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34 protocols using dithiothreitol (dtt)

1

Internalization of Nanoparticles via SLO Pores

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We modified the method reported by Walev et al. (2001) (link) to introduce GMNPs to cells. First, streptolysin O (SLO; Wako Pure Chemical) was activated by reduction with DTT (Nacalai Tesque). Stock solutions of SLO with a final concentration of ~5 U/μL were prepared.
HEK cells (5 × 105) were rinsed with PBS(−) and resuspended in 20 μL of PEG-GMNP solution (NanoImmunotech) and 5 μL of 5× HBPS (1 mM Ca2+, 1 mM Mg2+). These cells were incubated in a 37°C incubator for 12 min in the presence of 1 μL of SLO. The pore-forming activities of SLO were inactivated by adding DMEM containing 10% FBS (0.5–1 mL) for 20 min or longer.
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2

Decorin and Periostin Proteomics

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Samples immunoprecipitated with antibodies against decorin or periostin were subjected to SDS-PAGE, and the gels were stained using the Silver Quest Staining Kit (Invitrogen). The stained gel bands were cut out and treated with dithiothreitol (DTT, Nacalai Tesque, Kyoto, Japan) dissolved in ammonium hydrogen carbonate (Nacalai Tesque), followed by treatment with iodoacetamide (Wako, Osaka, Japan). After the gels were dried, 20 μl of 0.05 pmol/μl trypsin (AB SCIEX) solution was applied to each gel piece and incubated for 12–16 h at 37°C to digest proteins. Digested peptides were extracted by washing the gel pieces twice with 50% trifluoroacetic acid (TFA, Wako), followed by washing with 80% TFA. The purified peptide samples were injected onto a reversed-phase C18 column (HiQ sil C18W-3P, 3 μm, 120 Å; KYA TECH Corp.) and separated by nanoflow liquid chromatography (300 nL/min) on a nano LC Dina-A system (KYA TECH Corp.) in line with a Q-TRAP 5500 instrument (AB SCIEX) using a 75-min gradient of 5–100% acetonitrile in 0.1% formic acid.
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3

MDCK II Cell Culture Protocol

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Madin-Darby canine kidney (MDCK) II cells were cultured in Dulbecco’s modified Eagle’s medium (Nacalai Tesque, Kyoto, Japan) supplemented with 10% fetal calf serum (Nichirei Biosciences, Tokyo) and 1% penicillin-streptomycin (Nacalai Tesque) in a humidified atmosphere containing 5% CO2.
Capsaicin, FD4, and NEM were purchased from Sigma (St. Louis, MO). LatA was from Wako Pure Chemical Industries (Osaka, Japan). DTT was from Nacalai Tesque, and A-967079 was from Cayman (Ann Arbor, MI).
Antibodies to occludin (#71-1500), Zo-1 (#61-7300), and tricellulin (#700191) were purchased from Invitrogen (Grand Island, NY). Anti-claudin-1 (#13050-1-AP) and anti-cofilin (#3312) was purchased from Proteintech Group, Inc. (Rosemont, IL) and Cell Signaling Technology (Beverly, MA), respectively. Anti-β-actin (#125K4769) and anti-phospho-cofilin (Ser 3, #sc-21867-R) were from Sigma and Santa Cruz Biotechnology (Santa Cruz, CA), respectively. Horseradish peroxidase (HRP)-conjugated anti-mouse and anti-rabbit IgGs were from Kirkegaard & Perry Laboratories (Gaithersburg, MD).
All other reagents were of reagent grade and purchased from Nacalai Tesque unless otherwise noted.
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4

Detecting Ubiquitinated ARMC5 and SREBF1

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For detection of ubiquitinated ARMC5 in vivo, HEK293T cells or H295R cells were transfected with pRK5-HA-Ubiquitin-WT (Addgene, 17608) (31 (link)) and pcDNA3.1-FLAG-mArmc5. For detection of full-length SREBF1 in vivo, HEK293T cells were transfected with pRK5-HA-Ubiquitin-WT and pcDNA3.1-FLAG-Srebf1 with pcDNA3.1-myc or pcDNA3.1-myc-Armc5. Twenty-four hours after transfection, the cells were treated with 10 μM MG132 (Sigma-Aldrich) for 5 hours. The cells were lysed by boiling in a buffer containing 2% SDS, 150 mM NaCl, 10 mM Tris-HCl, and 1 mM DTT (Nacalai Tesque). These lysates were diluted ninefold in dilution buffer containing 150 mM NaCl, 10 mM Tris-HCl, and 1% Triton X-100 and immunoprecipitated with anti-FLAG M2 Affinity Gel (Sigma-Aldrich); washed 4 times with dilution buffer; eluted with 200 μg/mL FLAG peptide (Sigma-Aldrich); and subjected to Western blotting using rabbit anti-HA antibody (Cell Signaling Technology, 3724) and HRP-conjugated anti-rabbit IgG antibody (GE Healthcare, NA934V).
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5

Chemical Stress Response Protocols

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DTT (Nakalai Tesque), tunicamycin (Sigma Aldrich), antimycin A (Sigma Aldrich) and NAC (Sigma Aldrich) were respectively prepared as stock solutions of 1 M in water, 2 mg/ml in dimethyl sulfoxide (DMSO), 20 mM in DMSO and 0.5 M in water, and stored at −30 °C. Hydrogen peroxide was obtained as a 35% water solution (Nakalai Tesque). For chemical-stress imposition, DTT, tunicamycin or Hydrogen peroxide was added into cultures during the exponential and fermentative growing phase.
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6

Recombinant Protein Expression in E. coli

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Recombinant proteins were expressed in E. coli BL21 (Promega) as GST fusion proteins by induction at 25°C for 2.5 h with 100 μM isopropyl-1-thio-β-D-galactopyranoside (GE Healthcare). The bacteria were lysed in a sonication buffer [PBS containing 0.1% NP-40 (v/v), 1 μM DTT, and 1% protease inhibitors (v/v) (Nacalai Tesque, Kyoto, Japan)], sonicated for 10 min on ice, and centrifuged for 10 min at 14,000 rpm at 4°C. The supernatant was mixed with 500 μl of equilibrated glutathione-Sepharose 4B (GE Healthcare) at 4°C for 1 h followed by washing five times with the sonication buffer. For preparation of cell lysates, MT-1 cells and HeLa cells transfected with plasmids were incubated with or without (−)-DHMEQ. The cells were then lysed in L buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM EDTA, 1% Triton X-100, and 0.1% protease inhibitors (v/v) (Nakalai Tesque)] on ice for 30 min and centrifuged for 10 min at 14,000 rpm at 4°C.
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7

ER Stress Induction in Cell Culture

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Dithiothreitol (DTT; Nakarai Tesque; 1 M stock solution in water), tunicamycin (Sigma-Aldrich; 2 mg/mL stock solution in dimethylsulfoxide) and ethanol were added into the medium 4 hr after culture start, and the culturing was continued without changing the aeration status. When ER stress-inducing agents were added into the static cultures, the conical tubes were immediately and gently inverted five times for mixing.
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8

Native PAGE Analysis of α2-Macroglobulin Purification

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Purified human α2-macroglobulin protein (725 kDa) was obtained from Enzo Life Science (New York, USA), anti-human monoclonal mouse α2-macroglobulin (immunoglobulin (Ig)G1 clone) from R&D Systems (Minneapolis, MN, USA), and goat anti-mouse IgG (H + L)-horseradish peroxidase (HRP) conjugate from Bio-Rad Laboratories (Hercules, CA, USA). Native PAGE™ Sample Buffer, Native PAGE Running Buffer, Dark Blue Cathode Buffer, Native Mark Unstained Protein Standard, and Light Blue Cathode Buffer were obtained from Thermo Fisher Scientific (Waltham, MA, USA). DTT, Blocking One and Peroxidase Stain 3,3′-Diaminobenzidine kit (Brown Stain) were purchased from Nacalai Tesque (Kyoto, Japan). Immune-Blot® polyvinylidene difluoride membrane, Sequi-Blot™ membrane, Precision Plus Protein™ Dual Color Standards and Mini-PROTEAN® TGX™ were obtained from Bio-Rad Laboratories. Perfect NT Gel, Perfect NT Gel System and SDS-PAGE Running Buffer were obtained from DRC (Tokyo, Japan), and ECL Prime Western Blotting Detection Reagent from GE Healthcare (Buckinghamshire, UK).
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9

Synthetic Dextrose Medium for Yeast Growth

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The standard synthetic dextrose (SD) medium contained 2% glucose, 0.67% yeast nitrogen base without amino acids (Difco), and appropriate auxotrophic requirements. For preculturing, yeast cells were aerobically incubated overnight at 30 °C in SD medium. The precultures were then diluted in SD medium to an OD600 of 0.20 and were further shaken aerobically at 30 °C. For culturing at 39 °C, the culturing temperature was shifted from 30 °C to 39 °C just after dilution of the precultures. A UV-1800 spectrophotometer (Shimazu) was used to measure the optical density at 600 nm (OD600) of cultures.
DTT (Nacalai Tesque) was dissolved in water to make a 1 M stock solution, which was then added to the cultures at the exponential growth phase.
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10

Purification of Ub2 Disulfide-Linked Fibrils

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To obtain Ub2S-S fibrils, 1 mg ml−1 solution of Ub2S-S was incubated at 368 K for 20 minutes in 50 mM sodium phosphate and 150 mM NaCl, pH 7.0. The solution was degassed, cooled to 277 K, before dithiothreitol (DTT, Nacalai Tesque) was added to a final concentration of 50 mM. The solution was then incubated at 277 K for more than 3 days, followed by centrifugation at 5,000 g for 10 minutes at 277 K and filtration using a 0.22 μm PVDF filter (Merck Millipore). The filtered sample was purified at 277 K in the presence of 5 mM DTT by using a Hiload 16/60 Superdex 75 pg size exclusion column (GE Healthcare). The first peak (elution volume of peak top: approximately 78 ml) in the size exclusion chromatography was collected as the dissociation intermediates.
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