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129 protocols using hydroxylamine

1

Synthesis of Gold Nanoparticles

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Tetraethylorthosilicate (TEOS), tetrakis (hydroxymethyl) phosphonium chloride (THPC), 3-aminopropyltrimethoxysilane (APTMS), sodium hydroxide, hydroxylamine (50% in H2O), potassium carbonate and chloroauric acid tetrahydrate (HAuCl4.4H2O) were obtained from Sigma-Aldrich. Ammonium hydroxide solution (30%) was purchased from Merck Company. All the reagents were analytical grade and used as received.
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2

FRET-based Binding Assay for 14-3-3θ

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The Site 2 and Sites 2,4 peptides were fluorescently labeled at the amidated C-terminus. Both peptides were labeled with the donor probe Alexa Fluor 488 NHS Ester, whereas the Site 2 peptide was additionally labeled with the acceptor probe Alexa Fluor 568 NHS Ester (Thermo Fisher Scientific). The labeling reaction was performed at 25 °C for 1 h in 20 mM MES pH 6.8 and 50 mM NaCl and at a peptide concentration of 5 mg mL−1 with a 2-fold molar excess of fluorescent dye. The labeling reaction was stopped with the addition of a 10-fold molar excess of hydroxylamine (Sigma-Aldrich Corporation). Labeled peptides were separated from any remaining unlabeled peptide using a Symmetry300 C18 reverse phase HPLC column (Waters Corporation, Milford, MA). The peptides were lyophilized, resuspended in 100 mM HEPES pH 7.5, and dialyzed against 25 mM HEPES pH 7.5, 50 mM NaCl and 1 mM MgCl2. The donor-labeled peptides were pre-incubated with 14-3-3θ at a 1:1 molar ratio (i.e., one peptide per 14-3-3θ dimer). The acceptor-labeled Site 2 peptide (at 5 μM concentration) was then titrated into the preformed complexes. The steady-state fluorescence emission spectra were recorded at 25 °C, with an excitation wavelength of 495 nm (5-nm slit width) and an emission wavelength of 520 nm (5-nm slit width).
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3

Biochemical Reagent Procurement Protocol

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DBDB was purchased from Prime Organics, Inc. (Mumbai, India). Hydroxylamine, sarcosine (N-methylglycine), potassium pyrophosphate, trifluoroacetic acid and acetonitrile were purchased from Sigma-Aldrich (St. Louis, MO). Glycerol was purchased from Fisher Scientific (Pittsburg, PA). Catalase was from USB Corporation (Cleveland, OH).
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4

CSF Proteomic Analysis via TMT Labeling

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The CSF samples (100 µl) were mixed with 50 µl 8 M guanidine hydrochloride solution (Sigma-Aldrich) and 15.6 µl 1 M triethylammonium bicarbonate buffer (TEAB) (Sigma-Aldrich). Cysteine disulfides were reduced by addition of 4.2 µl 200 mM tris(2-carboxyethyl)phosphine (TCEP) (Thermo Scientific) and incubation at 55 °C for 1 hour after which the samples were allowed to cool to room temperature. To alkylate cysteines, 4.3 µl 400 mM iodoacetamide (Sigma) were added, followed by incubation at room temperature in the dark for 30 min. TMT 10-plex reagents (Thermo Scientific) were dissolved in acetonitrile (ACN) to a concentration of 19.5 mg/mL and 19.5 µl of the reagent solution were added to each sample, after which they were incubated for 1 hour at room temperature. The TMT labeling reaction was then quenched by adding 9.7 µl of 5% (v/v) hydroxylamine (Sigma-Aldrich) to the samples, after which they were pooled into TMT sets.
The study samples were randomly distributed over the TMT sets, the discovery study (120 samples) comprising 14 TMT sets and the validation study (60 samples) comprising seven. A reference sample, prepared by pooling aliquots of all CSF samples in the respective study was labeled with TMT-131 and used for inter-TMT set data normalization.
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5

Antibody-Based Detection of E. coli and MS2 Bacteriophage

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Optical qPCR tubes (8× strip, catalog
no. 401428) and separate caps (8× strip, catalog no. 401425)
were obtained from Agilent Technologies (Santa Clara, CA). Rabbit
polyclonal anti-E. coli antibodies were obtained
from Fitzgerald (Acton, MA). Rabbit polyclonal anti-MS2 antibodies
were obtained from Tetracore (Rockville, MD). E. coli (strain MB1457), and bacteriophage MS2 (strain 15597-B1) were obtained
from the American Type Culture Collection (Manassas, VA). Phosphate
buffered saline (PBS) tablets (10 mM Phosphate, 2.7 mM potassium chloride,
140 mM sodium chloride, pH 7.4) were purchased from Bioline (Taunton,
MA). Anonymized human serum was obtained from the Gulf Coast Regional
Blood Center (Houston, TX). Fluorescein isothiocyanate (FITC) was
obtained from Pierce (Rockford, IL). 1-Ethyl-3-(3-(dimethylamino)propyl)
carbodiimide hydrochloride (EDC), N-hydroxysuccinimide
(NHS), bovine serum albumin (BSA), Tween-20, hydroxylamine, 6-mercapto-1-hexanol,
dimethyl sulfoxide (DMSO), anhydrous chromium trioxide, 96.7% sulfuric
acid, dithiobis(succinimidyl propionate) (DSP), and sodium cyanoborohydride
were purchased from Sigma-Aldrich (St. Louis, MO).
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6

Quantifying GCL Degradation in Mycobacteria

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For induction assays in which GCL was added to the growth medium, GCL degradation was monitored by a colorimetric method typically used for the analysis of ester molecules (Yang et al., 2006 (link)). The reaction between the ester group of GCL and hydroxylamine leads to the formation of hydroxamic acid in alkaline solution. This hydroxamic acid forms a highly colored complex with ferric ions, which can be quantified by spectrophotometry at 520 nm. GCL was quantified as described by Cirou et al. (2012) (link) and Barbey et al. (2018) (link). Briefly, culture supernatants were centrifuged at 5000 × g for 5 min, and 200 μl of the resulting supernatant was successively mixed with 250 μl of 2 M hydroxylamine (Sigma-Aldrich)/3.5 M NaOH (Merck) (1:1, v/v) and 250 μl of 10% iron chloride (Sigma-Aldrich) prepared in 4 M HCl/95% ethanol (Merck) (1:1, v/v). The absorbance of the mixture at 520 nm was analyzed against a blank consisting of the same mixture but with the culture supernatant s replaced with non-inoculated 7H9 medium without GCL. Non-inoculated 7H9 medium supplemented with GCL was incubated and analyzed under the same conditions as the inoculated media to check the stability of GCL.
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7

Plant Cell Culture Optimization

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Murashige and Skoog medium, 2,4-dichlorophenoxyacetic acid (2,4-D), kinetin, 2-(N-morpholino)ethanesulfonic acid (MES), triphenil-tetrazolium chloride (TTC), xylenol orange, EDTA, succinate, 4-morpholinepropanesulfonic acid (MOPS), Polyvinylpyrrolidone (PVP-40), hydroxylamine, sulphanilamide, α-naphthylamine, ampicillin, NP40, safranin, Salicylhydroxamic acid (SHAM), kalium-cyanide (KCN), linoleic acid, fatty acid free bovine serum albumin (BSA), luminol, p-Coumaric acid, Carbonyl cyanide-p-trifluoromethoxyphenylhydrazone (FCCP), were obtained from Sigma-Aldrich. ProBond Purification System was purchased from Invitrogen. Amicon Ultra 30K Centrifugal Filter Units were purchased from Merck. IPTG was obtained from Duchefa Biochemie, cytochrome c was purchased from Fluka. Primary and secondary antibodies were purchased from Agrisera Antibodies. All other chemicals were of analytical or HPLC grade, and were purchased from Reanal, Hungary. Pierce BCA Protein Assay Kit, GeneJET Plant RNA Purification Kit, and RevertAid First-Strand cDNA Synthesis Kit were obtained from Thermo Scientific; SensiFAST SYBR No-ROX Kit was purchased from Bioline.
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8

Gold-coated Manganese Ferrite Nanoparticle Synthesis

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Gold-coated manganese ferrite core-shell nanoparticles were prepared by the growth and coalescence of the gold-decorated nanoparticles as obtained in the previous section. The procedure was based on a previously reported “seeding” method [30 (link)]. Briefly, to a 1.5 mL aqueous solution of MnFe2O4 decorated with gold nanoparticles ([Au] = 0.6 mM), 2.4 mL of HAuCl4 (0.01%) and 100 µL of hydroxylamine (product number 255580 from Sigma-Aldrich, St. Louis, MO, USA) (40 mM) were added. Additional growth was promoted by the further addition of 100 µL of 1% HAuCl4. Purification was conducted by washing with water through magnetic decantation and, at the end, the particles were dispersed in ethanol. In order to monitor the gold shell formation, absorption spectra were measured in 10 s intervals.
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9

Peptide Synthesis and Modification

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Synthetic peptide GCLGNAK was acquired from AnaSpec (San Jose, CA). Palmitoyl chloride, dithiothreitol (DTT), hydroxylamine (HA), and ammonium bicarbonate (ABC) were purchased from Sigma-Aldrich (St. Louis, MO). Trifluoroacetic acid (TFA), formic acid (FA), and iodoacetamide (IAM) were purchased from Pierce (Rockford, IL). RapiGest was obtained from Waters (Milford, MA). 2,5-dihydroxybenzoic acid (DHB) was obtained from Bruker Daltonics (Billerica, MA). Acetonitrile (ACN) and isopropanol (IPA) were obtained from Burdick and Jackson (Muskegon, MI).
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10

Purification and Analysis of ADP-Ribosylated Peptides

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Products of ADP-ribosylation reactions containing 10 μg of protein were purified using standard TCA precipitation and resuspended in PBA buffer (100 mM HEPES pH 8.5, 150 mM NaCl, 2 mM MgCl2). If required, cysteines were reduced in 10 mM dithiotreitol for 30 min at room temperature and alkylated with 10 mM iodoacetamide for 30 min at room temperature in the dark. Proteins were digested with 100 ng trypsin (Promega) overnight at 37 °C and peptides bound to m-aminophenylboronic acid agarose beads (Sigma) for 1 h at 4 °C. The beads were washed extensively with PBA buffer and the ADP-ribosylated peptides eluted with 1 M hydroxylamine (Sigma) pH 7.0 overnight at room temperature. Eluates were purified using C18 ZipTips (Millipore) according to manufacturer instructions and analysed by nano-LC-MS (ThermoFisher U3000 nanoLC and Orbitrap XL mass spectrometer)39 (link). The raw mass spectrometry and tandem mass spectra were converted to.mgf format using Compass39 (link) and searched against the SwissProt database using Mascot (Matrix Science). Search parameters employed a precursor tolerance of 7 p.p.m. and a fragment ion tolerance of 0.8 Da. Quantification of precursor ions employed Skyline40 (link). ADP-ribosylation sites were identified based on a characteristic +15.0109 Da shift on glutamate and aspartate residues41 (link).
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