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26 protocols using 3 hexafluoro 2 propanol

1

Preparation of Homogenous hIAPP(20-29) Samples

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To prepare homogenous
monomer solutions, one milligram of hIAPP(20–29) was carefully
dissolved in 100 μL of 1,1,1,3,3,3-hexafluoro-2-propanol (≥99%,
Sigma-Aldrich) for 1 h with occasional vortexing. The solution was
then centrifuged at 15 000 rpm and 4 °C for 30 min, after
which the top 80% of the total volume was removed and divided into
10 μL aliquots. Aliquots were frozen in liquid nitrogen and
lyophilized for 5 h. The lyophilized hIAPP(20–29) aliquots
were stored at −20 °C.
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2

Preparing FFNT Nanostructures from L-diphenylalanine

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In order to prepare an
FFNT solution, we dissolved the l-diphenylalanine peptide
(Bachem, Bubendorf, Switzerland) in 1,1,1,3,3,3-hexafluoro-2-propanol
(Sigma-Aldrich, Ireland) at an initial concentration of 100 mg/mL.
The initial concentration of FFNTs was then further diluted in deionized
water (ddH2O) to a final concentration of 2 mg/mL to allow
the FFNTs to self-assemble. Fresh stock solutions were prepared for
each experiment.
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3

Preparation and Characterization of Amyloid-Beta Peptides

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Aβ peptides were purchased from Yale University and ChinaPeptides, and were prepared as previously described [40] (link). Briefly, lyophilized Aβ peptide was first dissolved in 1, 1, 1, 3, 3, 3-hexafluoro-2-propanol (Sigma-Aldrich). After evaporation of the peptide solution, anhydrous DMSO was added to the preparation to achieve the stock solution. The peptide solution was then sonicated at room temperature for 30 min. After sonication, Aβ peptides were snap-frozen in liquid nitrogen, and stored at −80 °C until the day of experiment. Presence of monomers, dimers, and oligomers was confirmed by Tris-Tricine gel electrophoresis as shown previously [40] (link). Aβ peptides were diluted to the indicated working concentration on the day of the experiment.
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4

Membrane Reconstitution of FP1 Peptide

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The composition of membranes used in this study is consistent with our previous study [14 (link)]. The desired amount of POPC, POPS, cholesterol and 0.5% (mol:mol) spin-labeled lipids in chloroform were mixed well and dried by N2 flow. The mixture was evacuated in a vacuum drier overnight to remove any trace of chloroform. To prepare MLVs, the lipids were resuspended and fully hydrated using 1 mL of pH 7 or pH 5 buffer (5 mM HEPES, 10 mM MES, 150 mM NaCl, and 0.1 mM EDTA, pH 7 or pH 5) at room temperature (RT) for 2 hours. To reconstitute FP1 without GGGKKKK in membrane, the desired amounts of peptide were dissolved in 1,1,1,3,3,3-hexafluoro-2-propanol (Sigma, St. Louis, MO) and well mixed with the lipids in chloroform. The mixtures were dried and fully hydrated to generate the MLVs. To prepare SUVs for CD and ITC measurements, the lipids were resuspended in pH 7 or pH 5 buffer and sonicated in an ice bath for 20 minutes or when the suspension became clear. The SUVs solution was then further clarified by ultracentrifugation at 13,000 rpm for 10 min.
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5

Amyloid-beta Peptide Preparation

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Anti-ATG5 and anti-ATG12 were purchased from Cell Signaling Technology (MA, USA) and anti-tubulin was from Millipore (MA, USA). Synthetic Aβ1–40 peptides (Invitrogen, Camarillo, CA, USA) were dissolved in 1, 1, 1, 3, 3, 3-hexafluoro-2-propanol (Sigma, Saint Louis, MO, USA) and sequentially lyophilized. Lyophilized peptide was redissolved in dimethylsulfoxide (DMSO).
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6

Electrospun Collagen Nanofiber Matrix for Tissue Regeneration

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In order to reconstitute the microenvironment of traumatized tissue, type I bovine collagen (Elastin Products Company, Owensville, MO, USA) was dissolved in 1,1,1,3,3,3-hexafluoro-2-propanol (Sigma Aldrich, St. Louis, MO, USA) and electrospun as previously described [13 (link), 14 (link)]. The collagen nanofiber matrix was adhered to coverslips or polymeric culture dish inserts using a medical silicone adhesive (Factor 2, Lakeside, AZ, USA), and briefly crosslinked in 25% glutaraldehyde vapor for 10 min. A 2.5% concentration of collagen electrospun at 0.8 mL/hr yielded a fiber diameter of 100 microns or less and had a 0.89 correlation coefficient with the fibers seen in traumatized muscle. To provide a non-collagen nanofibrous matrix comparison, 1.6 g of poly L-lactic acid (PLLA, Polysciences, Warrington, PA, USA) was dissolved in 10 mL chloroform and 1 mL of DMF followed by vortex-mixing overnight at room temperature and then electrospun at 0.4 mL/hr. When indicated, commercially available 6-well polycaprolactone (PCL) nanofiber plates (700 nm diameter fibers randomly oriented) were also used for the experiments (Nanofiber Solutions, Hilliard, OH, USA).
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7

Amyloid-beta Peptide Preparation

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Aβ was prepared as previously described (Puzzo et al., 2012 ; Ripoli et al., 2013 (link); Stine et al., 2003 (link)). Briefly, the lyophilized peptide American Peptide, Sunnyvale, CA, USA) was suspended in 1,1,1,3,3,3-hexafluoro-2-propanol (Sigma, St. Louis, MO, USA) to 1 mM. After the complete evaporation of 1,1,1,3,3,3-hexafluoro-2-propanol to allow complete monomerization, the Aβ film was dissolved in dimethyl sulfoxide (DMSO; Sigma), sonicated for 15 minutes, aliquoted, and stored at −20 °C. Different protocols were used to obtain preparations of Aβ42 or Aβ40 enriched in monomers mAβ42 and mAβ40) or oligomers (oAβ42 and oAβ40). For mAβ42 and mAβ40, the DMSO-Aβ solution was diluted in artificial CSF (ACSF) immediately before use to the final concentration (200 pM and 200 nM). For oAβ42 and oAβ40, the DMSO-Aβ solution was incubated in PBS at 4 °C for 12 hours and 1 week, respectively, to allow oligomerization. These oligomerized Aβ solutions were then diluted in ACSF to the final concentration, calculated based on the MW of the monomeric peptides. The oligomerization status of these solutions was routinely tested by western blot (WB) analysis. Scramble Aβ42 and Aβ40 (AnaSpec Inc, San Jose, CA, USA) were prepared following the same procedure.
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8

Amyloid-beta Oligomer Preparation

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1‐42 peptide (American peptide, USA and Bachem, Switzerland) was prepared as previously described (Byun et al., 2015). In brief, Aβ1‐42 peptide was dissolved in 1,1,1,3,3,3‐hexafluoro‐2‐propanol (Sigma, USA) and lyophilized in a Speedvac (Labconco, USA). Dry peptide was dissolved in anhydrous dimethyl sulfoxide (Sigma, USA) at a final concentration of 1 mM and diluted in DMEM or cell culture medium. During treatment in cell culture, most of Aβ consisted predominantly of oligomers and a few monomers (Kim et al., 2012).
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9

PCL Scaffolds Loaded with P11-4 Peptide

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Poly-ε-caprolactone (PCL, Mn: 50,000, CELLINK, Göthenburg, Sweden) was solubilized overnight in 1,1,1,3,3,3-hexafluoro-2-propanol (Sigma-Aldrich, St. Louis, MO, USA) at 100 mg/ml under stirring. PCL solutions were placed into a 5-ml plastic syringe (Becton, Dickson and Company, Franklin Lakes, NJ, USA) with a 27G metallic needle and electrospun into scaffolds at the following processing conditions; flow rate 2 ml/h, 20-cm distance and electrical voltage 18kV. The fibers were collected on an aluminum foil-covered rotating stainless-steel mandrel (120 rpm) at 25°C. After electrospinning, the scaffolds were kept under vacuum for 2 days to ensure solvent evaporation before SAP physical adsorption. SAP P11-4 (Curodont Repair, Credentis AG, Windisch, Switzerland) solutions were prepared by resuspending the peptide in sterile deionized water (DI) at different concentrations, namely: 0.1 mg/ml, 1 mg/ml, 1.25 mg/ml, and 2.5 mg/ml. The desiccated fibrous scaffolds were cut (15×15 mm2) and immersed in the distinct P11-4 solutions for 24 h at 37°C to allow the physisorption on the fibers’ surface. Next, the scaffolds were left to dry for 24 h, then assigned to the following groups: PCL-P11-4 0.1 mg/ml, PCL-P11-4 1 mg/ml, PCL-P11-4 1.25 mg/ml, PCL-P11-4 2.5 mg/ml, and non-modified/pristine PCL (control).
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10

Membrane Reconstitution of Viral Fusion Peptide

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The composition of membranes used in this study is consistent with our previous study [14] (link). The desired amounts of POPC, POPS, Chol, and 0.5% (mol:mol) spin-labeled lipids in chloroform were mixed well and dried by N2 flow. The mixture was evacuated in a vacuum drier overnight to remove any trace of chloroform. To prepare MLVs, the lipids were resuspended and fully hydrated using 1 mL of pH 7 or pH 5 buffer (5 mM HEPES, 10 mM MES, 150 mM NaCl, and 0.1 mM EDTA (pH 7 or pH 5)] at room temperature for 2 h. To reconstitute FP1 without GGGKKKK in membrane, the desired amounts of peptide were dissolved in 1,1,1,3,3,3-hexafluoro-2-propanol (Sigma) and well mixed with the lipids in chloroform. The mixtures were dried and fully hydrated to generate the MLVs. To prepare SUVs for CD and ITC measurements, the lipids were resuspended in pH 7 or pH 5 buffer and sonicated in an ice bath for 20 min or when the suspension became clear. The SUV solution was then further clarified by ultracentrifugation at 13,000 rpm for 10 min.
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