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12 protocols using d phenylalanine

1

Amino Acid Synthesis and Characterization

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d-Alanine, d-Arginine, d-Asparticacid, d-Asparagine, d-Glutamicacid, d-Histidine, d-Isoleucine, d-Leucine, d-Lysine, d-Methionine, d-Phenylalanine, d-Proline, d-Serine, d-Threonine, d-Tryptophan, d-Tyrosine, d-Valine, KBr (spectral grade), bovine serum albumin (BSA), glutathione and 3,3′,5,5′-tetramethylbenzidine (TMB) were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA). d-Cystine and d-Glutarnine were purchased from Aladdin Reagent Co, Ltd. (Shanghai, China). All other chemicals and reagents were of analytical grade. All aqueous solutions were prepared with Milli-Q water.
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2

Comprehensive Phytochemical Analysis

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Chemicals and reagents: Chromatography grade methanol and acetonitrile were purchased from Merck (Darmstadt, Germany). High liquid chromatography grade formic acid was purchased from Fluka (Buchs, Switzerland). Ultrapure water was prepared using a Milli-Q water purification system (Millipore Corp., Billerica, MA, USA). The following standard compounds were obtained from Aladdin: rutin, kaempferol, quercetin, apigenin, quercetin 3-β-d-glucoside, luteolin, d-phenylalanine, and hydroxysafflor yellow A. Narigenin was obtained from Sigma-Aldrich (St. Louis, MO, USA). kaempferol-3-O-β-rutinoside, kaempferol-3-O-β-d-glucoside, and carthamin were synthesized in our laboratory. All other chemicals were of analytical grade, with purities higher than 98%.
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3

Immobilization of Phenylalanine Enantiomers

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3-Aminopropyltriethoxysilane (98%, APTES), glutaraldehyde (GA), D-phenylalanine and L-phenylalanine were purchased from Sigma (USA). The support of immobilization (MCF-41, pore size of 2–12 nm, BET of 800 m2 g−1) was purchased from Nanjing XFNANO Materials Tech Co., Ltd. (China). Other reagents, such as DL-phenylalanine, methanol, acetone and toluene were purchased from Sinopharm Chemical Reagent Co., Ltd. (Shanghai, China).
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4

Regulation of mTORC1 by Amino Acids

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Cells were serum-starved overnight in RPMI 1,640 medium without amino acids and were restimulated with RPMI supplemented with EAA (or MEM) or 0.4 mM L-leucine (LEU222.25, Bioshop) for the indicated times. For knockdown of ATP6V0c experiment, HeLa cells were transfected with either control or ATP6V0c-715 siRNA (Abcam) and HA-LAPTM4b 48 h prior to serum starvation. For the ccA experiments, cells were transfected with HA-LAPTM4b where indicated and then treated with 5 μM ccA (Sigma) for 1 h prior to stimulation. For Rag A (Q66L) rescue experiments, HeLa cells were transfected with CFP-Rag A (Q66L) for 48 h, starved for 1.5 h and stimulated with EAA with or without 20 mM D-phenylalanine (P1751, Sigma) for the indicated times. Cells were lysed in lysis buffer and mTORC1 activation was monitored using anti-pT389-S6K1 and anti-p4E-BP1 antibodies. All blots were imaged using the Odyssey Imaging system and quantified using Image Studio version 3.1.4 (LI-COR).
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5

Synthesis of PBI Derivative (D-PBI)

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The chemical structure of the PBI derivative (D-PBI) is reported in Figure 1. It was obtained according to the procedure reported in the literature (Gershberg et al., 2015 (link)).
Milli-Q grade water was used to dissolve the PBI derivative and all the organic compounds (D-phenylalanine, L-phenylalanine, D-serine, D-histidine), used in this contribution, were purchased from Sigma-Aldrich and used as received.
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6

Modulating NK Cell Activation Pathways

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NK cells were cultured in medium or with 200 U/ml IL-2 for 5, 10, 15, 20, or 24 h at 37°C and 5% CO2 prior to stimulation. Where indicated, the following inhibitors were added to cells 1 hr prior to stimulation: 10 mM L-glutamic acid γ-(p-nitroanilide) hydrochloride (GPNA) (Santa Cruz Biotechnology) (1M GPNA solution was prepared in DMSO and kept at 37°C immediately prior to its addition), 100 mM D-phenylalanine (Sigma-Aldrich) (dissolved in medium for 1 h at 37°C by vortexing every 5-10 min prior to addition); 100 nM rapamycin (Calbiochem) (109.4 μM rapamycin in DMSO stock was stored at -20° C, thawed, and diluted in medium prior to addition); 100 nM Torin-1 (ApexBio) (1.645 mM Torin-1 in DMSO stock was stored at -80°C, thawed, and diluted in medium before addition). Nunc maxisorp ELISA plates (Thermo Fisher Scientific) were washed twice with PBS and then coated with 5 μg/ml anti-NKG2D mAb (1D11, BioLegend) or 5 μg/ml control mouse IgG1 (MOPC-21, UCSF Monoclonal Antibody Core) in PBS for 24 h at 4°C. After coating, the plates were washed twice with PBS and blocked in complete medium for 10 min at room temperature (RT). For IFNγ measurements, GolgiSTOP was added to cells immediately prior to stimulation. Stimulation of 1.5 × 105 cells/well proceeded for 5 h at 37°C and 5% CO2.
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7

Murine Bone Marrow-Derived Macrophage Culture

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Murine bone marrow cells were cultured in six-well plates in the RPMI 1640 medium (Sigma), or nonessential amino acid RPMI 1640 medium (BioConcept) without or with supplementation of L-leucine (0.05 g/L) containing 10% FCS and supplemented with 0.05 mM 2-ME, 100 U/ml penicillin, and 100 µg/ml streptomycin. Bone marrow-derived macrophages were generated by adding 20 ng/ml M-CSF (BioLegend) to the cultures. After 7 days, macrophages were either stimulated with 100 ng/ml lipopolysaccharide (LPS) from Escherichia coli O111:B4 (Sigma) and 10 ng/ml recombinant mouse IFN-γ (rmIFN-γ; BioLegend) or with 10 ng/ml recombinant mouse IL-4 (rmIL-4; BioLegend) and 10 ng/ml recombinant mouse IL-13 (rmIL-13; BioLegend) for 6 h before cells were analyzed. For conditional deletion of CD98c in vitro, tamoxifen dissolved in DMSO (Roth) was added into the culture during the macrophage generating and during LPS + IFNγ or IL-4 + IL-13 stimulation or D-phenylalanine (Sigma) was added 1 h prior and during LPS + IFNγ or IL-4 + IL-13 stimulation.
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8

Inhibition of Amino Acid Transporters and mTORC1 in Cell Lines

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HT-29 cells were cultured in RPMI 1640 media with 10% fetal bovine serum (FBS; Gibco), and 1% penicillin/streptomycin. Caco-2 cells were cultured in DMEM media, with sodium pyruvate, 10% FBS, and 1% penicillin/streptomycin. Cells were treated with the SLC3A2/SLC7A5 inhibitors, 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH, 20mM, Sigma) or D-phenylalanine (25 mM, Sigma) 1h prior or 3h prior (respectively) to infection and maintained during the infection. Cells were treated with the mTORC1 agonist rapamycin (25mg/ml in DMSO, LC Labs) 1h prior to infection and maintained during the infection.
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9

Adipocyte Differentiation and Autophagy Assay

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D-Phenylalanine (Cat# P1751), L-Leucine methyl ester hydrochloride (Cat# L1002), L-γ-glutamyl-p-nitoanilide (γ-GPNA) (Cat# G6133), L-Leucine (Cat# L8000), cycloheximide (Cat# C4859), puromycin (Cat# P9620), polybrene (Cat# H9268), doxycycline (Cat# D9891), Protein A Sepharose beads (Cat# P9424), Anti-FLAG M2 Magnetic Beads (Cat# M8823), bicinchonic acid solution (BCA) (Cat# B9643), Copper (II) sulfate solution (Cat# C2284), troglitazone (Cat# T2573), insulin (Cat# I9278), IBMX (Cat# I5879), dexamethasone (Cat# D4902), Oil Red O solution (Cat# O1391), cOmplete protease inhibitor tablets (Cat# 4693124001) and Earle’s Balanced Salt Solution (EBSS) (Cat# E2888) were obtained from Sigma-Aldrich. Fetal Bovin Serum (FBS) (Cat# 10270-106), penicillin/streptomycin (Cat#15140-122), glutamine (Cat#25030-024), accutase (Cat#A11105-01), trypsin (Cat# 15090-046), Dulbecco’s Modified Eagle Medium (DMEM) (Cat# 21969-035), LysoTracker Deep Red (cat#L12492) and 50X MEM amino acid solution (Cat# 11130-036) were purchased from Thermo Fisher Scientific. Rapamycin (Cat# R-5000) and Bafilomycin A1 (Cat# B-1080) were obtained from LC laboratories.
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10

Biomaterial Synthesis and Characterization

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l-phenylalanine, d-phenylalanine, l-tryptophan, 2-hydroxyethyl methacrylate (HEMA), ethylene glycol dimethacrylate (EGDMA) and allyl mercaptan (CH2CHCH2SH) were delivered from Sigma-Aldrich (St. Louis, MI, USA). N,N′-azobisisobutyronitrile (AIBN) and other utilized chemicals were purchased from Merck AG (Germany). Artificial human plasma was supplied by Tokra Medical (Ankara, Turkey). SPR bare gold chips (SPRchipTM, Masidon, WI, USA) were supplied for the SPRimager II instrument by GWC Technologies (Masidon, WI, USA).
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