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7 protocols using δdi 4s

1

Glycosaminoglycan Characterization Protocol

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Actinase E was purchased from Kaken Pharmaceutical Co., Ltd., Tokyo, Japan. Chondroitinase ABC (ChaseABC) from Proteus vulgaris, chondroitinase ACII (ChaseACII) from Arthrobacter aurescens, Heparinase I, Heparinase II, Heparinase III from Flavobacterium heparinum, unsaturated disaccharides of CS (ΔDi-0S, ΔDi-4S, ΔDi-6S, ΔDiUA-2S, ΔDi-diSE, ΔDi-diSB, ΔDi-diSD, ΔDi-TriS), and of HS (ΔDi-0SHS, ΔDi-NS, ΔDi-6SHS, ΔDi-NS6S ΔDi-NSUA2S, ΔDi-TriSHS) were purchased from Seikagaku Corp., Tokyo, Japan. N1-Guanyl-1,7-diaminoheptane (GC7), an inhibitor of deoxyhypusine synthase32 (link), was a kindly supplied by Dr. M. H. Park, National Institutes of Health.
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2

Quantitative Analysis of Glycosaminoglycan Disaccharides

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The chromatographic system consists of an HP1100 system (Agilent Technologies, USA) and a Hypercarb column (2.0 mm i.d. 150 mm, 5 μm, Thermo Electron, USA). An API-4000 mass spectrometer (Applied Biosystems) equipped with a turbo ionspray ion source was used. Stock solution of Galß1,4GlcNAc(6S) (500 μg/ml), ΔDiHS-0S (100 μg/ml), ΔDiHS-NS (10 μg/ml), ΔDi-4S (100 μg/ml), ΔDi-6S (100 μg/ml) (Seikagaku, Tokyo, Japan), and internal standard (IS-chondrosine) (50 μg/ml) (Glycosyn, New Zealand) were prepared in water. Urine was centrifuged and supernatants digested overnight with 1 mU of chondroitinase b, 1 mU heparitinase, and 1 mU keratanase II (Seikagaku, Tokyo, Japan) in buffer solution (1% BSA, 50 mM Tris-HCl, 5 mg/ml Chondrosine). Recovered samples were analyzed by the liquid chromatography-tandem mass spectrometry (LC-MS/MS) system and normalized by creatinine concentration in urine. Disaccharide GAG concentrations were calculated by Analyst 1.5.1 software (AB SCIEX, Foster City, CA).
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3

Quantification of Glycosaminoglycan Disaccharides

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Disaccharides were produced from polymer GAGs by digestion with chondroitinase B, heparitinase, and keratanase II, resulting in DS (di-0S), HS (diHS-NS, diHS-0S), and KS (mono-sulfated KS, di-sulfated KS). Chondrosine was used as an internal standard (IS). Unsaturated disaccharides, [ΔDiHS-NS, ΔDiHS-0S, ΔDi-4S, mono-sulfated KS and di-sulfated KS were obtained from Seikagaku Corporation (Tokyo, Japan) and used to make standard curves. Stock solutions ΔDiHS-NS (100 μg/ml), ΔDiHS-0S (100 μg/ml), ΔDi-4S (250 μg/ml), mono- and di-sulfated KS (1000 μg/ml) and IS (5 mg/ml) were prepared separately in milliQ water. Standard working solutions of ΔDiHS-NS, ΔDiHS-0S, ΔDi-4S (7.8125, 15.625, 31.25, 62.5, 125, 250, 500, and 1000 ng/ml), and mono- and di-sulfated KS (80, 160, 310, 630, 1250, 2500, 5000, and 10,000 ng/ml) each mixed with IS solution (5 μg/ml) were prepared. Mass spectrometer apparatus, run condition, brain homogenate preparation, and disaccharide analysis were done as described in Supplementary Methods.
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4

Disaccharide Quantification Across GAGs

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Disaccharides were produced from polymer GAGs by digestion with chondroitinase B, heparitinase, and keratanase II, resulting in DS (di-0S), HS (diHS-NS, diHS-0S), and KS (mono-sulfated KS, di-sulfated KS). Chondrosine was used as an internal standard (IS). Unsaturated disaccharides, ΔDiHS-NS, ΔDiHS-0S, ΔDi-4S, mono-sulfated KS, and di-sulfated KS were obtained from Seikagaku (Tokyo, Japan) and used to make standard curves. Stock solutions ΔDiHS-NS (100 μg/mL), ΔDiHS-0S (100 μg/mL), and ΔDi-4S (250 μg/mL) and mono- and di-sulfated KS (1,000 μg/mL) and IS (5 mg/mL) were prepared separately in milliQ water. Standard working solutions of ΔDiHS-NS, ΔDiHS-0S, ΔDi-4S (7.8125, 15.625, 31.25, 62.5, 125, 250, 500, and 1,000 ng/mL) and mono- and di-sulfated KS (80, 160, 310, 630, 1,250, 2,500, 5,000, and 10,000 ng/mL), each mixed with IS solution (5 μg/mL), were prepared. Mass spectrometer apparatus, run condition, brain homogenate preparation, and disaccharide analysis were done as described in the supplemental methods.
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5

Quantification of Urinary and Plasma GAGs

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Concentrations of urinary and plasma GAGs and KS were measured by tandem mass spectroscopy as described elsewhere (16 (link)). Briefly, the chromatographic system consists of an HP1100 system (Agilent Technologies) and a Hypercarb column (Thermo Electron). The API-4000 mass spectrometer (Applied Biosystems) was equipped with a turbo ionspray ion source. Disaccharides of keratan, heparan, dermatan sulfate were used as standards [Galß1,4GlcNAc(6S), ΔDiHS-0S, ΔDiHS-NS, ΔDi-4S, ΔDi-6S (Seikagaku). Chondrosine was used as internal standard (Glycosyn). Urine or plasma was centrifuged, and the supernatants were digested overnight with 1 mU of chondroitinase b, 1mU heparitinase, and 1mU keratanase II (Seikagaku). Recovered samples were analyzed by the LC-MS/MS system and normalized by creatinine concentration in urine. Total GAGs refer to total glycosaminoglycans or the additive sum of all the GAGs measured (HS, DS and KS). Disaccharide GAG concentrations were calculated by Analyst 1.5.1 software (AB SCIEX). Each sample was measured in triplicate with three injections for each sample.
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6

Chondroitin Sulfate Analysis of Shark Fins

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Dried fins (without skin and cartilage) of Isurus oxyrinchus and Prionace glauca and raw fin (without skin) of Prionace glauca were kindly provided by Mrs. T. Mano and T. Wada (Nihon Pharmaceutical Co. Ltd.). Deep-sea elasmobranchs (sharks and rays) were collected by H. Tejima through gill net fisheries at the mouth of Tokyo Bay off Kanaya, Chiba, Japan (35.17°N, 139.79°E; 200–300 m depths). Fins from those elasmobranchs were kindly provided by H. Tejima, before being processed as food materials. Actinase E was from Kaken Pharmaceutical Co., Ltd., Tokyo, Japan. Chondroitinase ABC (ChaseABC) from Proteus vulgaris, chondroitinase ACII (ChaseACII) from Arthrobacter aurescens, unsaturated disaccharides (ΔDi-0S, ΔDi-4S, ΔDi-6S, ΔDiUA-2S, ΔDi-diSE, ΔDi-diSB, ΔDi-diSD, ΔDi-TriS) and CS-E were purchased from Seikagaku Corp., Tokyo, Japan. Dialysis membrane for desalting was from Spectrum Medical (Los Angelis, CA, USA).
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7

Chondroitin Sulfate Modulates Rat CFU-GM Progenitors

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A CFU-GM assay was performed as described previously [17 (link)]. A colony-forming cell assay for rat cells (MethoCult GFR3774, StemCell Technology) is recommended for the detection and quantification of rat CFU-GM progenitors in bone marrow samples. Briefly, 0.3 mL of cell suspension (2,500 cells/mL for SCE-UCBCs, 1 x 105 cells/mL for UCB-MNCs, and 1 x 106 cells/mL for adult MNCs) was added to 3 mL of MethoCult. Using a 2.5 mL syringe, 1.1 mL of the MethoCult mixture was dispensed into each of two wells of a 6-well plate and cultured. After 10 days, the cultures were photographed using a stereo microscope (M165FC, Leica), and the number of colonies in each of the two wells was counted using a Photoshop counting tool (Adobe) and then averaged. The percentage of colony-forming cells was calculated as the number of colonies divided by the number of seeded cells. The experiments were repeated 3 times (n = 3).
UCB-MNCs were cultured with PBS, Chase ABC (0.2 U/mL, Seikagaku Corporation), CS-A (from whale cartilage, 80% of which consists of ΔDi-4S (A-unit), 100 μg/mL, Seikagaku Corporation), or CS-E (from squid cartilage, 60–65% of which consists of ΔDi-di4, 6S (E-unit), 100 μg/mL, Seikagaku Corporation) (Fig 5). Data are shown as the percentage of the control (PBS). The experiments were repeated 4 times and statistically analyzed.
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