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21 protocols using d lactose

1

Synthesis and Purification of HA-8mer Nanoparticles

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HA-8mer was synthesized as previously described (Kanekiyo et al., 2013 (link); Weaver et al., 2016 (link)). Briefly, plasmids were transiently transfected into FreeStyle 293-F cells in FreeStyle 293 Expression Medium. After 5 days of culturing in conditions described above, cell culture supernatants collected by centrifugation and concentrated using a tangential flow filtration setup with a 30 kDa cutoff. In 100 mL aliquots, the concentrate was mixed with 2 mL of PBS-equilibrated Erythrina cristagalli lectin-immobilized resin (EY Laboratories) at 4°C and incubated overnight with gentle agitation. The resin was then loaded onto a 1.5 × 20 cm glass Econo-Column (Bio-Rad) and washed with five column-volumes of PBS by gravity flow. HA-8mer particles were eluted with two column-volumes of 0.2 M D-lactose (Sigma-Aldrich) in PBS and concentrated in a centrifugal concentrator with a 100 kDa cutoff. Size-exclusion FPLC was then performed using a Superdex 200 10/30 column (GE Healthcare) and purified HA-8mer was again concentrated as before.
Recombinant HPV16 L1 (Abcam ab119880) and recombinant HBsAg AD (Abcam ab193473) were reconstituted following the manufacturer’s guidelines. Nanoparticle formation of the expected size was confirmed by dynamic light scattering.
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2

Carbohydrate-Coupled Sepharose 6B Matrix Preparation

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Carbohydrate coupled Sepharose 6B matrix was prepared according to our previous study (24 (link)). In brief, epoxy-activated Sepharose 6B matrix (GE Healthcare, Sweden) was washed extensively with distilled water, and then mixed with four kinds of carbohydrates, including d-lactose, N-acetyl-d-glucosamine (d-GlcNAc), d-mannose, and l-fucose (Sigma-Aldrich, Buchs, Switzerland), at a final concentration of 200 µM in distilled water (pH 13.0). The mixtures were incubated at 30°C with gentle shaking for 16 h, and 1 M ethanolamine (pH 8.0) was used to block the remaining active groups after TBS washing. The carbohydrate coupled Sepharose 6B matrix was then washed extensively with TBS, and packed into Teflon columns with 100 mm long and 10 mm inner diameter, respectively.
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3

Modulation of Intestinal Microbiota in Mice

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Il10-/- mice were weaned 21 days after birth and supplemented with a 5 mM solution of either 2-fucosyllactose (2FL), 3-fucosyllactose (3FL), 3-sialyllactose (3SL), 6-sialyllactose (6SL) (Glycom A/S, Hørsholm, Denmark) or D-lactose (Sigma-Aldrich, Buchs, Switzerland) in sterile filtrated water ad libitum for 28 days. For depletion of intestinal microbiota, 4–6 weeks old mice were supplied with 0.5 g/L vancomycin (AppliChem), 1 g/L ampicillin (VWR), 1 g/L neomycin (Fisher Bioreagents) and 0.2% aspartame (Sigma) in drinking water for 6 days. Once per day, mice received intragastric gavage of 250 μL of a 1 g/L metronidazole (Sigma) solution. After antibiotic treatment, mice were treated with 10% PEG 3000 solution (Sigma) in drinking water to flush the remaining bacteria and antibiotic. Neo-colonization with specific bacterial strains was done by intragastric gavage of 250 μL containing 109 CFU of the respective strain in PBS. Fecal pellets were collected to monitor changes of the microbiota.
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4

Zinc Oxide Nanoparticle Protein Interactions

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ZnO NPs were purchased from Sumitomo (Tokyo, Japan) and prepared in DW (stock suspension, 5 mg/mL) for 30 min prior to experiments. Materials used were as follows: casein sodium salt from bovine milk (Sigma-Aldrich, St. Louis, MO, USA), skim milk (Seoul Milk, Seoul, Korea), D-(+)-lactose (Sigma-Aldrich), CaOH2 (Yakuri Pure Chemicals Co., Ltd., Osaka, Japan), calcium standard solution (Sigma-Aldrich), and pepsin from porcine gastric mucosa (622 units/mg; Sigma-Aldrich).
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5

Carbohydrate Quantification in Human Milk

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The total carbohydrate content in HM was estimated using a 3,5-dinitrosalicylic acid (DNS) solution prepared by solubilizing 1 g of DNS (Sigma, 128,848) in a 2 M NaOH (VWR Chemicals, 28,244.295) solution containing 30 g Na-K tartrate (VWR Chemicals, 27,068.233), and then deionised (DI) H2O was added to reach a total volume of 100 mL; this solution was referred to as the working DNS solution. The milk samples were diluted 25× with DI H2O, and 500 μL of each diluted sample was mixed with 500 μL of working DNS solution. The mixture was then boiled for five minutes and cooled down in running tap water. Then, 4 mL of DI H2O was added to each reaction, and the absorbance was read at 540 nm with a Synergy H4 Hybrid Reader (BioTek, USA). The concentration of carbohydrates in the milk was calculated from a D-lactose (Sigma, 61,345) standard curve with a concentration range of 0–100 mg/mL.
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6

Synthesis and Purification of HA-8mer Nanoparticles

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HA-8mer was synthesized as previously described (Kanekiyo et al., 2013 (link); Weaver et al., 2016 (link)). Briefly, plasmids were transiently transfected into FreeStyle 293-F cells in FreeStyle 293 Expression Medium. After 5 days of culturing in conditions described above, cell culture supernatants collected by centrifugation and concentrated using a tangential flow filtration setup with a 30 kDa cutoff. In 100 mL aliquots, the concentrate was mixed with 2 mL of PBS-equilibrated Erythrina cristagalli lectin-immobilized resin (EY Laboratories) at 4°C and incubated overnight with gentle agitation. The resin was then loaded onto a 1.5 × 20 cm glass Econo-Column (Bio-Rad) and washed with five column-volumes of PBS by gravity flow. HA-8mer particles were eluted with two column-volumes of 0.2 M D-lactose (Sigma-Aldrich) in PBS and concentrated in a centrifugal concentrator with a 100 kDa cutoff. Size-exclusion FPLC was then performed using a Superdex 200 10/30 column (GE Healthcare) and purified HA-8mer was again concentrated as before.
Recombinant HPV16 L1 (Abcam ab119880) and recombinant HBsAg AD (Abcam ab193473) were reconstituted following the manufacturer’s guidelines. Nanoparticle formation of the expected size was confirmed by dynamic light scattering.
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7

Glycoproteomic analysis of PANC-1 cells

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Dithiothreitol (DTT), PNGase F and sequencing grade trypsin were from Promega (Madison, WI). Optimal LC/MS grade acetonitrile (ACN), methanol (MeOH) and water were from Fisher Scientific (Pittsburgh, PA). Concanavalin A (ConA), wheat germ agglutinin (WGA), Ricinuscommunis agglutinin (RCA120), iodoacetamide (IAA), acetyl-D18 glucosamine, D-lactose, methyl α-D-mannopyranoside and manganese dichloride were obtained from Sigma-Aldrich (St. Louis, MO). Tris base, urea (UA), sodium chloride, ammonium bicarbonate (ABC) and calcium chloride (CaCl2) were obtained from Fisher Scientific (Pittsburgh, PA). Trifluoroacetic acid (TFA), triethylammonium bicarbonate (TEAB), N, N-dimethylformamide (DMF), 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium tetrafluoroborate (DMTMM), N-methylmorpholine (NMM) and dimethyl sulfoxide (DMSO) were purchased from Sigma-Aldrich (St. Louis, MO). Hydroxylamine solution was purchased from Alfa Aesar (Ward Hill, MA). C18 OMIX tips were obtained from Agilent (Santa Clara, CA). Hydrophilic interaction chromatography material (PolyHYDROXYETHYL A) was obtained from PolyLC (Columbia, MD). Microcon filters YM-30 (30 kDa) was purchased from Merck Millipore (Billerica, MA). PANC-1 pancreatic ductal adenocarcinoma cells were from ATCC (Manassas, VA). Duplex DiLeu tags were custom synthesized in our own lab.45 (link)
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8

Bifidobacterium breve UCC2003 Cultivation

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Bifidobacterium breve UCC2003 was routinely grown anaerobically at 37 °C on RCM (Oxoid) or De Man Rogosa Sharpe (mMRS) made from first principles67 (link), and supplemented with 0.05% L-cysteine and appropriate carbon sources. Escherichia coli EC101 cells were grown on LB supplemented with tetracycline (10 μg ml−1) or kanamycin (50 μg ml−1) for selection of plasmid-containing cells. B. breve UCC2003 transposon mutants were routinely grown on RCM supplemented with 0.5% ribose and 10 μg ml−1 tetracycline, or mMRS supplemented with 0.5% L-cysteine-HCl and appropriate carbon sources as indicated. D-ribose, D-glucose, starch (potato-derived) and D-lactose were purchased from Sigma.
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9

Synthesis of Fluorescent Lactose Derivatives

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All reagents were obtained from commercial sources. D-lactose, acetic anhydride, N,N-dimethylformamide (DMF), trichloroacetonitrile, 1,8-diazabicyclo [5.4.0]undec-7-ene (DBU), boron trifluoride diethyl etherate (BF3·Et2O), propargyl alcohol, sodium metal, Dowex-50 resin (H+ form), 5-bromovaleryl chloride, 2,4-dimethyl pyrrole, triethylamine (TEA), N-iodosuccimide (NIS) were purchased from Sigma Aldrich (St. Louis, MO, USA). Sodium azide, sodium ascorbate, copper (II) sulfate pentahydrate, sodium hydroxide (NaOH), sulfuric acid (H2SO4), sodium hydrogen carbonate (NaHCO3), magnesium sulfate (MgSO4), and ammonium carbonate [(NH4)2CO3] were procured from Daejung Chemical (Gyeonggi-do, South Korea) and used without further purification. Ethyl acetate (EtOAc), dichloromethane (CH2Cl2), tetrahydrofuran (THF), methanol, and other solvents were of analytical grade and were dried under calcium hydride prior to use, except THF.
All compounds were characterized by 1H- and 13C-NMR spectroscopy on a Bruker AM 250 spectrometer (Billerica, MA, USA) and high-resolution electrospray ionization mass spectrometry (HR-ESI-MS) on a SYNAPT G2-Si high definition mass spectrometer (Waters, London, United Kingdom).
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10

Glycoproteomic Analysis of PANC-1 Cells

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Dithiothreitol (DTT), sequencing grade trypsin were purchased from Promega. Concanavalin A (ConA), wheat germ agglutinin (WGA), Ricinus communis agglutinin (RCA120), iodoacetamide (IAA), acetyl-D18 glucosamine, D-lactose, methyl α-D-mannopyranoside, and manganese dichloride were obtained from Sigma-Aldrich. Tris base, urea (UA), sodium chloride, ammonium bicarbonate (ABC), calcium chloride (CaCl2), and ACS-grade and Optima LC/MS-grade solvents were obtained from Fisher Scientific. Formic acid (FA), 10% sodium dodecyl sulfate solution (SDS), trifluoroacetic acid (TFA), and dimethyl sulfoxide (DMSO) were purchased from Sigma-Aldrich. C18 OMIX tips and Phenylboronic acid (PBA) solid-phase extraction cartridges were obtained from Agilent. Hydrophilic interaction chromatography material (PolyHYDROXYETHYL A) was obtained from PolyLC. Microcon filters YM-30 (30 kDa) and amicon Ultra-0.5 ml centrifugal filters (10 kDa) were purchased from Merck Millipore. PANC-1 pancreatic ductal adenocarcinoma cells were from ATCC.
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