other:
Article Title: Dopamine controls the Sensitivity to Manganese induced Dopaminergic neurotoxicity in Caenorhabditis elegans
Article Snippet: For studying the effect of Manganese on C. elegans , different concentrations of MnCl 2 (Merck-CAS #: 13446-34-9) solutions were used.
Plasmid Preparation:Article Title: A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria
Article Snippet: .. Kits High-Pure plasmid isolation kit (Roche, catalog number: 11754777001) Gene-Clean Turbo kit (Q-BIOgene, catalog number: 1102-400) Enzymes Pfu DNA polymerase (Promega, catalog number: M7741) T4 DNA ligase (New England Biolabs, catalog number: M0202L) Restriction enzyme Nhe I (New England Biolabs, catalog number: R3131S) Restriction enzyme Bsr GI (New England Biolabs, catalog number: R3575S) Restriction enzyme Spe I (New England Biolabs, catalog number: R3133L) Chemicals and other consumables 0.22 μm filter membranes (Merck, catalog number: GSWP02500) Multiwell microtiter plates, 96-well, Flat Bottom (Falcon, catalog number: 353072) 50 ml plastic tubes (Falcon) 2-ml microcentrifuge tubes 1.5-ml microcentrifuge tubes Aluminum foil Petri dishes Chloramphenicol (Sigma-Aldrich, catalog number: C0378-25G) Kanamycin sulfate (Roche, catalog number: 10106801001) Absolute ethanol (Sigma-Aldrich, catalog number: 1009832500) 85% (v/v) glycerol (Sigma-Aldrich, catalog number: 1040942500) NaCl (Merck, catalog number: 1.06404.1000) NaOH (Merck, catalog number: 1.06498.0500) CaCl 2 (Merck, catalog number: 1.02382.1000) RbCl (Sigma-Aldrich, catalog number: R2252-100G) MnCl 2 (Merck, catalog number: 1.05927.0100) Potassium acetate (Merck, catalog number: 1.04820.1000) Acetic acid (glacial) (Merck, catalog number: 1.00063.1000) MOPS (Sigma-Aldrich, catalog number: M1254-250G) 3-methylbenzoate (Sigma-Aldrich, catalog number: 89890) Agar (Conda, catalog number: 1806) Agarose D1 (Conda, catalog number: 8019.22) Bacto TM tryptone (BD, catalog number: 211705) Bacto TM yeast (BD, catalog number: 212750) Competent E. coli DH10B cells (see Recipes) Solution for DH10B competent cells TBFI (see Recipes) Solution for DH10B competent cells TBFII (see Recipes) 30 mg/ml chloramphenicol and 50 mg/ml kanamycin (see Recipes) LB broth (see Recipes) LB agar with 30 μg/ml chloramphenicol and/or 50 μg/ml kanamycin (see Recipes) 0.5 M 3-methylbenzoate (see Recipes) 50% (v/v) and 70% (v/v) ethanol (see Recipes) .. ABI Prism 377 automated DNA sequencer (Applied Biosystems Inc.) Electroporator (Gene Pulser, Bio-Rad) Orbital shaker Flasks (50 ml, 1 L) Pipettes (Gilson, models: PIPETMAN P2, P10, P20, P100, P200, P1000, P5000) Centrifuge (Tomy, model: MX-301) Thermal Cycler (Applied Biosystems, model: 2720Thermal Cycler) Temperature chamber (Taitec, model: Thermo minder SM-10R) Water bath shaker (Taitec, model: Personal-11) Plate reader (Corona, model: MTP-880Lab) Autoclave (Tomy Seiko, model: LSX-500)
Isolation:Article Title: A SsrA/NIa-based Strategy for Post-Translational Regulation of Protein Levels in Gram-negative Bacteria
Article Snippet: .. Kits High-Pure plasmid isolation kit (Roche, catalog number: 11754777001) Gene-Clean Turbo kit (Q-BIOgene, catalog number: 1102-400) Enzymes Pfu DNA polymerase (Promega, catalog number: M7741) T4 DNA ligase (New England Biolabs, catalog number: M0202L) Restriction enzyme Nhe I (New England Biolabs, catalog number: R3131S) Restriction enzyme Bsr GI (New England Biolabs, catalog number: R3575S) Restriction enzyme Spe I (New England Biolabs, catalog number: R3133L) Chemicals and other consumables 0.22 μm filter membranes (Merck, catalog number: GSWP02500) Multiwell microtiter plates, 96-well, Flat Bottom (Falcon, catalog number: 353072) 50 ml plastic tubes (Falcon) 2-ml microcentrifuge tubes 1.5-ml microcentrifuge tubes Aluminum foil Petri dishes Chloramphenicol (Sigma-Aldrich, catalog number: C0378-25G) Kanamycin sulfate (Roche, catalog number: 10106801001) Absolute ethanol (Sigma-Aldrich, catalog number: 1009832500) 85% (v/v) glycerol (Sigma-Aldrich, catalog number: 1040942500) NaCl (Merck, catalog number: 1.06404.1000) NaOH (Merck, catalog number: 1.06498.0500) CaCl 2 (Merck, catalog number: 1.02382.1000) RbCl (Sigma-Aldrich, catalog number: R2252-100G) MnCl 2 (Merck, catalog number: 1.05927.0100) Potassium acetate (Merck, catalog number: 1.04820.1000) Acetic acid (glacial) (Merck, catalog number: 1.00063.1000) MOPS (Sigma-Aldrich, catalog number: M1254-250G) 3-methylbenzoate (Sigma-Aldrich, catalog number: 89890) Agar (Conda, catalog number: 1806) Agarose D1 (Conda, catalog number: 8019.22) Bacto TM tryptone (BD, catalog number: 211705) Bacto TM yeast (BD, catalog number: 212750) Competent E. coli DH10B cells (see Recipes) Solution for DH10B competent cells TBFI (see Recipes) Solution for DH10B competent cells TBFII (see Recipes) 30 mg/ml chloramphenicol and 50 mg/ml kanamycin (see Recipes) LB broth (see Recipes) LB agar with 30 μg/ml chloramphenicol and/or 50 μg/ml kanamycin (see Recipes) 0.5 M 3-methylbenzoate (see Recipes) 50% (v/v) and 70% (v/v) ethanol (see Recipes) .. ABI Prism 377 automated DNA sequencer (Applied Biosystems Inc.) Electroporator (Gene Pulser, Bio-Rad) Orbital shaker Flasks (50 ml, 1 L) Pipettes (Gilson, models: PIPETMAN P2, P10, P20, P100, P200, P1000, P5000) Centrifuge (Tomy, model: MX-301) Thermal Cycler (Applied Biosystems, model: 2720Thermal Cycler) Temperature chamber (Taitec, model: Thermo minder SM-10R) Water bath shaker (Taitec, model: Personal-11) Plate reader (Corona, model: MTP-880Lab) Autoclave (Tomy Seiko, model: LSX-500)
Virus:Article Title: Protocol to monitor activation of a two-component system in Dickeya dadantii during chicory leaf infection using Phos-tag gel.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CpxR (1:1,000) Laboratory collection N/A Goat anti-rabbit IgG (1:10,000) Cytiva NA934-1ML Bacterial and virus strains Dickeya dadantii strain EC3937 Laboratory collection N/A Chemicals, peptides, and recombinant proteins Bromophenol blue Sigma B8026 EDTA Acros organic 14785-0010 MnCl 2 (4H 2 O) Merck M3634 SDS 20% Euromedex EU0660 Tris Euromedex 26-128-3094-B Ammonium persulfate (APS) Merck A3678 Tetramethylethylenediamine (TEMED) Merck T9281 Methanol Carlo Erba 414942 Formic acid Scharlau Ac1085 NaOH Carlo Erba 480507 BSA Roche 10735086001 Glycerol anhydrous Euromedex EU6550 PBS solution 10X Euromedex ET330 Tween 20 Euromedex 2001-A 40% acrylamide/bis-acrylamide solution (37.5:1) Bio-Rad 1610148 Phos-tag acrylamide, 10 mg FUJIFILM Wako AAL-107 TG-SDS 10X (Tris-Glycine-SDS) Euromedex EU0510 TG 10X (Tris-Glycine) Euromedex EU0550 LB (lysogeny broth) broth Lennox BD Difco 240230 Granulated agar BD Difco 214530 Color prestained protein standard, broad range New England Biolabs P7719 Critical commercial assays ECL Prime western blotting detection reagent GE Healthcare 28980926 Experimental models: Organisms/strains Chicory leaves Supermarket N/A Software and algorithms GraphPad Prism 10 GraphPad Software http://www.graphpad.com Quantity One Bio-Rad 1709602 ImageJ software Schneider et al. 8 https://imagej.net/ij/ Other PowerPac basic power supply Bio-Rad 1645050 Mini-PROTEAN tetra vertical electrophoresis cell for mini precast gels Bio-Rad 1658004 Mini-PROTEAN tetra cell casting module Bio-Rad 1658015 Trans-Blot Turbo transfer system Bio-Rad 1704150 Trans-Blot Turbo Mini 0.2 μm nitrocellulose transfer packs Bio-Rad 1704158 (Continued on next page) STAR Protocols 6, 103999, September 19, 2025 3 ..
Recombinant:Article Title: Protocol to monitor activation of a two-component system in Dickeya dadantii during chicory leaf infection using Phos-tag gel.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CpxR (1:1,000) Laboratory collection N/A Goat anti-rabbit IgG (1:10,000) Cytiva NA934-1ML Bacterial and virus strains Dickeya dadantii strain EC3937 Laboratory collection N/A Chemicals, peptides, and recombinant proteins Bromophenol blue Sigma B8026 EDTA Acros organic 14785-0010 MnCl 2 (4H 2 O) Merck M3634 SDS 20% Euromedex EU0660 Tris Euromedex 26-128-3094-B Ammonium persulfate (APS) Merck A3678 Tetramethylethylenediamine (TEMED) Merck T9281 Methanol Carlo Erba 414942 Formic acid Scharlau Ac1085 NaOH Carlo Erba 480507 BSA Roche 10735086001 Glycerol anhydrous Euromedex EU6550 PBS solution 10X Euromedex ET330 Tween 20 Euromedex 2001-A 40% acrylamide/bis-acrylamide solution (37.5:1) Bio-Rad 1610148 Phos-tag acrylamide, 10 mg FUJIFILM Wako AAL-107 TG-SDS 10X (Tris-Glycine-SDS) Euromedex EU0510 TG 10X (Tris-Glycine) Euromedex EU0550 LB (lysogeny broth) broth Lennox BD Difco 240230 Granulated agar BD Difco 214530 Color prestained protein standard, broad range New England Biolabs P7719 Critical commercial assays ECL Prime western blotting detection reagent GE Healthcare 28980926 Experimental models: Organisms/strains Chicory leaves Supermarket N/A Software and algorithms GraphPad Prism 10 GraphPad Software http://www.graphpad.com Quantity One Bio-Rad 1709602 ImageJ software Schneider et al. 8 https://imagej.net/ij/ Other PowerPac basic power supply Bio-Rad 1645050 Mini-PROTEAN tetra vertical electrophoresis cell for mini precast gels Bio-Rad 1658004 Mini-PROTEAN tetra cell casting module Bio-Rad 1658015 Trans-Blot Turbo transfer system Bio-Rad 1704150 Trans-Blot Turbo Mini 0.2 μm nitrocellulose transfer packs Bio-Rad 1704158 (Continued on next page) STAR Protocols 6, 103999, September 19, 2025 3 ..
Western Blot:Article Title: Protocol to monitor activation of a two-component system in Dickeya dadantii during chicory leaf infection using Phos-tag gel.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CpxR (1:1,000) Laboratory collection N/A Goat anti-rabbit IgG (1:10,000) Cytiva NA934-1ML Bacterial and virus strains Dickeya dadantii strain EC3937 Laboratory collection N/A Chemicals, peptides, and recombinant proteins Bromophenol blue Sigma B8026 EDTA Acros organic 14785-0010 MnCl 2 (4H 2 O) Merck M3634 SDS 20% Euromedex EU0660 Tris Euromedex 26-128-3094-B Ammonium persulfate (APS) Merck A3678 Tetramethylethylenediamine (TEMED) Merck T9281 Methanol Carlo Erba 414942 Formic acid Scharlau Ac1085 NaOH Carlo Erba 480507 BSA Roche 10735086001 Glycerol anhydrous Euromedex EU6550 PBS solution 10X Euromedex ET330 Tween 20 Euromedex 2001-A 40% acrylamide/bis-acrylamide solution (37.5:1) Bio-Rad 1610148 Phos-tag acrylamide, 10 mg FUJIFILM Wako AAL-107 TG-SDS 10X (Tris-Glycine-SDS) Euromedex EU0510 TG 10X (Tris-Glycine) Euromedex EU0550 LB (lysogeny broth) broth Lennox BD Difco 240230 Granulated agar BD Difco 214530 Color prestained protein standard, broad range New England Biolabs P7719 Critical commercial assays ECL Prime western blotting detection reagent GE Healthcare 28980926 Experimental models: Organisms/strains Chicory leaves Supermarket N/A Software and algorithms GraphPad Prism 10 GraphPad Software http://www.graphpad.com Quantity One Bio-Rad 1709602 ImageJ software Schneider et al. 8 https://imagej.net/ij/ Other PowerPac basic power supply Bio-Rad 1645050 Mini-PROTEAN tetra vertical electrophoresis cell for mini precast gels Bio-Rad 1658004 Mini-PROTEAN tetra cell casting module Bio-Rad 1658015 Trans-Blot Turbo transfer system Bio-Rad 1704150 Trans-Blot Turbo Mini 0.2 μm nitrocellulose transfer packs Bio-Rad 1704158 (Continued on next page) STAR Protocols 6, 103999, September 19, 2025 3 ..
Software:Article Title: Protocol to monitor activation of a two-component system in Dickeya dadantii during chicory leaf infection using Phos-tag gel.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CpxR (1:1,000) Laboratory collection N/A Goat anti-rabbit IgG (1:10,000) Cytiva NA934-1ML Bacterial and virus strains Dickeya dadantii strain EC3937 Laboratory collection N/A Chemicals, peptides, and recombinant proteins Bromophenol blue Sigma B8026 EDTA Acros organic 14785-0010 MnCl 2 (4H 2 O) Merck M3634 SDS 20% Euromedex EU0660 Tris Euromedex 26-128-3094-B Ammonium persulfate (APS) Merck A3678 Tetramethylethylenediamine (TEMED) Merck T9281 Methanol Carlo Erba 414942 Formic acid Scharlau Ac1085 NaOH Carlo Erba 480507 BSA Roche 10735086001 Glycerol anhydrous Euromedex EU6550 PBS solution 10X Euromedex ET330 Tween 20 Euromedex 2001-A 40% acrylamide/bis-acrylamide solution (37.5:1) Bio-Rad 1610148 Phos-tag acrylamide, 10 mg FUJIFILM Wako AAL-107 TG-SDS 10X (Tris-Glycine-SDS) Euromedex EU0510 TG 10X (Tris-Glycine) Euromedex EU0550 LB (lysogeny broth) broth Lennox BD Difco 240230 Granulated agar BD Difco 214530 Color prestained protein standard, broad range New England Biolabs P7719 Critical commercial assays ECL Prime western blotting detection reagent GE Healthcare 28980926 Experimental models: Organisms/strains Chicory leaves Supermarket N/A Software and algorithms GraphPad Prism 10 GraphPad Software http://www.graphpad.com Quantity One Bio-Rad 1709602 ImageJ software Schneider et al. 8 https://imagej.net/ij/ Other PowerPac basic power supply Bio-Rad 1645050 Mini-PROTEAN tetra vertical electrophoresis cell for mini precast gels Bio-Rad 1658004 Mini-PROTEAN tetra cell casting module Bio-Rad 1658015 Trans-Blot Turbo transfer system Bio-Rad 1704150 Trans-Blot Turbo Mini 0.2 μm nitrocellulose transfer packs Bio-Rad 1704158 (Continued on next page) STAR Protocols 6, 103999, September 19, 2025 3 ..
Electrophoresis:Article Title: Protocol to monitor activation of a two-component system in Dickeya dadantii during chicory leaf infection using Phos-tag gel.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies CpxR (1:1,000) Laboratory collection N/A Goat anti-rabbit IgG (1:10,000) Cytiva NA934-1ML Bacterial and virus strains Dickeya dadantii strain EC3937 Laboratory collection N/A Chemicals, peptides, and recombinant proteins Bromophenol blue Sigma B8026 EDTA Acros organic 14785-0010 MnCl 2 (4H 2 O) Merck M3634 SDS 20% Euromedex EU0660 Tris Euromedex 26-128-3094-B Ammonium persulfate (APS) Merck A3678 Tetramethylethylenediamine (TEMED) Merck T9281 Methanol Carlo Erba 414942 Formic acid Scharlau Ac1085 NaOH Carlo Erba 480507 BSA Roche 10735086001 Glycerol anhydrous Euromedex EU6550 PBS solution 10X Euromedex ET330 Tween 20 Euromedex 2001-A 40% acrylamide/bis-acrylamide solution (37.5:1) Bio-Rad 1610148 Phos-tag acrylamide, 10 mg FUJIFILM Wako AAL-107 TG-SDS 10X (Tris-Glycine-SDS) Euromedex EU0510 TG 10X (Tris-Glycine) Euromedex EU0550 LB (lysogeny broth) broth Lennox BD Difco 240230 Granulated agar BD Difco 214530 Color prestained protein standard, broad range New England Biolabs P7719 Critical commercial assays ECL Prime western blotting detection reagent GE Healthcare 28980926 Experimental models: Organisms/strains Chicory leaves Supermarket N/A Software and algorithms GraphPad Prism 10 GraphPad Software http://www.graphpad.com Quantity One Bio-Rad 1709602 ImageJ software Schneider et al. 8 https://imagej.net/ij/ Other PowerPac basic power supply Bio-Rad 1645050 Mini-PROTEAN tetra vertical electrophoresis cell for mini precast gels Bio-Rad 1658004 Mini-PROTEAN tetra cell casting module Bio-Rad 1658015 Trans-Blot Turbo transfer system Bio-Rad 1704150 Trans-Blot Turbo Mini 0.2 μm nitrocellulose transfer packs Bio-Rad 1704158 (Continued on next page) STAR Protocols 6, 103999, September 19, 2025 3 ..
Concentration Assay:Article Title: The Rel stringent factor from Thermus thermophilus : crystallization and X-ray analysis
Article Snippet: .. The MnCl 2 (Merck) used to titrate Rel Tt NTD was dissolved in a matching buffer to a concentration of 400–1000 μ M . The titrations were performed on an affinity ITC instrument (TA Instruments) at 10°C by injecting 2 μl of the MnCl 2 solution for each titration point at 200 s intervals with the stirring rate set to 75 rev min −1 . .. Data analysis and modelling were performed as described previously (Garcia-Pino et al. , 2016 ; Talavera et al. , 2018 ) with NanoAnalyze (TA Instruments) and MicroCal Origin 7.0.
Titration:Article Title: The Rel stringent factor from Thermus thermophilus : crystallization and X-ray analysis
Article Snippet: .. The MnCl 2 (Merck) used to titrate Rel Tt NTD was dissolved in a matching buffer to a concentration of 400–1000 μ M . The titrations were performed on an affinity ITC instrument (TA Instruments) at 10°C by injecting 2 μl of the MnCl 2 solution for each titration point at 200 s intervals with the stirring rate set to 75 rev min −1 . .. Data analysis and modelling were performed as described previously (Garcia-Pino et al. , 2016 ; Talavera et al. , 2018 ) with NanoAnalyze (TA Instruments) and MicroCal Origin 7.0.
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