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40 protocols using e coli dh10b

1

Recombinant Protein Expression in P. pastoris

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The subcloning and construction of recombinant plasmids was carried out in E. coli DH10B (Invitrogen). The P. pastoris GS115 strain (Invitrogen) was used as a host for the expression of heterogenous proteins. The vectors pPIC3.5K and pPICZαA were purchased from Invitrogen. The vector pTSC (Yan et al., 2008 (link)) was stocked in this lab. pUC57-MCS7 (the original plasmid used for construction of recombinant expression vectors) was from GeneCreate Biological Engineering Co., Ltd, Wuhan, China. E. coli DH10B was cultured in Luria-Bertani medium [1% (w/v) tryptone, 0.5% (w/v) yeast extract, and 1% (w/v) NaCl, pH 7.0] at 37°C. The P. pastoris yeast strain was cultured in YPD medium [1% (w/v) yeast extract, 2% (w/v) peptone, 2% (w/v) dextrose]. YPDZ plates containing Zeocin (100 μg/mL) were used for the selection of positive P. pastoris transformants. Buffered minimal glycerol-complex medium (BMGY) was prepared with 2% (w/v) peptone, 1% (w/v) yeast extract, 1% (w/v) glycerol, 1.34% (w/v) yeast nitrogen base with ammonium sulfate but without amino acids, and 4 × 10−5% (w/v) biotin in 100 mM potassium phosphate buffer. The phosphate buffer was adjusted to pH 6.0. Buffered minimal methanol-complex medium (BMMY) was the same as BMGY, except that 0.5% (w/v) methanol was replaced with glycerol.
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2

Mycoplasma agalactiae Bacterial Culture

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The pathogenic M. agalactiae type strain PG2 [28 (link), 29 (link)] and the pdhB transposon mutant were grown at 37°C in SP4 medium supplemented with penicillin, pyruvate, and phenol red as an indicator, as described before [21 (link)]. Gentamicin sulphate (50 μg/ml) was added to both broth and agar plates for the propagation of the pdhB transposon mutant. E. coli DH10B (Invitrogen GmbH, Lofer, Austria) transformants containing the transposon vector pISM2062 or the M. agalactiae oriC vector pMM21–7 were grown in LB broth (10 g tryptone, 5 g yeast extract, and 5 g of NaCl per litre) supplemented with ampicillin (100 μg/ml), gentamicin sulphate (7 μg/ml) or tetracycline (100 μg/ml). The M. agalactiae pdhB mutant containing the complementation plasmid pPlacZ was grown in SP4 broth containing both tetracycline (2 μg/ml) and gentamicin (50 μg/ml). To monitor lacZ expression on the basis of blue-white colonies, M. agalactiae clones were grown on SP4 agar supplemented with 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-Gal) at a concentration of 160 μg/ml [30 (link)].
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3

Bacterial Strains and Culture Conditions

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All strains used in this study are listed in Table 1. The serotype 1/2a strain L. monocytogenes EGD-e (Bécavin et al., 2014 (link)) was used to generate the sensor strain for detection of membrane damage. E. coli DH10B (Invitrogen, Darmstadt, Germany) was used as a cloning host. L. lactis strain B1627 (strain collection Dzung B. Diep, NMBU, Norway) was used to produce nisin-containing culture supernatants and L. lactis MG1363 (Gasson, 1983 (link)) served as nisin-negative control. Bacteria were grown under standard conditions in LB (E. coli), BHI (L. monocytogenes) or GM17 (L. lactis) broth aerobically at 37°C with agitation (E. coli, L. monocytogenes) or 30°C without aeration (L. lactis; Kuipers et al., 1995 (link)). Where indicated chloramphenicol was added to the media at a final concentration of 20 μg/ml (E. coli) or 15 μg/ml (L. monocytogenes).
For preparation of supernatants, overnight (o/N) cultures of L. lactis strains were diluted in 20 ml of fresh GM17 broth in an Erlenmeyer flask to an optical density at 600 nm (OD600) of 0.1 and grown under standard conditions. Growth was monitored by measuring OD600. At the indicated timepoints, aliquots were collected and supernatants were prepared by centrifugation at 3200 × g for 3 min and filtration (pore size: 0.2 μm).
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4

Ionic Liquid Tolerance Engineering

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All chemicals used were reagent grade and purchased from Sigma-Aldrich (St. Louis, MO), unless otherwise noted. [EMIM]OAc, also known as [C2C1im]OAc, was purchased from Sigma-Aldrich and used as received. All strains and plasmids used in this work are listed at http://public-registry.jbei.org and are summarized in Additional file 5: Table S4. E. coli DH10B (Invitrogen, Carlsbad, CA) was used for cloning and manipulation of plasmids. Except for the experiments described in Table 1 from the Keio Collection, all IL tolerance assays were conducted with E. coli DH1. Mutants from the Keio collection were tested against the BW25113 wild-type strain. Plasmids were constructed using isothermal assembly with 40 bp overlapping homologous sequences and plasmid sequences were verified with restriction endonuclease digestion and Sanger Sequencing (Quintara Biosciences, Albany, CA). We defined the promoter sequence of the cydDC operon as the immediate upstream ~ 500 bp of cydC. Plasmid transformation was conducted as previously described [60 (link)] or else as expressly indicated.
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5

Plasmid Manipulation Protocols in Bacteria and Fungi

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The plasmids, bacterial and fungal strains used in this study are shown in Table S1. Routine DNA manipulations were done with E. coli DH10B (Invitrogen, Carlsband, CA, USA) as a host using standard molecular biology protocols [37] . pUC18T-mini-Tn7T-Gm-eyfp was generously gifted by Dr. H. P. Schweizer, Colorado State University, USA (Table S1) [38] (link). P. fluorescens ATCC 13525 (Pf13525) and its plasmid derivatives were grown at 30°C and maintained on Pseudomonas agar (Hi Media, India) containing 50 μg/ml ampicillin and 10 μg/ml gentamycin as and when required. Fungal cultures were grown in minimal medium at 27°C [25] (link), [30] (link).
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6

Cloning and Expression of Phage gp053

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The PCR fragment of gene 053 (GeneID: 14011712) from phage FV3 was obtained by amplification of the phage DNA using the primers presented in Supplementary Table S1. The purified PCR products were cleaved with NdeI and BamHI/XhoI (Thermo Fisher Scientific, Vilnius, Lithuania) and then inserted into the pET-16b or pET-21a (Novagene, Madison, WI, USA) vectors, digested with the appropriate restriction endonucleases. The resulting vectors were amplified in E. coli DH10B (Invitrogen, Dublin, Ireland) cells and verified by DNA sequencing. These vectors were used for the production of a recombinant full-length gp053 and the truncated gp053 mutants with various variations in length and His-tag (Supplementary Table S2). The construction scheme of the gp053 oligomers is presented in detail in Supplementary Figure S1.
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7

Enterobacteriaceae Isolation and Identification

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A total of 922 non-duplicate isolates (one per patient) of Enterobacteriaceae were collected from March 2005 to April 2010 from the Microbiology Laboratories of five hospitals and four private laboratories in Bejaia (Algeria). The isolates were recovered from various pathological specimens and were identified by the API 20E system (bioMérieux, Marcy l’Etoile, France) as follows: E. coli (n = 551); Klebsiella pneumoniae (n = 221); P. mirabilis (n = 125) and Salmonella sp. (n = 25).
E. coli J53AzR was used as recipient strains for conjugation experiments. E. coli DH10B (Invitrogen) was used in transformation experiments and E. coli ATCC 25922 was used as a quality control strain for antimicrobial susceptibility testing.
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8

E. coli Recombinant Protein Expression

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E. coli DH10B (Invitrogen, Waltham, MA) was used for plasmid cloning and recombinant protein expression. LB media (BD-Difco, Franklin Lakes, NJ) was utilized as the culture media. The working antibiotic concentrations were as follows: 50 μg/mL chloramphenicol (Daejung Chemicals, Siheung, Republic of Korea) and 50 μg/mL gentamicin (KisanBio, Seoul, Republic of Korea). Primers used in this study were synthesized and purchased from Macrogen (Seoul, Republic of Korea). AzF (Chem-Impex, Wood Dale, IL), a non-canonical amino acid, was included as a substrate for aaRS. Arabinose (Alfa Aesar, Haverhill, MA) and isopropyl β-d-1-thiogalactopyranoside (IPTG, Bioneer, Daejeon, Republic of Korea) were applied as inducers.
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9

Aspergillus fumigatus Strain Cultivation

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Aspergillus fumigatus strains used in this study are presented in Table 1. Fungal strains were routinely grown at 37°C on Aspergillus complete medium (ACM) according to Pontecorvo et al. [30] (link) containing 1% (w/v) glucose as carbon source and 5 mM ammonium tartrate as nitrogen source. For solid media 1% (w/v) agar was added. Minimal media (MM) containing 5 mM ammonium tartrate and 1% (w/v) glucose [31] (link) was used for phenotypic testing. For Aspergillus transformation MM was supplemented with 1 M sucrose to produce regeneration medium (RM). Liquid cultures were agitated by orbital shaking at 150 rpm unless otherwise stated. For propagation of plasmids, E. coli strain XL-10 (Agilent technologies) was grown in Luria-Bertani (LB medium) supplemented with ampicillin (100 µg/ml). The A. fumigatus BAC library was maintained in E. coli DH10B (Invitrogen, UK). Propagation of BAC clones was performed in LB supplemented with chloramphenicol (12.5 µg/ml). Reagents for recombineering were kindly provided by Donald L Court (Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK). The replication deficient λ phage (λ cI857 ind1 CroTYR26amber PGLN59amber rex< >tetra) [27] (link) was maintained in E. coli LE392 (Promega, UK). The BAC library as well as the reagents for recombineering in A. fumigatus, are available on request.
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10

Generating Recombinant Plasmids and Viruses

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The recombinant plasmids pBSC_IBSP4ncp#2 and #3 were electroporated into E. coli DH10B (Invitrogen) using an ECM 830 BTX electroporator. The electroporation conditions were as follows: 2.75 kV, 99 μs, 5 pulses, and 1 s between pulses. Colonies were grown at 37 °C in Luria-Bertani medium with chloramphenicol (20 μg/mL) at 37 °C for 18–20 h. Plasmid DNA was then purified with the QIAGEN Plasmid Midi Kit (Qiagen) and used as a template for in vitro transcription. MDBK cells were electroporated with the RNA as described above. Infectivity of the RNA was accessed by the IFA assay performed at 24, 48, and 72 h after the transfection. Progeny viruses were harvested and subjected to five passages in MDBK cells, with the infectivity monitored at each passage by the IFA assay.
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