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44 protocols using minilys

1

Herbarium DNA Extraction and Amplification

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Total genomic DNA was extracted from herbarium samples according to Krinitsina et al. (2015) (link). Following the homogenisation of plant fragments (MiniLys, Bertin Technologies, France), total DNA was extracted using the CTAB-method (Doyle and Doyle 1987 ) and further purified using AMPure Beads (Beckman Coulter, USA).
PCRs for two chloroplast markers (atpB-rbcL and trnL-trnF) and nrDNA (ITS region) were carried out in a Thermal Cycler T100 (Bio-Rad, USA) using primers and cycler programmes listed in Table 2. A 10 ng aliquot of DNA was used to make a 25 μl total volume reaction, containing 1 μM of each primer, 200 μM of each dNTP and 0.5 U Encyclo polymerases (Evrogen, Russia). PCR products were checked on 1.2% agarose gels and purified using AMPure Beads (Beckman Coulter, USA) according to the owner’s manual. AMPure Beads suspension was mixed with a solution containing PCR-product ratio 1 vol. PCR-mix: 1.2 vol. AMPure Beads for atpB-rbcL and ITS primer pairs and 1 vol. PCR-mix: 1.4 vol. AMPure Beads for rbcL, Tab C/Tab D and Tab E/Tab F primer pairs.
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2

Western Blot Analysis of Drebrin

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Following the electrophysiological recordings, slices were harvested, snap frozen and stored at -80° until needed. Each slice was lysed in 100 µl Ripa Buffer (50 mM Tris–HCL pH 7.4, 150 mM NaCl, 0.5% sodium deoxycholate, 1% NP40, 0.1% SDS) supplemented with protease inhibitors (Calbiochem set III) and phosphatase inhibitors (1 mM Na2MO4,1 mM NaF, 20 mM β-glycerophosphate, 1 mM Na3V04, 500 nM Cantharidin) using a tissue homogenizer (Minilys, Bertin instruments). Homogenates were centrifuged at 20,000 G and supernatant was collected for further protein quantification analysis using BCA Thermo Scientific Pierce Protein Assay. 30 µg of protein was loaded on an SDS-PAGE gel and western blot analysis was performed as previously described49 (link). Anti-Drebrin (M2F6, Enzo) was used at a concentration of 1:1000 and anti-α-Tubulin (Sigma) was used in 1:8000. Quantification of band densities was performed using FIJI. The area of the band and the mean grey value were measured to obtain a relative density. For relative quantifications, measurements were normalized to tubulin loading control.
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3

Hair Cortisol Extraction and Quantification

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Hair was cut as close as possible to the scalp from the posterior vertex of the head from mothers and their children. The samples were kept at room temperature until they were analyzed. From each hair sample, 3 cm was used for the analysis. Hair was placed in tubes (Precellys Lysing Kits, Bertin Technologies, Paris, France), grinded and pulverized at 5000 rounds per minute via a homogenizer (Minilys, Bertin Technologies, Paris, France). Following this, 1 mL of methanol was added to each tube at room temperature and stirred for 16 h. The samples were centrifuged (Biofuge 13, Heraeus Instruments, Athens, Greece) and the extracts were transferred to a glass tube and left at room temperature in order to evaporate until they dried. Afterwards, they were reconstituted with phosphate buffered saline (100 μL) (pH 8.0) and placed in a vortex for 1.5 min. Before analysis, the samples were placed in a vortex once more. Finally, to estimate cortisol levels, the automatic electrochemiluminescence immunoassay “Cortisol II” was used in the automatic analyzer Cobas e411-Roche Diagnostics (GmbH, Mannheim, Germany). The detection threshold, as indicated from the manufacturer’s instructions, was set at 0.054 μg/dL. Hair cortisol was then calculated and expressed in pg/mg of hair.
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4

Protein Extraction from Frozen Brain Tissue

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Sections of stored frozen DLPFC tissue were cut and transferred to pre-tared tubes for wet weight measurement. A 15× (wt/vol) volume of cold lysis buffer (0.1% SDS/50mM Tris, pH 8.2/1mM MgCl2/Halt Protease Inhibitor (ThermoFisher Scientific, Bremen, Germany)/Simple Step1+3 phosphatase inhibitor (GoldBio)/Benzonase (Invitrogen) was added to 2 mL ceramic bead tubes on ice. Frozen brain tissue was transferred by forceps into the bead tube, and the tissue was homogenized using a Minilys (Bertin Instruments, Rockville, M, USA) bead beater apparatus (30 s at 5000 rpm, 2 times). After a pulse spin, lysate was transferred to a 1.5 mL protein LoBind tube (Eppendorf). The bead tube was washed with ¼ the lysis buffer volume, also transferred to the new tube. Samples were heated for 10 min at 80 °C while shaking at 1400 rpm. After cooling, the samples were spun for 10 min at 10,000× g to pellet insoluble material, and the supernatants were transferred to fresh tubes. Protein concentrations were determined using the bicinchoninic acid assay (BCA) (ThermoFisher Scientific) with bovine serum albumin (BSA) as the standard.
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5

Western Blot Analysis of Brain and Vascular Proteins

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Cerebral blood vessels, peripheral blood vessels, or brain tissues were homogenized in PBS containing Triton 1%, SDS 1%, 5-mM EDTA, deoxycholate 1%, and protease inhibitors (Sigma) by shaking with beads in the Minilys (Bertin). Proteins homogenates (100 mg for hippocampus and 150 mg for blood vessels) were separated on acrylamide gel 4%e15% and transferred on nitrocellulose membranes. The membranes were heated for 15 minutes at 85 C in PBS buffer and then blocked with PBS, 5% milk. PS1dE9 full length and PS1 Cter were immunoblotted with anti-PS1 (antibody registry: AB_10706356) revealed with IRDye800 anti-rabbit antibody (antibody registry: AB_621843), anti-NeuN (antibody registry: AB_2298772) revealed with A680 anti-mouse antibody (antibody registry: AB_2535723), and anti-GAPDH (antibody registry: AB_10615768) revealed with IRDye800 anti-chicken antibody (antibody registry: AB_1850023).
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6

Isolation and Purification of RNA from Microfilariae

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Mf in RNAlater (Ambion) were first diluted via adding an equal volume of phosphate-buffered saline to the sample, and centrifuged at 2,000 × g at 4 °C for 10 min to pellet mf. The pelleted mf were then processed using the TriZol–chloroform isolation procedure after homogenization using a bead beater (Minilys, Bertin Instruments). The remaining suspension was reserved for Western blotting assays. Isolated RNA was then purified using Exiqon’s miRCURY RNA isolation kit, cell & plant, in accordance with the manufacturer’s instructions. Extracted RNA was then assayed for quality and rRNA depleted using Terminator 5′-phosphate–dependent exonuclease (Epicentre), in accordance with the manufacturer’s instructions, before being processed using a commercial purification kit (Zymo, RNA Clean & Concentrator-5) following manufacturer’s instructions (SI Appendix, Supplementary Methods). These samples were then assayed for RNA concentration before being sent to the University of Liverpool’s Centre for Genomic Resources for RNA sequencing using an Illumina HiSeq 4000. Raw fastq files were trimmed for adapters and quality, with a minimum quality window score of 20, and reads of less than 20 bases were discarded.
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7

Gut Cell Death in A. domesticus

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On days 3, 5, and 21, the percentage of dead cells in the A. domesticus gut was examined. Seven groups (one for each treatment) containing fifteen 1-day-old adults were set up and reared as described above. Five insects from each group were collected on the 3rd, 5th, and 21st days and gently anesthetized on ice. Then, the gut was isolated in 0.1 PBS buffer (pH 7.4; 400 μL; 4 °C). Subsequently, the tissue was gently homogenized (Minilys®, Bertin Technologies, Montigny-le-Bretonneux, France), and the resulting cell suspension was used to determine the percentage of dead cells by using flow cytometry (MUSE® Cell Analyzer, Millipore, Billerica, MA, USA), employing the Muse® Annexin V & Dead Cell Kit and following the provided kit protocol. Dead cells were identified as 7-AAD (Aminoactinomycin D—a fluorescent intercalator) positive.
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8

RNA Extraction from Punch Biopsy

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Half of the 3mm punch biopsy was placed into RNAlater TM solution (ThermoFisher Scientific), stored overnight at +4°C to ensure proper penetration of the tissue, then moved to -80°C until the extraction. Half of 3mm punch biopsy was homogenized with Minilys by Bertin Technologies with 30sec homogenizing/30sec break 3 cycle on ice until the tissue was completely homogenized. Homogenates were proceeded to RNA extraction with the Qiagen RNeasy Fibrous Tissue kit according to the manufacturer's protocol including in-column
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9

Quantitative Gene Expression Analysis

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Frozen lung tissue samples were homogenized using Precellys Lysing Kits (Bertin Technologies, Cat# P000918-LYSK0-A) and the homogenizer Minilys (Bertin Technologies) as described in the manufacturer’s protocol. Total RNA was extracted from homogenized samples using Qiazol Lysis® Reagent (QIAGEN, Cat#79306) according to the manufacturer's instructions. Subsequently, 1 µg of RNA was reverse transcribed into copy DNA (cDNA) via the RevertAid™ First Strand cDNA Synthesis Kit (ThermoFisher Scientific, Cat#K1622) according to the manufacturer's protocol. Each qPCR reaction mix contained 5 ng of cDNA in a total volume of 20 µl and was performed using the iTaq Universal SYBR Green Supermix (Bio-Rad Laboratories, Cat# 1725124). Primers for qPCR analysis were purchased from Eurofins-Genomics Germany and sequences are shown in Supplementary Table S6. Reactions (50 cycles, initial activation 98 °C, 2 min, denaturation 95 °C, 5 min, hybridization/elongation 60 °C, 10 min) were performed using the CFX-96 Real-Time PCR Detection System (BIO-RAD, Munich, Germany) and analyzed via the CFX Manager Software (BIO-RAD, Munich, Germany). The relative expression level of specific transcripts was calculated using the relative quantification ΔΔCq method by normalization to the housekeeping-gene 60S ribosomal protein L30 (RPL30) or Hypoxanthine–guanine phosphoribosyltransferase (HPRT).
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10

Quantifying Ear Inflammation Markers

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The ear skins suspended in PBS containing 0.1% Triton X-100 (Sigma-Aldrich) and Halt protease and phosphatase inhibitor cocktail (Thermo Fisher Scientific) were homogenized by using zirconium oxide beads and Minilys (Bertin Technologies). The amounts of cytokines and chemokines in ear homogenate were measured by BD Cytometric Bead Array Flex Set (BD Biosciences, catalog#: 560157, 560232) and LEGENDplex Mouse Proinflammatory Chemokine Panel (BioLegend, catalog#: 740451), according to the manufacturer’s protocol.
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