L histidine

All twenty amino acid standards (L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-threonine, L-tryptophan, L-valine, L-arginine, L-cysteine, L-glutamine, L-glycine, L-proline, L-tyrosine, L-alanine, L-aspartic acid, L-asparagine, L-glutamic acid, and L-serine) were purchased from Sigma-Aldrich (St. Louis, MO, USA).

Both essential oils were supplied from Fitovizyon Doğal ve Sağlıklı Yaşam San. Tic. Ltd. Şti. (FitoBio- https://www.fitobio.com/ access on 14 January 2025) (Istanbul, Türkiye). The quality of essential oils complies with ISO and European Pharmacopoeia quality monographs. Resomer^® RG 504 H type PLGA with acid termination, 50:50 lactide:glycolide ratio, 38,000–54,000 molecular weight and 0.45–0.60 dL/g inherent viscosity was purchased from Sigma-Aldrich (Product Number: 719900) (St. Louis, MO, USA). Polyvinyl alcohol (PVA), dichloromethane (DCM), calf thymus DNA (CT-DNA) and ethidium bromide, sodium ammonium phosphate tetrahydrate, magnesium chloride hexahydrate, potassium phosphate, disodium hydrogen phosphate dihydrate, 4-nitro-o-phenylenediamine, L-histidine, D-biotin, sodium dihydrogen phosphate monohydrate, sulfate heptahydrate, citric acid monohydrate and sodium azide were purchased from Sigma Aldrich (St. Louis, MO, USA). Tris base, Ethylenediaminetetraacetic acid (EDTA), and sodium chloride (NaCl) were purchased from Merck Millipore (Darmstadt, Germany). pBR322 Plasmid DNA was purchased from Thermo Fisher (Waltham, MA, USA). Agar was purchased from Difco and Nutrient broth was purchased from Oxoid (Basingstoke, UK). S. typhimurium TA100 and S. typhimurium TA98 mutant strains were purchased from Moltox (Boone, NC, USA).

Cation exchange resin, Dowex (H⁺) 50WX8-400, acetonitrile, methanol, o-phthalaldehyde (OPA)/2 mercaptoethanol, disodium hydrogen phosphate dihydrate, propionic acid, standards of amino acids (L-alanine (Ala), L-arginine (Arg), L-asparagine (Asn), L-aspartic acid (Asp), glycine (Gly), L-glutamic acid (Glu), L-glutamine (Gln), L-histidine (His), L-isoleucine (Ile), leucine (Leu), L-methionine (Met), L-phenylalanine (Phe), L-serine (Ser), L-threonine (Thr), L-tryptophan (Trp), L-tyrosine (Tyr), and L-valine (Val)) were obtained from Sigma-Aldrich (Madrid, Spain). Phytohormones (1-aminocyclopropane-l-carboxylic acid (ACC), trans-zeatin (tZ), zeatin riboside (Zr), isopentenil adenine (IPA), gibberelic acid GA1, GA3, GA4 were obtained from Olchem (Olomouc, Czech Republic), and indoleacetic acid (AIA), abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA)) from Santa Cruz Biotechnologies (Dallas, TX, USA). The solid-phase extraction (SPE) cartridges used with clean-up of sample purposes were Strata cartridges (Strata X-AW, 100 mg/3 mL), which were acquired from Phenomenex (Torrance, CA, USA).

Chemical scavengers for ROS and RNS, mannitol (MP Biomedicals), tiron (Sigma-Aldrich), sodium azide (Sigma-Aldrich), l-histidine (Sigma-Aldrich), and ebselen (TCI), were used. For direct plasma treatment, a final concentration of 200 mM mannitol, 20 mM tiron, 10 mM sodium azide, 10 mM l-histidine, or 1 mM ebselen was added to the water containing bacteriophages. Then, the samples with or without scavengers were treated with plasma for 2 min and incubated at 22°C for 1 h. For the plasma-activated water treatment, a final concentration of 200 mM mannitol, 20 mM tiron, 10 mM sodium azide, 10 mM l-histidine, or 1 mM ebselen was added to water before or after plasma treatment for 2 min. Then, the water with or without scavengers was incubated with an equal volume of water containing bacteriophages at 22°C for 1 h. The inactivation rates were examined as described above.

The preparation and starvation of primary cells were performed as described in Perland et al. (2017 (link)). Briefly, a pregnant female mouse was euthanized by cervical dislocation at embryonic day e14.5. Cortices were dissected from the embryos and placed in ice cold PBS (137.0 mM NaCl, 2.7 mM KCl, 8.1 mM Na₂HPO₄) supplemented with 10.0 mM glucose (all from Sigma-Aldrich, USA). The tissues were chemically dissociated using a DNase/Papain solution prior mechanical dissociation. Single cells were filtered through a 70 μm nylon cell strainer (BD Stockholm, Sweden) before plated at a density of 7.5 × 10⁴-1.5 × 10⁵ cells per well in PLL coated 6 well plates (Invitrogen, USA) using plating media. Following cell adhering, the plating media was replaced with growth media supplemented with B27 (Gibco®, Life technologies, USA). 75% of the medium was changed every third day and the cells grew for 10 days before starvation experiment. The control medium was prepared using EBSS (Gibco®, Life technologies, USA) supplemented with 2.0 mM GlutaMAX™ and the amino acids glycine, L-alanine, L-arginine, L-asparagine, L-cysteine, L-histidine, L-isoleucine, L-leucine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-serine, L-threonine, L-tryptophan, L-tyrosine, and L-valine (Sigma-Aldrich, USA) was added in the same concentrations as in the Neurobasal® A medium. The starved medium was prepared using EBSS supplemented with L-arginine, L-cysteine, L-lysine, L-methionine, L-phenylalanine, L-proline, L-threonine, L-tryptophan, and L-tyrosine (Sigma-Aldrich, USA) in the same concentrations as in the Neurobasal® A medium. Both the control and starvation medium was supplemented with 1.0 mM Sodium-Pyruvate, 1% Penicillin-Streptomycin, 2% B-27® (50X), 4X MEM Vitamin Solution (100X) (Gibco®, Life technologies, USA) and 10.9 mM HEPES (1 M) buffer solution (Gibco®, Life technologies, USA). Hence, the starved cells were deprived of glycine, L-alanine, L-asparagine, L-glutamine, L-histidine, L-isoleucine, L-leucine, L-serine and L-valine, which are among the most common amino acids transported by the SLC38 family and their precursors. The experiment was run in triplicates in each treatment group (starved vs. control cells) and the cells were treated in the limited amino acid medium or the complete amino acid medium for 3, 7, or 12 h before RNA was extracted using RNeasy Midi Kit (Qiagen, Germany), following the manufacturers protocol. cDNA synthesis was performed using the High-Capacity RNA-to-cDNA kit (Invitrogen, USA) according to the manufacturers protocol and the cDNA from the triplicates in each treatment group were pooled. The cDNA concentrations were measured using a ND-spectrophotometer (NanoDrop Technologies, USA).