smai  (New England Biolabs)


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    Name:
    SmaI
    Description:
    SmaI 10 000 units
    Catalog Number:
    r0141l
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    261
    Size:
    10 000 units
    Category:
    Restriction Enzymes
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    New England Biolabs smai
    SmaI
    SmaI 10 000 units
    https://www.bioz.com/result/smai/product/New England Biolabs
    Average 99 stars, based on 93 article reviews
    Price from $9.99 to $1999.99
    smai - by Bioz Stars, 2020-07
    99/100 stars

    Images

    1) Product Images from "RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation"

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp780

    Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.
    Figure Legend Snippet: Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.

    Techniques Used: Southern Blot, Staining, Produced, Generated

    2) Product Images from "Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿"

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.02346-06

    PFGE-based clustering of C. coli strains investigated in this study. All 68 strains were analyzed by PFGE with SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Two strains (1004 A
    Figure Legend Snippet: PFGE-based clustering of C. coli strains investigated in this study. All 68 strains were analyzed by PFGE with SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Two strains (1004 A

    Techniques Used:

    PFGE profiles of group I strains. Nineteen MDR strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. The line labeled “a” indicates
    Figure Legend Snippet: PFGE profiles of group I strains. Nineteen MDR strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. The line labeled “a” indicates

    Techniques Used: Labeling

    A conserved SmaI PFGE pattern (type a ) was disseminated among MDR strains of different STs.
    Figure Legend Snippet: A conserved SmaI PFGE pattern (type a ) was disseminated among MDR strains of different STs.

    Techniques Used:

    PFGE profiles of group II strains. Forty-two strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Strains which were not resistant to all six antibiotics
    Figure Legend Snippet: PFGE profiles of group II strains. Forty-two strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Strains which were not resistant to all six antibiotics

    Techniques Used:

    PFGE profiles of 13 strains with various STs but a conserved PFGE profile (type a ). Cluster analysis of the SmaI and KpnI patterns was performed by BioNumerics as described in Materials and Methods.
    Figure Legend Snippet: PFGE profiles of 13 strains with various STs but a conserved PFGE profile (type a ). Cluster analysis of the SmaI and KpnI patterns was performed by BioNumerics as described in Materials and Methods.

    Techniques Used:

    3) Product Images from "The Streptococcus milleri Population of a Cystic Fibrosis Clinic Reveals Patient Specificity and Intraspecies Diversity ▿"

    Article Title: The Streptococcus milleri Population of a Cystic Fibrosis Clinic Reveals Patient Specificity and Intraspecies Diversity ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.00414-10

    ApaI fingerprints of multiple isolates from two patients with closely related SmaI profiles reveal that the strains are genetically different enough to rule out patient-to-patient transmission. The multiple isolates were recovered at different times (shown
    Figure Legend Snippet: ApaI fingerprints of multiple isolates from two patients with closely related SmaI profiles reveal that the strains are genetically different enough to rule out patient-to-patient transmission. The multiple isolates were recovered at different times (shown

    Techniques Used: Transmission Assay

    4) Product Images from "Staphylococcus spp., Streptococcus canis, and Arcanobacterium phocae of healthy Canadian farmed mink and mink with pododermatitis"

    Article Title: Staphylococcus spp., Streptococcus canis, and Arcanobacterium phocae of healthy Canadian farmed mink and mink with pododermatitis

    Journal: Canadian Journal of Veterinary Research

    doi:

    Pulsed-field gel electrophoresis (PFGE)-based dendrogram of 21 SmaI digested S. delphini genomic DNA from healthy and diseased mink from 2 unrelated farms in Canada. Scale bar represents percent similarity based on Dice coefficients and UPGMA clustering. Asterisk (*) indicates 2 isolates taken from the same individual mink.
    Figure Legend Snippet: Pulsed-field gel electrophoresis (PFGE)-based dendrogram of 21 SmaI digested S. delphini genomic DNA from healthy and diseased mink from 2 unrelated farms in Canada. Scale bar represents percent similarity based on Dice coefficients and UPGMA clustering. Asterisk (*) indicates 2 isolates taken from the same individual mink.

    Techniques Used: Pulsed-Field Gel, Electrophoresis

    5) Product Images from "Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation"

    Article Title: Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation

    Journal: PeerJ

    doi: 10.7717/peerj.224

    Methylation analysis of Moloney vector 5′ LTR using MSRE-qPCR. (A) Sequence of 5′ long terminal repeat (LTR) and untranslated region of Moloney murine leukemia virus. The U3, R and U5 sequences within the LTR are shown and demarcated by vertical lines. Also shown are direct repeats (DR1 and DR2), Tata box, polyadenylation signal (Poly A), negative control region (NCR), binding site for ELP/NR5A1, and primer binding site (PBS). The CpG nucleotides are marked underneath by ‘*’ to indicate putative sites of methylation. The methylation sensitive SmaI and methylation insensitive MscI restriction enzyme sites are shown in red and green, respectively. > > > and
    Figure Legend Snippet: Methylation analysis of Moloney vector 5′ LTR using MSRE-qPCR. (A) Sequence of 5′ long terminal repeat (LTR) and untranslated region of Moloney murine leukemia virus. The U3, R and U5 sequences within the LTR are shown and demarcated by vertical lines. Also shown are direct repeats (DR1 and DR2), Tata box, polyadenylation signal (Poly A), negative control region (NCR), binding site for ELP/NR5A1, and primer binding site (PBS). The CpG nucleotides are marked underneath by ‘*’ to indicate putative sites of methylation. The methylation sensitive SmaI and methylation insensitive MscI restriction enzyme sites are shown in red and green, respectively. > > > and

    Techniques Used: Methylation, Plasmid Preparation, Real-time Polymerase Chain Reaction, Sequencing, Negative Control, Binding Assay

    6) Product Images from "Aspartoacylase-LacZ Knockin Mice: An Engineered Model of Canavan Disease"

    Article Title: Aspartoacylase-LacZ Knockin Mice: An Engineered Model of Canavan Disease

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0020336

    Generation of aspa lacZ mice by homologous recombination. A, Genomic structure of the murine aspa locus, which spans 6 exons (black boxes). Homologous recombination of the targeting vector inserts the βgeo cassette (blue box), encoding β-Galactosidase (lacZ), into intron 1 of the intact aspa gene. This cassette is flanked by frt-sites (green circles). Additional loxP sites flank exon 2 (red triangles). The vector includes a DTA cassette for negative selection. In the targeted allele, exon 1 is spliced to the splice acceptor site preceding βgeo, and transcription is terminated at the introduced pA site. The conditional aspa flox allele is produced by breeding aspa lacZ mutants to FLP-deleter mice [40] for recombination of the βgeo cassette in vivo . Note that frt and loxP sites are not drawn to scale. βgeo, β-galactosidase-neomycin resistance cassette; SA, splice acceptor; pA, polyadenylation site, DTA, Diphteria toxin gene. B, For Southern blot analysis genomic DNA was digested with SmaI/ApaI. The neo probe (white box in A) detected the expected 7.5 kb band in heterozygotes and homozygotes. C, Genomic PCR of littermates with primers 1 3 produces the expected amplicons in aspa +/+ (336 bp), aspa lacZ/+ (387 bp and 336 bp) and aspa lacZ/lacZ (387 bp) animals. The upstream loxP site was detected by PCR with primers 1 2 yielding a 307 bp band. D, Q-RT-PCR using a TaqMan probe for quantification of aspa mRNA levels in brains of aspa +/+ , aspa lacZ/+ , and aspa lacZ/lacZ mice (n = 3) confirms the attenuation of transcription downstream of exon 2 in the targeted allele. E, Representative Western blot of whole brain lysates of a spa +/+ , aspa lacZ/+ and aspa lacZ/lacZ mice (aged 4 months, n = 3). The 37 kD protein ASPA was detected in aspa +/+ and aspa lacZ/+ mice but not in aspa lacZ/lacZ mutants. β-Galactosidase is expressed in aspa lacZ/+ and aspa lacZ/lacZ brain but not controls. α-Tubulin was used as loading control. F. Representative picture of a male aspa lacZ/lacZ mutant (asterisk) and an aspa +/+ littermate at P70.
    Figure Legend Snippet: Generation of aspa lacZ mice by homologous recombination. A, Genomic structure of the murine aspa locus, which spans 6 exons (black boxes). Homologous recombination of the targeting vector inserts the βgeo cassette (blue box), encoding β-Galactosidase (lacZ), into intron 1 of the intact aspa gene. This cassette is flanked by frt-sites (green circles). Additional loxP sites flank exon 2 (red triangles). The vector includes a DTA cassette for negative selection. In the targeted allele, exon 1 is spliced to the splice acceptor site preceding βgeo, and transcription is terminated at the introduced pA site. The conditional aspa flox allele is produced by breeding aspa lacZ mutants to FLP-deleter mice [40] for recombination of the βgeo cassette in vivo . Note that frt and loxP sites are not drawn to scale. βgeo, β-galactosidase-neomycin resistance cassette; SA, splice acceptor; pA, polyadenylation site, DTA, Diphteria toxin gene. B, For Southern blot analysis genomic DNA was digested with SmaI/ApaI. The neo probe (white box in A) detected the expected 7.5 kb band in heterozygotes and homozygotes. C, Genomic PCR of littermates with primers 1 3 produces the expected amplicons in aspa +/+ (336 bp), aspa lacZ/+ (387 bp and 336 bp) and aspa lacZ/lacZ (387 bp) animals. The upstream loxP site was detected by PCR with primers 1 2 yielding a 307 bp band. D, Q-RT-PCR using a TaqMan probe for quantification of aspa mRNA levels in brains of aspa +/+ , aspa lacZ/+ , and aspa lacZ/lacZ mice (n = 3) confirms the attenuation of transcription downstream of exon 2 in the targeted allele. E, Representative Western blot of whole brain lysates of a spa +/+ , aspa lacZ/+ and aspa lacZ/lacZ mice (aged 4 months, n = 3). The 37 kD protein ASPA was detected in aspa +/+ and aspa lacZ/+ mice but not in aspa lacZ/lacZ mutants. β-Galactosidase is expressed in aspa lacZ/+ and aspa lacZ/lacZ brain but not controls. α-Tubulin was used as loading control. F. Representative picture of a male aspa lacZ/lacZ mutant (asterisk) and an aspa +/+ littermate at P70.

    Techniques Used: Mouse Assay, Homologous Recombination, Plasmid Preparation, Selection, Produced, In Vivo, Southern Blot, Polymerase Chain Reaction, Reverse Transcription Polymerase Chain Reaction, Western Blot, Mutagenesis

    7) Product Images from "Identification of fusB-Mediated Fusidic Acid Resistance Islands in Staphylococcus epidermidis Isolates ▿"

    Article Title: Identification of fusB-Mediated Fusidic Acid Resistance Islands in Staphylococcus epidermidis Isolates ▿

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.00592-11

    Dendrogram produced by BioNumerics software, showing distances calculated by Dice similarity index of SmaI-digested DNA fragments among 34 fusB- carrying S. epidermidis isolates. The degree of similarity is shown in the scale. Different degrees of gray
    Figure Legend Snippet: Dendrogram produced by BioNumerics software, showing distances calculated by Dice similarity index of SmaI-digested DNA fragments among 34 fusB- carrying S. epidermidis isolates. The degree of similarity is shown in the scale. Different degrees of gray

    Techniques Used: Produced, Software

    8) Product Images from "First Report of the Local Spread of Vancomycin-Resistant Enterococci Ascribed to the Interspecies Transmission of a vanA Gene Cluster-Carrying Linear Plasmid"

    Article Title: First Report of the Local Spread of Vancomycin-Resistant Enterococci Ascribed to the Interspecies Transmission of a vanA Gene Cluster-Carrying Linear Plasmid

    Journal: mSphere

    doi: 10.1128/mSphere.00102-20

    Bacterial strains used in this study and their pulsed-field gel electrophoresis (PFGE) patterns and drug susceptibilities. The superscript italic “a” indicates results of PFGE analysis of SmaI-digested DNA isolated from the locally spread strains. Pulse time varied from 5.3 to 34.9 s during the 20.0 h of electrophoresis. The superscript italic “b” indicates the following abbreviations and definitions: VAN, vancomycin; TEC, teicoplanin; LZD, linezolid; AMP, ampicillin; GEN, gentamicin; KAN, kanamycin; STR, streptomycin; ERY, erythromycin; CHL, chloramphenicol; TET, tetracycline; MIN, minocycline; CIP, ciprofloxacin; CRO, ceftriaxone; CMZ, cefmetazole; MEM, meropenem. To determine the MICs, E. raffinosus strains were grown for 48 h because their growth rate was low.
    Figure Legend Snippet: Bacterial strains used in this study and their pulsed-field gel electrophoresis (PFGE) patterns and drug susceptibilities. The superscript italic “a” indicates results of PFGE analysis of SmaI-digested DNA isolated from the locally spread strains. Pulse time varied from 5.3 to 34.9 s during the 20.0 h of electrophoresis. The superscript italic “b” indicates the following abbreviations and definitions: VAN, vancomycin; TEC, teicoplanin; LZD, linezolid; AMP, ampicillin; GEN, gentamicin; KAN, kanamycin; STR, streptomycin; ERY, erythromycin; CHL, chloramphenicol; TET, tetracycline; MIN, minocycline; CIP, ciprofloxacin; CRO, ceftriaxone; CMZ, cefmetazole; MEM, meropenem. To determine the MICs, E. raffinosus strains were grown for 48 h because their growth rate was low.

    Techniques Used: Pulsed-Field Gel, Electrophoresis, Isolation

    9) Product Images from "Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach"

    Article Title: Diversity of Proteolytic Clostridium botulinum Strains, Determined by a Pulsed-Field Gel Electrophoresis Approach

    Journal:

    doi: 10.1128/AEM.71.3.1311-1317.2005

    Digestion patterns of five proteolytic C. botulinum strains, two of type A (ATCC 3502 and ATCC 19397), two of type B (FT 243 and 4B), and one of type F (ATCC 35415), using the rare-cutting restriction enzymes SacII and SmaI. The pulse time ramp was 1
    Figure Legend Snippet: Digestion patterns of five proteolytic C. botulinum strains, two of type A (ATCC 3502 and ATCC 19397), two of type B (FT 243 and 4B), and one of type F (ATCC 35415), using the rare-cutting restriction enzymes SacII and SmaI. The pulse time ramp was 1

    Techniques Used:

    10) Product Images from "The preparation of HL-60 cells vaccine expressing BCG heat shock protein 70 and detection of its immunogenicity in vitro"

    Article Title: The preparation of HL-60 cells vaccine expressing BCG heat shock protein 70 and detection of its immunogenicity in vitro

    Journal: Human Vaccines & Immunotherapeutics

    doi: 10.4161/hv.21321

    Figure 2. Identification of recombinant plasmid pDisplay-HSP70. Lane 1: DNA marker (DL2000); Lane 2: PCR product of HSP70; Lane 3: plasmid pDisplay digested with BglII and SmaI; Lane 4: HSP70 digested with BglII and SmaI; Lane 5: recombinant plasmid
    Figure Legend Snippet: Figure 2. Identification of recombinant plasmid pDisplay-HSP70. Lane 1: DNA marker (DL2000); Lane 2: PCR product of HSP70; Lane 3: plasmid pDisplay digested with BglII and SmaI; Lane 4: HSP70 digested with BglII and SmaI; Lane 5: recombinant plasmid

    Techniques Used: Recombinant, Plasmid Preparation, Marker, Polymerase Chain Reaction

    11) Product Images from "Molecular Epidemiology, Sequence Types, and Plasmid Analyses of KPC-Producing Klebsiella pneumoniae Strains in Israel ▿"

    Article Title: Molecular Epidemiology, Sequence Types, and Plasmid Analyses of KPC-Producing Klebsiella pneumoniae Strains in Israel ▿

    Journal: Antimicrobial Agents and Chemotherapy

    doi: 10.1128/AAC.01818-09

    A comparison of bla KPC-2 -carrying plasmids originated from two K. pneumoniae clones and two E. coli clones isolated in the same time period. Plasmid restriction analysis of transformants carrying these plasmids showed identity between the K. pneumoniae plasmids (K) and the E. coli plasmids (E). Plasmids from both organisms were digested with BglII (lanes 2 to 5), EcoRV (lanes 6 to 9), and SmaI (lanes 10 to 13) prior to electrophoresis. GeneRuler 1-kb DNA ladder (Fermentas Life Sciences), lane 1 (M); E. coli 386, lanes 2, 6, and 10; K. pneumoniae 523 PFGE type R, lanes 3, 7, and 11; E. coli 547, lanes 4, 8, and 12); K. pneumoniae 531, PFGE type, lanes 5, 9, and 13.
    Figure Legend Snippet: A comparison of bla KPC-2 -carrying plasmids originated from two K. pneumoniae clones and two E. coli clones isolated in the same time period. Plasmid restriction analysis of transformants carrying these plasmids showed identity between the K. pneumoniae plasmids (K) and the E. coli plasmids (E). Plasmids from both organisms were digested with BglII (lanes 2 to 5), EcoRV (lanes 6 to 9), and SmaI (lanes 10 to 13) prior to electrophoresis. GeneRuler 1-kb DNA ladder (Fermentas Life Sciences), lane 1 (M); E. coli 386, lanes 2, 6, and 10; K. pneumoniae 523 PFGE type R, lanes 3, 7, and 11; E. coli 547, lanes 4, 8, and 12); K. pneumoniae 531, PFGE type, lanes 5, 9, and 13.

    Techniques Used: Clone Assay, Isolation, Plasmid Preparation, Electrophoresis

    12) Product Images from "High-Temperature Ethanol Fermentation and Transformation with Linear DNA in the Thermotolerant Yeast Kluyveromyces marxianus DMKU3-1042 ▿"

    Article Title: High-Temperature Ethanol Fermentation and Transformation with Linear DNA in the Thermotolerant Yeast Kluyveromyces marxianus DMKU3-1042 ▿

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.01854-08

    Transformation of a K. marxianus ura3 mutant with a linear DNA of S. cerevisiae URA3 (Sc URA3 ). (A) The K. marxianus ura3 mutant was not transformed with the intact Sc URA3 plasmid (pRS316) but with SmaI-digested pRS316 (4.8 kb) and the Sc URA3 PCR fragment (1.7 kb). (B) Southern blot hybridization of chromosomal DNA of S. cerevisiae BY4704 (lane 1), K. marxianus wild-type (WT) DMKU3-1042 (lane 2), ura3 mutant RAK3605 (lane 3), and nine Sc URA3 transformants from strain RAK3605 (lanes 4 to 12). Chromosomal DNA was digested with BamHI, run on a 0.8% agarose gel, transferred to a nylon membrane, and hybridized with a digoxigenin-labeled Sc URA3 probe. The bands indicated by an arrowhead are likely the authentic K. marxianus URA3 that cross-hybridizes with Sc URA3 . M, DNA size marker.
    Figure Legend Snippet: Transformation of a K. marxianus ura3 mutant with a linear DNA of S. cerevisiae URA3 (Sc URA3 ). (A) The K. marxianus ura3 mutant was not transformed with the intact Sc URA3 plasmid (pRS316) but with SmaI-digested pRS316 (4.8 kb) and the Sc URA3 PCR fragment (1.7 kb). (B) Southern blot hybridization of chromosomal DNA of S. cerevisiae BY4704 (lane 1), K. marxianus wild-type (WT) DMKU3-1042 (lane 2), ura3 mutant RAK3605 (lane 3), and nine Sc URA3 transformants from strain RAK3605 (lanes 4 to 12). Chromosomal DNA was digested with BamHI, run on a 0.8% agarose gel, transferred to a nylon membrane, and hybridized with a digoxigenin-labeled Sc URA3 probe. The bands indicated by an arrowhead are likely the authentic K. marxianus URA3 that cross-hybridizes with Sc URA3 . M, DNA size marker.

    Techniques Used: Transformation Assay, Mutagenesis, Plasmid Preparation, Polymerase Chain Reaction, Southern Blot, Hybridization, Agarose Gel Electrophoresis, Labeling, Marker

    13) Product Images from "Oxacilin-resistant Coagulase-negative staphylococci (CoNS) bacteremia in a general hospital at S?o Paulo city, Brasil"

    Article Title: Oxacilin-resistant Coagulase-negative staphylococci (CoNS) bacteremia in a general hospital at S?o Paulo city, Brasil

    Journal: Brazilian Journal of Microbiology

    doi: 10.1590/S1517-83822008000400006

    PFGE profile of SmaI-digested chromosomal DNA of CoNS isolates, obtained from patients in 9 de Julho Hospital in São Paulo city, Brazil. λ lamba ladder DNA markers; lanes 1–5 S. epidermidis ; lanes 6,7 and 10: S. haemolyticus ; lane 8: S. hominis ; lane 9: S. warneri ; lane 11: S. cohnii spp urealyticus .
    Figure Legend Snippet: PFGE profile of SmaI-digested chromosomal DNA of CoNS isolates, obtained from patients in 9 de Julho Hospital in São Paulo city, Brazil. λ lamba ladder DNA markers; lanes 1–5 S. epidermidis ; lanes 6,7 and 10: S. haemolyticus ; lane 8: S. hominis ; lane 9: S. warneri ; lane 11: S. cohnii spp urealyticus .

    Techniques Used:

    14) Product Images from "Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages"

    Article Title: Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0162526

    Selection for loss of antibiotic resistance in ST59/SCC mec V (5C2 5) MRSA strain PM1. (A) Cartoon representation of MES structures in PM1 and the generated colonies PM1-1 to PM1-5. (B) SmaI-digested PFGE of PM1 and PM1-1 to PM1-5 and the Southern blot. The SmaI-digested DNA separated by PFGE is shown in the left. The DNA was transferred to a nylon membrane and detected by Southern blot hybridization with DIG-labeled cat -, ermB - and IS 1216V -specific probes, which are shown on the right. Abbreviations: E r , erythromycin resistant; K r , kanamycin resistant; S r , streptomycin resistant; C r , chloramphenicol resistant.
    Figure Legend Snippet: Selection for loss of antibiotic resistance in ST59/SCC mec V (5C2 5) MRSA strain PM1. (A) Cartoon representation of MES structures in PM1 and the generated colonies PM1-1 to PM1-5. (B) SmaI-digested PFGE of PM1 and PM1-1 to PM1-5 and the Southern blot. The SmaI-digested DNA separated by PFGE is shown in the left. The DNA was transferred to a nylon membrane and detected by Southern blot hybridization with DIG-labeled cat -, ermB - and IS 1216V -specific probes, which are shown on the right. Abbreviations: E r , erythromycin resistant; K r , kanamycin resistant; S r , streptomycin resistant; C r , chloramphenicol resistant.

    Techniques Used: Selection, Generated, Southern Blot, Hybridization, Labeling

    15) Product Images from "Characteristics of Community-Associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) Strains Isolated from Skin and Soft-Tissue Infections in Uruguay"

    Article Title: Characteristics of Community-Associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) Strains Isolated from Skin and Soft-Tissue Infections in Uruguay

    Journal: International Journal of Microbiology

    doi: 10.1155/2009/472126

    (a) Pulsed-field gel electrophoresis (PFGE) patterns of the SmaI-digested genomic DNA obtained from CA-MRSA isolates in Uruguay. Lane 1, pulsotype A (strain IH 23); lane 2, pulsotype B (strain IH 48); lane 3, pulsotype C (strain IH 46); lane 4, pulsotype D (strain IH 7); lane 5, pulsotype E (strain IH 22) and lane 6 pulsotype F (strain IH 69). (b) Pulsed-field gel electrophoresis (PFGE) patterns of the SmaI-digested genomic DNA obtained from CA-MRSA isolates in Uruguay. Lane 1, pulsotype A1 (strain IH 36); lane 2, pulsotype A (strain IH 44); lane 3, pulsotype A2 (strain IH 9).
    Figure Legend Snippet: (a) Pulsed-field gel electrophoresis (PFGE) patterns of the SmaI-digested genomic DNA obtained from CA-MRSA isolates in Uruguay. Lane 1, pulsotype A (strain IH 23); lane 2, pulsotype B (strain IH 48); lane 3, pulsotype C (strain IH 46); lane 4, pulsotype D (strain IH 7); lane 5, pulsotype E (strain IH 22) and lane 6 pulsotype F (strain IH 69). (b) Pulsed-field gel electrophoresis (PFGE) patterns of the SmaI-digested genomic DNA obtained from CA-MRSA isolates in Uruguay. Lane 1, pulsotype A1 (strain IH 36); lane 2, pulsotype A (strain IH 44); lane 3, pulsotype A2 (strain IH 9).

    Techniques Used: Pulsed-Field Gel, Electrophoresis

    16) Product Images from "ICESluvan, a 94-Kilobase Mosaic Integrative Conjugative Element Conferring Interspecies Transfer of VanB-Type Glycopeptide Resistance, a Novel Bacitracin Resistance Locus, and a Toxin-Antitoxin Stabilization System"

    Article Title: ICESluvan, a 94-Kilobase Mosaic Integrative Conjugative Element Conferring Interspecies Transfer of VanB-Type Glycopeptide Resistance, a Novel Bacitracin Resistance Locus, and a Toxin-Antitoxin Stabilization System

    Journal: Journal of Bacteriology

    doi: 10.1128/JB.02165-12

    PFGE of SmaI-digested total DNA of recipient, donor, and transconjugants from filter matings. Lanes 1 and 9, low-range PFGE marker; lane 2, ICE Slu van donor S. lutetiensis 5-F9; lane 3, recipient BM4110 containing pIP964; lane 4, 1st-generation transconjugant/2nd-generation donor BM4110 ICE Slu van pIP964; lane 5, 2nd-generation transconjugant JH2-2 ICE Slu van pIP964; lane 6, 2nd-generation transconjugant UV202 ICE Slu van pIP964; lane 7, recipient JH2-2; lane 8, recipient UV202. Vancomycin, streptomycin, and rifampin and fusidic acid resistance are indicated by plus signs opposite Van r , Str r , and Rif r Fus r , respectively. The presence of ICE Slu van was verified by vanB PCR and visual inspection of the SmaI PFGE pattern, where ICE Slu ). The presence of the pheromone-responsive plasmid pIP964 was verified by rep pCF10 and agg PCRs.
    Figure Legend Snippet: PFGE of SmaI-digested total DNA of recipient, donor, and transconjugants from filter matings. Lanes 1 and 9, low-range PFGE marker; lane 2, ICE Slu van donor S. lutetiensis 5-F9; lane 3, recipient BM4110 containing pIP964; lane 4, 1st-generation transconjugant/2nd-generation donor BM4110 ICE Slu van pIP964; lane 5, 2nd-generation transconjugant JH2-2 ICE Slu van pIP964; lane 6, 2nd-generation transconjugant UV202 ICE Slu van pIP964; lane 7, recipient JH2-2; lane 8, recipient UV202. Vancomycin, streptomycin, and rifampin and fusidic acid resistance are indicated by plus signs opposite Van r , Str r , and Rif r Fus r , respectively. The presence of ICE Slu van was verified by vanB PCR and visual inspection of the SmaI PFGE pattern, where ICE Slu ). The presence of the pheromone-responsive plasmid pIP964 was verified by rep pCF10 and agg PCRs.

    Techniques Used: Marker, Polymerase Chain Reaction, Plasmid Preparation

    17) Product Images from "Characterization of Vancomycin-Resistant Enterococcus faecium Isolated from Swine in Three Michigan Counties ▿ Isolated from Swine in Three Michigan Counties ▿ ‖"

    Article Title: Characterization of Vancomycin-Resistant Enterococcus faecium Isolated from Swine in Three Michigan Counties ▿ Isolated from Swine in Three Michigan Counties ▿ ‖

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02346-09

    PFGE of SmaI-digested genomic DNA from six vanA -containing Enterococcus faecium isolates from swine in three Michigan counties.
    Figure Legend Snippet: PFGE of SmaI-digested genomic DNA from six vanA -containing Enterococcus faecium isolates from swine in three Michigan counties.

    Techniques Used:

    Related Articles

    Real-time Polymerase Chain Reaction:

    Article Title: Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation
    Article Snippet: .. Methylation-sensitive restriction enzyme qPCR (MSRE-qPCR) Genomic DNA (60 ng), isolated using DNeasy Kits, was digested with 5 units of SmaI (methylation sensitive) or MscI (methylation insensitive) or incubated in the absence of restriction enzyme (uncut) in the manufacturer supplied buffer (New England Biolabs, Massachusetts, USA) in a 50 µl reaction volume at 37°C for 4 h. The reaction was terminated by inactivating the enzymes at 80°C for 20 min. An aliquot of the digest (5 µl) containing 6 ng of genomic DNA was then used in qPCR using primers (SK160 and SK161, ) targeting the 5′ Moloney murine leukemia virus LTR and 5′ untranslated region (UTR) ( ). .. The PCR was carried out using SsoAdvanced SYBR Green Supermix (Bio-Rad, Hercules, CA, USA; Catalog no. 1725261) in a Bio-Rad CFX96 thermocycler.

    Agarose Gel Electrophoresis:

    Article Title: Aspartoacylase-LacZ Knockin Mice: An Engineered Model of Canavan Disease
    Article Snippet: .. DNA was digested with ApaI and SmaI (NEB, Ipswich, MA), separated on a 0.7% agarose gel, blotted onto Hybond N+ membrane (GE Healthcare, Dassel, Germany) and probed with a 600 bp 32 P-labelled fragment of the Neo-cassette. .. Mice were genotyped by PCR using Primer 1 as forward primer and Primer 3 as reversed primer resulting in a 336 bp band for the wild-type allele and a 387 bp band for the synthetic allele.

    Article Title: Staphylococcus spp., Streptococcus canis, and Arcanobacterium phocae of healthy Canadian farmed mink and mink with pododermatitis
    Article Snippet: .. Genomic DNA from both species was digested with SmaI (New England BioLabs, Ipswich, Massachusetts, USA) before electrophoresis in a 1.0% agarose gel, using a CHEF-III electrophoresis unit (Bio-Rad Laboratories, Hercules, California, USA) in 0.5× Trisborate-ethylenediamine tetra-acetic acid (EDTA) buffer containing 200 μM thiourea (Fisher Scientific, Fair Lawn, New Jersey, USA). .. For S. delphini, gels were run at 14°C at 6V/cm with an angle of 120° and a linear ramping from 4 s to 10 s for 12 h, followed by 13 s to 20 s for 6 h. For S. canis, gels were run under the same conditions, but with linear ramping from 1 s to 20 s over 16 h. Gel images were analyzed using BioNumerics software v5.1 (Applied Maths, Austin, Texas, USA).

    Plasmid Preparation:

    Article Title: Oncosuppressive Suicide Gene Virotherapy "PVH1-yCD/5-FC" for Pancreatic Peritoneal Carcinomatosis Treatment: NF?B and Akt/PI3K Involvement
    Article Snippet: .. Recombinant PV-H1 virus constructions for yCD and GFP expression The PV-H1-based vector DNA, phH1Δ800 , was linearized with SmaI restriction enzyme and subsequently dephosphorylated by the calf intestinal phosphatase (New England Biolabs-OZYME, Saint Quentin Yveline; France). .. The yCD gene was isolated from yeast genomic DNA (strain D4916 from Sigma-Aldrich) using specific probes: Forward: 5′-att ctcgag c gccaccatgg tgacagggggaatg-3′ containing a Kozak sequence (bold type) and XhoI restriction site (underlined), and Reverse: 5′-att ggatcc ctactcaccaatatcttcaaacc-3′ containing BamH1 restriction site (underlined), and was phosphorylated with T4 Polynucleotide Kinase (New England Biolabs-Ozyme, Montigny-Le-Bretonneux; France).

    Methylation:

    Article Title: Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation
    Article Snippet: .. Methylation-sensitive restriction enzyme qPCR (MSRE-qPCR) Genomic DNA (60 ng), isolated using DNeasy Kits, was digested with 5 units of SmaI (methylation sensitive) or MscI (methylation insensitive) or incubated in the absence of restriction enzyme (uncut) in the manufacturer supplied buffer (New England Biolabs, Massachusetts, USA) in a 50 µl reaction volume at 37°C for 4 h. The reaction was terminated by inactivating the enzymes at 80°C for 20 min. An aliquot of the digest (5 µl) containing 6 ng of genomic DNA was then used in qPCR using primers (SK160 and SK161, ) targeting the 5′ Moloney murine leukemia virus LTR and 5′ untranslated region (UTR) ( ). .. The PCR was carried out using SsoAdvanced SYBR Green Supermix (Bio-Rad, Hercules, CA, USA; Catalog no. 1725261) in a Bio-Rad CFX96 thermocycler.

    Isolation:

    Article Title: Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation
    Article Snippet: .. Methylation-sensitive restriction enzyme qPCR (MSRE-qPCR) Genomic DNA (60 ng), isolated using DNeasy Kits, was digested with 5 units of SmaI (methylation sensitive) or MscI (methylation insensitive) or incubated in the absence of restriction enzyme (uncut) in the manufacturer supplied buffer (New England Biolabs, Massachusetts, USA) in a 50 µl reaction volume at 37°C for 4 h. The reaction was terminated by inactivating the enzymes at 80°C for 20 min. An aliquot of the digest (5 µl) containing 6 ng of genomic DNA was then used in qPCR using primers (SK160 and SK161, ) targeting the 5′ Moloney murine leukemia virus LTR and 5′ untranslated region (UTR) ( ). .. The PCR was carried out using SsoAdvanced SYBR Green Supermix (Bio-Rad, Hercules, CA, USA; Catalog no. 1725261) in a Bio-Rad CFX96 thermocycler.

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation
    Article Snippet: .. Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min. .. The purified genomic DNA was re-digested with 100 U of ApaI completely (for first digestion with XhoI, PstI and SmaI) or 100 U of PstI (for first digestion with SpeI and ApaLI).

    Electrophoresis:

    Article Title: Staphylococcus spp., Streptococcus canis, and Arcanobacterium phocae of healthy Canadian farmed mink and mink with pododermatitis
    Article Snippet: .. Genomic DNA from both species was digested with SmaI (New England BioLabs, Ipswich, Massachusetts, USA) before electrophoresis in a 1.0% agarose gel, using a CHEF-III electrophoresis unit (Bio-Rad Laboratories, Hercules, California, USA) in 0.5× Trisborate-ethylenediamine tetra-acetic acid (EDTA) buffer containing 200 μM thiourea (Fisher Scientific, Fair Lawn, New Jersey, USA). .. For S. delphini, gels were run at 14°C at 6V/cm with an angle of 120° and a linear ramping from 4 s to 10 s for 12 h, followed by 13 s to 20 s for 6 h. For S. canis, gels were run under the same conditions, but with linear ramping from 1 s to 20 s over 16 h. Gel images were analyzed using BioNumerics software v5.1 (Applied Maths, Austin, Texas, USA).

    Incubation:

    Article Title: Gammaretroviral vector encoding a fluorescent marker to facilitate detection of reprogrammed human fibroblasts during iPSC generation
    Article Snippet: .. Methylation-sensitive restriction enzyme qPCR (MSRE-qPCR) Genomic DNA (60 ng), isolated using DNeasy Kits, was digested with 5 units of SmaI (methylation sensitive) or MscI (methylation insensitive) or incubated in the absence of restriction enzyme (uncut) in the manufacturer supplied buffer (New England Biolabs, Massachusetts, USA) in a 50 µl reaction volume at 37°C for 4 h. The reaction was terminated by inactivating the enzymes at 80°C for 20 min. An aliquot of the digest (5 µl) containing 6 ng of genomic DNA was then used in qPCR using primers (SK160 and SK161, ) targeting the 5′ Moloney murine leukemia virus LTR and 5′ untranslated region (UTR) ( ). .. The PCR was carried out using SsoAdvanced SYBR Green Supermix (Bio-Rad, Hercules, CA, USA; Catalog no. 1725261) in a Bio-Rad CFX96 thermocycler.

    Pulsed-Field Gel:

    Article Title: Nisin H Is a New Nisin Variant Produced by the Gut-Derived Strain Streptococcus hyointestinalis DPC6484
    Article Snippet: .. Molecular fingerprinting of S. hyointestinalis isolates was performed by pulsed-field gel electrophoresis (PFGE) as described by Simpson et al. (2002) ( ) using SmaI restriction endonucleases and DNA molecular weight markers (9.42 to 242.50 kb; New England BioLabs, Beverly, MA). .. DNA fragments were resolved with a CHEF (contour-clamped homogeneous electric field) DRIII pulsed-field system (Bio-Rad Laboratories) at 6 V/cm for 18 h with a 1- to 30-s linear ramp time to resolve bands.

    Expressing:

    Article Title: Oncosuppressive Suicide Gene Virotherapy "PVH1-yCD/5-FC" for Pancreatic Peritoneal Carcinomatosis Treatment: NF?B and Akt/PI3K Involvement
    Article Snippet: .. Recombinant PV-H1 virus constructions for yCD and GFP expression The PV-H1-based vector DNA, phH1Δ800 , was linearized with SmaI restriction enzyme and subsequently dephosphorylated by the calf intestinal phosphatase (New England Biolabs-OZYME, Saint Quentin Yveline; France). .. The yCD gene was isolated from yeast genomic DNA (strain D4916 from Sigma-Aldrich) using specific probes: Forward: 5′-att ctcgag c gccaccatgg tgacagggggaatg-3′ containing a Kozak sequence (bold type) and XhoI restriction site (underlined), and Reverse: 5′-att ggatcc ctactcaccaatatcttcaaacc-3′ containing BamH1 restriction site (underlined), and was phosphorylated with T4 Polynucleotide Kinase (New England Biolabs-Ozyme, Montigny-Le-Bretonneux; France).

    Recombinant:

    Article Title: Oncosuppressive Suicide Gene Virotherapy "PVH1-yCD/5-FC" for Pancreatic Peritoneal Carcinomatosis Treatment: NF?B and Akt/PI3K Involvement
    Article Snippet: .. Recombinant PV-H1 virus constructions for yCD and GFP expression The PV-H1-based vector DNA, phH1Δ800 , was linearized with SmaI restriction enzyme and subsequently dephosphorylated by the calf intestinal phosphatase (New England Biolabs-OZYME, Saint Quentin Yveline; France). .. The yCD gene was isolated from yeast genomic DNA (strain D4916 from Sigma-Aldrich) using specific probes: Forward: 5′-att ctcgag c gccaccatgg tgacagggggaatg-3′ containing a Kozak sequence (bold type) and XhoI restriction site (underlined), and Reverse: 5′-att ggatcc ctactcaccaatatcttcaaacc-3′ containing BamH1 restriction site (underlined), and was phosphorylated with T4 Polynucleotide Kinase (New England Biolabs-Ozyme, Montigny-Le-Bretonneux; France).

    Molecular Weight:

    Article Title: Nisin H Is a New Nisin Variant Produced by the Gut-Derived Strain Streptococcus hyointestinalis DPC6484
    Article Snippet: .. Molecular fingerprinting of S. hyointestinalis isolates was performed by pulsed-field gel electrophoresis (PFGE) as described by Simpson et al. (2002) ( ) using SmaI restriction endonucleases and DNA molecular weight markers (9.42 to 242.50 kb; New England BioLabs, Beverly, MA). .. DNA fragments were resolved with a CHEF (contour-clamped homogeneous electric field) DRIII pulsed-field system (Bio-Rad Laboratories) at 6 V/cm for 18 h with a 1- to 30-s linear ramp time to resolve bands.

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    New England Biolabs smai restriction enzyme
    Schematic representation of recombinant parvoviral vector constructions. The upper diagram depicts the empty vector DNA clone PVH1-Δ800 which has 800-bp deletion in the VP coding region and carries a multiple cloning sequence <t>(MluI/SmaI</t> polylinker) at the VP2 translation initiation site. DNA inserts encoding for <t>GFP</t> or catalytic yCD were introduced in polylinker using XhoI and BamH1 restriction enzymes. The resulting rPVH1-GFP and rPVH1-yCD plasmids were used for the production of corresponding non-replicative recombinant parvoviruses.
    Smai Restriction Enzyme, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 90/100, based on 97 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Schematic representation of recombinant parvoviral vector constructions. The upper diagram depicts the empty vector DNA clone PVH1-Δ800 which has 800-bp deletion in the VP coding region and carries a multiple cloning sequence (MluI/SmaI polylinker) at the VP2 translation initiation site. DNA inserts encoding for GFP or catalytic yCD were introduced in polylinker using XhoI and BamH1 restriction enzymes. The resulting rPVH1-GFP and rPVH1-yCD plasmids were used for the production of corresponding non-replicative recombinant parvoviruses.

    Journal: PLoS ONE

    Article Title: Oncosuppressive Suicide Gene Virotherapy "PVH1-yCD/5-FC" for Pancreatic Peritoneal Carcinomatosis Treatment: NF?B and Akt/PI3K Involvement

    doi: 10.1371/journal.pone.0070594

    Figure Lengend Snippet: Schematic representation of recombinant parvoviral vector constructions. The upper diagram depicts the empty vector DNA clone PVH1-Δ800 which has 800-bp deletion in the VP coding region and carries a multiple cloning sequence (MluI/SmaI polylinker) at the VP2 translation initiation site. DNA inserts encoding for GFP or catalytic yCD were introduced in polylinker using XhoI and BamH1 restriction enzymes. The resulting rPVH1-GFP and rPVH1-yCD plasmids were used for the production of corresponding non-replicative recombinant parvoviruses.

    Article Snippet: Recombinant PV-H1 virus constructions for yCD and GFP expression The PV-H1-based vector DNA, phH1Δ800 , was linearized with SmaI restriction enzyme and subsequently dephosphorylated by the calf intestinal phosphatase (New England Biolabs-OZYME, Saint Quentin Yveline; France).

    Techniques: Recombinant, Plasmid Preparation, Clone Assay, Sequencing

    (A) PFGE macrorestriction patterns of Streptococcus hyointestinalis strains restricted with SmaI. Lane 1, S. hyointestinalis DPC6484; lane 2, S. hyointestinalis LMG14579; lane 3, S. hyointestinalis LMG14581; lane 4, S. hyointestinalis LMG14582; lane 5, S. hyointestinalis LMG14583; lane 6, S. hyointestinalis LMG14585; lane 7, S. hyointestinalis LMG14586; lane 8, S. hyointestinalis LMG14587. (B) (i) PCR amplification of strains of S. hyointestinalis template DNA with nshT -, nshH -, nshF -, and nshR -specific primers. Lanes correspond to those in panel A. (ii) Comparison of antimicrobial activities of S. hyointesinalis strains DPC6484 (H), LMG14579, LMG14581, LMG14582, LMG14583, LMG14585, LMG14586, and LMG14587 against the indicator strain, L. delbrueckii subsp. bulgaricus LMG6901. Wells are labeled with H (for nisin H) and with the last two digits of the strain designation for the other strains.

    Journal: Applied and Environmental Microbiology

    Article Title: Nisin H Is a New Nisin Variant Produced by the Gut-Derived Strain Streptococcus hyointestinalis DPC6484

    doi: 10.1128/AEM.00212-15

    Figure Lengend Snippet: (A) PFGE macrorestriction patterns of Streptococcus hyointestinalis strains restricted with SmaI. Lane 1, S. hyointestinalis DPC6484; lane 2, S. hyointestinalis LMG14579; lane 3, S. hyointestinalis LMG14581; lane 4, S. hyointestinalis LMG14582; lane 5, S. hyointestinalis LMG14583; lane 6, S. hyointestinalis LMG14585; lane 7, S. hyointestinalis LMG14586; lane 8, S. hyointestinalis LMG14587. (B) (i) PCR amplification of strains of S. hyointestinalis template DNA with nshT -, nshH -, nshF -, and nshR -specific primers. Lanes correspond to those in panel A. (ii) Comparison of antimicrobial activities of S. hyointesinalis strains DPC6484 (H), LMG14579, LMG14581, LMG14582, LMG14583, LMG14585, LMG14586, and LMG14587 against the indicator strain, L. delbrueckii subsp. bulgaricus LMG6901. Wells are labeled with H (for nisin H) and with the last two digits of the strain designation for the other strains.

    Article Snippet: Molecular fingerprinting of S. hyointestinalis isolates was performed by pulsed-field gel electrophoresis (PFGE) as described by Simpson et al. (2002) ( ) using SmaI restriction endonucleases and DNA molecular weight markers (9.42 to 242.50 kb; New England BioLabs, Beverly, MA).

    Techniques: Polymerase Chain Reaction, Amplification, Labeling

    Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.

    Journal: Nucleic Acids Research

    Article Title: RIP140 in thyroid hormone-repression and chromatin remodeling of Crabp1 gene during adipocyte differentiation

    doi: 10.1093/nar/gkp780

    Figure Lengend Snippet: Alterations of restriction enzyme accessibility in the juxtaposed region of Crabp1 promoter along the course of adipocyte differentiation. ( A ) Detection of nucleosome array. Chromatin of MNase partially digested nuclei was separated on agarose gels followed by Southern blot analysis (left panel) and EtBr staining (right panel). A probe used covering the TIS (HinfI-PvuII) was used for Southern blot analysis. ( B–F ) Nuclei (differentiation Days 0, 4, 8) were digested with the indicated restriction enzymes and the recovered chromatin DNAs were completely re-digested with ApaI ( B–D ) or PstI ( E and F ) (the relationship of specific restriction site and each individual nucleosome was depicted in panel G), followed by Southern blot analyses using probe 1 ( D ) or probe 2 (B–C and E–F). ( G ) Schematic description of restriction enzyme digestion, nucleosomes, and predicted fragments detected with probes on the Southern blots. Complete digestion with ApaI produced 1.3 kb, and complete digestion with PstI produced 1.65 kb fragments. The generated fragments by digestion with XhoI, PstI, SmaI, SpeI and ApaLI for the corresponding nucleosome are 0.93, 0.67, 0.86, 0.55 and 0.65 kb, respectively. Nucleosomes on this array were named N5 to N-1, from the 5′- to the 3′-ends of this chromatin segment. Experiments were performed for least three times.

    Article Snippet: Isolated nuclei from differentiating 3T3-L1 cells were digested with 100 U of PstI, XhoI, SmaI, SpeI and ApaLI (New England Biolabs) for 30 min.

    Techniques: Southern Blot, Staining, Produced, Generated

    PFGE-based clustering of C. coli strains investigated in this study. All 68 strains were analyzed by PFGE with SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Two strains (1004 A

    Journal: Applied and Environmental Microbiology

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    doi: 10.1128/AEM.02346-06

    Figure Lengend Snippet: PFGE-based clustering of C. coli strains investigated in this study. All 68 strains were analyzed by PFGE with SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Two strains (1004 A

    Article Snippet: PFGE was performed using SmaI and KpnI (New England Biolabs) by following the protocol described by Ribot et al. ( ) with a few minor modifications; specifically, the prerestriction step was eliminated and the gels were electrophoresed for 22 h. TIFF images of banding patterns resulting from PFGE and fla typing were analyzed by BioNumerics (version 4.6; Applied Maths).

    Techniques:

    PFGE profiles of group I strains. Nineteen MDR strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. The line labeled “a” indicates

    Journal: Applied and Environmental Microbiology

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    doi: 10.1128/AEM.02346-06

    Figure Lengend Snippet: PFGE profiles of group I strains. Nineteen MDR strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. The line labeled “a” indicates

    Article Snippet: PFGE was performed using SmaI and KpnI (New England Biolabs) by following the protocol described by Ribot et al. ( ) with a few minor modifications; specifically, the prerestriction step was eliminated and the gels were electrophoresed for 22 h. TIFF images of banding patterns resulting from PFGE and fla typing were analyzed by BioNumerics (version 4.6; Applied Maths).

    Techniques: Labeling

    A conserved SmaI PFGE pattern (type a ) was disseminated among MDR strains of different STs.

    Journal: Applied and Environmental Microbiology

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    doi: 10.1128/AEM.02346-06

    Figure Lengend Snippet: A conserved SmaI PFGE pattern (type a ) was disseminated among MDR strains of different STs.

    Article Snippet: PFGE was performed using SmaI and KpnI (New England Biolabs) by following the protocol described by Ribot et al. ( ) with a few minor modifications; specifically, the prerestriction step was eliminated and the gels were electrophoresed for 22 h. TIFF images of banding patterns resulting from PFGE and fla typing were analyzed by BioNumerics (version 4.6; Applied Maths).

    Techniques:

    PFGE profiles of group II strains. Forty-two strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Strains which were not resistant to all six antibiotics

    Journal: Applied and Environmental Microbiology

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    doi: 10.1128/AEM.02346-06

    Figure Lengend Snippet: PFGE profiles of group II strains. Forty-two strains were characterized by PFGE using SmaI and KpnI, and cluster analysis of the patterns was performed by BioNumerics as described in Materials and Methods. Strains which were not resistant to all six antibiotics

    Article Snippet: PFGE was performed using SmaI and KpnI (New England Biolabs) by following the protocol described by Ribot et al. ( ) with a few minor modifications; specifically, the prerestriction step was eliminated and the gels were electrophoresed for 22 h. TIFF images of banding patterns resulting from PFGE and fla typing were analyzed by BioNumerics (version 4.6; Applied Maths).

    Techniques:

    PFGE profiles of 13 strains with various STs but a conserved PFGE profile (type a ). Cluster analysis of the SmaI and KpnI patterns was performed by BioNumerics as described in Materials and Methods.

    Journal: Applied and Environmental Microbiology

    Article Title: Clonal Population Structure and Specific Genotypes of Multidrug-Resistant Campylobacter coli from Turkeys ▿

    doi: 10.1128/AEM.02346-06

    Figure Lengend Snippet: PFGE profiles of 13 strains with various STs but a conserved PFGE profile (type a ). Cluster analysis of the SmaI and KpnI patterns was performed by BioNumerics as described in Materials and Methods.

    Article Snippet: PFGE was performed using SmaI and KpnI (New England Biolabs) by following the protocol described by Ribot et al. ( ) with a few minor modifications; specifically, the prerestriction step was eliminated and the gels were electrophoresed for 22 h. TIFF images of banding patterns resulting from PFGE and fla typing were analyzed by BioNumerics (version 4.6; Applied Maths).

    Techniques: