escherichia coli dh5α  (Thermo Fisher)


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    Structured Review

    Thermo Fisher escherichia coli dh5α
    ( a ) Remote effect of emissions of the PGPB Azospirillum brasilense Cd and Bacillus pumilus ES4 and the control bacterium <t>Escherichia</t> coli <t>DH5α</t> on growth of the microalgae Chlorella sorokiniana , ( b ) growth in the presence of the CO 2 absorbant LiOH•H 2 O, 0.3 g and ( c ) 0.5 g. ( d ) Remote effect of emissions on the volume of C. sorokiniana cells, ( e ) Growth of the PGPB in the culture medium, and ( f ), Increase in pH in the medium. The control bacterium ( E. coli ) was used only in experiments measuring the potential effect of produced CO 2 on microalgae growth and metabolite production. Values on curves denoted by different capital letters differ significantly using one-way ANOVA combined with LSD post-hoc analysis at P
    Escherichia Coli Dh5α, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 100 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus"

    Article Title: Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus

    Journal: Scientific Reports

    doi: 10.1038/srep41310

    ( a ) Remote effect of emissions of the PGPB Azospirillum brasilense Cd and Bacillus pumilus ES4 and the control bacterium Escherichia coli DH5α on growth of the microalgae Chlorella sorokiniana , ( b ) growth in the presence of the CO 2 absorbant LiOH•H 2 O, 0.3 g and ( c ) 0.5 g. ( d ) Remote effect of emissions on the volume of C. sorokiniana cells, ( e ) Growth of the PGPB in the culture medium, and ( f ), Increase in pH in the medium. The control bacterium ( E. coli ) was used only in experiments measuring the potential effect of produced CO 2 on microalgae growth and metabolite production. Values on curves denoted by different capital letters differ significantly using one-way ANOVA combined with LSD post-hoc analysis at P
    Figure Legend Snippet: ( a ) Remote effect of emissions of the PGPB Azospirillum brasilense Cd and Bacillus pumilus ES4 and the control bacterium Escherichia coli DH5α on growth of the microalgae Chlorella sorokiniana , ( b ) growth in the presence of the CO 2 absorbant LiOH•H 2 O, 0.3 g and ( c ) 0.5 g. ( d ) Remote effect of emissions on the volume of C. sorokiniana cells, ( e ) Growth of the PGPB in the culture medium, and ( f ), Increase in pH in the medium. The control bacterium ( E. coli ) was used only in experiments measuring the potential effect of produced CO 2 on microalgae growth and metabolite production. Values on curves denoted by different capital letters differ significantly using one-way ANOVA combined with LSD post-hoc analysis at P

    Techniques Used: Produced

    2) Product Images from "Non-contact positions impose site selectivity on Cre recombinase"

    Article Title: Non-contact positions impose site selectivity on Cre recombinase

    Journal: Nucleic Acids Research

    doi:

    Modulation of Cre-E262G recombination at mutant lox sites. Shown are recombination frequencies for wt and the indicated mutant Cre recombinases at loxP and at mutant lox sites that differ from loxP at positions 11 and 12. Escherichia coli DH5α carrying a resident pBAD construct expressing the indicated cre mutant was transformed with the indicated lox 2 neo plasmids and cre expression induced for 1 h before plating non-selectively to yield about 200 colonies/experiment. Sensitivity to kanamycin, signifying excisive recombination, was determined by replica plating. The frequencies shown are calculated from at least two independent experiments.
    Figure Legend Snippet: Modulation of Cre-E262G recombination at mutant lox sites. Shown are recombination frequencies for wt and the indicated mutant Cre recombinases at loxP and at mutant lox sites that differ from loxP at positions 11 and 12. Escherichia coli DH5α carrying a resident pBAD construct expressing the indicated cre mutant was transformed with the indicated lox 2 neo plasmids and cre expression induced for 1 h before plating non-selectively to yield about 200 colonies/experiment. Sensitivity to kanamycin, signifying excisive recombination, was determined by replica plating. The frequencies shown are calculated from at least two independent experiments.

    Techniques Used: Mutagenesis, Construct, Expressing, Transformation Assay

    Related Articles

    Clone Assay:

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: Therefore, genes, tags, and any regulatory elements of interest from PCR amplification can be directly cloned into GECs after digestion. .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ].

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Other fragments were cloned into the Kpn I/Hin dIII sites of pQE-80L vector. .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Centrifugation:

    Article Title: Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus
    Article Snippet: In experiments that measured the potential effect of CO2 , Escherichia coli DH5α (Invitrogen, Carlsbad, CA) served as the negative control for microalgal growth and promoting metabolites because it does not have any plant growth-promoting effects; it also served as a positive control in the CO2 experiment because it produces CO2 , as any E. coli . .. Bacteria were then harvested by centrifugation at 3720 × g for 7 min, rinsed twice in 0.85% saline solution, and subsequently transferred to minimal mineral Brunner’s medium (DSMZ medium 457) composed of (in g L−1 ): Na2 HPO4 (2.44), KH2 PO4 (1.52), (NH4 )2 SO4 (0.50), MgSO4 •7H2 O (0.20), CaCl2 •2H2 O (0.05), EDTA (0.50), FeSO4 •7H2 O (0.20), and (in μg·L−1 ): ZnSO4 •7H2 O (0.10), MnCl2 •4H2 O (0.03), H3 BO3 (0.30), CoCl2 •6H2 O (0.20), CuCl2 •2H2 O (0.01), NiCl2 •6H2 O (0.02), Na2 MoO4 •2H2 O (0.03).

    Amplification:

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: Therefore, genes, tags, and any regulatory elements of interest from PCR amplification can be directly cloned into GECs after digestion. .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ].

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: The DNA sequences encoding mHMGB1 -186-200, mHMGB1 -196-210, mHMGB1 -196-205, mHMGB1 -198-207, mHMGB1 -201-210 and mHMGB1 -201-205 (rHMGB1 lacking amino acid residues 186-200, 196-210, 196-205, 198-207, 201-210 and 201-205 respectively) were amplified by one-step opposite-direction PCR using MutanBEST Kit (TaKaRa) according to the manufacturer's instructions (taking pUC19-rHMGB1 as template). .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Positive Control:

    Article Title: Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae
    Article Snippet: .. E. coli Dh5α (Life Technologies) was used as a positive control. ..

    Article Title: Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus
    Article Snippet: .. In experiments that measured the potential effect of CO2 , Escherichia coli DH5α (Invitrogen, Carlsbad, CA) served as the negative control for microalgal growth and promoting metabolites because it does not have any plant growth-promoting effects; it also served as a positive control in the CO2 experiment because it produces CO2 , as any E. coli . .. For initial culturing of the microalga, 10 mL axenic C. sorokiniana culture, cultivated in sterile mineral medium (C30), was added to a sterile flask containing 90 mL sterile C30 medium, composed of (in g·L−1 ): KNO3 (25), MgSO4 •7H2 O (10), KH2 PO4 (4), K2 HPO4 (1), FeSO4 •7H2 O (1), and (in μg·L−1 ): H3 BO3 (2.86), MnCl2 •4H2 O (1.81), ZnSO4 •7H2 O (0.11), CuSO4 •5H2 O (0.09), NaMoO4 (0.021), pH 5.25 and incubated at 27 ± 2 °C on a rotary shaker at 120 rpm under 60 μmol photon·m−2 ·s−1 continuous light intensity for 6 days .

    Construct:

    Article Title: Non-contact positions impose site selectivity on Cre recombinase
    Article Snippet: .. Plasmids were constructed and propagated using Escherichia coli DH5α (Invitrogen). ..

    Article Title: Bacillus thuringiensis subsp. kurstaki HD1 as a factory to synthesize alkali-labile ChiA74?sp chitinase inclusions, Cry crystals and spores for applied use
    Article Snippet: .. All constructs (Figure A) were propagated in E. coli DH5α [supE44, DlacU169 (F80lacZDM15 ) hsdR17 recA1 end A1 gyrA96 thi-1 relA1 ] (Invitrogen, Carlsbad CA, USA) and then used for transforming the acrystalliferous strain of B. thuringiensis subsp. israelensis 4Q7, (hereafter 4Q7), and B. thuringiensis subsp. kurstaki HD1 (hereafter HD1) (Bacillus Genetic Stock Center, Columbus, OH). .. Plasmid pGLO is a vector that harbors the green fluorescent protein (gfp ) gene under the control arabinose (araC ) promoter and contains an ampicillin (bla ) resistance gene marker (Bio-Rad, Hercules CA, USA).

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: We constructed a set of alternative GECs for labeling a desired protein with different tags at the N- or C-terminus (Table ). .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ].

    Article Title: Improving Acetate Tolerance of Escherichia coli by Rewiring Its Global Regulator cAMP Receptor Protein (CRP)
    Article Snippet: .. Materials The host strain E. coli DH5α ∆crp was constructed by knocking out crp from E. coli DH5α (Invitrogen, San Diego, US) according to previously established protocol [ ]. .. Overnight culture was prepared in Luria-Bertani (LB) medium containing 1% tryptone (Oxoid, Hampshire, UK), 0.5% yeast extract (Merck, Damstadt, Germany), and 1% sodium chloride (Merck, Damstadt, Germany).

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: After being sequenced, the fragments encoding rHMGB1 A box and B box were separately ligated into the Kpn I/Hin dIII cloning sites in the pQE-80L/DHFR prokaryotic expression vector (pQE-80L/DHFR vector constructed by us from pQE-80L). .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Real-time Polymerase Chain Reaction:

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: .. Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Quantifications were carried out from 25 ng of community DNA using a “TaqMan® Universal PCR Master Mix, NoAmpErase® UNG” (Applied Biosystems) as recommended by the manufacturer, with 800 nM of each primer, and 300 nM of TaqMan probe, in a 25 μL reaction volume.

    Incubation:

    Article Title: Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae
    Article Snippet: Plates were centrifuged at 500 × g for 10 min then incubated at 37°C with 5% CO2 for 2 h. After incubation, neutrophils were lysed with water, the content of each well serially diluted in BHI and plated on sBHI-agar for overnight incubation and enumeration of CFU. .. E. coli Dh5α (Life Technologies) was used as a positive control.

    Article Title: Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus
    Article Snippet: In experiments that measured the potential effect of CO2 , Escherichia coli DH5α (Invitrogen, Carlsbad, CA) served as the negative control for microalgal growth and promoting metabolites because it does not have any plant growth-promoting effects; it also served as a positive control in the CO2 experiment because it produces CO2 , as any E. coli . .. For initial culturing of the microalga, 10 mL axenic C. sorokiniana culture, cultivated in sterile mineral medium (C30), was added to a sterile flask containing 90 mL sterile C30 medium, composed of (in g·L−1 ): KNO3 (25), MgSO4 •7H2 O (10), KH2 PO4 (4), K2 HPO4 (1), FeSO4 •7H2 O (1), and (in μg·L−1 ): H3 BO3 (2.86), MnCl2 •4H2 O (1.81), ZnSO4 •7H2 O (0.11), CuSO4 •5H2 O (0.09), NaMoO4 (0.021), pH 5.25 and incubated at 27 ± 2 °C on a rotary shaker at 120 rpm under 60 μmol photon·m−2 ·s−1 continuous light intensity for 6 days .

    Article Title: Characterization of a minimal pKW2124 replicon from Weissella cibaria KLC140 and its application for the construction of the Weissella expression vector pKUCm1
    Article Snippet: .. All Weissella species were incubated anaerobically at 37°C in de Man-Rogosa-Sharpe (MRS) medium (Difco, Detroit, MI, USA) and E. coli DH5α (Invitrogen, Carlsbad, CA, USA) was grown with shaking in Luria-Bertani (LB) medium (Difco) at 37°C. .. Ampicillin sulfate (Sigma, St. Louis, MO, USA) was added to the E. coli growth medium for selection at 50 μg/ml.

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce). .. After blocked with 5% non-fat milk in phosphate buffered saline containing 0.1% Tween 20 (PBS-T), the membranes were incubated with mouse anti-His monoclonal antibody (Qiagen).

    Luciferase:

    Article Title: Murine immunization with CS21 pili or LngA major subunit of enterotoxigenic Escherichia coli (ETEC) elicits systemic and mucosal immune responses and inhibits ETEC gut colonization
    Article Snippet: E. coli DH5α (Life Technologies, Grand Island, NY), and CS21+ or CS8+ ETEC strains were cultured on Luria broth (LB), Terrific broth (TB) or TB agar plates at 37 °C overnight ( ). .. CS21+ ETEC E0934A strain was electroporated with plasmid pCM17 containing luciferase genes ( , ).

    Cell Culture:

    Article Title: What an Escherichia coli Mutant Can Teach Us About the Antibacterial Effect of Chlorophyllin
    Article Snippet: .. Bacteria Strains and Cell Culture Experiments were performed with E. coli DH5α (Invitrogen, Carlsbad, CA, USA), E. coli NR698 (MC4100 lptD4213 ; kindly provided by M. Grabowicz, Princeton University, NJ, USA) [ ] and B. subtilis 168 (trpC2 ; laboratory stock). ..

    Article Title: Chronic Prosthetic Hip Infection Caused by a Small-Colony Variant of Escherichia coli
    Article Snippet: E. coli DH5α was purchased from Gibco-BRL (Eggenstein, Germany). .. Unless otherwise stated, bacteria were cultured on Trypticase soy agar (TSA; Oxoid, Unipath Ltd., Basingstoke, England) supplemented with 7% defibrinated sheep blood (Oxoid, Unipath Ltd.) for 48 h at 37°C under aerobic conditions.

    Article Title: Improving Acetate Tolerance of Escherichia coli by Rewiring Its Global Regulator cAMP Receptor Protein (CRP)
    Article Snippet: Materials The host strain E. coli DH5α ∆crp was constructed by knocking out crp from E. coli DH5α (Invitrogen, San Diego, US) according to previously established protocol [ ]. .. M9 minimal medium was used for cells cultured under acetate stress, which is composed of the following chemicals (per liter): 6.78 g Na2 HPO4 , 3 g KH2 PO4 , 0.5 g NaCl, 1 g NH4 Cl, 0.49 g MgSO4 .7H2 O, 0.011 g CaCl2 , 2 g glucose and 1 ml of trace metal stock solution.

    Article Title: Murine immunization with CS21 pili or LngA major subunit of enterotoxigenic Escherichia coli (ETEC) elicits systemic and mucosal immune responses and inhibits ETEC gut colonization
    Article Snippet: .. E. coli DH5α (Life Technologies, Grand Island, NY), and CS21+ or CS8+ ETEC strains were cultured on Luria broth (LB), Terrific broth (TB) or TB agar plates at 37 °C overnight ( ). .. CS21+ ETEC E0934A strain was electroporated with plasmid pCM17 containing luciferase genes ( , ).

    Expressing:

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce). .. After blocked with 5% non-fat milk in phosphate buffered saline containing 0.1% Tween 20 (PBS-T), the membranes were incubated with mouse anti-His monoclonal antibody (Qiagen).

    Western Blot:

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Then, all of these prokaryotic expression vectors were separately transformed into E. coli DH5α and induced by IPTG to express the corresponding His-tagged proteins, which were determined by Western blot. .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Transformation Assay:

    Article Title: Non-contact positions impose site selectivity on Cre recombinase
    Article Snippet: Plasmids were constructed and propagated using Escherichia coli DH5α (Invitrogen). .. Transformation of DH5α and BS583 with the loxK2 2 plasmid pBS584 yielded the indicator/selector strains BS1491 and BS1494, respectively.

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Then, all of these prokaryotic expression vectors were separately transformed into E. coli DH5α and induced by IPTG to express the corresponding His-tagged proteins, which were determined by Western blot. .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Electroporation:

    Article Title: Characterization of a minimal pKW2124 replicon from Weissella cibaria KLC140 and its application for the construction of the Weissella expression vector pKUCm1
    Article Snippet: All Weissella species were incubated anaerobically at 37°C in de Man-Rogosa-Sharpe (MRS) medium (Difco, Detroit, MI, USA) and E. coli DH5α (Invitrogen, Carlsbad, CA, USA) was grown with shaking in Luria-Bertani (LB) medium (Difco) at 37°C. .. Weissella and other electroporation host bacteria were selected using chloramphenicol (USB Corporation, Santa Clara, CA, USA) with the following appropriate concentrations, 6.0 μg/ml for Weissella, Lactobacillus and Bifidobacterium, 5.0 μg/ml for Lactococcus and Leuconostoc , and 3.0 μg/ml for Streptococcus .

    Chromatography:

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce). .. The expressed proteins were purified by Ni2+ -NTA chromatography kit (Qiagen) under the natural condition following the instructions of the manufacturer.

    Infection:

    Article Title: Chronic Prosthetic Hip Infection Caused by a Small-Colony Variant of Escherichia coli
    Article Snippet: E. coli Z-2376 was obtained from two different specimens of the scar area of a patient with a prosthetic hip infection. .. E. coli DH5α was purchased from Gibco-BRL (Eggenstein, Germany).

    Article Title: Use of Chimeric Type IV Secretion Systems to Define Contributions of Outer Membrane Subassemblies for Contact-Dependent Translocation
    Article Snippet: E. coli DH5α (GIBCO-BRL) was used for plasmid constructions and the type VI secretion system (T6SS) killing assay. .. E. coli MG1655 ( E. coli Genetic Stock Center) served as donors in the conjugation assays and for the phage infection assays.

    Generated:

    Article Title: Non-contact positions impose site selectivity on Cre recombinase
    Article Snippet: Plasmids were constructed and propagated using Escherichia coli DH5α (Invitrogen). .. Lysogenization of DH5Δ lac U169 ( ) with the resulting phage generated the loxP 2 lacZ indicator strain BS583.

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Except for manure microcosm experiments, standard curves correlating the detection threshold of the fluorescence signal (Cq) to known concentrations of target DNA were generated by qPCR on pure template DNA obtained as follows: pB10 was extracted from E. coli DH5α(pB10) using a Wizard® Plus SV Minipreps kit (Promega, Madison, WI, USA), DNA was then linarized by digestion with Bam HI (Promega), and repurified using a QIAquick® PCR purification kit (Qiagen).

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: The DNA sequences encoding rHMGB1 A box, B box, tHMGB1 and mHMGB1 -211-215, mHMGB1 - 206-215, mHMGB1 -201-215, mHMGB1 -196-215, mHMGB1 -191-215 (rHMGB1 lacking amino acid residues 211-215, 206-215, 201-215, 196-215 and 191-215 respectively) were generated by PCR taking pUC19-rHMGB1 as template. .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Polymerase Chain Reaction:

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Quantifications were carried out from 25 ng of community DNA using a “TaqMan® Universal PCR Master Mix, NoAmpErase® UNG” (Applied Biosystems) as recommended by the manufacturer, with 800 nM of each primer, and 300 nM of TaqMan probe, in a 25 μL reaction volume.

    Article Title: Characterization of a minimal pKW2124 replicon from Weissella cibaria KLC140 and its application for the construction of the Weissella expression vector pKUCm1
    Article Snippet: Paragraph title: BACTERIAL STRAINS, PLASMIDS, PCR PRIMERS, AND GROWTH CONDITIONS ... All Weissella species were incubated anaerobically at 37°C in de Man-Rogosa-Sharpe (MRS) medium (Difco, Detroit, MI, USA) and E. coli DH5α (Invitrogen, Carlsbad, CA, USA) was grown with shaking in Luria-Bertani (LB) medium (Difco) at 37°C.

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: The DNA sequences encoding mHMGB1 -186-200, mHMGB1 -196-210, mHMGB1 -196-205, mHMGB1 -198-207, mHMGB1 -201-210 and mHMGB1 -201-205 (rHMGB1 lacking amino acid residues 186-200, 196-210, 196-205, 198-207, 201-210 and 201-205 respectively) were amplified by one-step opposite-direction PCR using MutanBEST Kit (TaKaRa) according to the manufacturer's instructions (taking pUC19-rHMGB1 as template). .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Recombinant:

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Paragraph title: Preparation of recombinant proteins and C peptide ... Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Article Title: An engineered autotransporter-based surface expression vector enables efficient display of Affibody molecules on OmpT-negative E. coli as well as protease-mediated secretion in OmpT-positive strains
    Article Snippet: .. E. coli DH5α (Invitrogen) was used for OmpT-mediated release of recombinant protein into the medium. .. Construction of expression vectors DNA fragments encoding ZIgG , His6 , OmpT cleavage site and ABP were subcloned into the vector pMK90 [ ], containing parts of the aidA gene under control of the aidA promoter [ ].

    In Vivo:

    Article Title: Murine immunization with CS21 pili or LngA major subunit of enterotoxigenic Escherichia coli (ETEC) elicits systemic and mucosal immune responses and inhibits ETEC gut colonization
    Article Snippet: E. coli DH5α (Life Technologies, Grand Island, NY), and CS21+ or CS8+ ETEC strains were cultured on Luria broth (LB), Terrific broth (TB) or TB agar plates at 37 °C overnight ( ). .. E9034A/pCM17, used for in vivo challenge mice experiments, was cultured in LB broth supplemented with Kanamycin at 37 °C overnight and then sub-cultured in DMEM/F12 (1:1) medium (25 mM glucose, 15 mM HEPES and 0.5% mannose) at ratio of 1:10 for 3 hours at 37 °C.

    Fluorescence:

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Except for manure microcosm experiments, standard curves correlating the detection threshold of the fluorescence signal (Cq) to known concentrations of target DNA were generated by qPCR on pure template DNA obtained as follows: pB10 was extracted from E. coli DH5α(pB10) using a Wizard® Plus SV Minipreps kit (Promega, Madison, WI, USA), DNA was then linarized by digestion with Bam HI (Promega), and repurified using a QIAquick® PCR purification kit (Qiagen).

    Conjugation Assay:

    Article Title: Use of Chimeric Type IV Secretion Systems to Define Contributions of Outer Membrane Subassemblies for Contact-Dependent Translocation
    Article Snippet: E. coli DH5α (GIBCO-BRL) was used for plasmid constructions and the type VI secretion system (T6SS) killing assay. .. E. coli MG1655 ( E. coli Genetic Stock Center) served as donors in the conjugation assays and for the phage infection assays.

    Isolation:

    Article Title: Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae
    Article Snippet: Neutrophil killing assays Human neutrophils were isolated and purified from venous blood using the PolyMorphPrep kit (Axis-Shield) as per the manufacturer's instructions and seeded into 96-well plates at 2* 105 cells/well. .. E. coli Dh5α (Life Technologies) was used as a positive control.

    Subcloning:

    Article Title: An engineered autotransporter-based surface expression vector enables efficient display of Affibody molecules on OmpT-negative E. coli as well as protease-mediated secretion in OmpT-positive strains
    Article Snippet: Bacterial strains Escherichia coli strain RR1∆M15 [ ] and E. coli strain DH5α (Invitrogen, Carlsbad, CA) were used for subcloning work. .. E. coli DH5α (Invitrogen) was used for OmpT-mediated release of recombinant protein into the medium.

    Microscopy:

    Article Title: Chronic Prosthetic Hip Infection Caused by a Small-Colony Variant of Escherichia coli
    Article Snippet: E. coli DH5α was purchased from Gibco-BRL (Eggenstein, Germany). .. The sizes of the colonies were determined by plate microscopy.

    Purification:

    Article Title: Maturation of molybdoenzymes and its influence on the pathogenesis of non-typeable Haemophilus influenzae
    Article Snippet: Neutrophil killing assays Human neutrophils were isolated and purified from venous blood using the PolyMorphPrep kit (Axis-Shield) as per the manufacturer's instructions and seeded into 96-well plates at 2* 105 cells/well. .. E. coli Dh5α (Life Technologies) was used as a positive control.

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Except for manure microcosm experiments, standard curves correlating the detection threshold of the fluorescence signal (Cq) to known concentrations of target DNA were generated by qPCR on pure template DNA obtained as follows: pB10 was extracted from E. coli DH5α(pB10) using a Wizard® Plus SV Minipreps kit (Promega, Madison, WI, USA), DNA was then linarized by digestion with Bam HI (Promega), and repurified using a QIAquick® PCR purification kit (Qiagen).

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce). .. The expressed proteins were purified by Ni2+ -NTA chromatography kit (Qiagen) under the natural condition following the instructions of the manufacturer.

    Sequencing:

    Article Title: Bacillus thuringiensis subsp. kurstaki HD1 as a factory to synthesize alkali-labile ChiA74?sp chitinase inclusions, Cry crystals and spores for applied use
    Article Snippet: These plasmids (pEHchiA74 and pEBchiA74) were used for deleting the signal peptide-encoding sequence of ChiA74 to obtain ChiA74Δsp (see below). .. All constructs (Figure A) were propagated in E. coli DH5α [supE44, DlacU169 (F80lacZDM15 ) hsdR17 recA1 end A1 gyrA96 thi-1 relA1 ] (Invitrogen, Carlsbad CA, USA) and then used for transforming the acrystalliferous strain of B. thuringiensis subsp. israelensis 4Q7, (hereafter 4Q7), and B. thuringiensis subsp. kurstaki HD1 (hereafter HD1) (Bacillus Genetic Stock Center, Columbus, OH).

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: Therefore, GECs saved both time and cost for cloning and sequencing of genes. .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ].

    Labeling:

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: We constructed a set of alternative GECs for labeling a desired protein with different tags at the N- or C-terminus (Table ). .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ].

    Mouse Assay:

    Article Title: Murine immunization with CS21 pili or LngA major subunit of enterotoxigenic Escherichia coli (ETEC) elicits systemic and mucosal immune responses and inhibits ETEC gut colonization
    Article Snippet: E. coli DH5α (Life Technologies, Grand Island, NY), and CS21+ or CS8+ ETEC strains were cultured on Luria broth (LB), Terrific broth (TB) or TB agar plates at 37 °C overnight ( ). .. E9034A/pCM17, used for in vivo challenge mice experiments, was cultured in LB broth supplemented with Kanamycin at 37 °C overnight and then sub-cultured in DMEM/F12 (1:1) medium (25 mM glucose, 15 mM HEPES and 0.5% mannose) at ratio of 1:10 for 3 hours at 37 °C.

    SDS Page:

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce). .. After blocked with 5% non-fat milk in phosphate buffered saline containing 0.1% Tween 20 (PBS-T), the membranes were incubated with mouse anti-His monoclonal antibody (Qiagen).

    Plasmid Preparation:

    Article Title: Non-contact positions impose site selectivity on Cre recombinase
    Article Snippet: Plasmids were constructed and propagated using Escherichia coli DH5α (Invitrogen). .. Transformation of DH5α and BS583 with the loxK2 2 plasmid pBS584 yielded the indicator/selector strains BS1491 and BS1494, respectively.

    Article Title: Bacillus thuringiensis subsp. kurstaki HD1 as a factory to synthesize alkali-labile ChiA74?sp chitinase inclusions, Cry crystals and spores for applied use
    Article Snippet: All constructs (Figure A) were propagated in E. coli DH5α [supE44, DlacU169 (F80lacZDM15 ) hsdR17 recA1 end A1 gyrA96 thi-1 relA1 ] (Invitrogen, Carlsbad CA, USA) and then used for transforming the acrystalliferous strain of B. thuringiensis subsp. israelensis 4Q7, (hereafter 4Q7), and B. thuringiensis subsp. kurstaki HD1 (hereafter HD1) (Bacillus Genetic Stock Center, Columbus, OH). .. Plasmid pGLO is a vector that harbors the green fluorescent protein (gfp ) gene under the control arabinose (araC ) promoter and contains an ampicillin (bla ) resistance gene marker (Bio-Rad, Hercules CA, USA).

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: .. Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Quantifications were carried out from 25 ng of community DNA using a “TaqMan® Universal PCR Master Mix, NoAmpErase® UNG” (Applied Biosystems) as recommended by the manufacturer, with 800 nM of each primer, and 300 nM of TaqMan probe, in a 25 μL reaction volume.

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ]. .. Plenty of REL sites in GECs provide a flexible platform for ad arbitrium modifying the vector by researcher themselves for their own individual study.

    Article Title: Transfer of Herb-Resistance Plasmid From Escherichia coli to Staphylococcus aureus Residing in the Human Urinary Tract
    Article Snippet: .. Plasmid Characterization Total plasmid DNA was prepared (Plasmid Extraction Kit, Beijing TIANGEN) and transferred into E. coli DH5α (Invitrogen, Carlsbad, CA, USA). ..

    Article Title: Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1
    Article Snippet: Other fragments were cloned into the Kpn I/Hin dIII sites of pQE-80L vector. .. Briefly, the lysates of E. coli DH5α expressing the corresponding proteins were subjected to SDS-PAGE and then transferred onto polyvinylidene difluoride membranes (Pierce).

    Article Title: Murine immunization with CS21 pili or LngA major subunit of enterotoxigenic Escherichia coli (ETEC) elicits systemic and mucosal immune responses and inhibits ETEC gut colonization
    Article Snippet: E. coli DH5α (Life Technologies, Grand Island, NY), and CS21+ or CS8+ ETEC strains were cultured on Luria broth (LB), Terrific broth (TB) or TB agar plates at 37 °C overnight ( ). .. CS21+ ETEC E0934A strain was electroporated with plasmid pCM17 containing luciferase genes ( , ).

    Article Title: Use of Chimeric Type IV Secretion Systems to Define Contributions of Outer Membrane Subassemblies for Contact-Dependent Translocation
    Article Snippet: .. E. coli DH5α (GIBCO-BRL) was used for plasmid constructions and the type VI secretion system (T6SS) killing assay. .. E. coli MG1655 ( E. coli Genetic Stock Center) served as donors in the conjugation assays and for the phage infection assays.

    Software:

    Article Title: Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group
    Article Snippet: .. Basically, sets of qPCR primers were designed to prime on both sides of a unique junction between building blocks of the element targeted for quantification: a unique assembly between two truncated transposons for plasmid pB10 (target coordinates 45968–46102; GenBank NC_004840), and both sides of a unique 97 kb-deletion in the chromosome of E. coli DH5α (target coordinates on K12 274654–372933; GenBank U00096; ; ). qPCRs were performed in triplicate using a “Step One Plus Real-Time PCR System” (Applied Biosystems, driver: StepOne Software v2.2) with thermocycling conditions set as follows: 2 min at 50°C, then 10 min at 95°C followed by 45 cycles of 15 s at 95°C and 1 min at 60°C. .. Quantifications were carried out from 25 ng of community DNA using a “TaqMan® Universal PCR Master Mix, NoAmpErase® UNG” (Applied Biosystems) as recommended by the manufacturer, with 800 nM of each primer, and 300 nM of TaqMan probe, in a 25 μL reaction volume.

    Negative Control:

    Article Title: Enhanced performance of the microalga Chlorella sorokiniana remotely induced by the plant growth-promoting bacteria Azospirillum brasilense and Bacillus pumilus
    Article Snippet: .. In experiments that measured the potential effect of CO2 , Escherichia coli DH5α (Invitrogen, Carlsbad, CA) served as the negative control for microalgal growth and promoting metabolites because it does not have any plant growth-promoting effects; it also served as a positive control in the CO2 experiment because it produces CO2 , as any E. coli . .. For initial culturing of the microalga, 10 mL axenic C. sorokiniana culture, cultivated in sterile mineral medium (C30), was added to a sterile flask containing 90 mL sterile C30 medium, composed of (in g·L−1 ): KNO3 (25), MgSO4 •7H2 O (10), KH2 PO4 (4), K2 HPO4 (1), FeSO4 •7H2 O (1), and (in μg·L−1 ): H3 BO3 (2.86), MnCl2 •4H2 O (1.81), ZnSO4 •7H2 O (0.11), CuSO4 •5H2 O (0.09), NaMoO4 (0.021), pH 5.25 and incubated at 27 ± 2 °C on a rotary shaker at 120 rpm under 60 μmol photon·m−2 ·s−1 continuous light intensity for 6 days .

    Selection:

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ]. .. The chloramphenicol (Cm) was employed as a selection marker in E. coli , which may be compatible to most of binary vectors available.

    Article Title: Characterization of a minimal pKW2124 replicon from Weissella cibaria KLC140 and its application for the construction of the Weissella expression vector pKUCm1
    Article Snippet: All Weissella species were incubated anaerobically at 37°C in de Man-Rogosa-Sharpe (MRS) medium (Difco, Detroit, MI, USA) and E. coli DH5α (Invitrogen, Carlsbad, CA, USA) was grown with shaking in Luria-Bertani (LB) medium (Difco) at 37°C. .. Ampicillin sulfate (Sigma, St. Louis, MO, USA) was added to the E. coli growth medium for selection at 50 μg/ml.

    Agarose Gel Electrophoresis:

    Article Title: Transfer of Herb-Resistance Plasmid From Escherichia coli to Staphylococcus aureus Residing in the Human Urinary Tract
    Article Snippet: Plasmid Characterization Total plasmid DNA was prepared (Plasmid Extraction Kit, Beijing TIANGEN) and transferred into E. coli DH5α (Invitrogen, Carlsbad, CA, USA). .. Plasmid DNA was separated on a 0.7% agarose gel, stained with ethidium bromide, and visualized under UV-light.

    Concentration Assay:

    Article Title: What an Escherichia coli Mutant Can Teach Us About the Antibacterial Effect of Chlorophyllin
    Article Snippet: Bacteria Strains and Cell Culture Experiments were performed with E. coli DH5α (Invitrogen, Carlsbad, CA, USA), E. coli NR698 (MC4100 lptD4213 ; kindly provided by M. Grabowicz, Princeton University, NJ, USA) [ ] and B. subtilis 168 (trpC2 ; laboratory stock). .. Prior to the experiments, cell concentration was determined optically at 590 nm and set to OD590 = 0.1 before cells were diluted in LB as required.

    Marker:

    Article Title: Bacillus thuringiensis subsp. kurstaki HD1 as a factory to synthesize alkali-labile ChiA74?sp chitinase inclusions, Cry crystals and spores for applied use
    Article Snippet: All constructs (Figure A) were propagated in E. coli DH5α [supE44, DlacU169 (F80lacZDM15 ) hsdR17 recA1 end A1 gyrA96 thi-1 relA1 ] (Invitrogen, Carlsbad CA, USA) and then used for transforming the acrystalliferous strain of B. thuringiensis subsp. israelensis 4Q7, (hereafter 4Q7), and B. thuringiensis subsp. kurstaki HD1 (hereafter HD1) (Bacillus Genetic Stock Center, Columbus, OH). .. Plasmid pGLO is a vector that harbors the green fluorescent protein (gfp ) gene under the control arabinose (araC ) promoter and contains an ampicillin (bla ) resistance gene marker (Bio-Rad, Hercules CA, USA).

    Article Title: BioVector, a flexible system for gene specific-expression in plants
    Article Snippet: .. A ccd B gene in REL sites (Figure ) served as a negative selection marker for E. coli DH5α as all GATEWAY entry vectors employ (Invitrogen) [ , , ]. .. The chloramphenicol (Cm) was employed as a selection marker in E. coli , which may be compatible to most of binary vectors available.

    Staining:

    Article Title: Transfer of Herb-Resistance Plasmid From Escherichia coli to Staphylococcus aureus Residing in the Human Urinary Tract
    Article Snippet: Plasmid Characterization Total plasmid DNA was prepared (Plasmid Extraction Kit, Beijing TIANGEN) and transferred into E. coli DH5α (Invitrogen, Carlsbad, CA, USA). .. Plasmid DNA was separated on a 0.7% agarose gel, stained with ethidium bromide, and visualized under UV-light.

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    Thermo Fisher max efficiency dh5α competent cells
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