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191 protocols using agar

1

Antibiotic Resistance in E. coli SIG-1

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E. coli SIG-1 (an ampicillin-resistant clinical isolate) was selected for in vitro and in vivo experiments. For susceptibility testing, Pseudomonas aeruginosa ATCC 27853 was used as control [36 ]. Culture media included trypticase soy broth and agar for in vivo studies and cation-adjusted Mueller–Hinton broth and agar for susceptibility testing (Becton–Dickinson, USA).
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2

Soft Agar Colony Formation Assay

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Substrate-independent cell proliferation was determined by soft agar colony formation assays performed in 6-well plates with a 1.5-mL bottom layer and 0.5-mL top layer containing 5.1 mg/mL agar (Difco Laboratories, Detroit, MI) in culture medium (DMEM plus supplements). Cells (1×10 4 / well) were dispersed as a single cell suspension in culture medium with 3.4 mg/mL agar, overlaid onto the bottom agar layer, and covered by the top layer. Cells were incubated for 2 to 3 h at room temperature and then at 37°C under 5% CO 2 . The top layer was covered with 400 μL of fresh culture medium every second day. Colony formation was quantified after 10 days using Giemsa staining.
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3

Bacterial Motility Assays: Swimming and Twitching

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Swimming plates contained 1% tryptone (Difco Laboratories, USA), 0.5% NaCl (Merck, Germany), and 0.3% agar (Difco Laboratories, USA). Bacteria were taken with a toothpick from colonies grown overnight on LB plates and inoculated onto swimming plates by stabbing the agar with the toothpick midway and incubated at 30°C for 24 h. Total of 8 different plates were used to calculate swimming potential by measuring the diameter of the bacterial colony formed. Twitching plates contained 1% tryptone (Difco Laboratories, USA), 0.5% yeast extract, 1% NaCl (Merck, Germany), and 1% agar (Difco Laboratories, USA). Bacteria were taken from colonies grown overnight on LB plates and inoculated onto twitching plates by stabbing the agar with the toothpick all through the agar and inoculated at 30°C for 24 h. Total of 10 replicates were used to calculate twitching potential by measuring diameter of bacterial spread at the bottom of the plate after removing the agar and dying the bacteria at the bottom using crystal violet 1% (c0775, Sigma, USA).
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4

Swarming Motility of P. aeruginosa

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After being inoculated into LB medium, P. aeruginosa PAO1 was cultivated at 37 °C and 150 rpm until OD600 = 1.0. Then, 1 μL of P. aeruginosa PAO1 bacterial medium was inoculated into the center of swarming solid medium (0.8% nutrient broth (BD), 0.5% glucose, 0.3% agar (BD)) and cultured at 30 °C for 16 h. Then, the colonies of the swarming plate were picked and added to the center of the cooled swarming solid medium (0.8% nutrient broth (BD), 0.5% glucose, 0.5% agar (BD)), which had been supplemented with compounds and cultured at 30 °C for 24 h [40 (link)].
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5

Soft Agar Colony Formation Assay

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One thousand arsenic treated BEAS-2B (miR-100-inhibitor) and BEAS-2B (miR-NC) cells were re-suspended in 1mL of complete medium (DMEM medium with 10%FBS) containing 0.6% agar and were then plated on top of a bottom layer that contains 1.2% agar (BD) with complete medium. Plates were cultureed under normal conditions for 2 weeks, and then cells colony were counted and photographed under a microscope (Nikon).
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6

Lentil Cultivar Susceptibility to Ascochyta Blight

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Lentil (L. culinaris) plants of Canadian cultivars Eston with complete susceptibility to both races of C. lentis, and CDC Robin with partial resistance to race 1 were grown in 4 inch pots containing commercial potting mixture as described previously9 (link). Isolates CT-30 (race 0) and CT-21 (race 1) of C. lentis were routinely maintained on oat-meal agar (OMA) plates containing 30 g blended quick oats (The Quaker Oats Company, Chicago, USA), 8.8 g agar (Becton, Dickinson and Company, Sparks, USA), and 1 L deionized water supplemented with 0.01% chloramphenicol (AMRESCO, Solon, USA). For infection assays, conidia were collected from 10-day-old OMA plates by flooding the sterile water.
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7

Characterization of IGF1R-Deficient R-Cells

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The igf1r deficient R‐cell line was isolated from mouse embryos with a targeted disruption of the igf1r gene by Dr. Renato Baserga's group (Sell et al., 1993). pBABE‐Puro retroviral expression vector (#RTV‐001‐PURO) and Platium‐E packaging cell line (#RV‐101) were bought from Cell Biolabs Inc. (San Diego, CA).
Agar (#214220), BrdU (#550891), 7‐AAD (#559925), mouse anti‐IGF1R (#556000), and FITC labeled mouse anti‐BrdU (#347583) was purchased from Becton, Dickinson and Company (San Jose, CA). Polybrene (sc‐134220), antibodies against GAPDH (sc‐25778), cyclin A (SC‐751), cyclin D (SC‐450), cyclin E (SC‐247), CDK2 (SC‐748), and normal mouse IgG (sc‐2025) were obtained from Santa Cruz Biotechnology Inc. (Santa Cruz, CA). IGF‐1R (#3027), pAkt (#9275), pErk (#9101), SUMO‐1 (#4940), CDK4 (#2906), p27 kip1 (#3698), InsR β (#3020), and phospho‐tyrosine (#9411) antibodies were purchased from Cell Signaling Technology (Danvers, MA). Cyclin B1 (ab181593) and CDK1 (ab18) antibodies were provided by Abcam (Cambridge, MA). qRT‐PCR primers for IGF1R (#Hs00609566_m1) and GAPDH (#Mm99999915_g1), puromycin (#A11138), and protein G Dynabeads (#10004D) were provided by Life Technologies (Carlsbad, CA).
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8

Cultivation of Aggregatibacter actinomycetemcomitans

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All strains (Table 1) were stored at −80°C. Aggregatibacter actinomycetemcomitans was grown on TSBYE medium containing 3% trypticase soy broth, 0.6% yeast extract with/without 1.5% agar (Becton Dickinson and Company), and incubated statically in a 37°C incubator with 5% humidified carbon dioxide.
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9

Aequorin-based Ca2+ Imaging in Arabidopsis

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Arabidopsis thaliana ecotype Col-0 constitutively expressing intracellular Ca2+ indicator aequorin (pMAQ2) is a gift from M. Knight and the principles of how the active aequorin is formed can be found in Knight et al. (1991) (link). Arabidopsis plants were grown in 150 mm × 15 mm round Petri dishes in half-strength Murashige and Skoog salts (MS; Gibco), supplemented with 1.5% (w/v) sucrose (Sigma), and 0.8% (w/v) agar (Becton Dickinson) adjusted to pH 6.0 with KOH in controlled an environmental room at 21 ± 2°C. The fluency rate of white light was ∼110 μmol m-2 s-1. The photoperiods were 16 h light/8 h dark cycles. Seeds were sterilized with 2.5% plant preservative mixture (Caisson Laboratories) and stratified at 4°C for 3 days in the dark, and then transferred to the growth room.
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10

Cultivation of Francisella tularensis

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Ft LVS and Ft SchuS4 were cultured aerobically at 37 °C in modified Mueller-Hinton broth (MHB) or agar (Becton Dickinson, Sparks, MD) supplemented with ferric pyrophosphate and Iso-Vitalex (Becton Dickinson, Sparks, MD). Ft LVS SodB mutant was grown in Brain-Heart Infusion (BHI) medium and the active mid-log phase bacteria were harvested and used for immunization.
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