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15 protocols using sodium borodeuteride

1

C57BL/6 Mice Animal Care Protocol

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C57BL/6 mice of 8 weeks years old (n = 120) were purchased from Shanghai jiesijie experimental animal Co., Ltd. All animal experiments were in accordance with the requirements of the Animal Experiment Ethics Committee of Fudan University and were approved. Animals were maintained on commercial normal diet (proteins 24.02%, fat 12.95%, carbohydrates 63.03%, 3.44 kcal/g) from Beijing Keao Xieli Feed Co., Ltd. Complete diet composition is listed in Table S1. The environment was kept at 23 ± 2°C, and 12 h light/dark cycle with light on at 06:00 a.m.
Reagents: Sodium dodecyl sulfate (SDS), 1‐hydroxybenzotriazole monohydrate (HOBt), sodium borodeuteride (NaBD4), formic acid (FA), trifluoroacetic acid (TFA), sodium hydroxide (NaOH), super‐2,5‐dihydroxybenzoic acid (super‐DHB), 10 × phosphate buffered solution (PBS), dimethyl sulfoxide (DMSO) and Sepharose CL‐4B were purchased from Sigma Aldrich. Acetonitrile (ACN) and ethanol (EtOH) were provided by Merck Millipore. NP‐40 and peptide‐N‐glycosidase F (PNGase F) were from New England Biolabs (Inc.). The FiltrEX™ 96‐well Clear Filter Plates with 0.2 μm PVDF Membrane were from Corning. Milli‐Q water (MQ) was provided by Milli‐Q system.
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2

Synthesis of Deuterated Methyl Compounds

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Dimethyl sulfoxide and pyridine were purchased from Merck (Germany), iodomethane and sodium borodeuteride from Sigma–Aldrich (USA), sodium hydroxide, chloroform, methanol, and ammonium hydroxide from Slavus (Slovakia), sodium sulfate, formic acid, and acetic anhydride from Lachema (Czech Republic), trifluoroacetic acid from AppliChem (Germany).
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3

Chemical Reagents for Cellular Assays

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Solvents for extraction and LC–MS (acetone, n-hexane/s, dichloromethane, acetonitrile, methanol and water) were of HPLC or Optima LC–MS grade and from Fisher Scientific (Hampton, NH, USA). Formic and acetic acid (both pro analysis grade), sodium borohydride (≥98.5%), sodium borodeuteride (98 atom-% D), sodium periodate (≥99.8%) and methanol-d4, (≥99.8 atom-% D) were from Sigma–Aldrich (St. Louis, MO, USA). All cell culture and assay reagents (DMSO, ouabain, veratrine, phosphate-buffered saline, trypsin, and methylthiazolyldiphenyltetrazolium bromide (MTT), supplements (fetal bovine serum; l-glutamine; sodium pyruvate, penicillinstreptomycin), and Roswell Park Memorial Institute (RPMI) culture medium were of the highest grade available and sourced from Sigma–Aldrich (St. Louis, MO, USA) and Fisher Scientific (Hampton, NH, USA). CTX3C was from Wako Chemicals USA (Richmond, VA, USA). Supplemented RPMI medium contained heat-inactivated fetal bovine serum (5% by volume), sodium pyruvate (1 mM), l-glutamine (2 mM), penicillin (50 units/mL), and streptomycin (50 ng/mL).
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4

Analysis of Cell Glycome Composition

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The total cell N-glycome and O-glycome of cell lines were prepared as described previously (60 , 61 (link)). O-Glycans were reduced with sodium borohydride or sodium borodeuteride (Sigma). Released glycans were permethylated with iodomethane and powdered sodium hydroxide (36 (link), 62 ). Permethylated glycans were fractionated by Sep-Pak C18 Classic Cartridge into 15, 35, 50, and 75% acetonitrile fractions and analyzed by MALDI-TOF and MALDI-TOF-TOF on an ABSciex 5800, as described previously (36 (link)). Glycan compositional assignment was confirmed by extensive MS/MS fragmentation analysis with manual interpretation and reconstruction of the precursor ions using GlycoWorkBench (63 (link)).
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5

Characterization of Hull-less Barley Polysaccharides

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Hull-less barley was cultivated in Qinghai Province, China. Enzymes (thermostable α-amylase, amyloglucosidase and papin) were provided by Aladdin Biochemical Technology Co., Ltd. (Shanghai, China). The β-glucan assay kit was from Megazyme International (Wicklow, Ireland). d-xylose was obtained from J&K Scientific Ltd. (Beijing, China). Other monosaccharide standards (d-arabinose, d-galactose, d-glucose, glucuronic acid, and galacturonic acid), deuterium oxide (D2O), dimethyl sulfoxide-d6 (DMSO-d6), methyl iodide, and sodium borodeuteride (98 atom% d) were bought from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA). All other used reagents were of analytical grade unless otherwise specified.
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6

Synthesis of Organometallic Compounds

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All reagents were purchased from Acros Organics or Sigma-Aldrich and used without further purification: hexachloroplatinic(IV) acid (H2PtCl6·6H2O, 99%, metals basis), silver nitrate (AgNO3, 99% metals basis), adamantane-1-thiol (C10H15SH, 95%), cyclohexyl mercaptan (HS-c-C6H11, 95%), 2-bromoadamantane (C10H15Br, 99.9%), sodium borohydride (NaBH4, 99.9%), sodium borodeuteride (NaBD4, 99.5%), potassium thioacetate (C2H3KOS, 99.9%), cesium acetate (CH3COOCs, 99% metals basis), methylene chloride [CH2Cl2, high-performance liquid chromatography (HPLC), Sigma-Aldrich], methanol (CH3OH, HPLC, Sigma-Aldrich), methanol-OD (CH3OD, 99.5 atom% D, Sigma-Aldrich), water-D2 (D2O, 99.9 atom% D, Sigma-Aldrich), water-18O (H218O, 98 atom% 18O, Sigma-Aldrich), ethanol (CH3CH2OH, HPLC, Sigma-Aldrich), ether (C2H5OC2H5, HPLC, Sigma-Aldrich), N,N-dimethylformamide (C3H7NO, HPLC, Sigma-Aldrich), and n-hexane (C6H14, HPLC, Sigma-Aldrich).
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7

Quantification of Intestinal Permeability

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Intestinal permeability was determined by quantification of urinary excreted sugars after ingestion of an oral sugar cocktail [42 (link)–44 (link)]. The oral sugar cocktail was taken by the HC subjects seven days after the endoscopic sigmoid colon mucosa and fecal specimens were collected. Fasted HC subjects were given an oral cocktail of 40 g sucrose, 2 g mannitol, 7.5 g lactulose mixed in 8 oz. of water and 1 g sucralose in two capsules at 6 AM, and then urine was collected for 24 hours. Urinary concentrations of excreted sugars were determined using gas chromatography and an internal standard as previously described [42 (link),44 (link)]. The intestinal permeability results were expressed as percent excretion of oral dose of the various sugars as previously described [42 (link),44 (link)].
Lactulose (4-o-β-D-galactopyranosyl-D-fructofuranose) was obtained from Bertek Pharmaceuticals, as brand name Kristalose. Mannitol (D-mannitol) and sucrose (α-D-glucopyranosyl-β-D-fructofuranoside) were obtained from Sigma Aldrich. Sucralose (1,6-dichloro-1,6-dideoxy-β-D-fructofuranosyl-4-chloro-4-deoxy-α-D-glucopyranoside) was supplied by Tate and Lyle. Trifluoroacetic acid ammonia, sodium borodeuteride, acetone, acetic anhydride and glacial acetic acid were purchased at their highest grade purity from Sigma Aldrich.
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8

Extraction and Characterization of Dendrobium nobile

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Dendrobium nobile Lindl. was obtained from Guizhou Chishui Guoli Dendrobium nobile Lindl. Development Co., Ltd. (Guizhou, China), dried and crushed, and then screened with 80 meshes.
MD2-IN-1, TLR4-IN-C34, IL-10, IL-6, IL-1 β, TNF-α ELISA kit were purchased from Shanghai Jianglai Biotechnology Co., Ltd. (Shanghai, China); mouse macrophage RAW264.7 was provided by Zhejiang Meisen Cell Technology Co., Ltd. (Wenzhou, China); DMEM High-Glucose Medium and FBS were acquired from Gibco (New York, NY, USA); CCK-8 Kit was purchased from Wuhan Doctor De Bioengineering Co., Ltd. (Wuhan, China); NO detection kit was obtained from Shanghai Biyuntian Biotechnology Co., Ltd. (Shanghai, China); trifluoroacetic acid, acetic acid, LPS, dimethyl sulfoxide, sodium borodeuteride, and acetic anhydride were purchased from Sigma (Kalamazoo, MI, USA).
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9

Carbohydrate Characterization Protocol

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Lactulose (4-o-β-D-galactopyranosyl-D-fructofuranose) was obtained from Bertek Pharmaceuticals, as brand name Kristalose. Mannitol (D-mannitol) and sucrose (α-D-glucopyranosyl-β-D-fructofuranoside) were obtained from Sigma Aldrich. Sucralose (1,6-dichloro-1,6-dideoxy-β-D-fructofuranosyl-4-chloro-4-deoxy-α-D-glucopyranoside) was supplied by Tate and Lyle. Trifluoroacetic acid ammonia, sodium borodeuteride, acetone, acetic anhydride and glacial acetic acid were purchased at their highest grade purity from Sigma Aldrich.
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10

Glycan Characterization Protocol

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Sialyl lewis A (SLA), sialyl lewis X (SLX), Lewis B, Lewis Y, lacto-N-tetraose (LNT), and lacto-N-neotetraose (LNnT) were purchased from Dextra Laboratories (Reading, UK). Lacto-N-fucopentaose (LNFP) I, II, and III were acquired from V-LABS, Inc. (Covington, LA). Cellohexaose (CelHex), maltohexaose (MalHex), A2F and NA2F glycans were purchased from Carbosynth Limited (Berkshire, UK). Synthetic N-linked glycan standards (N002 to N233) were obtained from Chemily Glycoscience (Atlanta, GA). Man9 N-glycan, H218O (97%) water, 2-aminopyridine, acetic acid, dimethyl sulfoxide (DMSO), sodium hydroxide, methyl iodide, chloroform, sodium borodeuteride, and cesium acetate were purchased from Sigma-Aldrich (St. Louis, MO). Pierce PepClean C18 spin columns were acquired from ThermoFisher Scientific.
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