pcdna3 1 myc 6xhis sec24d  (New England Biolabs)


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    AscI
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    AscI 2 500 units
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    r0558l
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    Restriction Enzymes
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    New England Biolabs pcdna3 1 myc 6xhis sec24d
    AscI
    AscI 2 500 units
    https://www.bioz.com/result/pcdna3 1 myc 6xhis sec24d/product/New England Biolabs
    Average 90 stars, based on 172 article reviews
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    pcdna3 1 myc 6xhis sec24d - by Bioz Stars, 2021-02
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    Images

    1) Product Images from "Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation"

    Article Title: Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation

    Journal: bioRxiv

    doi: 10.1101/2020.12.30.424839

    Sec24D is dynamically O-GlcNAcylated A. Myc-6xHis Sec24D was transiently expressed in HEK 293T cells treated with 50 μM TG, 5SG, or DMSO vehicle control for 6 hours. Sec24D was analyzed by tandem myc IP/Ni-NTA affinity purification and O-GlcNAc IB. B. Endogenous Sec24D was IP-ed from control Sec24D -/- (KO) HEK 293T cells treated with 50 μM TG or DMSO vehicle control for 6 hours and analyzed by O-GlcNAc IB. C. Six O-GlcNAc sites were identified on Sec24D by ETD MS: T9, S13, T35, S418, S421, T427.
    Figure Legend Snippet: Sec24D is dynamically O-GlcNAcylated A. Myc-6xHis Sec24D was transiently expressed in HEK 293T cells treated with 50 μM TG, 5SG, or DMSO vehicle control for 6 hours. Sec24D was analyzed by tandem myc IP/Ni-NTA affinity purification and O-GlcNAc IB. B. Endogenous Sec24D was IP-ed from control Sec24D -/- (KO) HEK 293T cells treated with 50 μM TG or DMSO vehicle control for 6 hours and analyzed by O-GlcNAc IB. C. Six O-GlcNAc sites were identified on Sec24D by ETD MS: T9, S13, T35, S418, S421, T427.

    Techniques Used: Affinity Purification

    2) Product Images from "Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract"

    Article Title: Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract

    Journal: Chromosoma

    doi: 10.1007/s00412-010-0307-4

    Enzyme Digestion Method for AFM of Lower-Order Structures. AFM images of Asc I restriction enzyme digestion products from (a) DNA-coated surface not treated with extract, (b) The control surface without DNA treated with 20-fold diluted egg extract and
    Figure Legend Snippet: Enzyme Digestion Method for AFM of Lower-Order Structures. AFM images of Asc I restriction enzyme digestion products from (a) DNA-coated surface not treated with extract, (b) The control surface without DNA treated with 20-fold diluted egg extract and

    Techniques Used:

    3) Product Images from "Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation"

    Article Title: Evidence for nutrient-dependent regulation of the COPII coat by O-GlcNAcylation

    Journal: bioRxiv

    doi: 10.1101/2020.12.30.424839

    Sec24D is dynamically O-GlcNAcylated A. Myc-6xHis Sec24D was transiently expressed in HEK 293T cells treated with 50 μM TG, 5SG, or DMSO vehicle control for 6 hours. Sec24D was analyzed by tandem myc IP/Ni-NTA affinity purification and O-GlcNAc IB. B. Endogenous Sec24D was IP-ed from control Sec24D -/- (KO) HEK 293T cells treated with 50 μM TG or DMSO vehicle control for 6 hours and analyzed by O-GlcNAc IB. C. Six O-GlcNAc sites were identified on Sec24D by ETD MS: T9, S13, T35, S418, S421, T427.
    Figure Legend Snippet: Sec24D is dynamically O-GlcNAcylated A. Myc-6xHis Sec24D was transiently expressed in HEK 293T cells treated with 50 μM TG, 5SG, or DMSO vehicle control for 6 hours. Sec24D was analyzed by tandem myc IP/Ni-NTA affinity purification and O-GlcNAc IB. B. Endogenous Sec24D was IP-ed from control Sec24D -/- (KO) HEK 293T cells treated with 50 μM TG or DMSO vehicle control for 6 hours and analyzed by O-GlcNAc IB. C. Six O-GlcNAc sites were identified on Sec24D by ETD MS: T9, S13, T35, S418, S421, T427.

    Techniques Used: Affinity Purification

    4) Product Images from "Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae"

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0006389

    Karyotype analysis of 21 GCRs containing strains by PFGE and aCGH. (A) PFGE analysis of 21 Can r 5FOA r strains. Intact chromosomes from the indicated GCR strains were transferred to nitrocellulose membranes and hybridized to a radiolabeled chromosome V essential gene YEL058W probe. Rearranged chromosome V sizes were estimated relative to the sizes of chromosomes from the RDKY3615 wild-type and the CAN r 5FOA r tlc1 mut 3 strain that were run as controls. (B) Analysis of circular chromosome V GCRs. Circular chromosome V GCRs were digested in the agarose plugs with Asc I for the indicated strains prior to PFGE. The intact and digested chromosome V was detected by hybridization with the YEL058W radiolabelled probe and the size of the resulting chromosome V fragment was estimated. (C) Karyotype analysis by aCGH of representative GCR containing strains is presented. The aGCH data of all GCRs analyzed in this study are present in the Figure S1 . The normalized log 2 ratio of the fluorescence intensities for each oligonucleotide relative to the reference strain is presented; in order to show all of the data points, it was necessary to use a different scale for the log 2 ratio for each chromosome. Chromosome numbers are indicated to the left of the panel.
    Figure Legend Snippet: Karyotype analysis of 21 GCRs containing strains by PFGE and aCGH. (A) PFGE analysis of 21 Can r 5FOA r strains. Intact chromosomes from the indicated GCR strains were transferred to nitrocellulose membranes and hybridized to a radiolabeled chromosome V essential gene YEL058W probe. Rearranged chromosome V sizes were estimated relative to the sizes of chromosomes from the RDKY3615 wild-type and the CAN r 5FOA r tlc1 mut 3 strain that were run as controls. (B) Analysis of circular chromosome V GCRs. Circular chromosome V GCRs were digested in the agarose plugs with Asc I for the indicated strains prior to PFGE. The intact and digested chromosome V was detected by hybridization with the YEL058W radiolabelled probe and the size of the resulting chromosome V fragment was estimated. (C) Karyotype analysis by aCGH of representative GCR containing strains is presented. The aGCH data of all GCRs analyzed in this study are present in the Figure S1 . The normalized log 2 ratio of the fluorescence intensities for each oligonucleotide relative to the reference strain is presented; in order to show all of the data points, it was necessary to use a different scale for the log 2 ratio for each chromosome. Chromosome numbers are indicated to the left of the panel.

    Techniques Used: Hybridization, Fluorescence

    5) Product Images from "Pulsed-Field Gel Electrophoresis in Differentiation of Erysipelothrix Species Strains"

    Article Title: Pulsed-Field Gel Electrophoresis in Differentiation of Erysipelothrix Species Strains

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.39.11.4032-4036.2001

    PFGE patterns produced from four strains of Erysipelothrix spp. by Sma I, Asc I, and Not I. Lanes: 1, E. rhusiopathiae strain ME-7, serovar 1a; 2, E. rhusiopathiae strain ATCC 19414, serovar 2; 3, E. tonsillarum strain ATCC 43339, serovar 7; 4, Erysipelothrix species strain 715, serovar 18; M, CHEF DNA Size Standard Lambda Ladder (Bio-Rad).
    Figure Legend Snippet: PFGE patterns produced from four strains of Erysipelothrix spp. by Sma I, Asc I, and Not I. Lanes: 1, E. rhusiopathiae strain ME-7, serovar 1a; 2, E. rhusiopathiae strain ATCC 19414, serovar 2; 3, E. tonsillarum strain ATCC 43339, serovar 7; 4, Erysipelothrix species strain 715, serovar 18; M, CHEF DNA Size Standard Lambda Ladder (Bio-Rad).

    Techniques Used: Produced

    6) Product Images from "Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France"

    Article Title: Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France

    Journal: Veterinary Research

    doi: 10.1186/s13567-015-0200-5

    Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the combination of Not I and Asc I restriction enzymes and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.
    Figure Legend Snippet: Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the combination of Not I and Asc I restriction enzymes and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Techniques Used: Software

    Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the Asc I restriction enzyme and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.
    Figure Legend Snippet: Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the Asc I restriction enzyme and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Techniques Used: Software

    7) Product Images from "Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization"

    Article Title: Intestinal Serum amyloid A suppresses systemic neutrophil activation and bactericidal activity in response to microbiota colonization

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1007381

    Intestinally-derived Saa regulates systemic neutrophil activity. (A) qRT-PCR of saa from whole 6 dpf larvae of the indicated genotypes (n = 4 replicates / genotype, 25–30 larvae / replicate) (B) Enumeration of intestine-associated lyz:DsRed + neutrophils along the anterior to posterior axis (segment 1 to segment 3) in 6 dpf larvae (n ≥ 25 larvae / genotype). (C) lyz:DsRed + neutrophil recruitment to caudal fin wound 6 hours following amputation in 6 dpf zebrafish larvae (n ≥ 25 larvae / genotype at 6 hour time point). (D) CFU quantification of bacterial concentration following 4 hour co-culture of lyz:DsRed + adult zebrafish neutrophils with P . aeruginosa ( P . a ., MOI 0.2) (8 replicates / genotype). (E) Representative stereoscope images of IEC specific mCherry expression in 6 dpf Tg(-0 . 349cldn15la : mCherry) rdu65 larvae compared to non-transgenic (NTG) controls. White dashed line indicates the intestine (scale bar = 500 μm). (F) Representative confocal micrograph of immunostained transverse section of Tg(-0 . 349cldn15la : mCherry) 6 dpf larvae labeled with the absorptive cell brush border-specific antibody 4E8 (scale bar = 20 μm). (G,H) qRT-PCR of cldn15la , fabp2 , and fabp10a (G) from sorted Tg(-0 . 349cldn15la : mCherry) + IECs and saa (H) from cldn15la : mCherry + and negative cells isolated from 6 dpf larvae of indicated genotypes (13,000 –0.349cldn15la:mCherry + or mCherry negative cells / replicate, 4 replicates / genotype, 30 larvae / replicate). (I) qRT-PCR of saa from 6 dpf larval dissected digestive tissue of the indicated genotypes (n = 4 replicates / genotype, 25–30 larvae / replicate) (J) Enumeration of intestine-associated lyz:DsRed + neutrophils in 6 dpf larvae (n = 30 larvae / genotype). (K) lyz:DsRed + neutrophil recruitment to caudal fin wound 6 hours following amputation in 6 dpf zebrafish larvae (n ≥ 18 larvae / genotype at 6 hour time point). (L) CFU quantification of bacterial concentration following 4 hour co-culture of lyz:DsRed + adult zebrafish neutrophils with P . aeruginosa ( P . a ., MOI 0.2) (3–6 replicates / genotype). (M) il1b qRT-PCR from lyz:DsRed + neutrophils co-cultured with and without P . a . ex vivo for 4 hours (n ≥ 2 replicates / condition). (N) CFU quantification of in vivo P . a . bacterial burden following systemic infection of larval zebrafish at 5 days post infection (dpi) (data from 3 independent experiments, n ≥ 30 larvae / genotype). Data in panels A-D and H-N were analyzed by one-way ANOVA with Tukey’s multiple comparisons test. A Mann-Whitney test was applied to panel G. For panels C and K, statistical comparisons were performed amongst samples within the same time point. Data are presented as mean ± SEM. * p
    Figure Legend Snippet: Intestinally-derived Saa regulates systemic neutrophil activity. (A) qRT-PCR of saa from whole 6 dpf larvae of the indicated genotypes (n = 4 replicates / genotype, 25–30 larvae / replicate) (B) Enumeration of intestine-associated lyz:DsRed + neutrophils along the anterior to posterior axis (segment 1 to segment 3) in 6 dpf larvae (n ≥ 25 larvae / genotype). (C) lyz:DsRed + neutrophil recruitment to caudal fin wound 6 hours following amputation in 6 dpf zebrafish larvae (n ≥ 25 larvae / genotype at 6 hour time point). (D) CFU quantification of bacterial concentration following 4 hour co-culture of lyz:DsRed + adult zebrafish neutrophils with P . aeruginosa ( P . a ., MOI 0.2) (8 replicates / genotype). (E) Representative stereoscope images of IEC specific mCherry expression in 6 dpf Tg(-0 . 349cldn15la : mCherry) rdu65 larvae compared to non-transgenic (NTG) controls. White dashed line indicates the intestine (scale bar = 500 μm). (F) Representative confocal micrograph of immunostained transverse section of Tg(-0 . 349cldn15la : mCherry) 6 dpf larvae labeled with the absorptive cell brush border-specific antibody 4E8 (scale bar = 20 μm). (G,H) qRT-PCR of cldn15la , fabp2 , and fabp10a (G) from sorted Tg(-0 . 349cldn15la : mCherry) + IECs and saa (H) from cldn15la : mCherry + and negative cells isolated from 6 dpf larvae of indicated genotypes (13,000 –0.349cldn15la:mCherry + or mCherry negative cells / replicate, 4 replicates / genotype, 30 larvae / replicate). (I) qRT-PCR of saa from 6 dpf larval dissected digestive tissue of the indicated genotypes (n = 4 replicates / genotype, 25–30 larvae / replicate) (J) Enumeration of intestine-associated lyz:DsRed + neutrophils in 6 dpf larvae (n = 30 larvae / genotype). (K) lyz:DsRed + neutrophil recruitment to caudal fin wound 6 hours following amputation in 6 dpf zebrafish larvae (n ≥ 18 larvae / genotype at 6 hour time point). (L) CFU quantification of bacterial concentration following 4 hour co-culture of lyz:DsRed + adult zebrafish neutrophils with P . aeruginosa ( P . a ., MOI 0.2) (3–6 replicates / genotype). (M) il1b qRT-PCR from lyz:DsRed + neutrophils co-cultured with and without P . a . ex vivo for 4 hours (n ≥ 2 replicates / condition). (N) CFU quantification of in vivo P . a . bacterial burden following systemic infection of larval zebrafish at 5 days post infection (dpi) (data from 3 independent experiments, n ≥ 30 larvae / genotype). Data in panels A-D and H-N were analyzed by one-way ANOVA with Tukey’s multiple comparisons test. A Mann-Whitney test was applied to panel G. For panels C and K, statistical comparisons were performed amongst samples within the same time point. Data are presented as mean ± SEM. * p

    Techniques Used: Derivative Assay, Activity Assay, Quantitative RT-PCR, Concentration Assay, Co-Culture Assay, Expressing, Transgenic Assay, Labeling, Isolation, Cell Culture, Ex Vivo, In Vivo, Infection, MANN-WHITNEY

    8) Product Images from "Integrated Physical and Genetic Mapping of Bacillus cereus and Other Gram-Positive Bacteria Based on IS231A Transposition Vectors"

    Article Title: Integrated Physical and Genetic Mapping of Bacillus cereus and Other Gram-Positive Bacteria Based on IS231A Transposition Vectors

    Journal: Infection and Immunity

    doi:

    PFGE profiles of total DNA from B. cereus strains restricted by Not I (A), Asc I (B), Sfi I (C), and I- Sce I (D). Y, yeast chromosome marker; λ, lambda ladder marker (New England Biolabs); HS, hot-spot candidate with one single mini-IS Kan r insertion; TS, B. cereus ATCC 14579 type strain; A1 and A2, ade mutants; G1, gua mutant; H1 and H2, his mutants; M1 and M2, met mutants; U1, ura mutant; Aph., aphenotypic double-insertion mutant.
    Figure Legend Snippet: PFGE profiles of total DNA from B. cereus strains restricted by Not I (A), Asc I (B), Sfi I (C), and I- Sce I (D). Y, yeast chromosome marker; λ, lambda ladder marker (New England Biolabs); HS, hot-spot candidate with one single mini-IS Kan r insertion; TS, B. cereus ATCC 14579 type strain; A1 and A2, ade mutants; G1, gua mutant; H1 and H2, his mutants; M1 and M2, met mutants; U1, ura mutant; Aph., aphenotypic double-insertion mutant.

    Techniques Used: Marker, Mutagenesis

    B. cereus chromosomal map. Based on the position of the dnaA gene and by comparison of the locations of other genes with those of B. subtilis ). plc , phospholipase C; inA , inhibitor A; pdh , pyruvate dehydrogenase. Nx and Ax correspond to Not I and Asc I restriction fragments, respectively. The hot-spot insertion site as well as eight other insertions generating auxotrophies are indicated. Aph represents an aphenotypic secondary transposition event.
    Figure Legend Snippet: B. cereus chromosomal map. Based on the position of the dnaA gene and by comparison of the locations of other genes with those of B. subtilis ). plc , phospholipase C; inA , inhibitor A; pdh , pyruvate dehydrogenase. Nx and Ax correspond to Not I and Asc I restriction fragments, respectively. The hot-spot insertion site as well as eight other insertions generating auxotrophies are indicated. Aph represents an aphenotypic secondary transposition event.

    Techniques Used: Planar Chromatography

    9) Product Images from "Sources of Listeria monocytogenes Contamination in a Cold-Smoked Rainbow Trout Processing Plant Detected by Pulsed-Field Gel Electrophoresis Typing"

    Article Title: Sources of Listeria monocytogenes Contamination in a Cold-Smoked Rainbow Trout Processing Plant Detected by Pulsed-Field Gel Electrophoresis Typing

    Journal: Applied and Environmental Microbiology

    doi:

    Dendrogram of Listeria monocytogenes isolates based on Asc I macrorestriction profiles. Similarity analysis was performed with the Dice coefficient and clustering by unweighted pair group method with arithmetic averages.
    Figure Legend Snippet: Dendrogram of Listeria monocytogenes isolates based on Asc I macrorestriction profiles. Similarity analysis was performed with the Dice coefficient and clustering by unweighted pair group method with arithmetic averages.

    Techniques Used:

    10) Product Images from "Genotypic characterization of Listeria monocytogenes isolated from humans in India"

    Article Title: Genotypic characterization of Listeria monocytogenes isolated from humans in India

    Journal: Annals of Tropical Medicine and Parasitology

    doi: 10.1179/1364859411Y.0000000023

    Dendrogram derived from a PFGE profile of Asc I macrorestriction showing restriction patterns among the L. monocytogenes isolated from humans. Isolate identification numbers correspond to isolate numbers in Table.
    Figure Legend Snippet: Dendrogram derived from a PFGE profile of Asc I macrorestriction showing restriction patterns among the L. monocytogenes isolated from humans. Isolate identification numbers correspond to isolate numbers in Table.

    Techniques Used: Derivative Assay, Isolation

    11) Product Images from "A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain"

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

    Journal: eLife

    doi: 10.7554/eLife.43322

    Validation of subclass-switched anti-PSD-95 K28/43R R-mAb. ( A ) Validation of the K28/43R R-mAb in heterologous cells. COS-1 cells transiently transfected to express human PSD-95 in a subset of cells were immunolabeled with K28/43 mAb (IgG2a) alone (top row), K28/43R R-mAb (IgG1) alone (middle row), or K28/43 mAb plus K28/43R R-mAb (bottom row). Immunolabeling in all samples was detected with a cocktail of anti-mouse IgG2a (red, for the K28/43 mAb) and anti-mouse IgG1 (green, for the K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Labeling in blue is for the DNA-specific dye Hoechst 33258 and shows nuclei of both transfected and untransfected cells. Scale bar in the lower right merged panel = 30 µm and holds for all panels in A. ( B ) Validation of the K28/43R R-mAb in brain sections. A brain section from an adult rat was immunolabeled with K28/43 mAb plus K28/43R R-mAb and immunolabeling detected with a cocktail of anti-mouse IgG2a (red, for K28/43 mAb) and anti-mouse IgG1 (green, for K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Cell nuclei are labeled with the DNA-specific dye Hoechst 33258 (blue). The region of interest shown is from cerebellar cortex. Scale bar in the left panel = 100 µm, and in the right merged panel = 30 µm. ( C ) Immunoblots against brain membranes and COS cell lysates over-expressing various members of the MAGUK superfamily of scaffolding proteins. To confirm expression of MAGUK proteins, immunoblots were probed with rabbit anti-PSD-95 (red). K28/86 is an anti-MAGUK mAb. Primary antibodies were detected with the appropriate combinations of fluorescently labeled species-specific anti-rabbit and subclass-specific anti-mouse IgG secondary Abs as indicated. Control indicates COS cells transfected with an empty vector.
    Figure Legend Snippet: Validation of subclass-switched anti-PSD-95 K28/43R R-mAb. ( A ) Validation of the K28/43R R-mAb in heterologous cells. COS-1 cells transiently transfected to express human PSD-95 in a subset of cells were immunolabeled with K28/43 mAb (IgG2a) alone (top row), K28/43R R-mAb (IgG1) alone (middle row), or K28/43 mAb plus K28/43R R-mAb (bottom row). Immunolabeling in all samples was detected with a cocktail of anti-mouse IgG2a (red, for the K28/43 mAb) and anti-mouse IgG1 (green, for the K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Labeling in blue is for the DNA-specific dye Hoechst 33258 and shows nuclei of both transfected and untransfected cells. Scale bar in the lower right merged panel = 30 µm and holds for all panels in A. ( B ) Validation of the K28/43R R-mAb in brain sections. A brain section from an adult rat was immunolabeled with K28/43 mAb plus K28/43R R-mAb and immunolabeling detected with a cocktail of anti-mouse IgG2a (red, for K28/43 mAb) and anti-mouse IgG1 (green, for K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Cell nuclei are labeled with the DNA-specific dye Hoechst 33258 (blue). The region of interest shown is from cerebellar cortex. Scale bar in the left panel = 100 µm, and in the right merged panel = 30 µm. ( C ) Immunoblots against brain membranes and COS cell lysates over-expressing various members of the MAGUK superfamily of scaffolding proteins. To confirm expression of MAGUK proteins, immunoblots were probed with rabbit anti-PSD-95 (red). K28/86 is an anti-MAGUK mAb. Primary antibodies were detected with the appropriate combinations of fluorescently labeled species-specific anti-rabbit and subclass-specific anti-mouse IgG secondary Abs as indicated. Control indicates COS cells transfected with an empty vector.

    Techniques Used: Transfection, Immunolabeling, Labeling, Western Blot, Expressing, Scaffolding, Plasmid Preparation

    12) Product Images from "The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori"

    Article Title: The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36261-y

    Isolation of transgenic silkworms. ( A , B) Schematic illustration of the piggyBac [3 × P3-EGFP, BmLP3-Gal4] and piggyBac [3 × P3-DsRed, UAS-EGT] vectors. ( C , D ) Digestion of the vectors with Asc I yielded the expected band sizes. Lane 1/3: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid; Lane 2/4: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid after Asc I digestion. BmLP3-Gal4-SV40 is about 4000 bp and UAS-EGT-SV40 is about 2100 bp. ( E ) Isolation of generation G0 transgenic silkworms by detection of EGFP (Gal4 transgenic line) and DsRed (UAS transgenic line) expression in the compound eyes of moths. E1/E3: Gal4/ UAS transgenic moth under white light. E2/E4: Gal4/UAS transgenic moth under fluorescent light. ( F ) Screening of generation G7 hybrid offspring from Gal4 and UAS transgenic lines by detection of both EGFP and DsRed expression in the eggs. F1/2/3: transgenic eggs under white/green fluorescent/red fluorescent light.
    Figure Legend Snippet: Isolation of transgenic silkworms. ( A , B) Schematic illustration of the piggyBac [3 × P3-EGFP, BmLP3-Gal4] and piggyBac [3 × P3-DsRed, UAS-EGT] vectors. ( C , D ) Digestion of the vectors with Asc I yielded the expected band sizes. Lane 1/3: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid; Lane 2/4: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid after Asc I digestion. BmLP3-Gal4-SV40 is about 4000 bp and UAS-EGT-SV40 is about 2100 bp. ( E ) Isolation of generation G0 transgenic silkworms by detection of EGFP (Gal4 transgenic line) and DsRed (UAS transgenic line) expression in the compound eyes of moths. E1/E3: Gal4/ UAS transgenic moth under white light. E2/E4: Gal4/UAS transgenic moth under fluorescent light. ( F ) Screening of generation G7 hybrid offspring from Gal4 and UAS transgenic lines by detection of both EGFP and DsRed expression in the eggs. F1/2/3: transgenic eggs under white/green fluorescent/red fluorescent light.

    Techniques Used: Isolation, Transgenic Assay, Agarose Gel Electrophoresis, Plasmid Preparation, Expressing

    13) Product Images from "Recombinant PRRSV expressing porcine circovirus sequence reveals novel aspect of transcriptional control of porcine arterivirus"

    Article Title: Recombinant PRRSV expressing porcine circovirus sequence reveals novel aspect of transcriptional control of porcine arterivirus

    Journal: Virus Research

    doi: 10.1016/j.virusres.2009.11.014

    Construction of recombinant PRRSV expressing PCV2 capsid gene. The boxed numbers 1a, 1b, 2a, 2b, 3–7 represent PRRSV open reading frame (ORF) 1a-ORF7, respectively. For the mutant PRRSV clones, only the region covering the 3′ part of ORF 1b through the 3′ end of the genome is shown. The pORF12 was constructed ( Yu et al., 2009 ) by inserting restriction sites (Pac I, Swa I and Asc I, a total of 23 nt) directly between ORF1b and ORF2 of the wild-type pAPRRS. pCPV was then constructed by inserting Pac I-PCV2 ORF2-Asc I in the same insertion site as pORF12.
    Figure Legend Snippet: Construction of recombinant PRRSV expressing PCV2 capsid gene. The boxed numbers 1a, 1b, 2a, 2b, 3–7 represent PRRSV open reading frame (ORF) 1a-ORF7, respectively. For the mutant PRRSV clones, only the region covering the 3′ part of ORF 1b through the 3′ end of the genome is shown. The pORF12 was constructed ( Yu et al., 2009 ) by inserting restriction sites (Pac I, Swa I and Asc I, a total of 23 nt) directly between ORF1b and ORF2 of the wild-type pAPRRS. pCPV was then constructed by inserting Pac I-PCV2 ORF2-Asc I in the same insertion site as pORF12.

    Techniques Used: Recombinant, Expressing, Mutagenesis, Clone Assay, Construct

    14) Product Images from "A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain"

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

    Journal: eLife

    doi: 10.7554/eLife.43322

    Cloning of V L and V H domain sequences from hybridomas into the R-mAb expression plasmid. ( A ) Agarose gel analysis of V L and V H domain PCR products amplified from cDNA synthesized from RNA extracted from the N59/36 (anti-NR2B/GRIN2B) and K39/25 (anti-Kv2.1/KCNB1) hybridomas. The expected size of mouse IgG V L and V H domains is ≈360 bp. ( B ) Agarose gel analysis of V H and digested V L fragments joined by fusion PCR (F-PCR) to the P1316-derived joining fragment to create a dual IgG chain cassette. ( C ) Agarose gel analysis of colony PCR samples of transformants from the N59/36 R-mAb project. ( D ) Agarose gel analysis of products of restriction enzyme digestion of N59/36 plasmid DNA with NotI and AscI. The plasmid backbone is seven kbp, and the intact insert comprising the V L and V H domains and the intervening joining fragment is 2.4 kbp. ( E ) Agarose gel analysis of PCR products of V L domain cDNA synthesized from RNA extracted from mouse splenocytes, the fusion partner Sp2/0-Ag14, and various hybridomas after digestion with the BciVI restriction enzyme to cleave the Sp2/0-Ag14-derived aberrant light chain product. The intact V L domains are ≈360 bp, and the digested aberrant light chains ≈180 bp.
    Figure Legend Snippet: Cloning of V L and V H domain sequences from hybridomas into the R-mAb expression plasmid. ( A ) Agarose gel analysis of V L and V H domain PCR products amplified from cDNA synthesized from RNA extracted from the N59/36 (anti-NR2B/GRIN2B) and K39/25 (anti-Kv2.1/KCNB1) hybridomas. The expected size of mouse IgG V L and V H domains is ≈360 bp. ( B ) Agarose gel analysis of V H and digested V L fragments joined by fusion PCR (F-PCR) to the P1316-derived joining fragment to create a dual IgG chain cassette. ( C ) Agarose gel analysis of colony PCR samples of transformants from the N59/36 R-mAb project. ( D ) Agarose gel analysis of products of restriction enzyme digestion of N59/36 plasmid DNA with NotI and AscI. The plasmid backbone is seven kbp, and the intact insert comprising the V L and V H domains and the intervening joining fragment is 2.4 kbp. ( E ) Agarose gel analysis of PCR products of V L domain cDNA synthesized from RNA extracted from mouse splenocytes, the fusion partner Sp2/0-Ag14, and various hybridomas after digestion with the BciVI restriction enzyme to cleave the Sp2/0-Ag14-derived aberrant light chain product. The intact V L domains are ≈360 bp, and the digested aberrant light chains ≈180 bp.

    Techniques Used: Clone Assay, Expressing, Plasmid Preparation, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Synthesized, Derivative Assay

    Cloning of anti-Kv2.1 D3/71 V L and V H domain cDNAs from a nonviable hybridoma. ( A ) Agarose gel analysis of PCR amplified V L and V H domains from cDNA synthesized from RNA extracted from the non-viable D3/71 hybridoma. The panel to the right shows the V L after digestion with the BciVI restriction enzyme to cleave the Sp2/0-Ag14-derived aberrant light chain product. The expected size of mouse IgG V L and V H domains is ≈360 bp, and of the cleaved aberrant V L domain is ≈180 bp. ( B ) Agarose gel analysis of D3/71 V H and digested V L fragments joined by fusion PCR (F-PCR) to the P1316 joining fragment to create a dual IgG chain cassette. ( C ) Agarose gel analysis of colony PCR samples of transformants from the of D3/71 R-mAb project. ( D ) Agarose gel analysis of products of restriction enzyme digestion of D3/71 plasmid DNA with NotI and AscI. The plasmid backbone is seven kbp, and the intact insert comprising the V L and V H domains and the intervening joining fragment is 2.4 kbp.
    Figure Legend Snippet: Cloning of anti-Kv2.1 D3/71 V L and V H domain cDNAs from a nonviable hybridoma. ( A ) Agarose gel analysis of PCR amplified V L and V H domains from cDNA synthesized from RNA extracted from the non-viable D3/71 hybridoma. The panel to the right shows the V L after digestion with the BciVI restriction enzyme to cleave the Sp2/0-Ag14-derived aberrant light chain product. The expected size of mouse IgG V L and V H domains is ≈360 bp, and of the cleaved aberrant V L domain is ≈180 bp. ( B ) Agarose gel analysis of D3/71 V H and digested V L fragments joined by fusion PCR (F-PCR) to the P1316 joining fragment to create a dual IgG chain cassette. ( C ) Agarose gel analysis of colony PCR samples of transformants from the of D3/71 R-mAb project. ( D ) Agarose gel analysis of products of restriction enzyme digestion of D3/71 plasmid DNA with NotI and AscI. The plasmid backbone is seven kbp, and the intact insert comprising the V L and V H domains and the intervening joining fragment is 2.4 kbp.

    Techniques Used: Clone Assay, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Amplification, Synthesized, Derivative Assay, Plasmid Preparation

    15) Product Images from "Rapid isolation of yeast genomic DNA: Bust n' Grab"

    Article Title: Rapid isolation of yeast genomic DNA: Bust n' Grab

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-4-8

    Schematic representation of the human β-globin locus and sequences upstream of the LCR 5'HS5 region A) The human β-globin locus YAC (β-YAC). The ~187 kb Eco RI genomic DNA fragment containing the human β-globin locus is shown as a line above the YAC map. The β-like globin genes and YAC arms are shown as black rectangles. The LCR HSs are denoted with arrows. YAC arms contain a centromere (CEN), an autonomous replication sequence (ARS1), selectable markers for tryptophan and lysine prototrophy (TRP1 and LYS2, respectively), and an MMTneo cassette for selection in mammalian cell culture. B) Wild-type sequence with pertinent restriction enzyme sites labeled above and below the line. The 683 bp Sca I- Sfi I probe used for Southern blot hybridization is indicated by the grey bar. C) A 55 bp loxP-Asc I site was inserted into the Sfi I site at nucleotide 31,061 by YIP-mediated homologous recombination. The numbering is based on GenBank file AF137396.
    Figure Legend Snippet: Schematic representation of the human β-globin locus and sequences upstream of the LCR 5'HS5 region A) The human β-globin locus YAC (β-YAC). The ~187 kb Eco RI genomic DNA fragment containing the human β-globin locus is shown as a line above the YAC map. The β-like globin genes and YAC arms are shown as black rectangles. The LCR HSs are denoted with arrows. YAC arms contain a centromere (CEN), an autonomous replication sequence (ARS1), selectable markers for tryptophan and lysine prototrophy (TRP1 and LYS2, respectively), and an MMTneo cassette for selection in mammalian cell culture. B) Wild-type sequence with pertinent restriction enzyme sites labeled above and below the line. The 683 bp Sca I- Sfi I probe used for Southern blot hybridization is indicated by the grey bar. C) A 55 bp loxP-Asc I site was inserted into the Sfi I site at nucleotide 31,061 by YIP-mediated homologous recombination. The numbering is based on GenBank file AF137396.

    Techniques Used: Sequencing, Selection, Cell Culture, Labeling, Southern Blot, Hybridization, Homologous Recombination

    16) Product Images from "The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori"

    Article Title: The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-36261-y

    Isolation of transgenic silkworms. ( A , B) Schematic illustration of the piggyBac [3 × P3-EGFP, BmLP3-Gal4] and piggyBac [3 × P3-DsRed, UAS-EGT] vectors. ( C , D ) Digestion of the vectors with Asc I yielded the expected band sizes. Lane 1/3: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid; Lane 2/4: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid after Asc I digestion. BmLP3-Gal4-SV40 is about 4000 bp and UAS-EGT-SV40 is about 2100 bp. ( E ) Isolation of generation G0 transgenic silkworms by detection of EGFP (Gal4 transgenic line) and DsRed (UAS transgenic line) expression in the compound eyes of moths. E1/E3: Gal4/ UAS transgenic moth under white light. E2/E4: Gal4/UAS transgenic moth under fluorescent light. ( F ) Screening of generation G7 hybrid offspring from Gal4 and UAS transgenic lines by detection of both EGFP and DsRed expression in the eggs. F1/2/3: transgenic eggs under white/green fluorescent/red fluorescent light.
    Figure Legend Snippet: Isolation of transgenic silkworms. ( A , B) Schematic illustration of the piggyBac [3 × P3-EGFP, BmLP3-Gal4] and piggyBac [3 × P3-DsRed, UAS-EGT] vectors. ( C , D ) Digestion of the vectors with Asc I yielded the expected band sizes. Lane 1/3: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid; Lane 2/4: agarose gel electrophoresis detection of piggyBac [3 × P3-EGFP, BmLP3-Gal4]/piggyBac [3 × P3-DsRed, UAS-EGT] vector plasmid after Asc I digestion. BmLP3-Gal4-SV40 is about 4000 bp and UAS-EGT-SV40 is about 2100 bp. ( E ) Isolation of generation G0 transgenic silkworms by detection of EGFP (Gal4 transgenic line) and DsRed (UAS transgenic line) expression in the compound eyes of moths. E1/E3: Gal4/ UAS transgenic moth under white light. E2/E4: Gal4/UAS transgenic moth under fluorescent light. ( F ) Screening of generation G7 hybrid offspring from Gal4 and UAS transgenic lines by detection of both EGFP and DsRed expression in the eggs. F1/2/3: transgenic eggs under white/green fluorescent/red fluorescent light.

    Techniques Used: Isolation, Transgenic Assay, Agarose Gel Electrophoresis, Plasmid Preparation, Expressing

    17) Product Images from "A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain"

    Article Title: A toolbox of IgG subclass-switched recombinant monoclonal antibodies for enhanced multiplex immunolabeling of brain

    Journal: eLife

    doi: 10.7554/eLife.43322

    Validation of subclass-switched anti-PSD-95 K28/43R R-mAb. ( A ) Validation of the K28/43R R-mAb in heterologous cells. COS-1 cells transiently transfected to express human PSD-95 in a subset of cells were immunolabeled with K28/43 mAb (IgG2a) alone (top row), K28/43R R-mAb (IgG1) alone (middle row), or K28/43 mAb plus K28/43R R-mAb (bottom row). Immunolabeling in all samples was detected with a cocktail of anti-mouse IgG2a (red, for the K28/43 mAb) and anti-mouse IgG1 (green, for the K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Labeling in blue is for the DNA-specific dye Hoechst 33258 and shows nuclei of both transfected and untransfected cells. Scale bar in the lower right merged panel = 30 µm and holds for all panels in A. ( B ) Validation of the K28/43R R-mAb in brain sections. A brain section from an adult rat was immunolabeled with K28/43 mAb plus K28/43R R-mAb and immunolabeling detected with a cocktail of anti-mouse IgG2a (red, for K28/43 mAb) and anti-mouse IgG1 (green, for K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Cell nuclei are labeled with the DNA-specific dye Hoechst 33258 (blue). The region of interest shown is from cerebellar cortex. Scale bar in the left panel = 100 µm, and in the right merged panel = 30 µm. ( C ) Immunoblots against brain membranes and COS cell lysates over-expressing various members of the MAGUK superfamily of scaffolding proteins. To confirm expression of MAGUK proteins, immunoblots were probed with rabbit anti-PSD-95 (red). K28/86 is an anti-MAGUK mAb. Primary antibodies were detected with the appropriate combinations of fluorescently labeled species-specific anti-rabbit and subclass-specific anti-mouse IgG secondary Abs as indicated. Control indicates COS cells transfected with an empty vector.
    Figure Legend Snippet: Validation of subclass-switched anti-PSD-95 K28/43R R-mAb. ( A ) Validation of the K28/43R R-mAb in heterologous cells. COS-1 cells transiently transfected to express human PSD-95 in a subset of cells were immunolabeled with K28/43 mAb (IgG2a) alone (top row), K28/43R R-mAb (IgG1) alone (middle row), or K28/43 mAb plus K28/43R R-mAb (bottom row). Immunolabeling in all samples was detected with a cocktail of anti-mouse IgG2a (red, for the K28/43 mAb) and anti-mouse IgG1 (green, for the K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Labeling in blue is for the DNA-specific dye Hoechst 33258 and shows nuclei of both transfected and untransfected cells. Scale bar in the lower right merged panel = 30 µm and holds for all panels in A. ( B ) Validation of the K28/43R R-mAb in brain sections. A brain section from an adult rat was immunolabeled with K28/43 mAb plus K28/43R R-mAb and immunolabeling detected with a cocktail of anti-mouse IgG2a (red, for K28/43 mAb) and anti-mouse IgG1 (green, for K28/43R R-mAb) subclass-specific Alexa Fluor conjugated secondary antibodies. Cell nuclei are labeled with the DNA-specific dye Hoechst 33258 (blue). The region of interest shown is from cerebellar cortex. Scale bar in the left panel = 100 µm, and in the right merged panel = 30 µm. ( C ) Immunoblots against brain membranes and COS cell lysates over-expressing various members of the MAGUK superfamily of scaffolding proteins. To confirm expression of MAGUK proteins, immunoblots were probed with rabbit anti-PSD-95 (red). K28/86 is an anti-MAGUK mAb. Primary antibodies were detected with the appropriate combinations of fluorescently labeled species-specific anti-rabbit and subclass-specific anti-mouse IgG secondary Abs as indicated. Control indicates COS cells transfected with an empty vector.

    Techniques Used: Transfection, Immunolabeling, Labeling, Western Blot, Expressing, Scaffolding, Plasmid Preparation

    18) Product Images from "An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands"

    Article Title: An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands

    Journal: Genome Research

    doi: 10.1101/gr.197402

    RLGS identifies DNA methylation in primary lung cancer. ( A ) Sections from RLGS profiles including RLGS fragment A2E54 (arrow). Sections from normal and tumor profiles from patient 14 as well as two lung cancer cell lines (H1299 and H125) are shown. The corresponding Asc I– Eco RV clone was found in plate 4, row I, and column 14, and this clone was confirmed by use in a mixing gel. ( B ) DNA from Asc I clone 4I14 corresponding to RLGS spot A2E54 was used for Southern analysis. DNAs from normal lung (NL), lung tumors (T), and adjacent normal tissue (N) from patients 10, 14, 17, and 18, as well as from three lung cancer cell lines H125, H1299, and A549 were digested with Asc I and Eco RV. DNA in the first lane was digested only with Eco RV and shows the size of the Eco RV fragment. In the double digests, hybridization to the large Eco RV band is indicative of protection of the Asc I site digestion by methylation. The smaller band is indicative of cutting by Asc I.
    Figure Legend Snippet: RLGS identifies DNA methylation in primary lung cancer. ( A ) Sections from RLGS profiles including RLGS fragment A2E54 (arrow). Sections from normal and tumor profiles from patient 14 as well as two lung cancer cell lines (H1299 and H125) are shown. The corresponding Asc I– Eco RV clone was found in plate 4, row I, and column 14, and this clone was confirmed by use in a mixing gel. ( B ) DNA from Asc I clone 4I14 corresponding to RLGS spot A2E54 was used for Southern analysis. DNAs from normal lung (NL), lung tumors (T), and adjacent normal tissue (N) from patients 10, 14, 17, and 18, as well as from three lung cancer cell lines H125, H1299, and A549 were digested with Asc I and Eco RV. DNA in the first lane was digested only with Eco RV and shows the size of the Eco RV fragment. In the double digests, hybridization to the large Eco RV band is indicative of protection of the Asc I site digestion by methylation. The smaller band is indicative of cutting by Asc I.

    Techniques Used: RLGS, DNA Methylation Assay, Hybridization, Methylation

    Outline of the RLGS procedure using Asc I as a restriction landmark enzyme.
    Figure Legend Snippet: Outline of the RLGS procedure using Asc I as a restriction landmark enzyme.

    Techniques Used: RLGS

    19) Product Images from "Validation of Binary Typing for Staphylococcus aureus Strains"

    Article Title: Validation of Binary Typing for Staphylococcus aureus Strains

    Journal: Journal of Clinical Microbiology

    doi:

    Physical mapping of the DNA probes on S. aureus ) restriction fragments. (A) PFGE macrorestriction patterns of S. aureus NCTC 8325 digested with Sma I, Sgr AI, and Asc I (lanes 1, 2, and 3, respectively). Restriction fragments are coded by descending molecular size. (B) Example of hybridization results with probe AW-15 to PFGE patterns of S. aureus NCTC 8325. Lanes are the same as for panel A. (C) Hybridization results of probe AW-15 depicted on the physical map of S. aureus NCTC 8325. (D) Mapping results of the 15 strain-specific DNA probes (AW-1 through AW-15) to the macro-restriction fragments of the S. aureus NCTC 8325 genome. NH, no hybridization of the strain-specific DNA probe to the macrorestriction fragments.
    Figure Legend Snippet: Physical mapping of the DNA probes on S. aureus ) restriction fragments. (A) PFGE macrorestriction patterns of S. aureus NCTC 8325 digested with Sma I, Sgr AI, and Asc I (lanes 1, 2, and 3, respectively). Restriction fragments are coded by descending molecular size. (B) Example of hybridization results with probe AW-15 to PFGE patterns of S. aureus NCTC 8325. Lanes are the same as for panel A. (C) Hybridization results of probe AW-15 depicted on the physical map of S. aureus NCTC 8325. (D) Mapping results of the 15 strain-specific DNA probes (AW-1 through AW-15) to the macro-restriction fragments of the S. aureus NCTC 8325 genome. NH, no hybridization of the strain-specific DNA probe to the macrorestriction fragments.

    Techniques Used: Hybridization

    20) Product Images from "DNA Repair Pathway Selection Caused by Defects in TEL1, SAE2, and De Novo Telomere Addition Generates Specific Chromosomal Rearrangement Signatures"

    Article Title: DNA Repair Pathway Selection Caused by Defects in TEL1, SAE2, and De Novo Telomere Addition Generates Specific Chromosomal Rearrangement Signatures

    Journal: PLoS Genetics

    doi: 10.1371/journal.pgen.1004277

    GCRs retaining hph belong to two size classes. ( A ) Digestion of the uGCR chrV divides the uGCR chrV into left telomeric, internal, and right telomeric fragments. Vertical arrows indicate the Asc I cleavage sites and relevant chromosomal features are labeled. ( B ) Southern blot using an hph probe of a pulsed-field gel (PFG) with DNA from the wild-type strain (RDKY6677) and 6 GCR-containing isolates (212, 214, 215, 217, 218, and 219) with and without Asc I digestion. The hph probe hybridizes to the intact chromosome and the internal and left telomeric fragments. ( C ) Southern blot of a second PFG with the same samples as in panel B using an MCM3 probe. The MCM3 probe hybridizes to the intact chromosome and the internal fragment.
    Figure Legend Snippet: GCRs retaining hph belong to two size classes. ( A ) Digestion of the uGCR chrV divides the uGCR chrV into left telomeric, internal, and right telomeric fragments. Vertical arrows indicate the Asc I cleavage sites and relevant chromosomal features are labeled. ( B ) Southern blot using an hph probe of a pulsed-field gel (PFG) with DNA from the wild-type strain (RDKY6677) and 6 GCR-containing isolates (212, 214, 215, 217, 218, and 219) with and without Asc I digestion. The hph probe hybridizes to the intact chromosome and the internal and left telomeric fragments. ( C ) Southern blot of a second PFG with the same samples as in panel B using an MCM3 probe. The MCM3 probe hybridizes to the intact chromosome and the internal fragment.

    Techniques Used: Labeling, Southern Blot, Pulsed-Field Gel

    21) Product Images from "Characterization of Recurrent and Sporadic Listeria monocytogenes Isolates from Raw Milk and Nondairy Foods by Pulsed-Field Gel Electrophoresis, Monocin Typing, Plasmid Profiling, and Cadmium and Antibiotic Resistance Determination"

    Article Title: Characterization of Recurrent and Sporadic Listeria monocytogenes Isolates from Raw Milk and Nondairy Foods by Pulsed-Field Gel Electrophoresis, Monocin Typing, Plasmid Profiling, and Cadmium and Antibiotic Resistance Determination

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.2.840-847.2001

    Dendrogram showing the relatedness of band patterns derived from PFGE of Asc I-restricted genomic DNA from 23 L. monocytogenes ) to compare profiles between gels.
    Figure Legend Snippet: Dendrogram showing the relatedness of band patterns derived from PFGE of Asc I-restricted genomic DNA from 23 L. monocytogenes ) to compare profiles between gels.

    Techniques Used: Derivative Assay

    22) Product Images from "Characterization of Listeria monocytogenes isolated from a fresh mixed sausage processing line in Pelotas-RS by PFGE"

    Article Title: Characterization of Listeria monocytogenes isolated from a fresh mixed sausage processing line in Pelotas-RS by PFGE

    Journal: Brazilian Journal of Microbiology

    doi: 10.1590/S1517-838220090003000021

    PFGE profiles obtained with the Apa I restriction enzime. P: L. monocytogenes H 2446 digested with Asc I; 1529: L. monocytogenes from the outgroup; 06; 08; 07; 19; 22; 18; 02; 12; 23; 11: Isolates of L. monocytogenes digested with Apa I.
    Figure Legend Snippet: PFGE profiles obtained with the Apa I restriction enzime. P: L. monocytogenes H 2446 digested with Asc I; 1529: L. monocytogenes from the outgroup; 06; 08; 07; 19; 22; 18; 02; 12; 23; 11: Isolates of L. monocytogenes digested with Apa I.

    Techniques Used:

    PFGE profiles obtained with the Asc I restriction enzyme. P: L. monocytogenes H 2446 digested with Asc I; B; E; C; J; D; M; G; A; K; H: isolates of L. monocytogenes digested with Asc I.
    Figure Legend Snippet: PFGE profiles obtained with the Asc I restriction enzyme. P: L. monocytogenes H 2446 digested with Asc I; B; E; C; J; D; M; G; A; K; H: isolates of L. monocytogenes digested with Asc I.

    Techniques Used:

    23) Product Images from "An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands"

    Article Title: An AscI Boundary Library for the Studies of Genetic and Epigenetic Alterations in CpG Islands

    Journal: Genome Research

    doi: 10.1101/gr.197402

    RLGS identifies DNA methylation in primary lung cancer. ( A ) Sections from RLGS profiles including RLGS fragment A2E54 (arrow). Sections from normal and tumor profiles from patient 14 as well as two lung cancer cell lines (H1299 and H125) are shown. The corresponding Asc I– Eco RV clone was found in plate 4, row I, and column 14, and this clone was confirmed by use in a mixing gel. ( B ) DNA from Asc I clone 4I14 corresponding to RLGS spot A2E54 was used for Southern analysis. DNAs from normal lung (NL), lung tumors (T), and adjacent normal tissue (N) from patients 10, 14, 17, and 18, as well as from three lung cancer cell lines H125, H1299, and A549 were digested with Asc I and Eco RV. DNA in the first lane was digested only with Eco RV and shows the size of the Eco RV fragment. In the double digests, hybridization to the large Eco RV band is indicative of protection of the Asc I site digestion by methylation. The smaller band is indicative of cutting by Asc I.
    Figure Legend Snippet: RLGS identifies DNA methylation in primary lung cancer. ( A ) Sections from RLGS profiles including RLGS fragment A2E54 (arrow). Sections from normal and tumor profiles from patient 14 as well as two lung cancer cell lines (H1299 and H125) are shown. The corresponding Asc I– Eco RV clone was found in plate 4, row I, and column 14, and this clone was confirmed by use in a mixing gel. ( B ) DNA from Asc I clone 4I14 corresponding to RLGS spot A2E54 was used for Southern analysis. DNAs from normal lung (NL), lung tumors (T), and adjacent normal tissue (N) from patients 10, 14, 17, and 18, as well as from three lung cancer cell lines H125, H1299, and A549 were digested with Asc I and Eco RV. DNA in the first lane was digested only with Eco RV and shows the size of the Eco RV fragment. In the double digests, hybridization to the large Eco RV band is indicative of protection of the Asc I site digestion by methylation. The smaller band is indicative of cutting by Asc I.

    Techniques Used: RLGS, DNA Methylation Assay, Hybridization, Methylation

    Outline of the RLGS procedure using Asc I as a restriction landmark enzyme.
    Figure Legend Snippet: Outline of the RLGS procedure using Asc I as a restriction landmark enzyme.

    Techniques Used: RLGS

    24) Product Images from "Molecular Epidemiology of an Outbreak of Febrile Gastroenteritis Caused by Listeria monocytogenes in Cold-Smoked Rainbow Trout"

    Article Title: Molecular Epidemiology of an Outbreak of Febrile Gastroenteritis Caused by Listeria monocytogenes in Cold-Smoked Rainbow Trout

    Journal: Journal of Clinical Microbiology

    doi:

    Macrorestriction patterns of L. monocytogenes with restriction enzyme Asc I. Lane 1, lambda ladder PFG marker; lane 2, LMU1 (isolated from patient); lane 3, LMU10 (isolated from patient); lane 4, LMK55 (isolated without an enrichment step from cold-smoked rainbow trout); lane 5, LMK65 (isolated through an enrichment step from cold-smoked rainbow trout); lane 6, low-range PFG marker.
    Figure Legend Snippet: Macrorestriction patterns of L. monocytogenes with restriction enzyme Asc I. Lane 1, lambda ladder PFG marker; lane 2, LMU1 (isolated from patient); lane 3, LMU10 (isolated from patient); lane 4, LMK55 (isolated without an enrichment step from cold-smoked rainbow trout); lane 5, LMK65 (isolated through an enrichment step from cold-smoked rainbow trout); lane 6, low-range PFG marker.

    Techniques Used: Marker, Isolation

    Related Articles

    Functional Assay:

    Article Title: The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori
    Article Snippet: .. The sequences were assembled into the intermediate plasmid pSL1180 (modified and stored in our laboratory) to generate a functional cassette, which was digested with Asc I and ligated into piggyBac [3 × P3-EGFP] using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA), yielding piggyBac [3 × P3-EGFP, Bm LP3-Gal4]. .. Similarly, a piggyBac vector with 3 × P3-DsRed as a screening marker was prepared as follows.

    Agarose Gel Electrophoresis:

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae
    Article Snippet: .. To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes. .. Southern blotting To determine telomere sizes, purified chromosomal DNA from each strain was digested with Xho I (New England Biolabs) and separated by electrophoresis through a 0.7% agarose gel.

    Size-exclusion Chromatography:

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae
    Article Snippet: .. To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes. .. Southern blotting To determine telomere sizes, purified chromosomal DNA from each strain was digested with Xho I (New England Biolabs) and separated by electrophoresis through a 0.7% agarose gel.

    Electrophoresis:

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae
    Article Snippet: .. To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes. .. Southern blotting To determine telomere sizes, purified chromosomal DNA from each strain was digested with Xho I (New England Biolabs) and separated by electrophoresis through a 0.7% agarose gel.

    Incubation:

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae
    Article Snippet: .. To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes. .. Southern blotting To determine telomere sizes, purified chromosomal DNA from each strain was digested with Xho I (New England Biolabs) and separated by electrophoresis through a 0.7% agarose gel.

    Modification:

    Article Title: The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori
    Article Snippet: .. The sequences were assembled into the intermediate plasmid pSL1180 (modified and stored in our laboratory) to generate a functional cassette, which was digested with Asc I and ligated into piggyBac [3 × P3-EGFP] using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA), yielding piggyBac [3 × P3-EGFP, Bm LP3-Gal4]. .. Similarly, a piggyBac vector with 3 × P3-DsRed as a screening marker was prepared as follows.

    Staining:

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae
    Article Snippet: .. To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes. .. Southern blotting To determine telomere sizes, purified chromosomal DNA from each strain was digested with Xho I (New England Biolabs) and separated by electrophoresis through a 0.7% agarose gel.

    Plasmid Preparation:

    Article Title: The expression of ecdysteroid UDP-glucosyltransferase enhances cocoon shell ratio by reducing ecdysteroid titre in last-instar larvae of silkworm, Bombyx mori
    Article Snippet: .. The sequences were assembled into the intermediate plasmid pSL1180 (modified and stored in our laboratory) to generate a functional cassette, which was digested with Asc I and ligated into piggyBac [3 × P3-EGFP] using T4 DNA ligase (New England Biolabs, Ipswich, MA, USA), yielding piggyBac [3 × P3-EGFP, Bm LP3-Gal4]. .. Similarly, a piggyBac vector with 3 × P3-DsRed as a screening marker was prepared as follows.

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    New England Biolabs asc i
    Enzyme Digestion Method for AFM of Lower-Order Structures. AFM images of <t>Asc</t> I restriction enzyme digestion products from (a) DNA-coated surface not treated with extract, (b) The control surface without DNA treated with 20-fold diluted egg extract and
    Asc I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 96/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Enzyme Digestion Method for AFM of Lower-Order Structures. AFM images of Asc I restriction enzyme digestion products from (a) DNA-coated surface not treated with extract, (b) The control surface without DNA treated with 20-fold diluted egg extract and

    Journal: Chromosoma

    Article Title: Atomic Force Microscope Imaging of Chromatin Assembled in Xenopus laevis Egg Extract

    doi: 10.1007/s00412-010-0307-4

    Figure Lengend Snippet: Enzyme Digestion Method for AFM of Lower-Order Structures. AFM images of Asc I restriction enzyme digestion products from (a) DNA-coated surface not treated with extract, (b) The control surface without DNA treated with 20-fold diluted egg extract and

    Article Snippet: Since the digestion efficiency of Asc I on chromatin was very low, the digestion buffer was changed to its optimum buffer, NEBuffer 4 (20 mM Tris-acetate, 50 mM potassium acetate, 10 mM magnesium acetate, 1 mM dithiothreitol, pH 7.9; New England Biolabs).

    Techniques:

    Karyotype analysis of 21 GCRs containing strains by PFGE and aCGH. (A) PFGE analysis of 21 Can r 5FOA r strains. Intact chromosomes from the indicated GCR strains were transferred to nitrocellulose membranes and hybridized to a radiolabeled chromosome V essential gene YEL058W probe. Rearranged chromosome V sizes were estimated relative to the sizes of chromosomes from the RDKY3615 wild-type and the CAN r 5FOA r tlc1 mut 3 strain that were run as controls. (B) Analysis of circular chromosome V GCRs. Circular chromosome V GCRs were digested in the agarose plugs with Asc I for the indicated strains prior to PFGE. The intact and digested chromosome V was detected by hybridization with the YEL058W radiolabelled probe and the size of the resulting chromosome V fragment was estimated. (C) Karyotype analysis by aCGH of representative GCR containing strains is presented. The aGCH data of all GCRs analyzed in this study are present in the Figure S1 . The normalized log 2 ratio of the fluorescence intensities for each oligonucleotide relative to the reference strain is presented; in order to show all of the data points, it was necessary to use a different scale for the log 2 ratio for each chromosome. Chromosome numbers are indicated to the left of the panel.

    Journal: PLoS ONE

    Article Title: Stabilization of Dicentric Translocations through Secondary Rearrangements Mediated by Multiple Mechanisms in S. cerevisiae

    doi: 10.1371/journal.pone.0006389

    Figure Lengend Snippet: Karyotype analysis of 21 GCRs containing strains by PFGE and aCGH. (A) PFGE analysis of 21 Can r 5FOA r strains. Intact chromosomes from the indicated GCR strains were transferred to nitrocellulose membranes and hybridized to a radiolabeled chromosome V essential gene YEL058W probe. Rearranged chromosome V sizes were estimated relative to the sizes of chromosomes from the RDKY3615 wild-type and the CAN r 5FOA r tlc1 mut 3 strain that were run as controls. (B) Analysis of circular chromosome V GCRs. Circular chromosome V GCRs were digested in the agarose plugs with Asc I for the indicated strains prior to PFGE. The intact and digested chromosome V was detected by hybridization with the YEL058W radiolabelled probe and the size of the resulting chromosome V fragment was estimated. (C) Karyotype analysis by aCGH of representative GCR containing strains is presented. The aGCH data of all GCRs analyzed in this study are present in the Figure S1 . The normalized log 2 ratio of the fluorescence intensities for each oligonucleotide relative to the reference strain is presented; in order to show all of the data points, it was necessary to use a different scale for the log 2 ratio for each chromosome. Chromosome numbers are indicated to the left of the panel.

    Article Snippet: To digest the DNA with Asc I (New England Biolabs) prior to PFGE, plugs were extensively washed in digestion buffer and incubated with 60 units of Asc I in 500 µl of 1X digestion buffer at 37C for 18 h. Finally, the plugs were extensively washed in 10 mM Tris pH 7.5, 50 mM EDTA pH 8 prior to resolving the chromosomes in a 1% Agarose gel run in a CHEF (clamped homogeneous electric field electrophoresis) apparatus in chilled (4°C) 0.5X TBE (89 mM Tris-borate, pH 8.3, 25 mM EDTA) under two different conditions; 7 V/cm with 75 sec or 90 sec fixed pulse times for 24 h. Gels were stained with 0.5 µg/ml ethidium bromide for 30 minutes to visualize the chromosomes.

    Techniques: Hybridization, Fluorescence

    PFGE patterns produced from four strains of Erysipelothrix spp. by Sma I, Asc I, and Not I. Lanes: 1, E. rhusiopathiae strain ME-7, serovar 1a; 2, E. rhusiopathiae strain ATCC 19414, serovar 2; 3, E. tonsillarum strain ATCC 43339, serovar 7; 4, Erysipelothrix species strain 715, serovar 18; M, CHEF DNA Size Standard Lambda Ladder (Bio-Rad).

    Journal: Journal of Clinical Microbiology

    Article Title: Pulsed-Field Gel Electrophoresis in Differentiation of Erysipelothrix Species Strains

    doi: 10.1128/JCM.39.11.4032-4036.2001

    Figure Lengend Snippet: PFGE patterns produced from four strains of Erysipelothrix spp. by Sma I, Asc I, and Not I. Lanes: 1, E. rhusiopathiae strain ME-7, serovar 1a; 2, E. rhusiopathiae strain ATCC 19414, serovar 2; 3, E. tonsillarum strain ATCC 43339, serovar 7; 4, Erysipelothrix species strain 715, serovar 18; M, CHEF DNA Size Standard Lambda Ladder (Bio-Rad).

    Article Snippet: DNA plugs were sliced, and DNAs were digested with Sma I (Takara Co. Ltd., Tokyo, Japan), Asc I (New England BioLabs), and Not I (Takara).

    Techniques: Produced

    Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the combination of Not I and Asc I restriction enzymes and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Journal: Veterinary Research

    Article Title: Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France

    doi: 10.1186/s13567-015-0200-5

    Figure Lengend Snippet: Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the combination of Not I and Asc I restriction enzymes and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Article Snippet: Each plug was divided, one part being digested with 40 U of Not I (New England Biolabs) and the other part with 40 U of Asc I (New England Biolabs) at 37 °C overnight.

    Techniques: Software

    Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the Asc I restriction enzyme and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Journal: Veterinary Research

    Article Title: Pulsed-field gel electrophoresis and multi locus sequence typing for characterizing genotype variability of Yersinia ruckeri isolated from farmed fish in France

    doi: 10.1186/s13567-015-0200-5

    Figure Lengend Snippet: Dendrogram of the PFGE profiles of Y. ruckeri (field isolates and reference strains) obtained using the Asc I restriction enzyme and the BioNumerics software. Origin/reference strains, host, biotype, serotype, pulsotype, number and region of origin are indicated. Clusters and subclusters are presented.

    Article Snippet: Each plug was divided, one part being digested with 40 U of Not I (New England Biolabs) and the other part with 40 U of Asc I (New England Biolabs) at 37 °C overnight.

    Techniques: Software