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    Thermo Fisher xbai digestion
    Stable transfection confirms that PAG sequences reduce transcription and steady-state levels of mRNAs from genes in the vicinity. ( A ) Schematic diagram of a bicistronic construct based on the two procyclin genes in the EP/PAG1 locus. Fragments derived from PAG1 were inserted into the unique <t>XbaI</t> site (X) in the forward or reverse orientation. ( B ) Northern blots were hybridized sequentially with probes corresponding to the open reading frames of <t>CAT</t> and BLE, then normalized with α-tubulin. ( C ) Nuclear run-on analysis of BLE and CAT in selected clones. Other single-stranded probes are as described in the legend to Figure 5 . The MARP signals minus background levels were set as 1 for each clone.
    Xbai Digestion, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 447 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 99 stars, based on 447 article reviews
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    95
    Millipore xbai
    Linear view of consensus optical maps with <t>DNA</t> sequence-based maps. Solid black arrows represent the locations of missing cuts in the consensus optical maps. The <t>XbaI</t> and NheI consensus optical maps extend to the left of the origin of the DNA sequence-based map because both optical maps had a missing cut at that position.
    Xbai, supplied by Millipore, used in various techniques. Bioz Stars score: 95/100, based on 654 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xbai/product/Millipore
    Average 95 stars, based on 654 article reviews
    Price from $9.99 to $1999.99
    xbai - by Bioz Stars, 2020-08
    95/100 stars
      Buy from Supplier

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    Stable transfection confirms that PAG sequences reduce transcription and steady-state levels of mRNAs from genes in the vicinity. ( A ) Schematic diagram of a bicistronic construct based on the two procyclin genes in the EP/PAG1 locus. Fragments derived from PAG1 were inserted into the unique XbaI site (X) in the forward or reverse orientation. ( B ) Northern blots were hybridized sequentially with probes corresponding to the open reading frames of CAT and BLE, then normalized with α-tubulin. ( C ) Nuclear run-on analysis of BLE and CAT in selected clones. Other single-stranded probes are as described in the legend to Figure 5 . The MARP signals minus background levels were set as 1 for each clone.

    Journal: Nucleic Acids Research

    Article Title: Bidirectional silencing of RNA polymerase I transcription by a strand switch region in Trypanosoma brucei

    doi: 10.1093/nar/gkp513

    Figure Lengend Snippet: Stable transfection confirms that PAG sequences reduce transcription and steady-state levels of mRNAs from genes in the vicinity. ( A ) Schematic diagram of a bicistronic construct based on the two procyclin genes in the EP/PAG1 locus. Fragments derived from PAG1 were inserted into the unique XbaI site (X) in the forward or reverse orientation. ( B ) Northern blots were hybridized sequentially with probes corresponding to the open reading frames of CAT and BLE, then normalized with α-tubulin. ( C ) Nuclear run-on analysis of BLE and CAT in selected clones. Other single-stranded probes are as described in the legend to Figure 5 . The MARP signals minus background levels were set as 1 for each clone.

    Article Snippet: The insert was excised with XhoI (cuts within the vector backbone 5′ to the PAG1 insert) and XbaI and cloned into the XhoI and XbaI sites of pG-mcs-CAT/EP2. pG-1240rev-CAT/EP2 (1240R ): the first 1240 bp of PAG1 were amplified by PCR from pG-1240-CAT/EP2 with the primers PAG1down3 and 1240up3 and cloned into the XhoI and XbaI sites of pG-mcs-CAT/EP2. pG-1240-neo-CAT/EP2 (1240F -neo): the same strategy was used as for pG-640-neo-CAT/EP2, however the neo fragment was cloned into XbaI site of pG-1240-CAT/EP2. pG-PAG1end-CAT/EP2 (ORFF ): to obtain the fragment with the PAG1 sequence from its internal HindIII site at 1087 to position 2458, a PCR was performed with the template pBS-711-HN ( ) and the primers M13r (Invitrogen) and PAG1up2.

    Techniques: Stable Transfection, Construct, Derivative Assay, Northern Blot, Clone Assay

    Dendrogram generated by BioNumerics software with 1% optimization and 1% position tolerance, showing the results of cluster analysis of band patterns after digestion of DNA from 42 isolates of Salmonella enterica serovar Typhimurium with the XbaI restriction

    Journal: Canadian Journal of Veterinary Research

    Article Title: Antimicrobial resistance, virulence-associated genes, and pulsed-field gel electrophoresis profiles of Salmonella enterica subsp. enterica serovar Typhimurium isolated from piglets with diarrhea in Korea

    doi:

    Figure Lengend Snippet: Dendrogram generated by BioNumerics software with 1% optimization and 1% position tolerance, showing the results of cluster analysis of band patterns after digestion of DNA from 42 isolates of Salmonella enterica serovar Typhimurium with the XbaI restriction

    Article Snippet: Briefly, agarose-embedded DNA was digested with 30 U of restriction enzyme XbaI (Fermentas International, Burlington, Ontario) overnight in a water bath at 37°C.

    Techniques: Generated, Software

    PFGE profiles, pulsotypes, seven-gene MLST profiles, ST, and K-type of the sequenced isolates. Dendogram generated by BioNumerics software version 7.6.1 showing the relationship of the isolates based on their banding patterns generated by XbaI restriction digestion. a, isolate name; b, pulsotype number; c, seven MLST housekeeping genes profile; d, sequence type; e, K-type.

    Journal: Scientific Reports

    Article Title: Molecular Characterization of Carbapenem Resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae Isolated from Lebanon

    doi: 10.1038/s41598-018-36554-2

    Figure Lengend Snippet: PFGE profiles, pulsotypes, seven-gene MLST profiles, ST, and K-type of the sequenced isolates. Dendogram generated by BioNumerics software version 7.6.1 showing the relationship of the isolates based on their banding patterns generated by XbaI restriction digestion. a, isolate name; b, pulsotype number; c, seven MLST housekeeping genes profile; d, sequence type; e, K-type.

    Article Snippet: Pulsed-field gel electrophoresis (PFGE) PFGE fingerprinting was performed using the XbaI restriction enzyme (ThermoScientific, Waltham, MA, USA), 1% SeaKem agarose gel, and the universal laboratory standard Salmonella enterica subsp. enterica serovar Braenderup (ATCC® BAA664™) according to the standard PulseNet protocol ( http://www.pulsenetinternational.org ).

    Techniques: Generated, Software, Sequencing

    NotI (A) or XbaI (B) PFGE profiles of Y. enterocolitica 1B/O8 clinical isolates from Poland (lanes 4 to 9) compared with profiles of bioserotype 1A/O7,8 (lanes 1 and 2) and 1B/O8 (lane 3) strains. The corresponding dendrograms illustrate genetic similarity of the NotI and XbaI profiles. The similarity values are shown in the dendrograms. PFGE genotypes are indicated in parentheses. Lanes in panels A and B: M, bacteriophage λ DNA ladder; 1, Y. enterocolitica 1A/O7,8 strain 323; 2, Y. enterocolitica 1A/O7,8 strain UG55; 3, reference 1B/O8 strain WA-314; 7, isolate 51/07; lanes in panel A: 4, 27/04; 5, 152/05; 6, 82/06; 8, 84/07; 9, 93-1/08; lanes in panel B: 4, 180/08; 5, 27/04; 6, 152/05. Sizes of DNA fragments are given in kilobases.

    Journal: Journal of Clinical Microbiology

    Article Title: Molecular Characterization of Human Clinical Isolates of Yersinia enterocolitica Bioserotype 1B/O8 in Poland: Emergence and Dissemination of Three Highly Related Clones ▿ Bioserotype 1B/O8 in Poland: Emergence and Dissemination of Three Highly Related Clones ▿ †

    doi: 10.1128/JCM.01321-08

    Figure Lengend Snippet: NotI (A) or XbaI (B) PFGE profiles of Y. enterocolitica 1B/O8 clinical isolates from Poland (lanes 4 to 9) compared with profiles of bioserotype 1A/O7,8 (lanes 1 and 2) and 1B/O8 (lane 3) strains. The corresponding dendrograms illustrate genetic similarity of the NotI and XbaI profiles. The similarity values are shown in the dendrograms. PFGE genotypes are indicated in parentheses. Lanes in panels A and B: M, bacteriophage λ DNA ladder; 1, Y. enterocolitica 1A/O7,8 strain 323; 2, Y. enterocolitica 1A/O7,8 strain UG55; 3, reference 1B/O8 strain WA-314; 7, isolate 51/07; lanes in panel A: 4, 27/04; 5, 152/05; 6, 82/06; 8, 84/07; 9, 93-1/08; lanes in panel B: 4, 180/08; 5, 27/04; 6, 152/05. Sizes of DNA fragments are given in kilobases.

    Article Snippet: For this reason, we performed additional PFGE analyses using the enzyme XbaI (Fermentas, Lithuania).

    Techniques:

    Interaction between the GYS1 XbaI polymorphism and physical activity (PA) in males. Kaplan Meier survival curves for males reporting normal to high physical activity (PA) level according to GYS1 XbaI genotype compared to males with low PA level.

    Journal: PLoS ONE

    Article Title: Variation in GYS1 Interacts with Exercise and Gender to Predict Cardiovascular Mortality

    doi: 10.1371/journal.pone.0000285

    Figure Lengend Snippet: Interaction between the GYS1 XbaI polymorphism and physical activity (PA) in males. Kaplan Meier survival curves for males reporting normal to high physical activity (PA) level according to GYS1 XbaI genotype compared to males with low PA level.

    Article Snippet: The XbaI polymorphism in GYS1 was genotyped using single base pair extension on AB3100 (Applied Biosystems) and the APOE polymorphisms were genotyped using allelic discrimination on AB7900 at the SWEGENE DNA genotyping Laboratory.

    Techniques: Activity Assay

    CV mortality in males and females according to the GYS1 XbaI (A) and APOE –219/ε2/ε3/ε4 (B) genotypes. Kaplan Meier survival curves illustrating a higher risk for CV mortality (HR 1.8 [1.2–2.6], p = 0.0016, p c = 0.0096) in male carriers of the GYS1 XbaI CT/TT-genotypes and in female carriers of the APOE –219TT/ε4 genotype combination (HR 2.3 [1.6–3.2], p

    Journal: PLoS ONE

    Article Title: Variation in GYS1 Interacts with Exercise and Gender to Predict Cardiovascular Mortality

    doi: 10.1371/journal.pone.0000285

    Figure Lengend Snippet: CV mortality in males and females according to the GYS1 XbaI (A) and APOE –219/ε2/ε3/ε4 (B) genotypes. Kaplan Meier survival curves illustrating a higher risk for CV mortality (HR 1.8 [1.2–2.6], p = 0.0016, p c = 0.0096) in male carriers of the GYS1 XbaI CT/TT-genotypes and in female carriers of the APOE –219TT/ε4 genotype combination (HR 2.3 [1.6–3.2], p

    Article Snippet: The XbaI polymorphism in GYS1 was genotyped using single base pair extension on AB3100 (Applied Biosystems) and the APOE polymorphisms were genotyped using allelic discrimination on AB7900 at the SWEGENE DNA genotyping Laboratory.

    Techniques:

    Structure of pBud-h I L-7 expression vector. The IL-7 gene was inserted into the SalI/XbaI site of pBudCE4.1

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Cloning and Expression of Recombinant Human Interleukin-7 in Chinese Hamster Ovary (CHO) Cells

    doi:

    Figure Lengend Snippet: Structure of pBud-h I L-7 expression vector. The IL-7 gene was inserted into the SalI/XbaI site of pBudCE4.1

    Article Snippet: After digestion with SalI and XbaI restriction endonucleases (Thermo Fisher Scientific, Vilnius, Lithuania), the gelpurified DNA fragment (Silica Bead DNA Gel Extraction Kit, Invitrogen, CA, USA) was inserted into the SalI/XbaI site of the pBudCE4.1 expression vector (Invitrogen) downstream of the CMV promoter to create pBud-h IL -7.

    Techniques: Expressing, Plasmid Preparation

    Agarose gel (1%) electrophoresis of restriction digestion of pBud-h IL-7 . lane M: DNA markers (GeneRuler 1 kb DNA Ladder,Thermo Fisher Scientific).Lane 1: pBud-hIL-7 cut with SalI and XbaI restriction endonucleases shows a 534 bp band expected for h IL-7 . Lane 2: uncut pBud-hIL-7 plasmid.

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Cloning and Expression of Recombinant Human Interleukin-7 in Chinese Hamster Ovary (CHO) Cells

    doi:

    Figure Lengend Snippet: Agarose gel (1%) electrophoresis of restriction digestion of pBud-h IL-7 . lane M: DNA markers (GeneRuler 1 kb DNA Ladder,Thermo Fisher Scientific).Lane 1: pBud-hIL-7 cut with SalI and XbaI restriction endonucleases shows a 534 bp band expected for h IL-7 . Lane 2: uncut pBud-hIL-7 plasmid.

    Article Snippet: After digestion with SalI and XbaI restriction endonucleases (Thermo Fisher Scientific, Vilnius, Lithuania), the gelpurified DNA fragment (Silica Bead DNA Gel Extraction Kit, Invitrogen, CA, USA) was inserted into the SalI/XbaI site of the pBudCE4.1 expression vector (Invitrogen) downstream of the CMV promoter to create pBud-h IL -7.

    Techniques: Agarose Gel Electrophoresis, Electrophoresis, Plasmid Preparation

    Colony-PCR and digestion products visualized on 1.2% agarose gels. A: Agarose gel electrophoresis of colony-PCR product. Lane 1: 1968 bp PCR product of fusion fragments, M: 100 bp-plus DNA size marker; B: BamHI and Xba XbaI digestion products of recombinant

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Construction of a Novel DNA Vaccine Candidate Encoding an HspX-PPE44-EsxV Fusion Antigen of Mycobacterium tuberculosis

    doi:

    Figure Lengend Snippet: Colony-PCR and digestion products visualized on 1.2% agarose gels. A: Agarose gel electrophoresis of colony-PCR product. Lane 1: 1968 bp PCR product of fusion fragments, M: 100 bp-plus DNA size marker; B: BamHI and Xba XbaI digestion products of recombinant

    Article Snippet: Then the generated HspX-PPE44-EsxV, along with vector, was digested with BamHI and XbaI restriction enzymes and ligated into pcDNA3.1 (+) (Invitrogen, USA) in BamHI and XbaI restriction sites at the 5´and 3´ ends ( ).

    Techniques: Polymerase Chain Reaction, Agarose Gel Electrophoresis, Marker, Recombinant

    Agarose gels of recombinant vector. a: digestion of pGH/HspX-PPE44-EsxV by BamHI and XbaI . lane 1: pGH (2940 bp) and HspX-PPE4-EsxV (1968 bp); lane; M: 1kb DNA size marker. B: Ligated pcDNA3.1 (+)/hspX-ppe44-esxV. The band is Recombinant pcDNA3.1 (+)

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Construction of a Novel DNA Vaccine Candidate Encoding an HspX-PPE44-EsxV Fusion Antigen of Mycobacterium tuberculosis

    doi:

    Figure Lengend Snippet: Agarose gels of recombinant vector. a: digestion of pGH/HspX-PPE44-EsxV by BamHI and XbaI . lane 1: pGH (2940 bp) and HspX-PPE4-EsxV (1968 bp); lane; M: 1kb DNA size marker. B: Ligated pcDNA3.1 (+)/hspX-ppe44-esxV. The band is Recombinant pcDNA3.1 (+)

    Article Snippet: Then the generated HspX-PPE44-EsxV, along with vector, was digested with BamHI and XbaI restriction enzymes and ligated into pcDNA3.1 (+) (Invitrogen, USA) in BamHI and XbaI restriction sites at the 5´and 3´ ends ( ).

    Techniques: Recombinant, Plasmid Preparation, Marker

    Schematic map of the pcDNA3.1 (+)/HspX-PPE44-EsxV-His plasmid. The fusion segment consisting of hspX, linker, ppe44, linker, esxV sequences, and a 6-polyhistidine-tag was designed between the BamHI and XbaI restriction sites of pcDNA3.1 (+) downstream

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Construction of a Novel DNA Vaccine Candidate Encoding an HspX-PPE44-EsxV Fusion Antigen of Mycobacterium tuberculosis

    doi:

    Figure Lengend Snippet: Schematic map of the pcDNA3.1 (+)/HspX-PPE44-EsxV-His plasmid. The fusion segment consisting of hspX, linker, ppe44, linker, esxV sequences, and a 6-polyhistidine-tag was designed between the BamHI and XbaI restriction sites of pcDNA3.1 (+) downstream

    Article Snippet: Then the generated HspX-PPE44-EsxV, along with vector, was digested with BamHI and XbaI restriction enzymes and ligated into pcDNA3.1 (+) (Invitrogen, USA) in BamHI and XbaI restriction sites at the 5´and 3´ ends ( ).

    Techniques: Plasmid Preparation

    Linear view of consensus optical maps with DNA sequence-based maps. Solid black arrows represent the locations of missing cuts in the consensus optical maps. The XbaI and NheI consensus optical maps extend to the left of the origin of the DNA sequence-based map because both optical maps had a missing cut at that position.

    Journal: Applied and Environmental Microbiology

    Article Title: Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

    doi: 10.1128/AEM.71.9.5511-5522.2005

    Figure Lengend Snippet: Linear view of consensus optical maps with DNA sequence-based maps. Solid black arrows represent the locations of missing cuts in the consensus optical maps. The XbaI and NheI consensus optical maps extend to the left of the origin of the DNA sequence-based map because both optical maps had a missing cut at that position.

    Article Snippet: Surface properties were assayed by digesting lambda DASH II bacteriophage DNA with 40 units of XbaI, HindIII, and NheI diluted in 200 μl of digestion buffer with 0.2% Triton X-100 (Sigma, St. Louis, MO) at 37°C to determine optimal digestion times, which ranged from 30 to 120 min.

    Techniques: Sequencing

    Whole-genome circular XbaI map of R. rubrum . The outermost circle (thick line) represents the consensus map created by Gentig from the single-molecule maps shown as arcs. The single-molecule maps were made from single DNA molecules digested with XbaI. The color ordering of the fragments is for contrast and is therefore random.

    Journal: Applied and Environmental Microbiology

    Article Title: Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

    doi: 10.1128/AEM.71.9.5511-5522.2005

    Figure Lengend Snippet: Whole-genome circular XbaI map of R. rubrum . The outermost circle (thick line) represents the consensus map created by Gentig from the single-molecule maps shown as arcs. The single-molecule maps were made from single DNA molecules digested with XbaI. The color ordering of the fragments is for contrast and is therefore random.

    Article Snippet: Surface properties were assayed by digesting lambda DASH II bacteriophage DNA with 40 units of XbaI, HindIII, and NheI diluted in 200 μl of digestion buffer with 0.2% Triton X-100 (Sigma, St. Louis, MO) at 37°C to determine optimal digestion times, which ranged from 30 to 120 min.

    Techniques:

    Comparisons of the XbaI, NheI, and HindIII optical maps to sequence data. (A, B, and C) Plots of optical map fragment sizes versus the DNA sequence-based map fragment sizes from the finished sequence for XbaI (A), NheI (B), and HindIII (C). The error bars represent the standard deviation of optical map fragment size about the mean. (D, E, F) Plots of the relative fragment sizing error [100 × (optical map fragment size - corresponding DNA sequence-based map fragment size)/corresponding DNA sequence-based map fragment size] versus DNA sequence-based map fragment size for XbaI ( D), NheI (E), and HindIII (F).

    Journal: Applied and Environmental Microbiology

    Article Title: Whole-Genome Shotgun Optical Mapping of Rhodospirillum rubrum

    doi: 10.1128/AEM.71.9.5511-5522.2005

    Figure Lengend Snippet: Comparisons of the XbaI, NheI, and HindIII optical maps to sequence data. (A, B, and C) Plots of optical map fragment sizes versus the DNA sequence-based map fragment sizes from the finished sequence for XbaI (A), NheI (B), and HindIII (C). The error bars represent the standard deviation of optical map fragment size about the mean. (D, E, F) Plots of the relative fragment sizing error [100 × (optical map fragment size - corresponding DNA sequence-based map fragment size)/corresponding DNA sequence-based map fragment size] versus DNA sequence-based map fragment size for XbaI ( D), NheI (E), and HindIII (F).

    Article Snippet: Surface properties were assayed by digesting lambda DASH II bacteriophage DNA with 40 units of XbaI, HindIII, and NheI diluted in 200 μl of digestion buffer with 0.2% Triton X-100 (Sigma, St. Louis, MO) at 37°C to determine optimal digestion times, which ranged from 30 to 120 min.

    Techniques: Sequencing, Standard Deviation