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21 protocols using microfuge 16

1

Selamectin Hemolytic Assay on Human Erythrocytes

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Selamectin was tested on human erythrocytes of blood group 0 obtained from a healthy patient. The blood was centrifuged at 5000 rpm for five minutes (Microfuge 16, Beckman coulter, Brea, CA, USA) and the erythrocytes were washed 5 times with a solution (TBS) containing 50 Mm Tris-HCl (pH 7.6) and 0.15 M NaCl. After the washes, the erythrocytes were diluted 10-fold using the TBS solution. A volume of 50 µL of drug at the concentrations mentioned above (50 to 0.4 μg/mL) was added to 50 µL of cell suspension and incubated at 37 °C for 1 h. Two controls were included in the assay, which were dissolved drug solvent and 0.1% Triton X-100, used as CTR- and CTR+, respectively. After incubation, the plate was centrifuged at 500× g for 5 min and 50 μL of supernatant from each well was transferred to a new 96-well plate (Microfuge 16, Beckman coulter, Brea, CA, USA). The supernatants were used to measure the absorbance of the released hemoglobin at 540 nm. The hemolysis percentage of each sample was calculated using the following formula: % Hemolysis=Abs 540 nm of the test sample Abs 540 nm of CTR(Abs 540 nm of CTR+Abs 540 nm of CTR×100
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2

Preparing Microalgal Samples for SEM Examination

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Before SEM examination, the microalgal samples were centrifuged at 5000 rpm (equivalent to relative centrifugal force of 1845× g) for 5 min (Microfuge 16, Beckman Coulter, Brea; CA, USA). The supernatant was decanted, and the pellet was fixed with 2.5% (v/v) glutaraldehyde for 4 to 6 h at 4 °C. The samples were washed three times, with 0.2% (v/v) sodium cacodylate buffer for 10 min each. The samples were then post-fixed with 1% (v/v) osmium tetroxide for 2 h at 4 °C and washed three times with sodium cacodylate buffer for 10 min each. After post-fixation, the samples were dehydrated gradually using a series of increasing acetone concentrations: 35%, 50%, 75%, 95% once for 10 min each, and 100% three times for 15 min each. After the drying process, the samples were mounted on aluminum stubs and coated with gold using a sputter coater. The samples were then observed using SEM (Model JEOL JSM-6400, Tokyo, Japan) with an accelerating voltage of 15.0  kV.
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3

Peptide Stability Evaluation in Human Plasma

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Peptide stability tests were performed according to a TCA stability assay based on the method used by Nguyen et al. [38 (link)]. Peptides were dissolved in water, mixed with human plasma* to a final concentration of 1.0 mg/mL, and incubated at 37 °C with agitation (300 rpm, Thermomixer, Eppendorf AG, Hamburg, Germany). After 0, 1, 2, 3, 6 and 24 h, 80 μL of the solution was taken and mixed with 15% TCA to obtain a final concentration of 3% (v/v). The samples were incubated in ice for 10 min and centrifuged for 10 min (12,000 rpm, Microfuge 16, Beckman Coulter, Brea, CA, USA). Supernatants were analyzed by RP-HPLC on column using a linear gradient of acetonitrile (5–100% over 15 min) with detection at 223 nm. Peptides were quantified by their peak areas relative to the initial peak areas (0 min). All stability tests were performed at least in triplicates. As control samples peptides dissolved only in water under the same conditions were used. To additionally assess the changes in the incubated samples (peptide degradation) mass spectrometry analysis was used. LC-MS experiments were performed using ESI-IT-TOF (Shimadzu, Kyoto, Japan).
* Blood was collected from healthy anonymous donors and EDTA was then used as an anticoagulant. The procedure was approved by the Independent Bioethics Commission for Research of the Medical University of Gdańsk (NKBBN/387/2014).
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4

Crystallization of Peptides CysZ4 and CysZ9

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The crystallization trials were carried out for two peptides, CysZ4 and CysZ9. Lyophilized samples were dissolved in MiliQ water to the concentration of 2 mg/mL (CysZ4) or 4 mg/mL (CysZ9). Samples were centrifuged for 10 min (14,000 rpm, Microfuge 16, Beckman Coulter, Brea, CA, USA). The precipitate was discarded, and the supernatant was used for the crystallization trials by the hanging-drop vapor-diffusion method at 18 °C. CysZ9 was crystalized in two conditions.
The first was 2.4 M sodium malonate pH 6.0. A single needle-shaped whisker crystal was cryoprotected in mother liquor supplemented with 70% (v/v) MPD and then flash-vitrified at 100 K in nitrogen gas stream.
The second was 0.2 M MgCl2, 10% MPD, 0.05 M sodium cacodylate pH 6.5, 0.001 M spermine. A cuboid single crystal with the dimensions of 0.13 mm was cryoprotected in mother liquor supplemented with 60% (v/v) MPD and then flash-vitrified at 100 K in nitrogen gas stream. For both crystals, X-ray diffraction data were collected using synchrotron radiation at beamline 14.2 of the BESSY II synchrotron (Berlin, Germany), equipped with a Rayonix MX-225 square CCD detector. The diffraction data were processed using HKL3000 [31 (link),32 ].
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5

Graphene-PImQ Colloidal Synthesis

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Graphite (5 mg) was added to deionized water containing PImQ (0.05 g L−1, 10 mL). The mixture was sonicated in an ice bath for 60 min using a tip-type ultrasonic homogenizer (Branson Sonifer 250, power output 20 W, Branson Ultrasonics, Danbury, CT, USA). The colloidal solution was centrifuged at 4000 rpm for 1 h using a microcentrifuge (Microfuge 16, Beckman Coulter, Brea, CA, USA). After centrifugation, homogeneous PImQ/graphene (0.1:1, (w/w)) was obtained from the supernatant. PImQ/graphene suspensions with different component ratios up to PImQ/graphene = 1:1 (w/w) were also prepared.
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6

Hollow Fiber Precursor Dispersion Preparation

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The hollow fiber precursor dispersion consists of a homogeneous mixture
of 1,4-butanediol diacrylate (BDA, 36.7 vol %; ChemCruz), ethanol
(41.8 vol %; Merck), demineralized water (21.5 vol %; MilliQ Water
Purification), Ludox TMA nanoparticles (7.8 wt %; Grace), and hexadecyltrimethylammonium
cations (CTA+, 17 mM; Sigma-Aldrich). A detailed composition
of all STrIPS fiber casting mixtures is given in the Supporting Information
(Figure S2). The photo-initiator 2-hydroxy-2-methylpropiophenone
(Sigma-Aldrich) is added to 0.3 vol % to the casting mixtures to polymerize
the BDA monomers after phase separation. Visualization of the oil
phase is accomplished by fluorescence labeling with Nile red (Sigma-Aldrich).
All chemicals purchased are of analytical grade.
Ludox TMA nanoparticles
are prepared by concentrating the particle stock dispersion from 34
to 45 wt % by the evaporation of water. The concentrate is centrifuged
to remove nanoparticle aggregates (15 min at 2500 rpm; Microfuge 16
Beckman Coulter), adjusted to pH 3 by the addition of 1 M HCl (Acros
Organics), and then dialyzed in water containing 50 mM NaCl (Merck).
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7

Ethanol-Induced Silica Droplet Dynamics

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20 mL solutions
of CTA+ (5 mM), water, Ludox TMA (5 wt %), and ethanol
(0, 5, 10, 20, 30, 40 vol %) are mixed. The dispersions are tip-sonicated
for 30 s (30% amplitude of a 500 W tip sonicator, 10 mm tip diameter;
Qsonica LCC) to redisperse aggregated silica particles. Separately,
10 mL solutions of water and ethanol (0, 5, 10, 20, 30, 40 vol %)
are prepared to which 2 mL of BDA is added. These solutions are shaken
vigorously. Subsequently, the BDA and water are separated via centrifugation
at 1000 rpm for 15 min (Microfuge 16 Beckman Coulter) and decantation.
The densities of the BDA phases as well as the Ludox dispersions are
determined with a calibrated pipette and an analytical balance (AG204
DeltaRange). A droplet of the BDA phase (15 μL) that has been
equilibrated with the alcoholic solutions of the respective ethanol
vol % is formed in the aqueous dispersion of Ludox TMA and CTA+ with the corresponding ethanol volume fraction. Videos of
the droplet shape during volume reduction (90 vol %) are recorded
on a pendant drop tensiometer (Dataphysics OCA25). The drop shapes
are analyzed with the ImageJ plugin pendent drop.55 (link)
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8

Isolation and Characterization of Rat Liver Microsomes

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Rat liver microsomes were obtained via differential centrifugation [22 (link)] (L-80XP, Microfuge® 16, Beckman Coulter Inc., Miami, FL, USA). The microsomes were stored in buffer [10 mM Tris-acetate, 1 mM ethylenediaminetetraacetic acid (EDTA), 100 mM PMSF, and 20% glycerol, pH: 7.4] at −80 °C until further use. Protein concentrations were determined by the BCA method and CYP450 content was determined by the method of Omura and Sato [23 (link)].
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9

Genomic DNA Extraction from S. aureus

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Total genomic DNA was extracted using the conventional boiling method [18 (link)]. Briefly, colonies from pure S. aureus cultures were suspended in 300 μL of TE (Tris-EDTA) (10 mM Tris-HCl pH 8.0 with 1 mM EDTA) buffer and vortexed to homogenise the cells. The suspension was boiled in a heating block at 100°C for 10 minutes with immediate cooling on ice for 5 minutes. The tubes were centrifuged (Beckman Coulter Microfuge 16, United States) at 14000 ×g for 5 minutes. The supernatant was transferred into a new sterile tube and stored at −20°C for PCR use. Nanodrop readings were taken to measure the concentration and purity of isolated DNA using the Thermo Scientific Nanodrop 2000, UV-Vis spectrophotometer (Wilmington, Delaware, USA). Readings within 1.8–1.9 at the ratio of 260/280 were regarded as pure DNA. Nuclease-free water (Thermo Fisher Scientific, Waltham, MA USA) was used to adjust the DNA concentration accordingly for PCR.
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10

SWNT-ssDNA Suspension and Characterization

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SWNT purchased from Sigma Aldrich ((6,5) chirality, 0.7–0.9 tube diameter, carbon <95 %, >93% carbon as SWNT) was suspended with a d(AT)15 or a biotin-modified d(AT)15 sequence of ssDNA (Integrated DNA Technologies) using previously developed methods.[1 , 8 (link)] Briefly, SWNT and ssDNA were added in a 2:1 DNA:SWNT mass ratio to NaCl in nanopure water (0.1 m) (normal saline). The suspension was sonicated for 20 minutes with a bath sonicator (Bransonic, M2800H) followed by ultrasonication with a 3 mm probe tip sonicator (QSonica Q125 Sonicator) for 40 minutes. Suspension was centrifuged (Beckman Coulter Microfuge 16) for 180 min at 16,100 RCF and the supernatant was collected and stored at 4 C. Concentration of the SWNT-ssDNA solution was obtained via UV-Vis (Beckman Coulter, DU 730) and diluted with normal saline to obtain experimental concentrations.[8 (link)]
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