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17 protocols using 2 4 dichlorophenoxyacetic acid

1

Graphene Oxide Functionalization and Applications

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All the chemicals in this study were of analytical grade and were used as received without any additional purification. Graphene oxide (GO) suspension (50 mg/mL) was provided by Graphenox (Moscow, Russia). The element composition of the GO suspension was provided by the manufacturer and included C–46%, O–49%, H–2.5%, and S < 1.5%. The hydrazine hydrate solution (100%), 2,4-Dichlorophenoxyacetic acid, and salicylic acid were purchased from Merck (Darmstadt, Germany). Hydrochloric acid HCl was provided by Himprom (Kemerovo, Russia).
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2

Cell Culture Protocols for Arabidopsis and Tobacco

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Arabidopsis (Arabidopsis thaliana cv. Landsberg erecta) cell line (Ath-Ler) [61 (link)] was grown in sterile Murashige-Skoog medium (4.4 g·L−1, pH 5.8; Duchefa Biochemie, Haarlem, The Netherlands) supplemented with vitamins, 3% sucrose, 0.232 µM kinetin and 5.37 µM 1-naphthaleneacetic acid (Merck Life Science, Darmstadt, Germany). Tobacco (Nicotiana tabacum cv. Bright Yellow 2) cell line (BY-2) [62 (link)] was grown in sterile Murashige-Skoog medium (4.3 g·L−1 pH 5.8) supplemented with 3% sucrose, 4 µM thiamin, 555 µM inositol, 1.47 mM KH2PO4, and 0.9 µM 2,4-dichlorophenoxyacetic acid (Merck Life Science, Darmstadt, Germany). Both cell lines were subcultured weekly into fresh media in a volume ratio of 1:10. The cells were cultivated at 23 °C in the dark and shaken at 120 rpm. Five-day-old cells were used for all experiments. As a stock material, cell calli of both cell lines were cultivated on the same solidified media (1.2% agar) and subcultured monthly.
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3

Investigating plant hormone effects on root morphology

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We embedded each of the following compounds in JM plates: 100 nM IAA (Sigma), 100 nM 1- ACC) (Sigma), 100 nM 2,4-dichlorophenoxyacetic acid (Sigma), 100 nM flg22 (PhytoTech labs), 100 nM 6-benzylaminopurine (BAP) (Sigma) and 100 nM zeatin (Sigma). As some of these compound stocks were initially solubilized in ethanol, we included comparable amounts of ethanol in the control treatments. Plates with each compound were inoculated with one of the Variovorax strains CL14, MF160, B4 or YR216 or with Burkholderia CL11. These strains were grown in separate tubes, then washed and OD600 was adjusted to 0.01 before spreading 100 μl on plates. In addition, we included uninoculated controls for each compound. We also included unamended JM plates inoculated with the RGI-inducing Arthrobacter CL28 co-inoculated with each of the Variovorax or Burkholderia strains, or alone. Thus, the experiment included 42 individual treatments. The experiment was repeated twice, with three independent replicates per experiment. Upon collection, root morphology was measured (‘Root and shoot image analysis’ in ‘Deconstructing the synthetic community to four modules of co-occurring strains’).
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4

Evaluating Juglone-PLGA Biocompatibility

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Juglone (Mw: 174.15 g/mol, CAS Number: 481-39-0), polyvinyl alcohol (PVA, Mw 31–50 kDa, 87–89 % hydrolyzed, CAS Number: 9002-89-5), PLGA (50:50 lactide:glicolide; inherent viscosity 0.45−0.60 dL/g, Mw ~38−54 kDa, CAS Number: 26780-50-7), and dichloromethane (DCM, CAS Number: 75-09-2) were purchased from Sigma-Aldrich (St. Louis, MO, USA).
Plant suspension cultures were established from alfalfa (Medicago sativa cv Verco) seeds kindly provided by Dr Satı Uzun (University of Erciyes, Turkey ) . 2,4-dichlorophenoxyacetic acid, kinetin, sucrose, and agar used for preparing the Murashige and Skoog (MS) medium were purchased from Sigma-Aldrich.
The mouse fibroblast cell line L929 was obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA). Dulbecco’s modified Eagle’s medium (DMEM) / Ham’s Nutrient Mixture F-12 medium, foetal bovine serum (FBS), penicillin, and L-glutamine used in the preparation of fibroblast cell cultures were purchased from Sigma-Aldrich. The Ames Microplate Format Mutagenicity Assay™ 98/100 kit and strains were provided from Anaria-Xenometrix (Mason, OH, USA). All the chemicals and solvents used for mutagenicity study were of analytical grade. Ultra-pure water was obtained from the Millipore MilliQ Gradient system (Merck Millipore, Burlington, MA, USA)
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5

Investigating plant hormone effects on root morphology

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We embedded each of the following compounds in JM plates: 100 nM IAA (Sigma), 100 nM 1- ACC) (Sigma), 100 nM 2,4-dichlorophenoxyacetic acid (Sigma), 100 nM flg22 (PhytoTech labs), 100 nM 6-benzylaminopurine (BAP) (Sigma) and 100 nM zeatin (Sigma). As some of these compound stocks were initially solubilized in ethanol, we included comparable amounts of ethanol in the control treatments. Plates with each compound were inoculated with one of the Variovorax strains CL14, MF160, B4 or YR216 or with Burkholderia CL11. These strains were grown in separate tubes, then washed and OD600 was adjusted to 0.01 before spreading 100 μl on plates. In addition, we included uninoculated controls for each compound. We also included unamended JM plates inoculated with the RGI-inducing Arthrobacter CL28 co-inoculated with each of the Variovorax or Burkholderia strains, or alone. Thus, the experiment included 42 individual treatments. The experiment was repeated twice, with three independent replicates per experiment. Upon collection, root morphology was measured (‘Root and shoot image analysis’ in ‘Deconstructing the synthetic community to four modules of co-occurring strains’).
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6

Regeneration Assays and Imaging of Arabidopsis

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Plants were grown as previously described (Efroni et al., 2015 (link)). Mutant alleles of jkd-4, nww and mp-S319 were previously characterized (Crawford et al., 2015 (link); Hassan et al., 2010 (link); Schlereth et al., 2010 (link)). Regeneration assays were performed as in Sena et al., (2009) (link). For hormonal treatment, root tips were cut at 80µm above the QC, moved to agar plates (1/2 MS, 0.5% sucrose, 0.8% agar, pH=5.7) containing 2,4-D (2,4-Dichlorophenoxyacetic acid; Sigma), BAP (6-benzylamino purine; Sigma) or both, and placed vertically in a growth chamber for recovery. For confocal imaging, seedlings were stained with propidium iodide (10µg/ml), mounted in water, and visualized using either Leica SPE or Leica SP5 confocal microscopes. For live imaging, cut roots of plants carrying the lineage marker, or the histone marker 35S:HG2B-mCherry, were placed between a coverslip and an agar block and imaged using an inverted SPE confocal at fixed intervals (also see Supplemental Experimental Procedures).
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7

Evaluation of ToxCast Phase II Chemicals

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Chemicals from the ToxCast Phase II library (ph 2 subset) were obtained from the National Center for Computational Toxicology (NCCT), U.S. EPA. The test library contained 777 samples, representing 768 unique chemicals; 9 chemicals were in duplicate to serve as internal quality controls. Chemicals were solubilized in dimethyl sulfoxide (DMSO) (≤2 × 10−2M, Table S1) and supplied in thirteen 96-well plates (62 samples per plate) (Evotec Inc., Branford, CT). Stock chemical plates were visually inspected under an inverted microscope to confirm solubility in each well (Table S1). All control chemicals, including sodium perchlorate (NaClO4), sodium nitrate (NaNO3), sodium thiocyanate (NaSCN), 2,4-dichlorophenoxyacetic acid (2,4-D), and 2,3-dichloro-1,4-napthoquinone (DCNQ) (Sigma Aldrich, St. Louis, MO), were initially solubilized in DMSO (EMD Millipore Corp., Darmstadt, Germany) at 2 × 10−2M. All chemicals in the ToxCast inventory supplied for testing undergo manual quality curation review prior to registration in EPA's DSSTox structure database (Richard et al., 2016 (link)), and are assigned DSSTox chemical identifiers (DTXSIDs, chemical names, CAS numbers) and mapped to chemical structures (DTXCIDs), wherever possible. These identifiers and maximum concentrations used in this study are provided in Table S1.
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8

Optimizing Heavy Metal Remediation Using Chemical Reagents

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Some of the chemicals, including 2,4-dichlorophenoxyacetic acid (the chemical formula of C8H6Cl2O3 and the purity of 99%) with a molecular weight of 221.04 g mol−1, lead nitrate (Pb(NO3)2, >99% purity) and nitric acid (HNO3, 95% purity) and sodium sulfate (Na2SO4, 99% purity) were provided by Sigma Aldrich (St. Louis, MO, USA). Other chemicals, i.e., CaCl2·2H2O, MgSO4·7H2O, KI, MnCl2·4H2O, FeCl3·6H2O, CuSO4·5H2O, H3BO3, CoCl2·6H2O, ZnSO4·7H2O, Na2MnO4·2H2O, EDTA, CaCl2·H2O and MgSO4·7H2O were bought from Merck Co, Germany. Sodium hydroxide (NaOH) and sulfuric acid (H2SO4) were also supplied by Merck Co (Darmstadt, Germany). The regulation of solution pH was carried out using 0.01 N H2SO4 and 0.01 N NaOH.
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9

Characterization of Herbicide Contaminants

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Metsulfuron methyl, MM (CAS: 74223-64-6, 99.3% purity, pKa: 3.3), 2,4-dichlorophenoxyacetic acid, 2,4-D (CAS: 94-75-7, 99.3% purity, pKa: 2.98) and paraquat, PQ (CAS: 75365-73-0, 98.0% purity) were purchased from Riedel-de Haën, Sigma-Aldrich. The 10 mM stock solutions at pH 6.0 ± 0.2 were prepared in 0.01 M NaCl. pH 6.0 ± 0.2 was adjust for all solutions using small volumes of HCl and/or NaOH solutions (1 M). pH measurements were performed by using a Cole Parmer Model 59003-25 pH meter with an Alpha® model PY-41 electrode.
The molecular structures of all contaminants are shown in Table S1 of the ESI. Considering the pKa values of 2,4-D and MM their anionic species are predominant at working pH; on the other hand, BAC-12, BAC-14 and PQ are quaternary ammonium salts, therefore they only form cations in aqueous solution.44 Calcium chloride CaCl2·2H2O (CAS: 10035-04-8, 99.0% purity) was supplied by Sigma-Aldrich Company. All other chemicals were analytical grade.
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10

Integrated ADME Characterization Protocol

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Optima HPLC grade methanol, Optima HPLC grade water, Optima HPLC grade acetonitrile, American Chemical Society (ACS) grade acetone, ACS grade methanol, ACS grade pentane, hydrochloric acid, ammonium acetate, dipotassium phosphate, monopotassium phosphate, magnesium chloride (MgCl2) and reduced glutathione (GSH) were purchased from Fisher Chemical (Fair Lawn, NJ, USA); NADPH, 1-aminobenzotriazole, methimazole, 1-naphthol and hydroxyacetone from Acros Organics (Morris Plain, NJ, USA); UDPGA, saccharolactone and 2,4-dichlorophenoxyacetic acid from Sigma-Aldrich (St. Louis, MO, USA); bupropion, benzydamine and alamethicin from Alfa Aesar (Ward Hill, MA, USA); oxcarbazepine from European Pharmacopoeia Reference Standard (Strasbourg, France); ticlopidine from Tokyo Chemical Industry (Tokyo, Japan); hydroxybupropion from Cerilliant Corporation (Round Rock, Texas, USA); deuterated acetone (acetone-d6) from Cambridge Isotope Labs (Cambridge, MA, USA); hydrogen peroxide (50%) from Univar (Redmond, WA, USA); HLM, rat liver microsomes (RLM), DLM and human lung microsomes (HLungM) from Sekisui XenoTech (Kansas City, KS, USA); human recombinant CYP (rCYP) bactosomes expressed in Escherichia coli (E. coli) from Cypex (Dundee, Scotland); human recombinant flavin monooxygenase (rFMO) supersomes and human recombinant UGT (rUGT) supersomes expressed in insect cells from Corning (Woburn, MA, USA).
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