mse i  (New England Biolabs)


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    MseI
    Description:
    MseI 2 500 units
    Catalog Number:
    r0525l
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    282
    Size:
    2 500 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs mse i
    MseI
    MseI 2 500 units
    https://www.bioz.com/result/mse i/product/New England Biolabs
    Average 99 stars, based on 123 article reviews
    Price from $9.99 to $1999.99
    mse i - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster"

    Article Title: A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0026775

    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.
    Figure Legend Snippet: Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Techniques Used: In Vivo, Mutagenesis, Irradiation, In Vitro, Incubation

    2) Product Images from "A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)"

    Article Title: A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)

    Journal: Nucleic Acids Research

    doi:

    Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.
    Figure Legend Snippet: Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Generated, Modification, Amplification, Methylation, Clone Assay

    Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.
    Figure Legend Snippet: Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.

    Techniques Used: Hybridization, Plasmid Preparation, Amplification

    3) Product Images from "Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India"

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India

    Journal: Indian journal of virology : an official organ of Indian Virological Society

    doi: 10.1007/s13337-011-0023-6

    Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria
    Figure Legend Snippet: Actual RFLP analyses of 2.7 kb of 23S rDNA PCR products of TP phytoplasma (amplified using primer pair P23S5F3/A23S3R3) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM, toria

    Techniques Used: Polymerase Chain Reaction, Amplification

    Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,
    Figure Legend Snippet: Actual RFLP analyses of 1.25 kb of 16S rDNA nested-PCR products of TP phytoplasma (amplified using primer pair R16F2n/R16R2) digested with Hin fI, Hae III, Rsa I, Alu I, Hha I and Mse I restriction enzymes; TPN, toria phyllody strain New Delhi; TPM,

    Techniques Used: Nested PCR, Amplification

    4) Product Images from "Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal"

    Article Title: Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal

    Journal: Journal of Clinical Microbiology

    doi:

    Mse I restriction patterns of B. burgdorferi sensu lato rrf-rrl spacer nested PCR products amplified directly from ticks or cultured strains. Lanes 1 and 10, D-15 marker; lanes 2 and 3, cultured B. burgdorferi sensu stricto (ZS 7) and B. lusitaniae (PotiB1), patterns A and E, respectively; lanes 4 and 5, tick-derived samples 58 and 151 (pattern E), respectively; Lane 6, tick-derived sample 132 (pattern F); lane 7, tick-derived sample 163 (patterns E and F); lane 8, tick-derived sample 156 (pattern H); lane 9, tick-derived sample 167 (pattern G).
    Figure Legend Snippet: Mse I restriction patterns of B. burgdorferi sensu lato rrf-rrl spacer nested PCR products amplified directly from ticks or cultured strains. Lanes 1 and 10, D-15 marker; lanes 2 and 3, cultured B. burgdorferi sensu stricto (ZS 7) and B. lusitaniae (PotiB1), patterns A and E, respectively; lanes 4 and 5, tick-derived samples 58 and 151 (pattern E), respectively; Lane 6, tick-derived sample 132 (pattern F); lane 7, tick-derived sample 163 (patterns E and F); lane 8, tick-derived sample 156 (pattern H); lane 9, tick-derived sample 167 (pattern G).

    Techniques Used: Nested PCR, Amplification, Cell Culture, Marker, Derivative Assay

    5) 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-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

    6) Product Images from "Analysis of the Genetic Variability of Genes Encoding the RNA III-Activating Components Agr and TRAP in a Population of Staphylococcus aureus Strains Isolated from Cows with Mastitis"

    Article Title: Analysis of the Genetic Variability of Genes Encoding the RNA III-Activating Components Agr and TRAP in a Population of Staphylococcus aureus Strains Isolated from Cows with Mastitis

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.11.4060-4067.2002

    Restriction polymorphism in the trap gene. The trap gene was amplified by PCR, digested with Mse I, and electrophoresed on a 3% agarose gel. Examples of the different restriction types obtained are shown: type 1 (lane 2), type 2 (lane 3), type 3 (lane 4), and type 4 (lane 5). Molecular weight markers (50-bp DNA ladder; Promega) are shown in lanes 1 and 6.
    Figure Legend Snippet: Restriction polymorphism in the trap gene. The trap gene was amplified by PCR, digested with Mse I, and electrophoresed on a 3% agarose gel. Examples of the different restriction types obtained are shown: type 1 (lane 2), type 2 (lane 3), type 3 (lane 4), and type 4 (lane 5). Molecular weight markers (50-bp DNA ladder; Promega) are shown in lanes 1 and 6.

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

    7) Product Images from "Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells"

    Article Title: Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells

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

    doi:

    Isolation of single fluorescent cells from bone marrow by micromanipulation and preparation of DNA after proteinase K (PK) treatment. After PK inactivation, the double-stranded DNA was digested with Mse I, leaving a TA overhang for adapter annealing and subsequent ligation. After primary amplification, 1/100 of the PCR products was reamplified in the presence of bio-UTP, and 2 μg were used for hybridization.
    Figure Legend Snippet: Isolation of single fluorescent cells from bone marrow by micromanipulation and preparation of DNA after proteinase K (PK) treatment. After PK inactivation, the double-stranded DNA was digested with Mse I, leaving a TA overhang for adapter annealing and subsequent ligation. After primary amplification, 1/100 of the PCR products was reamplified in the presence of bio-UTP, and 2 μg were used for hybridization.

    Techniques Used: Isolation, Micromanipulation, Ligation, Amplification, Polymerase Chain Reaction, Hybridization

    8) Product Images from "A method for measuring the distribution of the shortest telomeres in cells and tissues"

    Article Title: A method for measuring the distribution of the shortest telomeres in cells and tissues

    Journal: Nature Communications

    doi: 10.1038/s41467-017-01291-z

    Measuring TL in long-term telomerase inhibition with imetelstat (1 µM) treatment and after the removal of drug in H2087 cells. a Isolated DNA from H2087 cells with 1 µM imetelstat treatment for 0, 10, and 18 weeks, and post released from 18 weeks for 1, 2, 3, 4, and 5 weeks was digested with the same REs for TeSLA ( Bfa I/ Cvi AII/ Mse I/ Nde I) and then separated on 0.7% agarose gel for TRF analysis. b Interphase Q-FISH; cells from H2087 with 0 and 18 weeks 1 µM imetelstat treatment, and 5 weeks after drug removal were used to measure TL by Q-FISH. The results were quantified using TFL-Telo software ( n : numbers of nuclei were quantified for each time point as indicated above). Scale bar, 3 µm. c Results of TeSLA using DNA as indicated. Four TeSLA PCRs (30 pg of each reaction) were performed for each DNA sample
    Figure Legend Snippet: Measuring TL in long-term telomerase inhibition with imetelstat (1 µM) treatment and after the removal of drug in H2087 cells. a Isolated DNA from H2087 cells with 1 µM imetelstat treatment for 0, 10, and 18 weeks, and post released from 18 weeks for 1, 2, 3, 4, and 5 weeks was digested with the same REs for TeSLA ( Bfa I/ Cvi AII/ Mse I/ Nde I) and then separated on 0.7% agarose gel for TRF analysis. b Interphase Q-FISH; cells from H2087 with 0 and 18 weeks 1 µM imetelstat treatment, and 5 weeks after drug removal were used to measure TL by Q-FISH. The results were quantified using TFL-Telo software ( n : numbers of nuclei were quantified for each time point as indicated above). Scale bar, 3 µm. c Results of TeSLA using DNA as indicated. Four TeSLA PCRs (30 pg of each reaction) were performed for each DNA sample

    Techniques Used: Inhibition, Isolation, Agarose Gel Electrophoresis, Fluorescence In Situ Hybridization, Software

    9) Product Images from "The Core Promoter and Redox-sensitive Cis-elements as Key Targets for Inactivation of the Lysyl Oxidase Gene by Cadmium"

    Article Title: The Core Promoter and Redox-sensitive Cis-elements as Key Targets for Inactivation of the Lysyl Oxidase Gene by Cadmium

    Journal: Journal of nature and science

    doi:

    Enhancement of methylation at the LOX promoter region in CdR cells as determined by using the methylation promoter PCR kit. The same amount of genomic DNA isolated from control and CdR cells were digested with restriction enzyme Mse I then incubated with MBP to form a protein/DNA complex, methylated DNA was isolated using a separation column and amplified by PCR. PCR products as a 205 bp DNA fragment encompassing one RNA synthesis star site at −78 and MREs were analyzed on 2.2% agarose gel.
    Figure Legend Snippet: Enhancement of methylation at the LOX promoter region in CdR cells as determined by using the methylation promoter PCR kit. The same amount of genomic DNA isolated from control and CdR cells were digested with restriction enzyme Mse I then incubated with MBP to form a protein/DNA complex, methylated DNA was isolated using a separation column and amplified by PCR. PCR products as a 205 bp DNA fragment encompassing one RNA synthesis star site at −78 and MREs were analyzed on 2.2% agarose gel.

    Techniques Used: Methylation, Polymerase Chain Reaction, Isolation, Incubation, Amplification, Agarose Gel Electrophoresis

    10) Product Images from "A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes"

    Article Title: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

    Journal: Genome Research

    doi: 10.1101/gr.224102

    Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.
    Figure Legend Snippet: Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Techniques Used: Clone Assay, Methylation, Transformation Assay

    11) Product Images from "Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of Escherichia coli: High-Resolution Typing Method with Phylogenetic Significance"

    Article Title: Predictive Fluorescent Amplified-Fragment Length Polymorphism Analysis of Escherichia coli: High-Resolution Typing Method with Phylogenetic Significance

    Journal: Journal of Clinical Microbiology

    doi:

    Sizes (in base pairs) and approximate locations of FAFLP assay-predicted fragments in the E. coli K-12 MG1655 genome obtained with primer set Mse I+TA– Eco RI+0. The genes that the fragments are predicted to have been amplified from are also indicated. θ, an uncharacterized locus in E. coli bearing sequence similarity to characterized loci in other bacteria; ϕ, no matches were found, indicating a noncoding region; ∗, hypothetical, as yet uncharacterized genes.
    Figure Legend Snippet: Sizes (in base pairs) and approximate locations of FAFLP assay-predicted fragments in the E. coli K-12 MG1655 genome obtained with primer set Mse I+TA– Eco RI+0. The genes that the fragments are predicted to have been amplified from are also indicated. θ, an uncharacterized locus in E. coli bearing sequence similarity to characterized loci in other bacteria; ϕ, no matches were found, indicating a noncoding region; ∗, hypothetical, as yet uncharacterized genes.

    Techniques Used: Amplification, Sequencing

    12) Product Images from "NNK, a Tobacco-Specific Carcinogen, Inhibits the Expression of Lysyl Oxidase, a Tumor Suppressor"

    Article Title: NNK, a Tobacco-Specific Carcinogen, Inhibits the Expression of Lysyl Oxidase, a Tumor Suppressor

    Journal: International Journal of Environmental Research and Public Health

    doi: 10.3390/ijerph120100064

    Enhancement of methylation at the LOX promoter region in NNK-treated cells as determined by using the methylation promoter PCR kit. The same amount of genomic DNA isolated from control and NNK-treated cells were digested with restriction enzyme Mse I, then incubated with MBP to form a protein/DNA complex. Methylated DNA was isolated using a separation column and amplified by PCR. PCR products as a 205 bp DNA were analyzed on 2.2% agarose gels and densities of DNA bands measured by the 1D Scan software. One typical gel among three repeated experiments is presented.
    Figure Legend Snippet: Enhancement of methylation at the LOX promoter region in NNK-treated cells as determined by using the methylation promoter PCR kit. The same amount of genomic DNA isolated from control and NNK-treated cells were digested with restriction enzyme Mse I, then incubated with MBP to form a protein/DNA complex. Methylated DNA was isolated using a separation column and amplified by PCR. PCR products as a 205 bp DNA were analyzed on 2.2% agarose gels and densities of DNA bands measured by the 1D Scan software. One typical gel among three repeated experiments is presented.

    Techniques Used: Methylation, Polymerase Chain Reaction, Isolation, Incubation, Amplification, Software

    13) Product Images from "A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)"

    Article Title: A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)

    Journal: Nucleic Acids Research

    doi:

    Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.
    Figure Legend Snippet: Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.

    Techniques Used: Sequencing, Polymerase Chain Reaction, Generated, Modification, Amplification, Methylation, Clone Assay

    Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.
    Figure Legend Snippet: Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.

    Techniques Used: Hybridization, Plasmid Preparation, Amplification

    14) Product Images from "Transcriptional Reprogramming and Chromatin Remodeling Accompanies Oct4 and Nanog Silencing in Mouse Trophoblast Lineage"

    Article Title: Transcriptional Reprogramming and Chromatin Remodeling Accompanies Oct4 and Nanog Silencing in Mouse Trophoblast Lineage

    Journal: Stem Cells and Development

    doi: 10.1089/scd.2013.0328

    Chromatin remodeling at the Oct-Sox binding motif in Oct4 and Nanog. (A) Schematic showing the location of the Oct-Sox binding motif and adjacent restriction enzyme cut site within the forward and reverse primers for Oct4 and Nanog . Shown are the effects of open and condensed chromatin on the accessibility of Dde I and Mse I at Oct4 and Nanog , respectively. (B) qPCR analysis of restriction enzyme accessibility at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. As a negative control, the accessibility of Mse I at an intergenic region was assessed. Data are presented as the percentage of DNA cut by the respective restriction enzyme. An assay was performed on a total of three biological replicates. For each biological replicate, two PCR reactions were performed in duplicate. (C) Histone H3 ChIP analysis at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. The enrichment of histone H3 on Gapdh was utilized as a control. As a negative control, a rabbit nonspecific IgG was used. A total of two ChIP replicates were performed for each biological replicate. * P
    Figure Legend Snippet: Chromatin remodeling at the Oct-Sox binding motif in Oct4 and Nanog. (A) Schematic showing the location of the Oct-Sox binding motif and adjacent restriction enzyme cut site within the forward and reverse primers for Oct4 and Nanog . Shown are the effects of open and condensed chromatin on the accessibility of Dde I and Mse I at Oct4 and Nanog , respectively. (B) qPCR analysis of restriction enzyme accessibility at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. As a negative control, the accessibility of Mse I at an intergenic region was assessed. Data are presented as the percentage of DNA cut by the respective restriction enzyme. An assay was performed on a total of three biological replicates. For each biological replicate, two PCR reactions were performed in duplicate. (C) Histone H3 ChIP analysis at the Oct-Sox binding motif in Oct4 and Nanog at 0, 48, and 96 h after induction of Cdx2. The enrichment of histone H3 on Gapdh was utilized as a control. As a negative control, a rabbit nonspecific IgG was used. A total of two ChIP replicates were performed for each biological replicate. * P

    Techniques Used: Binding Assay, Real-time Polymerase Chain Reaction, Negative Control, Polymerase Chain Reaction, Chromatin Immunoprecipitation

    15) Product Images from "Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California"

    Article Title: Molecular Evidence of Bartonella spp. in Questing Adult Ixodes pacificus Ticks in California

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.39.4.1221-1226.2001

    PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with Taq I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .
    Figure Legend Snippet: PCR-RFLP of the gltA gene of tick samples. Assays were performed by digestion with Taq I, Hha I, and Mse I. Lane M, 100-bp molecular size ladder; lanes 1, 11, and 21, tick 22; lanes 2, 12, and 22, tick 70; lanes 3, 13, and 23, tick 75; lanes 4, 14, and 24, tick 81; lanes 5, 15, and 25, tick 12; lanes 6, 16, and 26, tick 143; lanes 7, 17, and 27, B. henselae ; lanes 8, 18, and 28, B. vinsonii subsp. berkhoffii ; lanes 9, 19, and 29, Bartonella strain cattle-1; lanes 10, 20, and 30, B. quintana .

    Techniques Used: Polymerase Chain Reaction

    16) Product Images from "Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)"

    Article Title: Genetic Characteristics of Borrelia coriaceae Isolates from the Soft Tick Ornithodoros coriaceus (Acari: Argasidae)

    Journal: Journal of Clinical Microbiology

    doi:

    16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.
    Figure Legend Snippet: 16S rRNA amplification products restricted with Hph I (a), Bfa I (b), and Mse I (c). Lanes: 1, CA434; 2, CA435; 3, Co53; 4, B. parkeri ; 5, CA4. Restriction fragments were resolved in 2.5% NuSieve-GTG agarose–1× TBE at 5 V/cm for 3.5 h.

    Techniques Used: Amplification

    17) Product Images from "Ti Plasmids from Agrobacterium Characterize Rootstock Clones That Initiated a Spread of Crown Gall Disease in Mediterranean Countries"

    Article Title: Ti Plasmids from Agrobacterium Characterize Rootstock Clones That Initiated a Spread of Crown Gall Disease in Mediterranean Countries

    Journal: Applied and Environmental Microbiology

    doi:

    RFLP analysis of amplified vir (418) and vir (1673). vir (418) was restriction digested with the enzymes Msp I (profiles M1 and M2) and Mse I (profiles S1 and S2). Digestion of vir (1673) was performed with the enzyme Cfo I (profiles C1 and C2). A 123-bp ladder (lanes L) was used as a DNA size marker.
    Figure Legend Snippet: RFLP analysis of amplified vir (418) and vir (1673). vir (418) was restriction digested with the enzymes Msp I (profiles M1 and M2) and Mse I (profiles S1 and S2). Digestion of vir (1673) was performed with the enzyme Cfo I (profiles C1 and C2). A 123-bp ladder (lanes L) was used as a DNA size marker.

    Techniques Used: Amplification, Marker

    18) Product Images from "Frequency of hybridization between Ostrinia nubilalis E-and Z-pheromone races in regions of sympatry within the United States"

    Article Title: Frequency of hybridization between Ostrinia nubilalis E-and Z-pheromone races in regions of sympatry within the United States

    Journal: Ecology and Evolution

    doi: 10.1002/ece3.639

    Estimates of directional selection using Tajima's D by analysis of 100-bp sliding windows with 25-bp iterations across the Ostrinia nubilalis pheromone gland fatty-acyl reductase ( pgfar ) gene. This figure was adapted from a similar analysis by Lassance et al. ( 35 ) to show the location single nucleotide polymorphisms (SNPs) detected by markers at Taq I, Nde II, and Mse I restriction endonuclease sites.
    Figure Legend Snippet: Estimates of directional selection using Tajima's D by analysis of 100-bp sliding windows with 25-bp iterations across the Ostrinia nubilalis pheromone gland fatty-acyl reductase ( pgfar ) gene. This figure was adapted from a similar analysis by Lassance et al. ( 35 ) to show the location single nucleotide polymorphisms (SNPs) detected by markers at Taq I, Nde II, and Mse I restriction endonuclease sites.

    Techniques Used: Selection

    19) Product Images from "EBV Latency Types Adopt Alternative Chromatin Conformations"

    Article Title: EBV Latency Types Adopt Alternative Chromatin Conformations

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1002180

    Quantitative 3C analysis confirms alternative loop formation between type I and type III latency types. 3C assay coupled with quantitative PCR was used to analyze chromatin architecture of the EBV genome in type I (Mutu) and type III (Mutu-LCL) latencies. EBV genome coordinates of all the Mse I fragments tested are indicated on the X-axis. A pink asterisk indicates fragment bearing the anchor primer. Loop formation between the anchor primer (pink box) and an Mse I fragment is indicated by dashed arrows. Data were analyzed using the ΔCt method, and Ct values generated by using 100 ng of EBV bacmid DNA Mse I digested and randomly ligated were used as the control. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis. (A) Quantitative 3C analysis using the anchor primer within the fragment containing Qp and several regions of the EBV genome. (B) Quantitative 3C analysis using the anchor primer within the fragment containing Cp and several regions of the EBV genome. (C) Quantitative 3C analysis using the anchor primer within the fragment chosen as control and several regions of the EBV genome.
    Figure Legend Snippet: Quantitative 3C analysis confirms alternative loop formation between type I and type III latency types. 3C assay coupled with quantitative PCR was used to analyze chromatin architecture of the EBV genome in type I (Mutu) and type III (Mutu-LCL) latencies. EBV genome coordinates of all the Mse I fragments tested are indicated on the X-axis. A pink asterisk indicates fragment bearing the anchor primer. Loop formation between the anchor primer (pink box) and an Mse I fragment is indicated by dashed arrows. Data were analyzed using the ΔCt method, and Ct values generated by using 100 ng of EBV bacmid DNA Mse I digested and randomly ligated were used as the control. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis. (A) Quantitative 3C analysis using the anchor primer within the fragment containing Qp and several regions of the EBV genome. (B) Quantitative 3C analysis using the anchor primer within the fragment containing Cp and several regions of the EBV genome. (C) Quantitative 3C analysis using the anchor primer within the fragment chosen as control and several regions of the EBV genome.

    Techniques Used: Real-time Polymerase Chain Reaction, Generated, Ligation

    Quantitative 3C analysis confirms changes in chromatin architecture in ΔCTCF-Qp and ΔCTCF-Qp compared to Wt EBV bacmid. 3C assay coupled with quantitative PCR was used to analyze EBV chromatin architecture in 293-EBV Wt bacmid, 293-EBV ΔCTCF-Qp and 293-EBV ΔCTCF-Cp stable cell lines. EBV genome coordinates of all the MseI fragments tested are indicated on the X-axis. A pink asterisk indicates the fragment bearing the anchor primer. Loop formation between the anchor primer (pink box) and a MseI fragment is indicated by dashed arrows. PCR amplification was analyzed using the ΔCt method, and Ct values generated by using 50 ng of EBV bacmid DNA Mse I digested and randomly ligated were used as the control. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis. (A) Quantitative 3C analysis using the anchor primer within the fragment containing Qp and several regions of the EBV genome. (B) Quantitative 3C analysis using the anchor primer within the fragment containing Cp and several regions of EBV genome. (C) Quantitative 3C analysis using the anchor primer within the fragment chosen as control and several regions of the EBV genome.
    Figure Legend Snippet: Quantitative 3C analysis confirms changes in chromatin architecture in ΔCTCF-Qp and ΔCTCF-Qp compared to Wt EBV bacmid. 3C assay coupled with quantitative PCR was used to analyze EBV chromatin architecture in 293-EBV Wt bacmid, 293-EBV ΔCTCF-Qp and 293-EBV ΔCTCF-Cp stable cell lines. EBV genome coordinates of all the MseI fragments tested are indicated on the X-axis. A pink asterisk indicates the fragment bearing the anchor primer. Loop formation between the anchor primer (pink box) and a MseI fragment is indicated by dashed arrows. PCR amplification was analyzed using the ΔCt method, and Ct values generated by using 50 ng of EBV bacmid DNA Mse I digested and randomly ligated were used as the control. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis. (A) Quantitative 3C analysis using the anchor primer within the fragment containing Qp and several regions of the EBV genome. (B) Quantitative 3C analysis using the anchor primer within the fragment containing Cp and several regions of EBV genome. (C) Quantitative 3C analysis using the anchor primer within the fragment chosen as control and several regions of the EBV genome.

    Techniques Used: Real-time Polymerase Chain Reaction, Stable Transfection, Polymerase Chain Reaction, Amplification, Generated, Ligation

    CTCF siRNA depletion disrupts chromatin architecture of EBV. (A) 293-EBV Wt cell lines were transfected with siRNA against CTCF (siCTCF) or a non-targeting control (siControl). After 72 hrs cells were harvested and then analyzed by western blot with antibody to CTCF (top panel) or loading control PCNA (lower panel) to check depletion efficiency. (B) RT-qPCR analysis of promoter utilization and EBNA1 and EBNA2 gene expression after CTCF depletion. Data are normalized to GFP mRNA and expressed as −ΔΔCt values. Each bar represents the mean ± SE of three independent experiments. (C and D) 3C assay was used to analyze chromatin conformation after depletion of CTCF. Representative gel images of 3C PCR analysis using the anchor primer within the fragment containing Qp promoter (C) or Cp promoter (D) and several regions of the EBV genome for 293-EBV Wt cell line transfected with siControl or siCTCF siRNA. Amplified regions are indicated above each gel. (E) 3C assay coupled with quantitative PCR was used to analyze EBV chromatin architecture in 293-EBV Wt bacmid transfected with siControl or siCTCF siRNA, using the anchor primer within the fragment containing Qp promoter (left panel) or Cp promoter (right panel) and several regions of EBV genome. EBV genome coordinates of all the Mse I fragments tested are indicated on the X-axis. A pink asterisk indicates fragment bearing the anchor primer. Loop formation between anchor primer (pink box) and a Mse I fragment is indicated by dashed arrows. PCR amplification was normalized by using 50 ng of EBV bacmid DNA Mse I digested and randomly ligated. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis.
    Figure Legend Snippet: CTCF siRNA depletion disrupts chromatin architecture of EBV. (A) 293-EBV Wt cell lines were transfected with siRNA against CTCF (siCTCF) or a non-targeting control (siControl). After 72 hrs cells were harvested and then analyzed by western blot with antibody to CTCF (top panel) or loading control PCNA (lower panel) to check depletion efficiency. (B) RT-qPCR analysis of promoter utilization and EBNA1 and EBNA2 gene expression after CTCF depletion. Data are normalized to GFP mRNA and expressed as −ΔΔCt values. Each bar represents the mean ± SE of three independent experiments. (C and D) 3C assay was used to analyze chromatin conformation after depletion of CTCF. Representative gel images of 3C PCR analysis using the anchor primer within the fragment containing Qp promoter (C) or Cp promoter (D) and several regions of the EBV genome for 293-EBV Wt cell line transfected with siControl or siCTCF siRNA. Amplified regions are indicated above each gel. (E) 3C assay coupled with quantitative PCR was used to analyze EBV chromatin architecture in 293-EBV Wt bacmid transfected with siControl or siCTCF siRNA, using the anchor primer within the fragment containing Qp promoter (left panel) or Cp promoter (right panel) and several regions of EBV genome. EBV genome coordinates of all the Mse I fragments tested are indicated on the X-axis. A pink asterisk indicates fragment bearing the anchor primer. Loop formation between anchor primer (pink box) and a Mse I fragment is indicated by dashed arrows. PCR amplification was normalized by using 50 ng of EBV bacmid DNA Mse I digested and randomly ligated. Data were obtained by three independent experiments and expressed as mean ± SE. Data generated by the anchor fragment self-ligation product were removed from analysis.

    Techniques Used: Transfection, Western Blot, Quantitative RT-PCR, Expressing, Polymerase Chain Reaction, Amplification, Real-time Polymerase Chain Reaction, Generated, Ligation

    20) Product Images from "Molecular Fingerprinting of Clostridium difficile Isolates: Pulsed-Field Gel Electrophoresis versus Amplified Fragment Length Polymorphism"

    Article Title: Molecular Fingerprinting of Clostridium difficile Isolates: Pulsed-Field Gel Electrophoresis versus Amplified Fragment Length Polymorphism

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.40.1.101-104.2002

    AFLP fingerprints obtained from 30 clinical C. difficile isolates (A1 to A15, B1 to B11, and C1 to C4) from three general hospitals and an unrelated control strain (U1). The fingerprints were obtained using a fluorescently labeled Eco RI primer and an unlabeled Mse I-plus-G primer. The dendrogram was created by unweighted pair group method with arithmetic mean clustering using the Pearson correlation coefficient.
    Figure Legend Snippet: AFLP fingerprints obtained from 30 clinical C. difficile isolates (A1 to A15, B1 to B11, and C1 to C4) from three general hospitals and an unrelated control strain (U1). The fingerprints were obtained using a fluorescently labeled Eco RI primer and an unlabeled Mse I-plus-G primer. The dendrogram was created by unweighted pair group method with arithmetic mean clustering using the Pearson correlation coefficient.

    Techniques Used: Labeling

    21) Product Images from "Isolation of Lyme Disease Borrelia from Puffins (Fratercula arctica) and Seabird Ticks (Ixodes uriae) on the Faeroe Islands"

    Article Title: Isolation of Lyme Disease Borrelia from Puffins (Fratercula arctica) and Seabird Ticks (Ixodes uriae) on the Faeroe Islands

    Journal: Journal of Clinical Microbiology

    doi:

    RFLP analysis. (A) Hybridization of Hpa I-digested total Borrelia DNA with an rrl -directed probe. (B) PCR-amplified rrf-rrl intergenic spacer fragments digested with Mse I and separated by PAGE.
    Figure Legend Snippet: RFLP analysis. (A) Hybridization of Hpa I-digested total Borrelia DNA with an rrl -directed probe. (B) PCR-amplified rrf-rrl intergenic spacer fragments digested with Mse I and separated by PAGE.

    Techniques Used: Hybridization, Polymerase Chain Reaction, Amplification, Polyacrylamide Gel Electrophoresis

    22) Product Images from "Cytogenetic Characterization and AFLP-Based Genetic Linkage Mapping for the Butterfly Bicyclus anynana, Covering All 28 Karyotyped Chromosomes"

    Article Title: Cytogenetic Characterization and AFLP-Based Genetic Linkage Mapping for the Butterfly Bicyclus anynana, Covering All 28 Karyotyped Chromosomes

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0003882

    Linkage map of LG1-12. Vertical bars represent chromosomes and show the mapping distance in centimorgan (cM) on the left and the corresponding markers on the right. Microsatellites are displayed in bold and start with “BA”, the two microsatellites with only FI polymorphism are placed underneath the LG's they belong to. AFLPs are named according to their selective primer extension and amplicon size. The “e” stands for the fluorescent Eco RI-based primer and the “m” stands for the non-fluorescent Mse I-based primer. AFLPs with two amplicon sizes per primer combination (e.g. eACCmCAA212-221 in LG03) are codominant. A vertical line indicates that markers are less than 1 cM apart (e.g. eACAmCGA119 and eAACmCAT370 in LG09).
    Figure Legend Snippet: Linkage map of LG1-12. Vertical bars represent chromosomes and show the mapping distance in centimorgan (cM) on the left and the corresponding markers on the right. Microsatellites are displayed in bold and start with “BA”, the two microsatellites with only FI polymorphism are placed underneath the LG's they belong to. AFLPs are named according to their selective primer extension and amplicon size. The “e” stands for the fluorescent Eco RI-based primer and the “m” stands for the non-fluorescent Mse I-based primer. AFLPs with two amplicon sizes per primer combination (e.g. eACCmCAA212-221 in LG03) are codominant. A vertical line indicates that markers are less than 1 cM apart (e.g. eACAmCGA119 and eAACmCAT370 in LG09).

    Techniques Used: Amplification

    23) Product Images from "Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays"

    Article Title: Methods for high throughput validation of amplified fragment pools of BAC DNA for constructing high resolution CGH arrays

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-5-6

    Three AFP sequence products. (A) Sequence read of an AFP derived from BAC RP11-124P12 with an Mse I restriction site 260 bp downstream of the T7 primer. (B) Sequence read of an AFP derived from BAC RP11-125E6 with an Mse I restriction site 127 bp downstream of the T7 primer. (C) Sequence read of an AFP derived from BAC RP11-124P22 with an Mse I restriction site 17 bp downstream of the T7 primer.
    Figure Legend Snippet: Three AFP sequence products. (A) Sequence read of an AFP derived from BAC RP11-124P12 with an Mse I restriction site 260 bp downstream of the T7 primer. (B) Sequence read of an AFP derived from BAC RP11-125E6 with an Mse I restriction site 127 bp downstream of the T7 primer. (C) Sequence read of an AFP derived from BAC RP11-124P22 with an Mse I restriction site 17 bp downstream of the T7 primer.

    Techniques Used: Sequencing, Derivative Assay, BAC Assay

    24) Product Images from "A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes"

    Article Title: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

    Journal: Genome Research

    doi: 10.1101/gr.224102

    Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.
    Figure Legend Snippet: Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Techniques Used: Clone Assay, Methylation, Transformation Assay

    25) Product Images from "Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS"

    Article Title: Preaxial polydactyly/triphalangeal thumb is associated with changed transcription factor-binding affinity in a family with a novel point mutation in the long-range cis-regulatory element ZRS

    Journal: European Journal of Human Genetics

    doi: 10.1038/ejhg.2009.225

    ( a ) Representative chromatogram of the heterozygous mutation (463 T > G) in ZRS. ( b ) Wild type. ( c ) Restriction analysis using Mse I restriction enzyme in all the sampled family members (normal and affected); the 268-bp mutant allele is indicated
    Figure Legend Snippet: ( a ) Representative chromatogram of the heterozygous mutation (463 T > G) in ZRS. ( b ) Wild type. ( c ) Restriction analysis using Mse I restriction enzyme in all the sampled family members (normal and affected); the 268-bp mutant allele is indicated

    Techniques Used: Mutagenesis

    26) Product Images from "Molecular Typing and Epidemiological Study of Salmonella enterica Serotype Typhimurium Isolates from Cattle by Fluorescent Amplified-Fragment Length Polymorphism Fingerprinting and Pulsed-Field Gel Electrophoresis"

    Article Title: Molecular Typing and Epidemiological Study of Salmonella enterica Serotype Typhimurium Isolates from Cattle by Fluorescent Amplified-Fragment Length Polymorphism Fingerprinting and Pulsed-Field Gel Electrophoresis

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.39.3.1057-1066.2001

    GeneScan 2.1 software-derived electropherograms showing examples of areas of polymorphism within FAFLP profiles for Eco RI plus A and Mse I plus T amplifications of serotype Typhimurium genomes. Segments of FAFLP profiles obtained from serotype Typhimurium H6 (profile A4), N59 (profile B5), N54 (profile C3), and #2 (profile D2) are represented. The fragment size scale (base pairs) is indicated above each segment. The solid arrowheads and peaks indicate a fragment characteristic of that profile (sizes are indicated in base pairs).
    Figure Legend Snippet: GeneScan 2.1 software-derived electropherograms showing examples of areas of polymorphism within FAFLP profiles for Eco RI plus A and Mse I plus T amplifications of serotype Typhimurium genomes. Segments of FAFLP profiles obtained from serotype Typhimurium H6 (profile A4), N59 (profile B5), N54 (profile C3), and #2 (profile D2) are represented. The fragment size scale (base pairs) is indicated above each segment. The solid arrowheads and peaks indicate a fragment characteristic of that profile (sizes are indicated in base pairs).

    Techniques Used: Software, Derivative Assay

    27) 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

    28) Product Images from "Identification of Bartonella Species Directly in Clinical Specimens by PCR-Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment"

    Article Title: Identification of Bartonella Species Directly in Clinical Specimens by PCR-Restriction Fragment Length Polymorphism Analysis of a 16S rRNA Gene Fragment

    Journal: Journal of Clinical Microbiology

    doi:

    PCR-RFLP of B. quintana and B. henselae from clinical specimens. Lane 1, 50-bp ladder, lanes 2 to 4, B. quintana H93-176; lanes 5 to 7, B. henselae B92-007003; lane 8, blank; lanes 9 to 11, B. quintana B93-007356; lane 12, 50-bp ladder. PCR products were left uncut (lanes 2, 5, and 9) or were cut with Dde I (lanes 3, 6, and 10) or Mse I (lanes 4, 7, and 11).
    Figure Legend Snippet: PCR-RFLP of B. quintana and B. henselae from clinical specimens. Lane 1, 50-bp ladder, lanes 2 to 4, B. quintana H93-176; lanes 5 to 7, B. henselae B92-007003; lane 8, blank; lanes 9 to 11, B. quintana B93-007356; lane 12, 50-bp ladder. PCR products were left uncut (lanes 2, 5, and 9) or were cut with Dde I (lanes 3, 6, and 10) or Mse I (lanes 4, 7, and 11).

    Techniques Used: Polymerase Chain Reaction

    Related Articles

    Polymerase Chain Reaction:

    Article Title: Genetic Diversity of Borrelia burgdorferi Sensu Lato in Ticks from Mainland Portugal
    Article Snippet: .. Intergenic spacer PCR products (10 μl) were digested with 5 U of Mse I (New England Biolabs) in a total volume of 15 μl. .. Restriction products were separated by electrophoresis on a 20% polyacrylamide TBE (Tris-borate-EDTA) gel (NOVEX) for 4 h at 80 V. The gels were stained with ethidium bromide and were visualized with a UV transilluminator.

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India
    Article Snippet: .. A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer. .. DNA fragment profiles in gels were visualized and recorded in gel documentation unit (XR documentation system, Bio-Rad, USA).

    Electrophoresis:

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India
    Article Snippet: .. A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer. .. DNA fragment profiles in gels were visualized and recorded in gel documentation unit (XR documentation system, Bio-Rad, USA).

    Agarose Gel Electrophoresis:

    Article Title: Molecular Characterization and Phylogeny of a Phytoplasma Associated with Phyllody Disease of toria (Brassica rapa L. subsp. dichotoma (Roxb.)) in India
    Article Snippet: .. A total volume of 7 μl of PCR products were digested with restriction endonucleases Alu I, Hae III, Hha I, Hin fI, Mse I and Rsa I (New England BioLabs, Waverley, MA, USA) at 37°C for 3 h. Resultant restriction fragments were visualized by electrophoresis through 2.8% agarose gel with Tris–EDTA as running buffer. .. DNA fragment profiles in gels were visualized and recorded in gel documentation unit (XR documentation system, Bio-Rad, USA).

    Derivative Assay:

    Article Title: A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)
    Article Snippet: .. DNA derived from human female blood (100 µg) was digested with 200 U of Mse I (New England Biolabs, NEB) in a total volume of 500 µl, for 3–4 h, then loaded directly onto the column with the first 5 ml eluting being reloaded. .. Fractions were collected across a salt gradient ( ) and analysed using PCR primers to amplify regions of known methylation status.

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    New England Biolabs mse i
    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the <t>DNA</t> substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by <t>Mse</t> I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.
    Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 123 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs mse i library dna
    Overall strategy for cloning methylated CpG islands. In step 1, genomic <t>DNA</t> was digested with <t>Mse</t> I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.
    Mse I Library Dna, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    New England Biolabs restriction endonucleases mse i
    Restriction profiles obtained after digestion of polymerase chain reaction products from the ITS1 locus with <t>Mse</t> I. lanes 1- 3-, 100-, 50-, and 10-bp ladder molecular weight markers; lanes 4 and 15, bovine genotype 2 isolates; lanes 5, 6, 14, and 16, human genotype 1 isolates including DE340 (lane 14); lanes 7 and 9–12, cervine genotype isolates including MH205 (lane 7), TK320 (lane 10), and DE302 (lane 11); lane 8, Cryptosporidium meleagridis isolate CS33; lanes 13 and 17, other novel genotype isolates such as VF383 (lane 13) and TK348 (lane 17)
    Restriction Endonucleases Mse I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Journal: PLoS ONE

    Article Title: A Photolyase-Like Protein from Agrobacterium tumefaciens with an Iron-Sulfur Cluster

    doi: 10.1371/journal.pone.0026775

    Figure Lengend Snippet: Photorepair of UV-lesions. (A) In vivo photoreactivation test. A. tumefaciens cells of the wild type (WT), the phrA − and the phrB − mutant were spread on LB agar plates, irradiated with UV-B light for 5 min and immediately transferred to darkness (−) or subjected to photoreactivating white light (+). Mean values of CFU ± SE; n = 8 to 14. (B and C) In vitro repair of pyrimidine dimers by PhrA and PhrB. Thymine dimers were created by UV-C illumination of the DNA substrate (first row, +/− UV-C), mixed with enzyme (second row) and incubated for the indicated times in photoreactivating blue light (405 nm, 150 µ mol m −2 s −1 ) or in darkness (*) (third row). Photorepaired DNA can be digested by Mse I (fourth row, +/− Mse I). Shown are representative gels from three independent repair experiments using PhrA or PhrB.

    Article Snippet: Subsequently, proteins were inactivated by heating to 95°C for 10 min and the DNA probe was digested with Mse I (NEB).

    Techniques: In Vivo, Mutagenesis, Irradiation, In Vitro, Incubation

    Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.

    Journal: Nucleic Acids Research

    Article Title: A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)

    doi:

    Figure Lengend Snippet: Restriction enzyme digests and sequencing of PCR products generated with primers specific for bisulfite-modified DNA. ( A ) Amplified fragments are digested with BstU I, Mse I, Msp I or Hha I. Following bisulfite modification, methylated CpG will be retained, digestion with BstU I or Hha I indicates methylation. Digestion with Mse I indicates conversion of unmethylated cytosines (CCAA to TTAA); failure to digest with Msp I indicates successful conversion (CCGG-TCGG or TTGG depending on methylation at internal CpG). ( B – D ) Several inserts were analysed for each region amplified from both tumour and normal DNA, representative examples are shown. The methylation status of all CpGs in the amplified region including the cloned Mse I fragment is graphically represented. Sequence amplified from normal DNA was analysed as shown in the top line, amplified DNA from tumour tissue is shown below. Methylated CpGs are shown as black circles, unmethylated CpGs are represented as white circles. The fragment cloned in the library is represented by a white box with a dashed line indicating the cloned inserts extended beyond the region analysed.

    Article Snippet: DNA derived from human female blood (100 µg) was digested with 200 U of Mse I (New England Biolabs, NEB) in a total volume of 500 µl, for 3–4 h, then loaded directly onto the column with the first 5 ml eluting being reloaded.

    Techniques: Sequencing, Polymerase Chain Reaction, Generated, Modification, Amplification, Methylation, Clone Assay

    Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.

    Journal: Nucleic Acids Research

    Article Title: A novel technique for the identification of CpG islands exhibiting altered methylation patterns (ICEAMP)

    doi:

    Figure Lengend Snippet: Schematic representation of the subtractive hybridisation procedure. The tester and driver are comprised of Mse I-digested DNA that bound to the MDB column at NaCl concentrations of between 0.75 and 0.85 M. The fractions were precipitated, pooled and split in a 3:1 ratio with the smaller aliquot, tester (in black) being spiked with 0.25 pg of an Mse I digested plasmid (white box). The ends of the driver aliquot were then filled in (shown as black boxes without ‘overhanging ends’). (1) Both are mixed and denatured at 95°C for 10 min. (2) Following hybridisation for 48 h at 68°C only the plasmid fragments and a background of tester:tester duplexes can re-anneal generating TA overhangs. (3) Linker/adaptors can be attached to these and can then (4) be amplified using a compatible primer.

    Article Snippet: DNA derived from human female blood (100 µg) was digested with 200 U of Mse I (New England Biolabs, NEB) in a total volume of 500 µl, for 3–4 h, then loaded directly onto the column with the first 5 ml eluting being reloaded.

    Techniques: Hybridization, Plasmid Preparation, Amplification

    Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Journal: Genome Research

    Article Title: A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes

    doi: 10.1101/gr.224102

    Figure Lengend Snippet: Overall strategy for cloning methylated CpG islands. In step 1, genomic DNA was digested with Mse I (red), which cuts between CpG islands, and Hpa II (blue), which cuts unmethylated CpG islands. Mse I fragments containing methylated CpG islands then are transformed into a bacterial strain that does not cut methylated DNA. However, brief bacterial passage leads to loss of methylation of these previously methylated sequences. In step 2, the library DNA is pooled and digested with Eag I (green), which cuts relatively large fragments within CpG islands, and these fragments are then subcloned.

    Article Snippet: In the second step, 100 μg of the Mse I library DNA were digested with 1,000 U of Eag I (NEB) according to the manufacturer’s conditions.

    Techniques: Clone Assay, Methylation, Transformation Assay

    Restriction profiles obtained after digestion of polymerase chain reaction products from the ITS1 locus with Mse I. lanes 1- 3-, 100-, 50-, and 10-bp ladder molecular weight markers; lanes 4 and 15, bovine genotype 2 isolates; lanes 5, 6, 14, and 16, human genotype 1 isolates including DE340 (lane 14); lanes 7 and 9–12, cervine genotype isolates including MH205 (lane 7), TK320 (lane 10), and DE302 (lane 11); lane 8, Cryptosporidium meleagridis isolate CS33; lanes 13 and 17, other novel genotype isolates such as VF383 (lane 13) and TK348 (lane 17)

    Journal: Emerging Infectious Diseases

    Article Title: Novel Cryptosporidium Genotypes in Sporadic Cryptosporidiosis Cases: First Report of Human Infections with a Cervine Genotype

    doi: 10.3201/eid0803.010194

    Figure Lengend Snippet: Restriction profiles obtained after digestion of polymerase chain reaction products from the ITS1 locus with Mse I. lanes 1- 3-, 100-, 50-, and 10-bp ladder molecular weight markers; lanes 4 and 15, bovine genotype 2 isolates; lanes 5, 6, 14, and 16, human genotype 1 isolates including DE340 (lane 14); lanes 7 and 9–12, cervine genotype isolates including MH205 (lane 7), TK320 (lane 10), and DE302 (lane 11); lane 8, Cryptosporidium meleagridis isolate CS33; lanes 13 and 17, other novel genotype isolates such as VF383 (lane 13) and TK348 (lane 17)

    Article Snippet: RFLP Analyses of PCR Products PCR products were purified by using QIAquick spin columns (Qiagen, Mississauga, ON) according to the manufacturer’s instructions before digestion with the restriction endonucleases Mse I (New England BioLabs, Mississauga, ON) for the ITS1 locus and Rsa I (New England BioLabs) for the COWP gene.

    Techniques: Polymerase Chain Reaction, Molecular Weight