Structured Review

Roche xbai
Pulsed field gel electrophoresis of <t>XbaI-digested</t> DNA from the 59 ExPEC strains included in the study . Strain designation, phylogenetic group, ST assignation, clinical and geographical origin of isolation, <t>PFGE</t> cluster ( > 85% similarity), and PCR result for virulence genes that exhibited significant differences within the pathogenic groups are shown at right. This unweighted pair-group method with arithmetic mean dendrogram was generated in BioNumerics software (Applied Maths, St-Martens-Latem, Belgium) by using Dice coefficient with a 1.0% band position tolerance. The scale above the dendrogram indicates percent similarity. AS: abdominal sepsis; UTI: urinary tract infection; CI: cystitis; IS: intestinal sepsis; NBM: Newborn Meningitis; US: urosepsis; P?: posible pyelonephritis; C: colibacillosis; RS: respiratory sepsis; AP: acute pyelonephritis; AB: asymptomatic bacteriuria.
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Images

1) Product Images from "Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution"

Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution

Journal: BMC Microbiology

doi: 10.1186/1471-2180-9-132

Pulsed field gel electrophoresis of XbaI-digested DNA from the 59 ExPEC strains included in the study . Strain designation, phylogenetic group, ST assignation, clinical and geographical origin of isolation, PFGE cluster ( > 85% similarity), and PCR result for virulence genes that exhibited significant differences within the pathogenic groups are shown at right. This unweighted pair-group method with arithmetic mean dendrogram was generated in BioNumerics software (Applied Maths, St-Martens-Latem, Belgium) by using Dice coefficient with a 1.0% band position tolerance. The scale above the dendrogram indicates percent similarity. AS: abdominal sepsis; UTI: urinary tract infection; CI: cystitis; IS: intestinal sepsis; NBM: Newborn Meningitis; US: urosepsis; P?: posible pyelonephritis; C: colibacillosis; RS: respiratory sepsis; AP: acute pyelonephritis; AB: asymptomatic bacteriuria.
Figure Legend Snippet: Pulsed field gel electrophoresis of XbaI-digested DNA from the 59 ExPEC strains included in the study . Strain designation, phylogenetic group, ST assignation, clinical and geographical origin of isolation, PFGE cluster ( > 85% similarity), and PCR result for virulence genes that exhibited significant differences within the pathogenic groups are shown at right. This unweighted pair-group method with arithmetic mean dendrogram was generated in BioNumerics software (Applied Maths, St-Martens-Latem, Belgium) by using Dice coefficient with a 1.0% band position tolerance. The scale above the dendrogram indicates percent similarity. AS: abdominal sepsis; UTI: urinary tract infection; CI: cystitis; IS: intestinal sepsis; NBM: Newborn Meningitis; US: urosepsis; P?: posible pyelonephritis; C: colibacillosis; RS: respiratory sepsis; AP: acute pyelonephritis; AB: asymptomatic bacteriuria.

Techniques Used: Pulsed-Field Gel, Electrophoresis, Isolation, Polymerase Chain Reaction, Generated, Software, Infection

2) Product Images from "The plasma membrane permease PfNT1 is essential for purine salvage in the human malaria parasite Plasmodium falciparum"

Article Title: The plasma membrane permease PfNT1 is essential for purine salvage in the human malaria parasite Plasmodium falciparum

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

doi: 10.1073/pnas.0602590103

Strategy for PfNT1 disruption by double crossover. ( A ) Gene disruption strategy. I, schematic representation of WT PfNT1 chromosomal locus; II, the plasmid vector pKEΔPfNT1 used for stable transformation of P. falciparum ; III, the proposed model of integration of the plasmid by double crossover into the PfNT1 chromosomal locus. ( B ) Southern blot analysis of XbaI (X) and XbaI plus HindIII (X+H) digested genomic DNA from WT and pfnt1 Δ parasites by using BSD-specific and PfNT1-specific probes (as indicated by the gray double-headed arrows in part III of A ).
Figure Legend Snippet: Strategy for PfNT1 disruption by double crossover. ( A ) Gene disruption strategy. I, schematic representation of WT PfNT1 chromosomal locus; II, the plasmid vector pKEΔPfNT1 used for stable transformation of P. falciparum ; III, the proposed model of integration of the plasmid by double crossover into the PfNT1 chromosomal locus. ( B ) Southern blot analysis of XbaI (X) and XbaI plus HindIII (X+H) digested genomic DNA from WT and pfnt1 Δ parasites by using BSD-specific and PfNT1-specific probes (as indicated by the gray double-headed arrows in part III of A ).

Techniques Used: Plasmid Preparation, Transformation Assay, Southern Blot

3) Product Images from "Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya"

Article Title: Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.42.4.1477-1482.2004

(Left panel) Gel picture showing two different digest patterns of MDR serovar Typhi from Kenya: PFGE pattern 1 (lanes 1 and 2) and PFGE pattern 2 (lanes 3 and 4) with SpeI restriction endonuclease. Lane M, 50-kb lambda molecular size ladder. (Right panel) Gel picture showing XbaI digest pattern I of MDR serovar Typhi from Kenya (lanes 1 to 3), a similar PFGE pattern of MDR serovar Typhi from South Africa (lane 4) but different from the digest patterns of MDR serovar Typhi from Hong Kong (lane 5), Pakistan (lane 6), and the fully sensitive serovar Typhi from 1988 to 1990 outbreaks in Kenya (lanes 7 to 9). Lane M, 50-kb lambda molecular size ladder.
Figure Legend Snippet: (Left panel) Gel picture showing two different digest patterns of MDR serovar Typhi from Kenya: PFGE pattern 1 (lanes 1 and 2) and PFGE pattern 2 (lanes 3 and 4) with SpeI restriction endonuclease. Lane M, 50-kb lambda molecular size ladder. (Right panel) Gel picture showing XbaI digest pattern I of MDR serovar Typhi from Kenya (lanes 1 to 3), a similar PFGE pattern of MDR serovar Typhi from South Africa (lane 4) but different from the digest patterns of MDR serovar Typhi from Hong Kong (lane 5), Pakistan (lane 6), and the fully sensitive serovar Typhi from 1988 to 1990 outbreaks in Kenya (lanes 7 to 9). Lane M, 50-kb lambda molecular size ladder.

Techniques Used:

4) Product Images from "Clonal Expansion and Microevolution of Quinolone-Resistant Salmonella enterica Serotype Typhi in Vietnam from 1996 to 2004 ▿"

Article Title: Clonal Expansion and Microevolution of Quinolone-Resistant Salmonella enterica Serotype Typhi in Vietnam from 1996 to 2004 ▿

Journal:

doi: 10.1128/JCM.00948-07

Representative XbaI and SpeI PFGE profiles obtained for the 91 S. enterica serotype Typhi isolates under study. The PFGE profile numbering is indicated. The dendrograms generated by the BioNumerics software show the results of cluster analysis on the
Figure Legend Snippet: Representative XbaI and SpeI PFGE profiles obtained for the 91 S. enterica serotype Typhi isolates under study. The PFGE profile numbering is indicated. The dendrograms generated by the BioNumerics software show the results of cluster analysis on the

Techniques Used: Generated, Software

5) Product Images from "Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing"

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkv095

J is inserted into some plasmids transfected in L. tarentolae . The 25.2S, 25.2L and 28.2 plasmids, shown in Figure 2 , were purified after amplification in L. tarentolae or E. coli . The DNA samples were digested with BamHI, EcoRI and XbaI, size-fractionated in a 0.7% agarose gel in 0.5×TBE, transferred to nitrocellulose and incubated with an anti-J antibody. ( A ) The plasmids 25.2L and 25.2S purified from L. tarentolae show specific bands recognized by the anti-J antibody. It is clear that J was not only formed in the inserted 2 kb 25.2L cSSR, but also in the adjacent 0.8 kb intergenic α-tubulin and the 1.7 kb α-tubulin-neo fragments. The small 25.2S insert fragment is not visible on the blot. No J-containing fragments are detected when the plasmids were isolated from E. coli or when the 28.2 plasmid was used. ( B ) J-containing DNA fragments are only detected after growth in the wild-type and not after growth in the JBP2-null L. tarentolae strain. This blot contains the 0.4 kb 25.2S insert band, albeit weak because these small fragments are lost during blotting. The 1.2 kb fragment in the 25.2S plasmid preparation is due to a modification of the BamHI site.
Figure Legend Snippet: J is inserted into some plasmids transfected in L. tarentolae . The 25.2S, 25.2L and 28.2 plasmids, shown in Figure 2 , were purified after amplification in L. tarentolae or E. coli . The DNA samples were digested with BamHI, EcoRI and XbaI, size-fractionated in a 0.7% agarose gel in 0.5×TBE, transferred to nitrocellulose and incubated with an anti-J antibody. ( A ) The plasmids 25.2L and 25.2S purified from L. tarentolae show specific bands recognized by the anti-J antibody. It is clear that J was not only formed in the inserted 2 kb 25.2L cSSR, but also in the adjacent 0.8 kb intergenic α-tubulin and the 1.7 kb α-tubulin-neo fragments. The small 25.2S insert fragment is not visible on the blot. No J-containing fragments are detected when the plasmids were isolated from E. coli or when the 28.2 plasmid was used. ( B ) J-containing DNA fragments are only detected after growth in the wild-type and not after growth in the JBP2-null L. tarentolae strain. This blot contains the 0.4 kb 25.2S insert band, albeit weak because these small fragments are lost during blotting. The 1.2 kb fragment in the 25.2S plasmid preparation is due to a modification of the BamHI site.

Techniques Used: Transfection, Purification, Amplification, Agarose Gel Electrophoresis, Incubation, Isolation, Plasmid Preparation, Modification

Maps of the plasmids containing convergent strand switch regions and telomeric repeats. The cSSRs and telomeric repeats were cloned into the HindIII and XbaI restriction sites of the 5.5 kb pGEM 7Zf α-neo-α backbone before transfection into wild-type L. tarentolae . The gene coding for neomycin phosphotransferase (yellow), which confers resistance to paromomycin, served as a selection marker after transfection. The intergenic α-tubulin gene fragments flanking the neomycin marker are indicated in light blue. The 25.2S plasmid has a 381 bp insert corresponding to the cSSR with a J-peak in chromosome 25 of L. tarentolae (position 412 392–412 772). The 25.2L plasmid contains a 2.0 kb insert covering the 25.2S region (positions 410 965–412 966). The plasmid 28.2 contains a 2.4 kb fragment. This fragment corresponds to the cSSR in chromosome 28 of L. tarentolae which contains no J in the wild-type (position 580 566–582 966). The telomeric sequence plasmids contain 10 copies of the wild-type telomeric repeat (GGGTTA) or a mutant version (GGGTTT). Plasmids were linearized with ScaI for gel extraction and SMRT sequencing. Plasmids were digested with BamHI, EcoRI and XbaI for DNA immunoblots.
Figure Legend Snippet: Maps of the plasmids containing convergent strand switch regions and telomeric repeats. The cSSRs and telomeric repeats were cloned into the HindIII and XbaI restriction sites of the 5.5 kb pGEM 7Zf α-neo-α backbone before transfection into wild-type L. tarentolae . The gene coding for neomycin phosphotransferase (yellow), which confers resistance to paromomycin, served as a selection marker after transfection. The intergenic α-tubulin gene fragments flanking the neomycin marker are indicated in light blue. The 25.2S plasmid has a 381 bp insert corresponding to the cSSR with a J-peak in chromosome 25 of L. tarentolae (position 412 392–412 772). The 25.2L plasmid contains a 2.0 kb insert covering the 25.2S region (positions 410 965–412 966). The plasmid 28.2 contains a 2.4 kb fragment. This fragment corresponds to the cSSR in chromosome 28 of L. tarentolae which contains no J in the wild-type (position 580 566–582 966). The telomeric sequence plasmids contain 10 copies of the wild-type telomeric repeat (GGGTTA) or a mutant version (GGGTTT). Plasmids were linearized with ScaI for gel extraction and SMRT sequencing. Plasmids were digested with BamHI, EcoRI and XbaI for DNA immunoblots.

Techniques Used: Clone Assay, Transfection, Selection, Marker, Plasmid Preparation, Sequencing, Mutagenesis, Gel Extraction, Western Blot

Related Articles

Clone Assay:

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: .. Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche). .. To amplify the libraries, they were grown on LB agar plates containing Ap (approximately 1.3 × 104 cells per plate) and incubated for 24 h at 37°C.

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: Paragraph title: DNA manipulations and cloning of mfsT and sdtR genes ... PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372.

Amplification:

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: .. Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche). .. The digested plasmid and the PCR product were purified by agarose gel electrophoresis, ligated with T4 DNA ligase (Roche), and introduced into the TOP10 strain by electroporation.

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Synthesized:

Article Title: N-Acetylaspartylglutamate Synthetase II Synthesizes N-Acetylaspartylglutamylglutamate
Article Snippet: .. The plasmid pFLAG-NAAGS-II was linearized with BamHI or XbaI, and antisense and sense digoxigenin-labeled cRNA probes were synthesized with SP6- and T7-RNA polymerase, respectively, and the digoxigenin/dNTP mixture (Roche Applied Science), according to the manufacturer's instructions. .. Paraformaldehyde-fixed and paraffin-embedded brain sections (4 μm) from 10-week-old C57BL/6 mice were hybridized to antisense and sense cRNA probes as described ( ).

Lambda DNA Preparation:

Article Title: Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya
Article Snippet: DNA in agarose plugs was digested by using 25 U each of XbaI and SpeI (Roche Diagnostics GmbH, Mannheim, Germany). .. A lambda DNA digest consisting of a ladder (∼22 fragments) of increasing size from 50 to ∼1,000 kb was included as a DNA size standard.

Article Title: Thin-foil magnetic force system for high-numerical-aperture microscopy
Article Snippet: Linearized lambda DNA (New England Biolabs, Beverly, MA; 48.5 kb) was labeled with digoxigenin-dUTP (Roche Molecular Biochemicals, Mannheim Germany) using the Klenow reaction (New England Biolabs). .. The DNA was then cut with XbaI and triple labeled with biotinylated dUTP (Roche Molecular Biochemicals) and biotinylated dATP and dCTP (Invitrogen Corp., Carlsbad, CA) using the Klenow reaction.

Construct:

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: The pXGlacZ::afaD fusion plasmid was constructed in a similar manner. .. Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche).

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: The metagenomic libraries were constructed with the same DNA used for the 16S rRNA gene libraries. .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche).

End-sequence Profiling:

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Then, plugs were incubated sequentially in the following solutions for the indicated times: 10 mL of lysis solution containing lysozyme at 0.5 mg/mL and DNase-free RNase at 10 mg/mL at 37°C for 24 hours with gentle shaking; 5 mL of sterile, ES buffer containing 1M EDTA (PH = 9–9.3); and Sarcosine 10% at 50°C for 1 hour and 10 mL of ESP solution containing proteinase K at 100 mg/mL and 1% sodium dodecyl sulfate at 50°C for 48 hours ( ). .. Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ).

Incubation:

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Then, plugs were incubated sequentially in the following solutions for the indicated times: 10 mL of lysis solution containing lysozyme at 0.5 mg/mL and DNase-free RNase at 10 mg/mL at 37°C for 24 hours with gentle shaking; 5 mL of sterile, ES buffer containing 1M EDTA (PH = 9–9.3); and Sarcosine 10% at 50°C for 1 hour and 10 mL of ESP solution containing proteinase K at 100 mg/mL and 1% sodium dodecyl sulfate at 50°C for 48 hours ( ). .. Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ).

Article Title: Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Article Snippet: Solidified agarose plugs were transferred to a tube containing 5 ml of lysis buffer (50 mM Tris, 50 mM EDTA, 1% Sarkosyl [pH 8.0]) and 25 μl of proteinase K (20 mg/ml) incubated in a shaking water bath at 54°C for 2 h. Plugs were washed two times with type 1 water for 15 min each time and four times with 0.01 M Tris-EDTA (Gibco BRL, Grand Island, N.Y.) for 15 min each time in a shaking water bath. .. Agarose-embedded DNA plugs were cut (2.0 mm) and restricted with 50 U of XbaI (Roche Molecular Biochemicals, Indianapolis, Ind.) for 2 h at 37°C.

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: The mixture was incubated at 37°C for 5 h with vigorous shaking (200–250 rpm) to ensure maximum aeration. .. PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372.

Expressing:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: Preparation of RNA for affinity purification Plasmid DNA was purified from a cDNA expression library prepared from adult human heart mRNA (Invitrogen). .. Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions.

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: .. Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Transformation Assay:

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. After phenol extraction, the fragments to be cloned were ligated with the vector at 22°C for approximately 1.5 h. The ligated plasmids were transformed in Escherichia coli and plated on LB agar plates containing ampicillin (100 μg/ml).

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: Ligation mixtures were incubated overnight at 16°C using T4 DNA ligase (Roche) and transformed by electroporation into E. coli DH10B cells (Invitrogen) using Micropulser (Bio-Rad) according to the manufacturer's instructions. .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche).

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Hybridization:

Article Title: The plasma membrane permease PfNT1 is essential for purine salvage in the human malaria parasite Plasmodium falciparum
Article Snippet: Paragraph title: Southern Blot Hybridization of the Disrupted PfNT1 Locus. ... Ten micrograms of genomic DNA from WT and pfnt1 Δ parasites was digested with XbaI and HindIII, separated on a 0.8% agarose gel, and transferred to positively charged nylon membrane (Roche Molecular Biochemicals).

Electroporation:

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche). .. The digested plasmid and the PCR product were purified by agarose gel electrophoresis, ligated with T4 DNA ligase (Roche), and introduced into the TOP10 strain by electroporation.

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: Ligation mixtures were incubated overnight at 16°C using T4 DNA ligase (Roche) and transformed by electroporation into E. coli DH10B cells (Invitrogen) using Micropulser (Bio-Rad) according to the manufacturer's instructions. .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche).

Southern Blot:

Article Title: The plasma membrane permease PfNT1 is essential for purine salvage in the human malaria parasite Plasmodium falciparum
Article Snippet: Paragraph title: Southern Blot Hybridization of the Disrupted PfNT1 Locus. ... Ten micrograms of genomic DNA from WT and pfnt1 Δ parasites was digested with XbaI and HindIII, separated on a 0.8% agarose gel, and transferred to positively charged nylon membrane (Roche Molecular Biochemicals).

Ligation:

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: Ligation mixtures were incubated overnight at 16°C using T4 DNA ligase (Roche) and transformed by electroporation into E. coli DH10B cells (Invitrogen) using Micropulser (Bio-Rad) according to the manufacturer's instructions. .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche).

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: .. PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Polymerase Chain Reaction:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: .. Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions. .. In initial experiments, 0.5 µg of NotI- and XbaI-digested DNAs were used as templates in separate in vitro transcription reactions with the RiboMAX kit (Promega).

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: .. Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche). .. The digested plasmid and the PCR product were purified by agarose gel electrophoresis, ligated with T4 DNA ligase (Roche), and introduced into the TOP10 strain by electroporation.

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: .. PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Affinity Purification:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: Paragraph title: Preparation of RNA for affinity purification ... Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions.

Pulsed-Field Gel:

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Paragraph title: Pulsed-field gel electrophoresis (PFGE). ... Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ).

Article Title: Characterization of Foodborne Outbreaks of Salmonella enterica Serovar Enteritidis with Whole-Genome Sequencing Single Nucleotide Polymorphism-Based Analysis for Surveillance and Outbreak Detection
Article Snippet: .. Pulsed-field gel electrophoresis was performed at MDH with XbaI (Roche) using standardized methods for PulseNet laboratories ( ). ..

Nucleic Acid Electrophoresis:

Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution
Article Snippet: .. Pulse Field Gel Electrophoresis (PFGE) Cleavage of the agarose-embedded DNA was achieved with 0.2 U/μl XbaI (Roche) according to instructions of the manufacturer. .. XbaI-digested genomic DNA was analyzed in 1% agarose gel in 0.5× Tris-boric acid-EDTA TBE buffer at 14°C by using CHEF MAPPER (BioRad).

Isolation:

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: .. Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Article Title: Thin-foil magnetic force system for high-numerical-aperture microscopy
Article Snippet: Paragraph title: A. Methods: Chromatin isolation and functionalization ... The DNA was then cut with XbaI and triple labeled with biotinylated dUTP (Roche Molecular Biochemicals) and biotinylated dATP and dCTP (Invitrogen Corp., Carlsbad, CA) using the Klenow reaction.

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche). .. To amplify the libraries, they were grown on LB agar plates containing Ap (approximately 1.3 × 104 cells per plate) and incubated for 24 h at 37°C.

Labeling:

Article Title: Thin-foil magnetic force system for high-numerical-aperture microscopy
Article Snippet: .. The DNA was then cut with XbaI and triple labeled with biotinylated dUTP (Roche Molecular Biochemicals) and biotinylated dATP and dCTP (Invitrogen Corp., Carlsbad, CA) using the Klenow reaction. .. Chromatin was formed from the DNA by incorporation of yeast nucleosomes using high-salt extraction of S. cerevisiae nuclear extracts, followed by a gradually decreased salt concentration to assemble nucleosomes onto the DNA.

Purification:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: .. Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions. .. In initial experiments, 0.5 µg of NotI- and XbaI-digested DNAs were used as templates in separate in vitro transcription reactions with the RiboMAX kit (Promega).

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche). .. The digested plasmid and the PCR product were purified by agarose gel electrophoresis, ligated with T4 DNA ligase (Roche), and introduced into the TOP10 strain by electroporation.

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: .. Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: .. PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Sequencing:

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: The pXGafaD::gfp fusion plasmid was constructed by amplifying the sequence of the intergenic region including parts of the 3′ end of the afaC gene and the 5′ end of the afaD gene with the afaC.NsiI and afaD.NheI primers. .. Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche).

Affinity Chromatography:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions. .. Reactions were supplemented with [α-32 P] UTP (500 Ci/mmol) to permit trace labelling of RNA for quantification and estimations of recoveries during affinity chromatography.

Lysis:

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Then, plugs were incubated sequentially in the following solutions for the indicated times: 10 mL of lysis solution containing lysozyme at 0.5 mg/mL and DNase-free RNase at 10 mg/mL at 37°C for 24 hours with gentle shaking; 5 mL of sterile, ES buffer containing 1M EDTA (PH = 9–9.3); and Sarcosine 10% at 50°C for 1 hour and 10 mL of ESP solution containing proteinase K at 100 mg/mL and 1% sodium dodecyl sulfate at 50°C for 48 hours ( ). .. Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ).

Article Title: Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Article Snippet: Solidified agarose plugs were transferred to a tube containing 5 ml of lysis buffer (50 mM Tris, 50 mM EDTA, 1% Sarkosyl [pH 8.0]) and 25 μl of proteinase K (20 mg/ml) incubated in a shaking water bath at 54°C for 2 h. Plugs were washed two times with type 1 water for 15 min each time and four times with 0.01 M Tris-EDTA (Gibco BRL, Grand Island, N.Y.) for 15 min each time in a shaking water bath. .. Agarose-embedded DNA plugs were cut (2.0 mm) and restricted with 50 U of XbaI (Roche Molecular Biochemicals, Indianapolis, Ind.) for 2 h at 37°C.

Mouse Assay:

Article Title: N-Acetylaspartylglutamate Synthetase II Synthesizes N-Acetylaspartylglutamylglutamate
Article Snippet: The plasmid pFLAG-NAAGS-II was linearized with BamHI or XbaI, and antisense and sense digoxigenin-labeled cRNA probes were synthesized with SP6- and T7-RNA polymerase, respectively, and the digoxigenin/dNTP mixture (Roche Applied Science), according to the manufacturer's instructions. .. Paraformaldehyde-fixed and paraffin-embedded brain sections (4 μm) from 10-week-old C57BL/6 mice were hybridized to antisense and sense cRNA probes as described ( ).

In Situ Hybridization:

Article Title: N-Acetylaspartylglutamate Synthetase II Synthesizes N-Acetylaspartylglutamylglutamate
Article Snippet: Paragraph title: In Situ Hybridization ... The plasmid pFLAG-NAAGS-II was linearized with BamHI or XbaI, and antisense and sense digoxigenin-labeled cRNA probes were synthesized with SP6- and T7-RNA polymerase, respectively, and the digoxigenin/dNTP mixture (Roche Applied Science), according to the manufacturer's instructions.

Plasmid Preparation:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: The vector backbone is pcDNA3, which permits in vitro synthesis of RNA from linearized library DNA. .. Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions.

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: The pXGlacZ::afaD fusion plasmid was constructed in a similar manner. .. Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche).

Article Title: Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing
Article Snippet: .. Cloning of L. tarentolae DNA segments into plasmids and plasmid isolation The Leishmania expression vector pGEM 7Zf α-neo-α ( ) was digested with HindIII and XbaI, gel extracted, phenol purified, and dephosphorylated with calf intestinal alkaline phosphatase (1 U/μl, Roche). .. The fragments to be inserted were obtained by polymerase chain reaction (PCR) amplification using L. tarentolae genomic DNA as a template, gel extracted and digested with HindIII and XbaI.

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: .. PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Article Title: N-Acetylaspartylglutamate Synthetase II Synthesizes N-Acetylaspartylglutamylglutamate
Article Snippet: .. The plasmid pFLAG-NAAGS-II was linearized with BamHI or XbaI, and antisense and sense digoxigenin-labeled cRNA probes were synthesized with SP6- and T7-RNA polymerase, respectively, and the digoxigenin/dNTP mixture (Roche Applied Science), according to the manufacturer's instructions. .. Paraformaldehyde-fixed and paraffin-embedded brain sections (4 μm) from 10-week-old C57BL/6 mice were hybridized to antisense and sense cRNA probes as described ( ).

Software:

Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution
Article Snippet: Pulse Field Gel Electrophoresis (PFGE) Cleavage of the agarose-embedded DNA was achieved with 0.2 U/μl XbaI (Roche) according to instructions of the manufacturer. .. The gel was stained with ethidium bromide (1 μg/mL), observed on the Gel Doc 2000 system (BioRad), and analyzed with the BioNumerics fingerprinting software (Applied Maths, St-Martens-Latem, Belgium).

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ). .. The banding patterns were clustered using weighted paired group (UPGMA) method by Gelcompar II software Version 4.0.

Article Title: Clonal Expansion and Microevolution of Quinolone-Resistant Salmonella enterica Serotype Typhi in Vietnam from 1996 to 2004 ▿
Article Snippet: PFGE of XbaI (Roche)- and SpeI (Roche)-digested genomic DNA was carried out with all 91 Nalr serotype Typhi isolates in this study, as described previously ( ). .. BioNumerics software (version 4.0) was used for image normalization and the construction of similarity matrices.

Selection:

Article Title: Combined metagenomic and phenomic approaches identify a novel salt tolerance gene from the human gut microbiome
Article Snippet: PCR products were purified with a Qiagen PCR purification kit and digested with XbaI and PstI (Roche Applied Science) for mfsT and with SalI and XbaI for sdtR , followed by ligation using the FastLink DNA ligase kit (Epicentre Biotechnologies) to similarly digested plasmid pCI372. .. Electrocompetent E. coli MKH13 and E. coli EPI300 were transformed with the ligation mixture and plated on LB agar plates containing 20 μg/ml Cm for selection.

Agarose Gel Electrophoresis:

Article Title: The AfaR small RNA controls expression of the AfaD-VIII invasin in pathogenic Escherichia coli strains
Article Snippet: Briefly, pXG30 was digested with NsiI (Fermentas) and XbaI (Roche), and the 3′ end of the afaD gene was amplified by PCR with the afaD.NsiI and afaD.XbaI oligonucleotides, treated with exonuclease I (Fermentas) and digested with XbaI (Roche). .. The digested plasmid and the PCR product were purified by agarose gel electrophoresis, ligated with T4 DNA ligase (Roche), and introduced into the TOP10 strain by electroporation.

Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution
Article Snippet: Pulse Field Gel Electrophoresis (PFGE) Cleavage of the agarose-embedded DNA was achieved with 0.2 U/μl XbaI (Roche) according to instructions of the manufacturer. .. XbaI-digested genomic DNA was analyzed in 1% agarose gel in 0.5× Tris-boric acid-EDTA TBE buffer at 14°C by using CHEF MAPPER (BioRad).

Article Title: Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya
Article Snippet: DNA in agarose plugs was digested by using 25 U each of XbaI and SpeI (Roche Diagnostics GmbH, Mannheim, Germany). .. PFGE of agarose plug inserts was then performed on a CHEF-DR III system (Bio-Rad Laboratories, Hercules, Calif.) on a horizontal 1% agarose gel for 20 h at 120 V, with a pulse time of 5 to 40 s at 14°C.

Article Title: Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Article Snippet: Agarose-embedded DNA plugs were cut (2.0 mm) and restricted with 50 U of XbaI (Roche Molecular Biochemicals, Indianapolis, Ind.) for 2 h at 37°C. .. The digested DNA plugs were loaded on the comb, and a 1% SeaKem agarose gel was prepared using 0.5× Tris-buffered EDTA buffer (Sigma, St. Louis, Mo.) and electrophoresed using a CHEF Mapper (Bio-Rad) with switch times of 2.12 to 63.8 s at 6 V/cm for 18 h at 14°C.

Article Title: Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿Novel Nickel Resistance Genes from the Rhizosphere Metagenome of Plants Adapted to Acid Mine Drainage ▿ †
Article Snippet: Metagenomic DNA was partially digested using Sau3AI, and fragments from 1 kb to 8 kb were collected directly from a 0.8% low-melting-point agarose gel with the QIAquick extraction gel (QIAGEN) for ligation into the dephosphorylated and BamHI-digested pSKII+ vector. .. To determine the average insert size for each library, the plasmids of 184 random clones were isolated and digested using either XbaI or EcoRI and XbaI restriction enzymes (Roche).

Article Title: The plasma membrane permease PfNT1 is essential for purine salvage in the human malaria parasite Plasmodium falciparum
Article Snippet: .. Ten micrograms of genomic DNA from WT and pfnt1 Δ parasites was digested with XbaI and HindIII, separated on a 0.8% agarose gel, and transferred to positively charged nylon membrane (Roche Molecular Biochemicals). ..

In Vitro:

Article Title: Combinatorial mRNA binding by AUF1 and Argonaute 2 controls decay of selected target mRNAs
Article Snippet: The vector backbone is pcDNA3, which permits in vitro synthesis of RNA from linearized library DNA. .. Twenty micrograms of library DNA was linearized in separate reactions with either NotI or XbaI and then purified with the High Pure PCR Product Purification Kit (Roche) per the manufacturer’s instructions.

Concentration Assay:

Article Title: Thin-foil magnetic force system for high-numerical-aperture microscopy
Article Snippet: The DNA was then cut with XbaI and triple labeled with biotinylated dUTP (Roche Molecular Biochemicals) and biotinylated dATP and dCTP (Invitrogen Corp., Carlsbad, CA) using the Klenow reaction. .. Chromatin was formed from the DNA by incorporation of yeast nucleosomes using high-salt extraction of S. cerevisiae nuclear extracts, followed by a gradually decreased salt concentration to assemble nucleosomes onto the DNA.

Article Title: Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Article Snippet: Proteinase K was added to a final concentration of 1 mg/ml, and 500 μl of cell suspensions was added to 500 μl of 1% SeaKem agarose (FMC, Rockland, Maine). .. Agarose-embedded DNA plugs were cut (2.0 mm) and restricted with 50 U of XbaI (Roche Molecular Biochemicals, Indianapolis, Ind.) for 2 h at 37°C.

Marker:

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Salmonella choleraesuis strain H9812 was used as a molecular size marker. .. Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ).

Article Title: Novel Plasmid-Encoded Ceftazidime-Hydrolyzing CTX-M-53 Extended-Spectrum ?-Lactamase from Salmonella enterica Serotypes Westhampton and Senftenberg ▿
Article Snippet: The genetic diversity of the Salmonella isolates was assessed by the PFGE of genomic DNA digested with XbaI (Roche, Mannheim, Germany), as described previously ( ). .. The running conditions and the molecular size marker were as described in the standardized PulseNet protocol ( ).

Article Title: Clonal Expansion and Microevolution of Quinolone-Resistant Salmonella enterica Serotype Typhi in Vietnam from 1996 to 2004 ▿
Article Snippet: PFGE of XbaI (Roche)- and SpeI (Roche)-digested genomic DNA was carried out with all 91 Nalr serotype Typhi isolates in this study, as described previously ( ). .. The running conditions and the molecular size marker (XbaI-digested DNA from S. enterica serotype Braenderup H9812) were the same as those described in the standardized PulseNet protocol ( ).

Staining:

Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution
Article Snippet: Pulse Field Gel Electrophoresis (PFGE) Cleavage of the agarose-embedded DNA was achieved with 0.2 U/μl XbaI (Roche) according to instructions of the manufacturer. .. The gel was stained with ethidium bromide (1 μg/mL), observed on the Gel Doc 2000 system (BioRad), and analyzed with the BioNumerics fingerprinting software (Applied Maths, St-Martens-Latem, Belgium).

Article Title: Prevalence of biofilm formation and vancomycin-resistant genes among Enterococcus faecium isolated from clinical and environmental specimens in Lorestan hospitals
Article Snippet: Agarose plugs containing genomic DNA were digested with XbaI (Roche, Manheim, Germany) according to the manufacturer’s recommendations ( ). .. After 24 hours, gels were stained with ethidium bromide and visualized under ultraviolet light.

Article Title: Characterization of Multidrug-Resistant Typhoid Outbreaks in Kenya
Article Snippet: DNA in agarose plugs was digested by using 25 U each of XbaI and SpeI (Roche Diagnostics GmbH, Mannheim, Germany). .. The gel was stained with ethidium bromide and photographed on a UV transilluminator (UVP, Inc., San Gabriel, Calif.).

Article Title: Analysis of Salmonella enterica Serotype Typhi Pulsed-Field Gel Electrophoresis Patterns Associated with International Travel
Article Snippet: Agarose-embedded DNA plugs were cut (2.0 mm) and restricted with 50 U of XbaI (Roche Molecular Biochemicals, Indianapolis, Ind.) for 2 h at 37°C. .. Gels were stained using ethidium bromide (1 mg/ml) and destained with two deionized water washes.

Article Title: N-Acetylaspartylglutamate Synthetase II Synthesizes N-Acetylaspartylglutamylglutamate
Article Snippet: The plasmid pFLAG-NAAGS-II was linearized with BamHI or XbaI, and antisense and sense digoxigenin-labeled cRNA probes were synthesized with SP6- and T7-RNA polymerase, respectively, and the digoxigenin/dNTP mixture (Roche Applied Science), according to the manufacturer's instructions. .. Sections were stained using anti-digoxigenin Ig-alkaline phosphatase conjugate and nitro blue tetrazolium chloride and 5-bromo-4-chloro-3-indolyl phosphate as substrate.

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  • xbai  (Roche)
    92
    Roche xbai
    Agarose gel of HindIII and <t>XbaI</t> -digested pcDNA3.1/ <t>Mtb32C/Mtb32N</t> . Lane 1: HindIII and Xba Idigested digested vector; the 1045 bp fragment consist of mtb32C and mtb32N ; lane 2: DNA size marker (1000 bp).
    Xbai, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 11 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xbai/product/Roche
    Average 92 stars, based on 11 article reviews
    Price from $9.99 to $1999.99
    xbai - by Bioz Stars, 2020-02
    92/100 stars
      Buy from Supplier

    92
    Roche xbai restriction enzyme
    a The differences in plasmid number from a selection of bacteria isolates. Several isolates contained up to eight plasmids b S1-PFGE and Southern blotting of plasmids carrying <t>NDM-1</t> from clinical isolates. Pulsed-field gel of S1-treated plasmid DNA of selected Enterobacteriaceae from clinical isolates stained with ethidium bromide. The molecular weight marker is S. braenderup H9812 cut with <t>XbaI</t> ( A ). Autodiagram of gel A showing plasmids carrying NDM-1 ( B )
    Xbai Restriction Enzyme, supplied by Roche, used in various techniques. Bioz Stars score: 92/100, based on 6 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/xbai restriction enzyme/product/Roche
    Average 92 stars, based on 6 article reviews
    Price from $9.99 to $1999.99
    xbai restriction enzyme - by Bioz Stars, 2020-02
    92/100 stars
      Buy from Supplier

    Image Search Results


    Agarose gel of HindIII and XbaI -digested pcDNA3.1/ Mtb32C/Mtb32N . Lane 1: HindIII and Xba Idigested digested vector; the 1045 bp fragment consist of mtb32C and mtb32N ; lane 2: DNA size marker (1000 bp).

    Journal: Reports of Biochemistry & Molecular Biology

    Article Title: Construction of Mtb72F Plasmid as a DNA Vaccine Candidate for Mycobacterium tuberculosis

    doi:

    Figure Lengend Snippet: Agarose gel of HindIII and XbaI -digested pcDNA3.1/ Mtb32C/Mtb32N . Lane 1: HindIII and Xba Idigested digested vector; the 1045 bp fragment consist of mtb32C and mtb32N ; lane 2: DNA size marker (1000 bp).

    Article Snippet: The purified mtb32N PCR product and pcDNA3.1/ Mtb32C were digested with XbaI and EcoRI (Roche Company).

    Techniques: Agarose Gel Electrophoresis, Plasmid Preparation, Marker

    Pulsed field gel electrophoresis of XbaI-digested DNA from the 59 ExPEC strains included in the study . Strain designation, phylogenetic group, ST assignation, clinical and geographical origin of isolation, PFGE cluster ( > 85% similarity), and PCR result for virulence genes that exhibited significant differences within the pathogenic groups are shown at right. This unweighted pair-group method with arithmetic mean dendrogram was generated in BioNumerics software (Applied Maths, St-Martens-Latem, Belgium) by using Dice coefficient with a 1.0% band position tolerance. The scale above the dendrogram indicates percent similarity. AS: abdominal sepsis; UTI: urinary tract infection; CI: cystitis; IS: intestinal sepsis; NBM: Newborn Meningitis; US: urosepsis; P?: posible pyelonephritis; C: colibacillosis; RS: respiratory sepsis; AP: acute pyelonephritis; AB: asymptomatic bacteriuria.

    Journal: BMC Microbiology

    Article Title: Extraintestinal pathogenic Escherichia coli O1:K1:H7/NM from human and avian origin: detection of clonal groups B2 ST95 and D ST59 with different host distribution

    doi: 10.1186/1471-2180-9-132

    Figure Lengend Snippet: Pulsed field gel electrophoresis of XbaI-digested DNA from the 59 ExPEC strains included in the study . Strain designation, phylogenetic group, ST assignation, clinical and geographical origin of isolation, PFGE cluster ( > 85% similarity), and PCR result for virulence genes that exhibited significant differences within the pathogenic groups are shown at right. This unweighted pair-group method with arithmetic mean dendrogram was generated in BioNumerics software (Applied Maths, St-Martens-Latem, Belgium) by using Dice coefficient with a 1.0% band position tolerance. The scale above the dendrogram indicates percent similarity. AS: abdominal sepsis; UTI: urinary tract infection; CI: cystitis; IS: intestinal sepsis; NBM: Newborn Meningitis; US: urosepsis; P?: posible pyelonephritis; C: colibacillosis; RS: respiratory sepsis; AP: acute pyelonephritis; AB: asymptomatic bacteriuria.

    Article Snippet: Pulse Field Gel Electrophoresis (PFGE) Cleavage of the agarose-embedded DNA was achieved with 0.2 U/μl XbaI (Roche) according to instructions of the manufacturer.

    Techniques: Pulsed-Field Gel, Electrophoresis, Isolation, Polymerase Chain Reaction, Generated, Software, Infection

    a The differences in plasmid number from a selection of bacteria isolates. Several isolates contained up to eight plasmids b S1-PFGE and Southern blotting of plasmids carrying NDM-1 from clinical isolates. Pulsed-field gel of S1-treated plasmid DNA of selected Enterobacteriaceae from clinical isolates stained with ethidium bromide. The molecular weight marker is S. braenderup H9812 cut with XbaI ( A ). Autodiagram of gel A showing plasmids carrying NDM-1 ( B )

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Common isolation of New Delhi metallo-beta-lactamase 1-producing Enterobacteriaceae in a large surgical hospital in Vietnam

    doi: 10.1007/s10096-015-2345-6

    Figure Lengend Snippet: a The differences in plasmid number from a selection of bacteria isolates. Several isolates contained up to eight plasmids b S1-PFGE and Southern blotting of plasmids carrying NDM-1 from clinical isolates. Pulsed-field gel of S1-treated plasmid DNA of selected Enterobacteriaceae from clinical isolates stained with ethidium bromide. The molecular weight marker is S. braenderup H9812 cut with XbaI ( A ). Autodiagram of gel A showing plasmids carrying NDM-1 ( B )

    Article Snippet: NDM-1-positive bacterial isolates were genotyped by pulsed-field gel electrophoresis (PFGE), using XbaI restriction enzyme (Roche Diagnostic, Mannheim, Germany) to digest the bacterial genomes in agarose blocks.

    Techniques: Plasmid Preparation, Selection, Southern Blot, Pulsed-Field Gel, Staining, Molecular Weight, Marker

    PFGE profiles of representative S. enterica subsp. enterica strains after digestion with XbaI. As a molecular weight standard (M), S. enterica serovar Braenderup reference strain H9812 was used (lanes 1, 15, and 20). Lanes 2 to 14 represent the 13 different

    Journal:

    Article Title: Poultry-Associated Salmonella enterica subsp. enterica Serovar 4,12:d:- Reveals High Clonality and a Distinct Pathogenicity Gene Repertoire ▿ Serovar 4,12:d:- Reveals High Clonality and a Distinct Pathogenicity Gene Repertoire ▿ †

    doi: 10.1128/AEM.02187-08

    Figure Lengend Snippet: PFGE profiles of representative S. enterica subsp. enterica strains after digestion with XbaI. As a molecular weight standard (M), S. enterica serovar Braenderup reference strain H9812 was used (lanes 1, 15, and 20). Lanes 2 to 14 represent the 13 different

    Article Snippet: PFGE using the restriction enzyme XbaI (Roche Diagnostics, Mannheim, Germany) was performed according to the standardized PulseNet Salmonella protocol ( ).

    Techniques: Molecular Weight