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6 protocols using mgso4

1

Bacterial Growth Media and Antibiotic Protocols

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All chemicals used in the study were purchased from Sigma-Aldrich unless stated otherwise. LB medium: 10 g l−1 tryptone, 5 g l−1 yeast extract, and 10 g l−1 NaCl. For agar plates, 15 g l−1 agar was added. M9 medium: 6.8 g l−1 Na2HPO4, 3 g l−1 KH2PO4, 0.5 g l−1 NaCl, 1 g l−1 NH4Cl), 0.34 g l−1 thiamine, 0.2% casamino acids (BD Biosciences), 0.4% glucose, 2 mM MgSO4, and 100 μM CaCl2. Antibiotic concentrations: where appropriate, the media contained ampicillin at a final concentration of 100 μg ml−1 from a 100 mg ml−1 aqueous stock solution and chloramphenicol at a final concentration of 25 μg ml−1 from a 34 mg ml−1 stock solution in absolute ethanol; for pOSIP-KO-mediated chromosomal integration, 50 μg mL−1 kanamycin-sulfate was used. The indicated concentrations of antibiotics were used for both LB and M9 media. Inducer concentration: an isopropyl-d-1-thiogalactopyranoside gradient was prepared at 0, 1, 5, 10, 20, 30, 50, 70, 100, 200, and 500 μM final concentrations, diluted from a stock in DMSO. Phosphate-buffered saline (PBS): 8 g l−1 NaCl, 0.2 g l−1 KCl, 1.44 g l−1 Na2HPO4, and 0.24 g l−1 KH2PO4. Kanamycin (2 mg ml−1) was added to the PBS before sampling in order to terminate protein expression.
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2

Cultivation of Klebsiella Strains

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Klebsiella strains were purchased from Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures and from Public Health England National Collection of Type Cultures (NCTC) and are described in Supplementary Information (Suppl. Table S4). Unless otherwise stated, Klebsiella strains were prepared by culturing in Lysogeny Broth (LB) medium (Roth) or Casamino Acids (CAA) (0.5% BactoTM Casamino acids, 5.2 mM K2HPO4, 1 mM MgSO4) medium (BD Biosciences) at 28 °C, 30 °C or 37 °C (as indicated in Suppl. Table 1) with shaking (200 rpm); overnight cultures were prepared by inoculation from frozen stocks. Clinical Klebsiella strains used for agar overlay assay have been isolated in Lithuanian University of Health Sciences, Kaunas clinics, and are described in Suppl. Table S2.
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3

Nematode and Bacterium Culture Protocol

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All chemicals used for nematode culture and bacterium culture were from Sigma-Aldrich (NaCl [7647–14–5]; cholesterol [57–88–5]; MgSO4 [10034–99–8]; CaCl2 [10035–04–8]; KH2PO4 [7778–77–0]; K2HPO4 [7758–11–4]) or BD (peptone [211820]; tryptone [211699]; yeast extract [212750]). Spermidine was from Sigma-Aldrich (124–20–9), LysoTracker Blue DND-22 was from Life Technologies (L-7525), and Recombinant SLO protein was from Sigma-Aldrich (401470–29–9).
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4

Bacterial Growth Media Formulations

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All the chemicals used in the study were purchased from Sigma-Aldrich unless stated otherwise. LB medium: 10 g/l tryptone, 5 g/l yeast extract, and 10 g/l NaCl. For agar plates, 15 g/l agar was added. M9 medium: 6.8 g/l Na2HPO4, 3 g/l KH2PO4, 0.5 g/l NaCl, 1 g/l NH4Cl, 0.34 g/l thiamine, 0.2% casamino acids (BD Biosciences), 0.4% glucose, 2 mM MgSO4, and 100 μM CaCl2. The LB medium for overnight culture contained ampicillin and kanamycin at concentrations of 100 μg/ml to maintain the plasmids. The mixed medium for the microfluidic culture contained ampicillin and kanamycin at concentrations of 1 μg/ml at which the cells can grow normally and the plasmids can be maintained.
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5

Carbohydrate Quantification Protocol

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Sucrose, D-(−)-fructose, D-(+)-glucose, D-(+)-xylose, D-(+)-galactose, D-(+)-mannose, D-(+)-cellobiose, Folin–Ciocalteu′s phenol reagent, albumin from bovine serum (BSA), KNaC4H4·4H2O, NaOH, Na2CO3, CuSO4, and 3,5-Dinitrosalicylic acid were purchased from Sigma-Aldrich (St. Louis, MO, USA). The electrophoresis reagents were from Bio-Rad (Hercules, CA, USA). K2HPO4, MgSO4, HCl, CaCl2, NaCl, MnSO4, and FeSO4 were from J.T. Baker (S.A. de C.V., Toluca, Estado de México, México) Bacto Yeast Extract from BD Biosciences (San Jose, CA, USA).
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6

Colorimetric RT-LAMP Assay for SARS-CoV-2 Detection

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RT-LAMP reaction was performed in a total volume of 20 μL containing the following components: 8 U Bst 2.0 (NEB), 7.5 U RTx (NEB) and 1 × colorimetric buffer mix [1.6 μM FIP/BIP primers, 0.4 μM LF/LB primers, 0.2 μM F3/B3 primers Gene N-A24 (link), 10 mM (NH4)2SO4 (Merck), 50 mM KCl (BDH), 8 mM MgSO4 (BDH), 0.1% Tween 20, 0.2 mM Phenol Red (Sigma), 1.4 mM each dNTP (NZYTech)]. For the in-house-made assay, we used the same colorimetric buffer mix, 0.5 μL of MashUP RT (6.8 mg/mL) and 1 μL of Bst LF (7.6 mg/mL) 50 × diluted. WarmStart colorimetric LAMP 2 × master mix (M1800S, NEB) was also used with the above final primer concentration.
When the complexometric indicator MX-Zn was used, samples were assembled as described above, but without Phenol Red. After 30 min, 2 μL of 5 mM Murexide and 1 μL of 50 mM of ZnCl2 were added to the reaction, in a post-LAMP workspace. All reactions were performed in a thermocycler at 65 °C and pictures were taken at the indicated time points. Figures depicting the readout of the RT-LAMP assays are representative of three independent experiments.
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