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27 protocols using aspartate

1

Aspartate Rescue of Cancer Cell Proliferation

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The BC cells used were purchased from ATCC (ATCC; Manassas, VA, USA). All the cell lines used in this study were of human origin and were cultured at 37℃ in a humidi ed atmosphere of 5% CO2. MCF7 and MDA-MB-231 cells were cultured in DMEM (0020916, Biological Industries, Israel) supplemented with 10% fetal bovine serum (FBS, 1618326, Biological Industries, Israel) and 1% penicillin-streptomycin.
Aspartate was purchased from Sigma Aldrich (Sigma Aldrich, St. Louis, MO, USA) and used at a concentration of 5 mM [40, 41] (link) in the rescue experiment, consistent with prior in vitro studies linking cancer cell proliferation to Aspartate metabolism.
For the vertepor n (ab143294, Abcam, Cambridge, United Kingdom) / UCPH-101 (ab120309, Abcam) response experiments, MCF7 and MDA-MB-231 cells were given either vehicle or 10 µm vertepor n / UCPH-101.
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2

Corn Cob-based Enzymatic Hydrolysis

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Carboxymethyl cellulose, birch wood xylan, 2,2′-azino-di-[3-ethylbenzothiazoline-6-sulphonic acid] (ABTS), dinitrosalicylic acid, sodium-potassium tartrate, bovine serum albumin (BSA), manganese sulphate, copper sulphate, tyrosine, leucine, cellobiose, avicel, xylose, tryptophan, aspartate, glutamate, hydrogen peroxide, and media components were products of Sigma-Aldrich (St Louis, MO, USA). Corn cob was purchased from a local market. The corn cob was sun-dried and powdered into fine particles which was utilized as carbon source in the basal media. Further processing on the powdered corn cob was carried out using standard sieve to an average size of 1 mm. All other chemicals used were of analytical grade.
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3

Metabolite Profiling of Isotope-Labeled Compounds

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[15N1]-cholamine bromide hydrobromide salt (15N1-cholamine) was obtained from the Metabolite Standards Synthesis Center (SRI International).24 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride (DMTMM) was purchased from ACROS organics (Thermo Fisher Scientific). The following metabolite standards and reagents were purchased from Sigma-Aldrich: isoleucine, leucine, valine, alanine, glutamate, glutamine, aspartate, glycine, phenylalanine, histidine, tyrosine, tryptophan, serine, threonine, cysteine, cystine, N-acetyl-aspartate (N-AcAsp), formate, fumarate, 3-phosphoglycerate (3-PG), citrate, malate, alpha-ketoglutarate (α-KG), succinate, pyruvate, acetate, lactate, hydrochloric acid (HCl) and sodium hydroxide (NaOH). [U-13C]-pyruvate, [U-13C]-lactate, 1-13C-acetate, 2-13C-acetate and 1,2-13C2-acetate were purchased from Cambridge Isotope Laboratories (Andover, MA). Reduced glutathione (GSH) and oxidized glutathione (GSSG) were purchased from ACROS organics (Thermo Fisher). 18 MΩ water was obtained using an ultrapure water system (Barnstead, Dubuque, IA).
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4

Isolation and purification of phytochemicals

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Standard amino acids (alanine (Ala), arginine (Arg), aspartate (Asp), asparagine (Asn), γ-aminobutyric acid (GABA), glycine (Gly), glutamate (Glu), glutamine (Gln), histidine (His), isoleucine (Ile), leucine (Leu), lysine (Lys), phenylalanine (Phe), proline (Pro), serine (Ser), threonine (Thr), tyrosine (Tyr) and valine (Val)) were purchased from Sigma.
Standards flavonols (quercetin 3-glucoside, quercetin 3-glucoronide and kaempferol 3-glucoside); phenolic acids (caffeic acid, gallic acid, caftaric acid and isoferulic acid); flavanols and procyanidins (catechin, epicatechin, epicatechin gallate, epigallocatechin, epigallocatechin gallate, B1, B2, C1); stilbenes (trans-piceid, trans-resveratrol and trans-piceatannol) and other compounds (phloretin, naringenin, naringenin glucoside and taxifolin) were purchased from Extrasynthesis (France). Stilbenes, for the majority, have been purified in the MIB laboratory (such as the monomers trans-astringin and trans-isorhapontin, the dimers trans-ε-viniferin, trans-ω-viniferin, trans-δ-viniferin, pallidol, parthenocissin A, vitisinol C and ampelopsin A, the trimers miyabenol C and α-viniferin, and the tetramers: hopeaphenol, isohopeaphenol, r2-viniferin and r-viniferin).
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5

Comparative Analysis of Glutinous and Japonica Rice Huangjiu

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Huangjiu samples in Shaoxing region (S1, S2) fermented by glutinous rice and japonica rice, respectively, were provided by Zhejiang Pagoda Brand Shaoxing Rice Wine Co., Ltd., Shaoxing City, Zhejiang Province, China. The samples were brewed using the same Jianhu water, wheat Qu (a saccharification starter) and Jiuyao (a fermentation starter) with the same ratio. And the same brewing technique including soaking and steaming rice, fermentation (primary fermentation at 28°C for 3–5 days, then secondary fermentation at medium-low temperatures for about 90 days), filtration, pressing, clarification and storage was applied. All of the samples were stored at 4°C and they were analyzed within 1 month after being transferred to the laboratory.
The regents, aspartate, leucine, lysine, proline, histidine, arginine, 2-octanol (internal standard) and n-alkane standards (C5–C30) of chromatographic grade and purity ≥98.0% were obtained from Sigma Aldrich (Shanghai, China).
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6

Metabolic Regulation of Cell Cycle and Oxidative Stress

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Gelatin, sodium dodecyl sulfate (SDS), dithiothreitol, NaCl, EDTA, heparin, trichloroacetic acid, trypan blue, propidium iodide, RNase, cesium chloride, M199 medium, dimethyl-α-ketoglutarate, aspartate, hydrogen peroxide, glutamine, dialyzed fetal bovine serum, trypsin, 6-diazo-5-oxo-L-norleucine (DON), mercaptoethanol, streptomycin, penicillin, bis-2-(5-phenylacetomido-1,3,4-thiadiazol-2-yl)ethyl sulfide (BPTES), glutamate, ammonium chloride, and diethylamine NONOate (DEA-NO), K2HPO4, ATP, NAD, hydrazine, bovine liver glutamate dehydrogenase, and asparagine were from Sigma-Aldrich (St. Louis, MO). Endothelial cell growth factor was from Becton Dickinson Biosciences (Bedford, MA). Rainbow molecular weight markers were from GE Healthcare (Piscataway, NJ). Lipofectamine and 5-(and-6)-chloromethyl-2,7-dichlorodihydrofluorescein diacetate acetyl ester (CM-H2DCFDA) were from Life Technologies Corporation (Carlsbad, CA). CB-839 and NG-nitro-L-arginine methyl ester (L-NAME), were from Selleckchem (Houston, TX). Antibodies against GLS1, cyclin D1, cyclin E, cyclin A, p21, p27, p53, and β-actin were from Santa Cruz Biotechnology (Santa Cruz, CA), an antibody against phospho-retinoblastoma protein was from Cell Signaling Technologies (Beverley, MA), and an antibody against HO-1 was from Assay Designs (Ann Arbor, MI). [3H]Thymidine (20 Ci/mmol) was from Perkin Elmer (Boston, MA).
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7

Metabolic Knockout CRISPR Library Screening

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The human metabolic knockout pooled CRISPR library was a gift from David Sabatini (Addgene # 110066). The library consists of 29,790 sgRNAs targeting 2,981 metabolism‐related genes, with ~10 sgRNA/gene, as well as 500 intergenic control sgRNAs in a Cas9‐ expressing lentiviral vector. For lentivirus production, the psPAX2 (a gift from Didier Trono; Addgene plasmid # 12260) and VSV.G (a gift from Tannishtha Reya; Addgene plasmid # 14888) packaging plasmids were used. plentiCRISPR v3 was bought from Horizon (Cross et al, 2016 (link)) and pLKO.2 was a kind gift from Sebastian Nijman (Ludwig Cancer Research, Oxford, UK). For the competition assay, the pKAM‐GFP plasmid (a gift from Archibald Perkins, Addgene plasmid #101865) was used to tag the cells with GFP. The plasmids used for the FUCCI system, pLL3.7 m‐mTurquoise2‐SLBP(18‐126)‐IRES‐H1‐mMaroon1 and pLL3.7 m‐Clover‐Geminin(1‐110)‐IRES‐mKO2‐Cdt(30‐120) were a gift from Michael Lin (Addgene plasmids #83842 and #83841, respectively).
Etoposide, NCS from Streptomyces carzinostaticus ≥ 90%, and aspartate were obtained from Sigma‐Aldrich. Phenformin and Carboplatin were obtained from MedChem Express. TTFA was obtained from Abcam.
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8

Bacterial Kynurenine Metabolism Assay

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L. reuteri (F 275T = ATCC 23272T = DSM 20016T = JCM 1112T = LMG 9213T = LMG 13557T) bacteria were obtained from the American Type Culture Collection (Manassas, VA, USA). 3H-L-kynurenine (3H-KYN) (16 Ci/mmol) was purchased from Amersham (Buckinghamshire, UK). Aminooxyacetic acid (AOAA), aspartate, α-aminoadipate, glutamine, pyruvate, α-ketoglutarate, α-ketoisocaproate, α-ketoisovalerate, oxaloacetate, 2-amino-2-norbornanecarboxylic acid (BCH) and PF-04859989 were obtained from Sigma-Aldrich (St. Louis, MO, USA). L-Kynurenine sulfate (L-KYN) was acquired from Sai Advantium (Hyderabad, India) and D-kynurenine sulfate (D-KYN) from Shanghai Hanhong Chemical Co. (Shanghai, China). BFF-122 [(S)-(-)-9-(4-aminopiperazine-1-yl)-8-fluoro-3-methyl-6-oxo-2,3,5,6-tetrahydro-4H-1-oxa-3a-azaphenalene-5-carboxylic acid] was kindly provided by Dr. Y. Kajii (Mitsubishi-Tanabe Pharma Corp., Yokohama, Japan). All other chemicals used were purchased from commercial suppliers and were of the highest available purity.
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9

Mitochondrial Dynamics Protein Analysis

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Antibodies to the following proteins were used: Drp1 (BD Biosciences), Drp1 S637-PO4 (Cell Signaling), Actin (Millipore), Fis1 (Alexis Corps), Mff (Sigma-Aldrich), Mfn1 (Chen et al., 2003 (link)), Mfn2 (Sigma), Opa1 (in house monoclonal), ClpP (Proteintech Group), Oxa1 (Proteintech Group), Tom20 (Santa Cruz BioTech), Hsp60 (Santa Cruz BioTech), Yme1L (Proteintech Group), Myc (Covance). Oligomycin (Sigma-Aldrich), antimycin A (Sigma-Aldrich), atpenin A5 (Santa Cruz BioTech), CCCP (Sigma-Aldrich) and atractyloside (Sigma-Aldrich) were used at 1 μM. Concentrations of other compounds: rotenone (Sigma-Aldrich), 200 nM; KCN (Sigma-Aldrich), 1 mM; o-phenanthroline (Sigma-Aldrich), 0.5 mM; aspartate, 1 mM; ADP (Sigma-Aldrich), 200 μM; β-NADH (Sigma-Aldrich), 2 mM. Unless otherwise indicated, substrates (pyruvate, malate, succinate, α-ketoglutarate) were used at 5 mM.
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10

Neurotransmitter Receptor Assay

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All reagents are of molecular biology grade. Chemicals including GABA, acetylcholine, glutamate, glycine, aspartate, histamine, serotonin, picrotoxin, fipronil, and ivermectin were purchased from Sigma-Aldrich (Saint-Quentin-Fallavier, France). GABA, acetylcholine, glutamate, glycine, aspartate, histamine, and serotonin were directly dissolved in the recording solution, whereas picrotoxin, fipronil, and ivermectin were first prepared at 10 mM DMSO and then diluted in recording solution to the final concentrations in which DMSO did not exceed 0.1%.
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