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5 protocols using flat bottomed plates

1

Plasma Anti-OVA IgG ELISA Assay

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Plasma anti-OVA IgG titers were measured using ELISA as follows: 96-well flat-bottomed plates (Nunc) were coated overnight with OVA (Sigma-Aldrich) in phosphate-buffered saline (PBS). After washes with PBS/0.05% Tween 20 (PBS-Tween), non specific binding sites were blocked with PBS/5% foetal calf serum (FCS). Plates were then incubated with plasma. Horse raddish peroxidase conjugated polyclonal rabbit anti-rat IgG (Abcam) was added. Finally, TMB substrate (Thermoscientific) added to each well. The reaction was stopped with 2N H2SO4 and plates read at 450 nm using an automatic Infinite M200 microplate reader (Tecan). Titers were expressed as ×103 of the highest plasma dilution, giving an optical density at least twice the blank value.
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2

Bacterial Growth and Induction Assay

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Escherichia coli DH10B bacteria bearing or lacking (as a reference) the viral chimera were grown overnight in LB at 37 °C. Thereafter, the growth culture was diluted and the bacteria were grown until their O.D.600 reached 0.2. Subsequently, 50 μL of bacterial culture was dispensed into 96-well flat-bottomed plates (Nunc, Roskilde, Denmark) containing 50 μL of the different treatments. Unless stated otherwise, IPTG was added to the cells to final concentrations ranging from 0 to 100 μM. d-glucose was added to a concentration of 1%. Moreover, 96-well plates were incubated for 16 h at 37 °C in an Infinite 200 from the Tecan Group (Männedorf, Switzerland) at a constant high shaking rate. O.D.600 readings were recorded every 15 min. For every measurement, duplicates or triplicates were conducted.
For the Escherichia coli LB650 bacteria, the same protocol was used, except that growth was done in LBK overnight. Subsequently, the bacteria were diluted and grown until their O.D.600 reached 0.2, after which the media was replaced to LB and diluted twofold with the various treatments in each well. Unless stated otherwise, IPTG was added to the LB650 bacteria to a final concentration of 10 μM.
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3

4T1 Breast Cancer Mouse Model

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Inbred Balb/c mice (6–8 weeks-old) and documented 4T1 cell line were obtained from the Pasteur Institute (Tehran, Iran). Chitosan (100–300 kDa; 75–85% degree of deacetylation) and 4-hydroxycyclophosphamide as the active form of cyclophosphamide were purchased from Sigma (St. Louis, MO, USA). Flat-bottomed plates were bought form Nunc (Kamstrup, Denmark). Mouse cytokine enzyme-linked immunosorbent assay (ELISA) kits were obtained from eBiosciences (Frankfurt, Germany). RPMI (Roswell Park Memorial Institute) 1640 and fetal bovine serum (FBS) were bought from Invitrogen (Gibco, Grand Island, NY, USA). Collagen Type I was isolated from fresh bovine tendon using a method of trypsin digestion and acetic acid dissolution described previously in Ma et al (2003) [16 (link)].
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4

Confirmation of Mutation Rate by Sanger Sequencing

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Confirmation of mutation rate was conducted by Sanger sequencing. Specifically, the transformation of the library was performed into Escherichia coli XL10‐Gold bacteria (Agilent). Forty‐four colonies were isolated and grown overnight in LB at 37°C. The growth culture was diluted, and the bacteria were grown in secondary culture in LB until reaching an O.D.600 of 0.07–0.1. The bacteria were then divided into 96‐well flat‐bottomed plates (Nunc; Roskilde, Denmark) to a final volume of 100 μl per well with 100 μM of isopropyl‐β‐d‐1‐thiogalactopyranoside (IPTG). The plate was incubated for 16 h at 30°C in a Synergy 2 multidetection microplate reader (Biotek; Winooski, Vermont) or Infinite 20 (Tecan Group; Männedorf, Switzerland) at a constant high shaking rate. O.D.600 readings were recorded every 15 min. For all measurements, duplicates were conducted. Ampicillin and D‐glucose were added to all growth media to a final concentration of 100 μg/ml and 1%, respectively. Finally, the plasmid of each colony was isolated and sequenced by Sanger sequencing.
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5

CD4+ T Cell Activation Modulation

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To stimulate CD4+ T cells, we coated 96-well flat-bottomed plates (Nunc) with anti-CD3ε (2.5 μg/mL) by overnight incubation at 4 °C. CD4+ T cells were negatively isolated with a CD4+ T cell isolation kit (Miltenyi Biotec, Bergisch-Gladbach, Germany) in accordance with the manufacturer’s instructions. CD4+ T cell purity was determined by flow cytometry (CD3+, CD4+ cells >90 % purification). Immediately after cell preparation, CD4+ T cells were added to the coating plate (1 × 105 cells/well). C60-P, C60(OH)36, or NAC was added to the well 30 min before the addition of anti-CD28 (1 μg/mL). After incubation of the cells for 3 days at 37 °C (95 % room air, 5 % CO2), the amount of IL-2 released into an aliquot of culture supernatant was measured with an IL-2 ELISA kit (eBioscience) in accordance with the manufacturer’s instructions.
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