leukemic cell lines demonstrate the presence of mutant gDNA in the MOLT-4 cell line (pointed by an arrow head) but not in other leukemic cell lines in this experiment. D. Direct sequence analysis of a gDNA e PCR product shows selective enrichment of the R46X mutation. E, F. Sequence chromatograms of the heterozygous DNA mutations detected in two T-ALL cell lines are shown.

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

    Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.
    Figure Legend Snippet: Analysis of SDHB R46X mRNA mutation. A. The SDHB gene has 843 bp coding nucleotides spread to 8 exons within ∼35 kb at chromosome band 1p36.13. The 5′- portion of the gene shows the position of the R46X mutation and the mitochondrial signal peptide cleavage site (filled circle). B. Sequence chromatograms of RT-PCR products show samples that have high (top), low (middle), or undetectable (bottom) amounts of mutant R46X sequences. C. Quantification of the mutant fraction involved Taq I RE digestion of fluorescently-labeled RT-PCR products and capillary gel electrophoresis. The red peaks denote the molecular weight marker. D. The agarose gel electrophoresis shows variable fractions of mutant RT-PCR products from normal PBMCs detected by Taq I RE digestion, which releases two bands 159 and 126 bp in size from the wild-type sequence (also see Fig. S1A ). E. Fractions of Taq I RE resistant transcripts in the purified PBMC cell types are shown in an agarose gel. The negative image is presented to enhance the visibility of mutant transcripts.

    Techniques Used: Mutagenesis, Sequencing, Reverse Transcription Polymerase Chain Reaction, Labeling, Nucleic Acid Electrophoresis, Molecular Weight, Marker, Agarose Gel Electrophoresis, Purification

    11) Product Images from "The association of NR1H3 gene with lipid deposition in the pig"

    Article Title: The association of NR1H3 gene with lipid deposition in the pig

    Journal: Lipids in Health and Disease

    doi: 10.1186/s12944-016-0269-5

    The electrophoresis of PCR- Taq I-RFLP for NR1H3 exon 5-A201C in pigs. Note: The individual with 348 and 113 bp fragments had genotype AA (lanes 1, 2, 3, 6, 7, 9, 10, 13, 14), the individual with 348, 290, 113, and 58 bp fragments had genotype AC (lanes 4, 5, 8, 11, 12), and the individual with 290, 113, and 58 bp fragments had genotype CC (lanes 15, 16)
    Figure Legend Snippet: The electrophoresis of PCR- Taq I-RFLP for NR1H3 exon 5-A201C in pigs. Note: The individual with 348 and 113 bp fragments had genotype AA (lanes 1, 2, 3, 6, 7, 9, 10, 13, 14), the individual with 348, 290, 113, and 58 bp fragments had genotype AC (lanes 4, 5, 8, 11, 12), and the individual with 290, 113, and 58 bp fragments had genotype CC (lanes 15, 16)

    Techniques Used: Electrophoresis, Polymerase Chain Reaction

    12) Product Images from "Reliable molecular identification of nine tropical whitefly species"

    Article Title: Reliable molecular identification of nine tropical whitefly species

    Journal: Ecology and Evolution

    doi: 10.1002/ece3.1204

    Displays two 2% agarose gels showing the restriction fragment length polymorphism profiles obtained by digesting the COI with Alu I (A) and Ase I + Taq I (B) enzyme from Lecanoideus floccissimus (lane 1) , Aleurotrachelus socialis (lane 2) , Bemisia tabaci (Sample 1, lane 3) , B. tabaci (Sample 2, lane 4) , Trialeurodes vaporiariorum (lane 5) , Aleurodicus dispersus (lane 6) , Aleurothrixus floccosus (lane 7) , Aleurotrachelus trachoides (lane 8) , Trialeurodes variabilis (lane 9) , Aleuronudus melzeri (lane 10). Molecular size markers are shown on the right and left side of the figure. Number filled in black corresponds to fragments size expected based on available sequence information and those in red to fragments expected by sequence variation due to intraspecies variation detected by RFLP-PCR of the COI amplicon.
    Figure Legend Snippet: Displays two 2% agarose gels showing the restriction fragment length polymorphism profiles obtained by digesting the COI with Alu I (A) and Ase I + Taq I (B) enzyme from Lecanoideus floccissimus (lane 1) , Aleurotrachelus socialis (lane 2) , Bemisia tabaci (Sample 1, lane 3) , B. tabaci (Sample 2, lane 4) , Trialeurodes vaporiariorum (lane 5) , Aleurodicus dispersus (lane 6) , Aleurothrixus floccosus (lane 7) , Aleurotrachelus trachoides (lane 8) , Trialeurodes variabilis (lane 9) , Aleuronudus melzeri (lane 10). Molecular size markers are shown on the right and left side of the figure. Number filled in black corresponds to fragments size expected based on available sequence information and those in red to fragments expected by sequence variation due to intraspecies variation detected by RFLP-PCR of the COI amplicon.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Amplification

    13) Product Images from "Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma"

    Article Title: Epigenetic control of the ubiquitin carboxyl terminal hydrolase 1 in renal cell carcinoma

    Journal: Journal of Translational Medicine

    doi: 10.1186/1479-5876-7-90

    UCHL1 promoter DNA methylation in RCC lesions, tumor adjacent kidney epithelium and RCC cell lines . A) Representative COBRA analysis of three RCC tumor lesions and one RCC cell line. Genomic DNA extracted from tumor lesions (2874TU, 2876TU and 2878) and the cell line MZ1940RC was treated with bisulfite and amplified by nested PCR as described in the Methods section. The resulting 265 bp amplicons were either digested with Taq I (+) or left untreated (-) and subsequently separated in 2% agarose gels in TAE buffer. A 100 base pair DNA ruler loaded in the first lane served as length standard. B) Distribution pattern for UCHL1 promoter DNA methylation in tumor adjacent kidney epithelium, autologous primary RCC lesions and RCC cell lines. Grey bars represent samples with unmethylated (U), striped bars with partially methylated (P) and black bars with fully methylated (M) CpG islets within the UCHL1 promoter core region as indicated.
    Figure Legend Snippet: UCHL1 promoter DNA methylation in RCC lesions, tumor adjacent kidney epithelium and RCC cell lines . A) Representative COBRA analysis of three RCC tumor lesions and one RCC cell line. Genomic DNA extracted from tumor lesions (2874TU, 2876TU and 2878) and the cell line MZ1940RC was treated with bisulfite and amplified by nested PCR as described in the Methods section. The resulting 265 bp amplicons were either digested with Taq I (+) or left untreated (-) and subsequently separated in 2% agarose gels in TAE buffer. A 100 base pair DNA ruler loaded in the first lane served as length standard. B) Distribution pattern for UCHL1 promoter DNA methylation in tumor adjacent kidney epithelium, autologous primary RCC lesions and RCC cell lines. Grey bars represent samples with unmethylated (U), striped bars with partially methylated (P) and black bars with fully methylated (M) CpG islets within the UCHL1 promoter core region as indicated.

    Techniques Used: DNA Methylation Assay, Combined Bisulfite Restriction Analysis Assay, Amplification, Nested PCR, Methylation

    14) Product Images from "A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA"

    Article Title: A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr051

    The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.
    Figure Legend Snippet: The β-gt can specifically modify 5hmC residues at a high efficiency. ( a ) Oligonucleotides that were either incubated in the presence or absence of the β-gt were digested with Taq I, treated with alkaline phosphatase, 5′-end labeled using T4 polynucleotide kinase and digested to 5′-mononucleotides using DNase I and Snake Venom Phosphodiesterase. Radiolabeled mononucleotides were analyzed by two-dimensional TLC. C, 3′-deoxyribocytosine-5′-monophosphate; T, 3′-deoxyribothymidine-5′-monophosphate; 5meC, 3′-deoxyribo-N5-methylcytosine-5′-monophosphate; 5hmC, 3′-deoxyribo-N5-hydroxymethylcytosine-5′-monophosphate. ( b ) HPLC coupled to tandem mass spectrometry was used to measure the efficiency of the β-gt reaction. Substrates analyzed were 2.7 kb linear PCR products of pUC18: the dC substrate contained only cytosine residues; the 5meC substrate was created by methylating the CpG dinucleotide of the cytosine substrate; the 5hmC substrate was created by using d5hmC in place of dCTP in the PCR reactions; the β-glu-5hmC substrate was created by incubating the 5hmC substrate with the β-gt in the presence of UDP-glucose. Control DNA was prepared from salmon sperm. LC/MS/MS chromatograms of the cytosine residues from each of the substrates are presented. Abbreviations: dC, 3′-deoxyribocytosine; 5me(dC), 3′-deoxyribo-N5-methylcytosine; 5hm(dC), 3′-deoxyribo-N5-hydroxymethylcytosine; 5-glu-hm(dC), 3′-deoxyribo-N5-(β- d -glucosyl(hydroxymethyl))cytosine. Asterisks indictes that cytosines are only 5meC modified at CpG sequences.

    Techniques Used: Incubation, Labeling, Thin Layer Chromatography, High Performance Liquid Chromatography, Mass Spectrometry, Polymerase Chain Reaction, Liquid Chromatography with Mass Spectroscopy, Modification

    15) Product Images from "Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken"

    Article Title: Determination of Polymorphisms in Pituitary Genes of the Native Afghani Naked Neck Chicken

    Journal: The Journal of Poultry Science

    doi: 10.2141/jpsa.0180087

    The electrophoretic profile of PIT-1 intron 5 digested with Taq I. Lanes 1 and 4 are heterozygous (AB) genotypes, lanes 2 and 3 are homozygous (BB) genotypes, and lanes 5 and 6 are homozygous (AA) genotypes. M shows the molecular weight marker (100 bp ladder).
    Figure Legend Snippet: The electrophoretic profile of PIT-1 intron 5 digested with Taq I. Lanes 1 and 4 are heterozygous (AB) genotypes, lanes 2 and 3 are homozygous (BB) genotypes, and lanes 5 and 6 are homozygous (AA) genotypes. M shows the molecular weight marker (100 bp ladder).

    Techniques Used: Molecular Weight, Marker

    16) Product Images from "SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation"

    Article Title: SIP1 is downregulated in hepatocellular carcinoma by promoter hypermethylation

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-11-223

    Methylation analysis of promoter regions by COBRA . Photographs are representative of tumor-specific methylation in three promoter regions. Amplicons of P1 and P2 are cut with Bst UI (left and middle), and Taq I digestion is applied to the PCR products of the P3 region (right). N: normal; T: tumor; M: marker.
    Figure Legend Snippet: Methylation analysis of promoter regions by COBRA . Photographs are representative of tumor-specific methylation in three promoter regions. Amplicons of P1 and P2 are cut with Bst UI (left and middle), and Taq I digestion is applied to the PCR products of the P3 region (right). N: normal; T: tumor; M: marker.

    Techniques Used: Methylation, Combined Bisulfite Restriction Analysis Assay, Polymerase Chain Reaction, Marker

    17) Product Images from "Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California"

    Article Title: Coyotes (Canis latrans) as the Reservoir for a Human Pathogenic Bartonella sp.: Molecular Epidemiology of Bartonella vinsonii subsp. berkhoffii Infection in Coyotes from Central Coastal California

    Journal: Journal of Clinical Microbiology

    doi:

    PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).
    Figure Legend Snippet: PCR (lanes 2 to 5) and PCR-RFLP (lanes 6 to 9, Taq I digestion; lanes 10 to 13, Hha I digestion) analyses of the gltA ). Lanes 1 and 14, standard 100-bp molecular ladder; lanes 2, 6, and 10, coyote isolates; lanes 3, 7, and 11, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 4, 8, and 12, B. vinsonii ATCC VR152; lanes 5, 9 and 13, B. henselae (strain U-4, University of California, Davis).

    Techniques Used: Polymerase Chain Reaction

    PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).
    Figure Legend Snippet: PCR-RFLP analysis (lanes 2 to 11, Taq I digestion; lanes 12 to 21, Mse I digestion) of the gltA ). Lanes 1 and 22, standard 100-bp molecular ladder; lanes 2 to 9 and 12 to 19, coyote isolates; lanes 10 and 20, B. vinsonii subsp. berkhoffii ATCC 51672; lanes 11 and 21, B. henselae (strain U-4; University of California, Davis).

    Techniques Used: Polymerase Chain Reaction

    18) Product Images from "Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum x Solanum pennellii introgression lines"

    Article Title: Bin mapping of tomato diversity array (DArT) markers to genomic regions of Solanum lycopersicum x Solanum pennellii introgression lines

    Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

    doi: 10.1007/s00122-011-1759-5

    Digested-PCR products of DArT marker sequences reveal predicted polymorphisms and chromosomal locations. CAPs analysis of DArT marker sequences from parental and introgression lines. SYBR Safe-stained 2% TAE agarose gels highlighting the polymorphisms observed between Heinz, M82, S. pennellii and different IL lines DNAs. a Taq I digestion of PCR-amplified DNA corresponding to S. lycopersicum DArT marker 441173 using primers DArT39 and DArT40. b Mnl I digestion of PCR-amplified DNA corresponding to S. pennellii DArT marker 436990 using primers DArT41 and DArT42. Template DNA; S. lycopersicum cv. Heinz (H), S. lycopersicum cv. M82 (M82), S. pennellii ( Sp ), Introgression lines (IL), molecular weight Hyperladder IV (BIOLINE) (M)
    Figure Legend Snippet: Digested-PCR products of DArT marker sequences reveal predicted polymorphisms and chromosomal locations. CAPs analysis of DArT marker sequences from parental and introgression lines. SYBR Safe-stained 2% TAE agarose gels highlighting the polymorphisms observed between Heinz, M82, S. pennellii and different IL lines DNAs. a Taq I digestion of PCR-amplified DNA corresponding to S. lycopersicum DArT marker 441173 using primers DArT39 and DArT40. b Mnl I digestion of PCR-amplified DNA corresponding to S. pennellii DArT marker 436990 using primers DArT41 and DArT42. Template DNA; S. lycopersicum cv. Heinz (H), S. lycopersicum cv. M82 (M82), S. pennellii ( Sp ), Introgression lines (IL), molecular weight Hyperladder IV (BIOLINE) (M)

    Techniques Used: Polymerase Chain Reaction, Marker, Staining, Amplification, Molecular Weight

    19) Product Images from "Phenotypic and Molecular Characterization of Tetracycline- and Erythromycin-Resistant Strains of Streptococcus pneumoniae"

    Article Title: Phenotypic and Molecular Characterization of Tetracycline- and Erythromycin-Resistant Strains of Streptococcus pneumoniae

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.47.7.2236-2241.2003

    Different fingerprinting profiles obtained by digesting the tet (M) amplicons from 64 tet (M)-positive pneumococci with four endonucleases. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon. Lanes 1a to 1e, different Aci I profiles ( Aci I 1 to Aci I 5 ). Lanes 2a and 2b, different Rsa I profiles ( Rsa I 1 and Rsa I 2 ). Lane 3, Mse I profile. Lane 4, Taq I profile.
    Figure Legend Snippet: Different fingerprinting profiles obtained by digesting the tet (M) amplicons from 64 tet (M)-positive pneumococci with four endonucleases. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon. Lanes 1a to 1e, different Aci I profiles ( Aci I 1 to Aci I 5 ). Lanes 2a and 2b, different Rsa I profiles ( Rsa I 1 and Rsa I 2 ). Lane 3, Mse I profile. Lane 4, Taq I profile.

    Techniques Used: Marker, Amplification

    HRRA patterns of two tet (M)-positive pneumococci with restriction types A and B. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon of the strain exhibiting restriction type A; lanes A1 to A4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively. Lane B, undigested tet (M) amplicon of the strain exhibiting restriction type B; lanes B1 to B4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively.
    Figure Legend Snippet: HRRA patterns of two tet (M)-positive pneumococci with restriction types A and B. Lane M, molecular size marker (100-bp ladder). Lane A, undigested tet (M) amplicon of the strain exhibiting restriction type A; lanes A1 to A4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively. Lane B, undigested tet (M) amplicon of the strain exhibiting restriction type B; lanes B1 to B4, restriction profiles yielded by endonucleases Aci I, Rsa I, Mse I, and Taq I, respectively.

    Techniques Used: Marker, Amplification

    20) Product Images from "Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis"

    Article Title: Differentiation of Clinical Mycobacterium tuberculosis Complex Isolates by gyrB DNA Sequence Polymorphism Analysis

    Journal: Journal of Clinical Microbiology

    doi:

    RFLP patterns of PCR products obtained by Rsa I digestion (a), Sac II digestion (b), and Taq I (c) digestion of the 1,020-bp gyrB PCR fragment. Lanes: 1 and 9, 100-bp ladder; 2, M. tuberculosis ; 3, M. bovis resistant to PZA; 4 and 5, M. bovis susceptible to PZA; 6, M. africanum subtype I; 7, M. africanum subtype II; 8, M. microti .
    Figure Legend Snippet: RFLP patterns of PCR products obtained by Rsa I digestion (a), Sac II digestion (b), and Taq I (c) digestion of the 1,020-bp gyrB PCR fragment. Lanes: 1 and 9, 100-bp ladder; 2, M. tuberculosis ; 3, M. bovis resistant to PZA; 4 and 5, M. bovis susceptible to PZA; 6, M. africanum subtype I; 7, M. africanum subtype II; 8, M. microti .

    Techniques Used: Polymerase Chain Reaction

    21) Product Images from "Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales"

    Article Title: Dynamic Evolution of Telomeric Sequences in the Green Algal Order Chlamydomonadales

    Journal: Genome Biology and Evolution

    doi: 10.1093/gbe/evs007

    Results of terminal restriction fragment (TRF) analysis. Genomic DNA samples from the Chloromonadinia (TEL159), the Stephanosphaeria (TEL106), and the Dunaliellinia (TEL173) were digested by Taq I (T), Mbo I (M), Alu I (A), or Rsa I (R) restriction endonuclease (−, non-digested) and separated on an 0.9% agarose gel (marker lengths in kilo bases). Control algal DNA samples for the Arabidopsis type (TTTAGGG) and the Chlamydomonas type (TTTTAGGG) were included. The hybridization pattern of the probes specific for the telomeric types—the Arabidopsis type (ATSB), the Chlamydomonas type (CHSB), the human type (HUSB), and the chlorarachniophyte nucleomorph type (CASB) is shown ( table 1 ). Only the part of minisatellite probes is shown here, full version of the TRF analysis is available as supplementary fig. S2 ( Supplementary Material online)
    Figure Legend Snippet: Results of terminal restriction fragment (TRF) analysis. Genomic DNA samples from the Chloromonadinia (TEL159), the Stephanosphaeria (TEL106), and the Dunaliellinia (TEL173) were digested by Taq I (T), Mbo I (M), Alu I (A), or Rsa I (R) restriction endonuclease (−, non-digested) and separated on an 0.9% agarose gel (marker lengths in kilo bases). Control algal DNA samples for the Arabidopsis type (TTTAGGG) and the Chlamydomonas type (TTTTAGGG) were included. The hybridization pattern of the probes specific for the telomeric types—the Arabidopsis type (ATSB), the Chlamydomonas type (CHSB), the human type (HUSB), and the chlorarachniophyte nucleomorph type (CASB) is shown ( table 1 ). Only the part of minisatellite probes is shown here, full version of the TRF analysis is available as supplementary fig. S2 ( Supplementary Material online)

    Techniques Used: Agarose Gel Electrophoresis, Marker, Hybridization

    22) Product Images from "Toll-like receptor triggering in cord blood mesenchymal stem cells"

    Article Title: Toll-like receptor triggering in cord blood mesenchymal stem cells

    Journal: Journal of Cellular and Molecular Medicine

    doi: 10.1111/j.1582-4934.2009.00653.x

    The TNFα promoter is methylated in USSCs. (A) TNFα mRNA was detected by means of non-quantitative RT-PCR in monocytes (Mono), immature DC (imDC), DC stimulated with LPS for 6 hrs (DC, 6-hr LPS), tolerogenic DC (tolDC), tolerogenic DC stimulated with LPS for 6 hrs (tolDC, 6-hr LPS) and USSCs from donor 5016 (USSC-5016). The promoter of TNFα in imDC appeared to be unmethylated, as demonstrated by the resistance of methylation-specific genomic PCR products to Taq I digestion. (B) The TNF-α promoter in USSCs from two different donors (USSC-5016 and -DD) is methylated, as methylation-specific genomic PCR products derived from these cells are sensitive to Taq I digestion, irrespective of LPS or flagellin stimulation for 2 hrs. Arrows indicate full-length (183 bp; upper arrow), 141 bp and 42 bp products.
    Figure Legend Snippet: The TNFα promoter is methylated in USSCs. (A) TNFα mRNA was detected by means of non-quantitative RT-PCR in monocytes (Mono), immature DC (imDC), DC stimulated with LPS for 6 hrs (DC, 6-hr LPS), tolerogenic DC (tolDC), tolerogenic DC stimulated with LPS for 6 hrs (tolDC, 6-hr LPS) and USSCs from donor 5016 (USSC-5016). The promoter of TNFα in imDC appeared to be unmethylated, as demonstrated by the resistance of methylation-specific genomic PCR products to Taq I digestion. (B) The TNF-α promoter in USSCs from two different donors (USSC-5016 and -DD) is methylated, as methylation-specific genomic PCR products derived from these cells are sensitive to Taq I digestion, irrespective of LPS or flagellin stimulation for 2 hrs. Arrows indicate full-length (183 bp; upper arrow), 141 bp and 42 bp products.

    Techniques Used: Methylation, Quantitative RT-PCR, Polymerase Chain Reaction, Derivative Assay

    23) Product Images from "Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter"

    Article Title: Further examination of the Xist promoter-switch hypothesis in X inactivation: Evidence against the existence and function of a P0 promoter

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

    doi:

    The RNA detected by CJ11–CJ12 is found in the cytoplasm and is exclusively derived from autosomal Rps12 expression. ( A ) Nuclear and cytoplasmic distribution of the “P 0 RNA” isolated from male (M) and female (F) fibroblasts (Fib) and ES cells, RNA was reverse transcribed and amplified with CJ11 and CJ12. Xist ), which spans exons 3 to 6 of Xist. ( B ) Taq I and Hin fI restriction maps for pS12X and Rps12 fragments bounded by CJ11 and CJ12. Sizes are shown for polymorphic fragments. Asterisks indicate RFLP positions. ( C ) RFLP analysis of CJ11–CJ12 RT-PCR products. PCR products were diluted and extended one cycle to minimize heteroduplex formation and then digested with Taq I or Hin fI. Polymorphic restriction fragments were detected by hybridization to radiolabeled nested oligonucleotide CJ10. + and − indicate the presence or absence, respectively, of restriction enzyme during incubation. ( D ) Sensitivity of the RFLP assay of CJ11–CJ12 amplification. A constant amount of Rps12 RT-PCR product was mixed with 10-fold dilutions of pS12X PCR product, digested with Taq I, and visualized by hybridization to CJ10 oligonucleotide. pS12X fragments were visible at 10 −3 dilution (shown) and at 10 −4 dilution on the original autoradiogram (data not shown).
    Figure Legend Snippet: The RNA detected by CJ11–CJ12 is found in the cytoplasm and is exclusively derived from autosomal Rps12 expression. ( A ) Nuclear and cytoplasmic distribution of the “P 0 RNA” isolated from male (M) and female (F) fibroblasts (Fib) and ES cells, RNA was reverse transcribed and amplified with CJ11 and CJ12. Xist ), which spans exons 3 to 6 of Xist. ( B ) Taq I and Hin fI restriction maps for pS12X and Rps12 fragments bounded by CJ11 and CJ12. Sizes are shown for polymorphic fragments. Asterisks indicate RFLP positions. ( C ) RFLP analysis of CJ11–CJ12 RT-PCR products. PCR products were diluted and extended one cycle to minimize heteroduplex formation and then digested with Taq I or Hin fI. Polymorphic restriction fragments were detected by hybridization to radiolabeled nested oligonucleotide CJ10. + and − indicate the presence or absence, respectively, of restriction enzyme during incubation. ( D ) Sensitivity of the RFLP assay of CJ11–CJ12 amplification. A constant amount of Rps12 RT-PCR product was mixed with 10-fold dilutions of pS12X PCR product, digested with Taq I, and visualized by hybridization to CJ10 oligonucleotide. pS12X fragments were visible at 10 −3 dilution (shown) and at 10 −4 dilution on the original autoradiogram (data not shown).

    Techniques Used: Derivative Assay, Expressing, Isolation, Amplification, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Hybridization, Incubation, RFLP Assay

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    Sequencing:

    Article Title: Methyltransferase-directed covalent coupling of fluorophores to DNA covalent coupling of fluorophores to DNA †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04229eClick here for additional data file.
    Article Snippet: .. Preparation of sequence-specifically modified DNA Plasmid DNA (pUC19, NEB) (50 ng μL–1 ), an AdoMet cofactor analogue (150 μM Ado-6-amine or Ado-6-azide), and M.TaqI DNA methyltransferase (0.1 mg ml–1 ) were incubated in CutSmart buffer (New England Biolabs) for 2 h at 60 °C. .. Subsequently, 1 μL of proteinase K was added and the reaction was incubated for 1 h at 55 °C.

    Modification:

    Article Title: Methyltransferase-directed covalent coupling of fluorophores to DNA covalent coupling of fluorophores to DNA †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04229eClick here for additional data file.
    Article Snippet: .. Preparation of sequence-specifically modified DNA Plasmid DNA (pUC19, NEB) (50 ng μL–1 ), an AdoMet cofactor analogue (150 μM Ado-6-amine or Ado-6-azide), and M.TaqI DNA methyltransferase (0.1 mg ml–1 ) were incubated in CutSmart buffer (New England Biolabs) for 2 h at 60 °C. .. Subsequently, 1 μL of proteinase K was added and the reaction was incubated for 1 h at 55 °C.

    Incubation:

    Article Title: Small Fragment Homologous Replacement: Evaluation of Factors Influencing Modification Efficiency in an Eukaryotic Assay System
    Article Snippet: .. For Dam and SssI methylation, 1 µg of SDF-PCR-WT was incubated with 2 units of methyltransferase (New England Biolabs, Ipswich, MA, USA) in a final reaction volume of 20 µl. .. To create a Dam/SssI methylated fragment, we performed a second SssI methylation step on previously Dam methylated samples.

    Article Title: Methyltransferase-directed covalent coupling of fluorophores to DNA covalent coupling of fluorophores to DNA †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04229eClick here for additional data file.
    Article Snippet: .. Preparation of sequence-specifically modified DNA Plasmid DNA (pUC19, NEB) (50 ng μL–1 ), an AdoMet cofactor analogue (150 μM Ado-6-amine or Ado-6-azide), and M.TaqI DNA methyltransferase (0.1 mg ml–1 ) were incubated in CutSmart buffer (New England Biolabs) for 2 h at 60 °C. .. Subsequently, 1 μL of proteinase K was added and the reaction was incubated for 1 h at 55 °C.

    Article Title: An innovative platform for quick and flexible joining of assorted DNA fragments
    Article Snippet: .. For M.SssI assays, a 1055-bp PCR product, using the pET28-M.SacI plasmid as template, was amplified (using the primers TaqI-Fw and TaqI-Rw), purified, quantified and incubated with methyltransferase as manufacturer instructions (NEB). ..

    Article Title: An innovative platform for quick and flexible joining of assorted DNA fragments
    Article Snippet: .. The 1055-bp secondary product was then purified, quantified and incubated with methyltransferase as manufacturer instructions (NEB; except we increased incubation time to 4 h). .. Methylated DNA was purified and 400 ng used for type IIS assays in duplicates and “Digestion inhibition” and “Methylation efficiency” as described above.

    Polymerase Chain Reaction:

    Article Title: An innovative platform for quick and flexible joining of assorted DNA fragments
    Article Snippet: .. For M.SssI assays, a 1055-bp PCR product, using the pET28-M.SacI plasmid as template, was amplified (using the primers TaqI-Fw and TaqI-Rw), purified, quantified and incubated with methyltransferase as manufacturer instructions (NEB). ..

    Plasmid Preparation:

    Article Title: Methyltransferase-directed covalent coupling of fluorophores to DNA covalent coupling of fluorophores to DNA †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc04229eClick here for additional data file.
    Article Snippet: .. Preparation of sequence-specifically modified DNA Plasmid DNA (pUC19, NEB) (50 ng μL–1 ), an AdoMet cofactor analogue (150 μM Ado-6-amine or Ado-6-azide), and M.TaqI DNA methyltransferase (0.1 mg ml–1 ) were incubated in CutSmart buffer (New England Biolabs) for 2 h at 60 °C. .. Subsequently, 1 μL of proteinase K was added and the reaction was incubated for 1 h at 55 °C.

    Article Title: An innovative platform for quick and flexible joining of assorted DNA fragments
    Article Snippet: .. For M.SssI assays, a 1055-bp PCR product, using the pET28-M.SacI plasmid as template, was amplified (using the primers TaqI-Fw and TaqI-Rw), purified, quantified and incubated with methyltransferase as manufacturer instructions (NEB). ..

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  • 99
    New England Biolabs taq α i restriction endonuclease
    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved <t>Taq</t> <t>α</t> I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .
    Taq α I Restriction Endonuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/taq α i restriction endonuclease/product/New England Biolabs
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    88
    New England Biolabs restriction enzyme taq i
    Restriction enzyme digestion patterns obtained with <t>Taq</t> I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the <t>Taq</t> I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.
    Restriction Enzyme Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 88/100, based on 13 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    New England Biolabs taq i
    Genotyping of <t>phlD</t> -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.
    Taq I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 94/100, based on 9 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Alignment of Mu Terminal Inverted Repeats (TIRs). ClustalW was used to align all known active and potentially active Mu elements. Strings of four or more consecutive bases that are entirely conserved among all elements are shaded in red. The conserved Taq α I site is shaded in blue. Mu4, 5, and 6 are inactive and are not included [reviewed in [5] ]. Mu9 is MuDR. Only the first 39 bp of the Mu10, 11, and 12 TIRs have been sequenced [62] . However, the primer used to amplify the TIR ended in a 3′ GTC, allowing for the assumption that the sequence continues as GAC (shown as small case) and that the Taq α I site remains intact. Of the most recently discovered Mu elements (13–19), only Mu13 has been confirmed to actively move and create new mutations [58] . TIR sequences obtained from [3] , [58] , [62] – [68] .

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing

    Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Manhattan plot of la1-mu1 Taq α I sequencing. ( A ) Manhattan plot showing the distribution of reads from la1-mu1 genomic DNA mapped throughout the B73 genome. Alternating colors represent each of the ten maize chromosomes. Each x-axis pixel represents a bin of 1 Mb and the logarithmic y-axis denotes the number of reads mapping to each bin. The red line represents the known genetic map position for the la1 reference mutation. Each triangle below the plot represents the approximate location of mapped MFS. ( B ) Expanded Manhattan plot of a 1 Mb interval corresponding to the approximate map position of la1 . Same as top with each x-axis pixel representing a bin of 1 kb. Filtered genes in the 1 Mb interval are shown as black rectangles. MFS mapping to this interval are shown as inverted red triangles.

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing, Mutagenesis

    Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Journal: PLoS ONE

    Article Title: Identification of the Maize Gravitropism Gene lazy plant1 by a Transposon-Tagging Genome Resequencing Strategy

    doi: 10.1371/journal.pone.0087053

    Figure Lengend Snippet: Mu - Taq α I Library Construction. Digesting genomic DNA with Taq α I creates a library of fragments. Fragments containing a Mu -MFS junction will all contain a degenerate 39 nt Mu TIR tag along with 31–35 nt of flanking genomic sequence at one end of the 2×75 nt paired-end read. These fragments are computationally identified and the Mu flanking sequence (MFS) is mapped to the maize reference genome.

    Article Snippet: Approximately 5 µg of DNA was digested by 30 units Taq α I restriction endonuclease (New England BioLabs, Inc.) according to the manufacturer’s instructions.

    Techniques: Sequencing

    Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Journal: Journal of Clinical Microbiology

    Article Title: Detection and Identification of Bartonella Species Pathogenic for Humans by PCR Amplification Targeting the Riboflavin Synthase Gene (ribC)

    doi: 10.1128/JCM.41.3.1069-1072.2003

    Figure Lengend Snippet: Restriction enzyme digestion patterns obtained with Taq I. Digestion mixtures were electrophoresed on 1.5% agarose gels. On each panel, the gel is flanked by a 100-bp ladder (Invitrogen Life Technologies) (lane MW). (A) The three species illustrated are unambiguously identified by the Taq I pattern. However, for the species illustrated in panel B, the Taq I patterns are similar to one another, although clearly distinct from that of the species in panel A.

    Article Snippet: Each reaction mixture in which amplicons were detected was subjected to digestion with the restriction enzyme Taq I (New England Biolabs).

    Techniques:

    Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Journal: Applied and Environmental Microbiology

    Article Title: Changes in Populations of Rhizosphere Bacteria Associated with Take-All Disease of Wheat

    doi: 10.1128/AEM.67.10.4414-4425.2001

    Figure Lengend Snippet: Genotyping of phlD -containing bacteria present in the soils of Mount Vernon, Wash. Representative results for the growth chamber assays are shown. The phlD sequences were amplified using gene-specific primers B2BF and BPR4 and subsequently digested with either Hae III or Taq I. Set 1 includes samples of several terminal phlD + dilutions and isolates obtained from rhizospheres of wheat grown in soils A and B. Set 2 includes three isolates of a different genotype obtained from a Lind, Wash., soil for contrast. A known 2,4-DAPG-producing, BOX D genotype strain of Pseudomonas fluorescens (Q8r1–96) was used as a positive control for comparison (lane C). The sizes of individual fragments were determined based on the 100-bp ladder shown in lanes M.

    Article Snippet: To determine the genotype of phlD + populations, amplification products were digested with Hae III or Taq I (New England Biolabs, Beverly, Mass.).

    Techniques: Amplification, Positive Control

    COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.

    Journal: OMICS : a Journal of Integrative Biology

    Article Title: HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer

    doi: 10.1089/omi.2017.0016

    Figure Lengend Snippet: COBRA. Taq I (A) and Hpy 188I (B) restriction enzymes were used for region-1 and region-2, respectively. (−), No restriction digestion; M, marker. An amplicon having an Hpy 188I cutting site was used with (+) and without (Uncut) a restriction enzyme.

    Article Snippet: To analyze the methylation status, amplicons were restriction digested with Taq I and Hpy 188I (New England BioLabs, Ipswich, MA), as previously described (Xiong and Laird, ).

    Techniques: Combined Bisulfite Restriction Analysis Assay, Marker, Amplification