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38 protocols using nuclepore track etched membrane

1

Real-Time PCR for Bonamia ostreae Detection

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Efficiency, LOD and LOQ of both real‐time PCR approaches were established using Bonamia ostreae isolated from highly infected oysters (Mialhe et al., 1988). Isolated parasites were counted using a Malassez‐cell hemocytometer, and suspension concentration was adjusted before performing 1:10 serial dilutions in 0.22 µm filtered seawater (FSW). Each dilution was filtered onto a 1 µm pore size 47 mm diameter polycarbonate membrane (Whatman® Nuclepore™ Track‐Etched Membranes), stored at −80°C until being used for DNA or RNA extraction. A total of 5 separate diluted series from 10 to 106 parasites per membrane were tested in real‐time PCR for DNA detection. A total of 4 separate diluted series from 3 × 10−1 parasites to 3 × 107 parasites per membrane were tested in real‐time PCR for RNA detection.
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2

Conjugation of EGF to Nanoparticles

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EGF Recombinant Human Protein (ThermoFisher, 1mg/mL, 1X PBS) was functionalized by adding 2% v/v of Propargyl-N-hydroxysuccinimidyl ester (Sigma-Aldrich, 0.44 M in DMSO, wt 225.20 g) and incubated on ice for 6 h. The functionalized EGF was then dialyzed in 1x PBS via D-Tube Dialyzers (Millipore) overnight to remove excessive NHS ester. The conjugation was completed by mixing 5 μL of functionalized EGF with membrane-wrapped NP (NP: EGF, 1:50000). The catalyst was prepared by mixing a 0.10 M solution of L-Ascorbic acid with a 5.10 mM solution of CuSO4·5H2O (1:1 v/v). And 3 μL of catalyst was added to the mixture of alkyne-functionalized EGF and azide-presenting NP. The final volume of the mixture was brought to 100 μL with 0.1x PBS. To generate NP-EGF with different EGF loading, membrane-wrapped NP with different wrapping times were used (Figure S5). The crosslinking reaction was maintained at room temperature overnight. Subsequently, excessive EGF and catalyst were removed by dialysis with Nuclepore Track-Etched Membranes (Whatman, Pore Size 0.03 μm, Diameter 25 mm) in 0.1x PBS overnight.
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Cell Invasion Assay Using Boyden Chambers

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Cell invasion assays were performed in Boyden chambers, as previously described (38 (link)). Briefly, 4×104 cells/chamber were allowed to invade in Matrigel for 18 h at 37°C, 5% CO2 using 8 µm pore size Nuclepore Track-Etched Membranes (Whatman, Maidstone, UK) coated with 50 µg Matrigel (BD Biosciences) and 10% FBS in DMEM as a source of chemoattractants. At the end of the assay, cells on the lower filter surface were fixed with ethanol, stained with haematoxylin and counted in 10 random fields/filter at ×200 magnification. The extent of cell invasion was expressed as a percentage of the basal cell invasion (CTRL), considered 100%.
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4

Liposome Flotation Assay for Protein Binding

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Liposome generation and flotation was performed as described in Vollmer et al., 2015 (link). In short, E. coli polar lipids (Avanti Polar Lipids) dissolved in chloroform and supplemented with 0.2 mol% 18:1 Liss Rhodamine PE (Avanti Polar Lipids) were vacuum-dried on a rotary evaporator, dissolved as liposomes in PBS by freeze/thawing cycles and extruded by passages through Nuclepore Track-Etched Membranes (Whatman) with defined pore sizes using an Avanti Mini-Extruder to generate small unilamellar liposomes of defined sizes. For liposome flotations, proteins (6 μM) were mixed 1:1 with liposomes (6 mg/mL) and floated for 2 hr at 55,000 rpm in a TLS-55 rotor (Beckman) at 25°C through a sucrose gradient. Binding efficiency was determined by Western blot analysis using an EGFP antibody (Roche, 11814460001, 1:2000). As secondary antibody, an anti-mouse, horseradish peroxidase conjugated antibody (Calbiochem, 401215, 1:5000) was used. The ImageQuant LAS-4000 system (Fuji) and the AIDA software were used to compare band intensities of start materials with floated liposome fraction.
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5

Microplastics in Bottled Water

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Bottled water (still, low mineralization) marketed in 1.5 L single use PET bottles from the five top-selling five brands, was purchased from local retailers by the consumers’ organization OCU (Organization of Consumers and Users of Spain). Still water in 1.5 L PET bottles is the most common format sold in the country and the five brands selected represented about 40% or the market share for that type of water in Spain. We sampled 45 L for each brand (225 L for all brands). In all cases, water was bottled in origin at their respective springs as indicated in their labels.
Water was stored in a dark place protected from extreme temperatures and filtered as soon as possible using Whatman Nuclepore Track-Etched Membranes, 25 mm, pore size 0.8 μm, made of black polycarbonate. Black filters were used to make it easy the visual identification of anthropogenic particles, many of which were white or transparent. We conducted vacuum filtration using multiple filters for each brand, filtering a set of bottles with each filter. Each bottle underwent filtration in three 0.5 L aliquots, with the cap being recapped after each aliquot. This process required the caps to be removed three times per bottle (and repositioned twice), replicating the typical handling of bottled water by consumers.
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6

Preparation of Lipid Vesicles for Microscopy

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An appropriate amount of chloroform was added to a vial containing lipid or lipid mixture with 1 mol% Rhod-PE for fluorescence observation to obtain 17 mM lipid solutions. The lipid we used is DOPC, SOPC, or POPE. The lipid mixture we used consisted of 50 mol% DOPC and 50 mol% DOPE or 50 mol% DOPC, 20 mol% DOPE, and 30 mol% DOPS. After the chloroform was evaporated with Ar, the vial was placed under vacuum for at least 120 min to obtain a dried lipid film. The dried lipid film was hydrated with DI water under gentle agitation. Suspensions of the hydrated lipid film that contained multilamellar, micrometer-sized vesicles were obtained, followed by extrusion 21 times through a 50 nm polycarbonate membrane filter (Nuclepore track-etched membranes, Whatman, Inc., UK) using an extruder (Avanti Polar Lipids, Inc., USA). The SUV dispersion was stored at 4 °C for future use. The prepared SUV dispersion was spin-coated on the SU-8 microwell templates, which were cleaned with IPA and DI water at a rate of 100 rpm for 30 s and 1000 rpm for 30 s, followed by drying in a freeze dryer for more than 6 h to remove any traces of the aqueous solution.
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7

Fabrication of Microfluidic Device

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The device was fabricated on a commercial 6cm polystyrene tissue culture dish (Falcon). 11 holes of diameter 1.5mm were drilled at the dish bottom (Fig. S1, Step 1). A UV-curable adhesive was spread on the bottom surface using a sharp blade (NOA81, Norland Products, Fig. S1, step 2). A semi-permeable polycarbonate membrane (Whatman® Nuclepore Track-Etched Membranes, pore diameter 0.1μm) was placed on the adhesive layer (Fig. S1, step 3). The device was cured under UV-light for 2 minutes (365nm 20W LED, Shenzen Yonton Opto). The membrane covered 9 drilled holes, thus leaving 2 holes uncovered, which will serve as inlets. A circular Polydimethylsiloxane (PDMS) stamp of 150μm thickness and 20 mm diameter was prepared using a metal mold of the same dimensions. The PDMS stamp was placed on a 24x24 mm2 coverslip (Fig. S1, Step 4). The UV-curable adhesive was flown between the coverslip and PDMS by capillary, thus forming a spacer of thickness 150μm (Fig. S1, Step 5). The spacer was half-cured by UV-exposure, and the PDMS was pealed off (Fig. S1, Step 6).
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8

Fabrication of Microfluidic Device

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The device was fabricated on a commercial 6cm polystyrene tissue culture dish (Falcon). 11 holes of diameter 1.5mm were drilled at the dish bottom (Fig. S1, Step 1). A UV-curable adhesive was spread on the bottom surface using a sharp blade (NOA81, Norland Products, Fig. S1, step 2). A semi-permeable polycarbonate membrane (Whatman® Nuclepore Track-Etched Membranes, pore diameter 0.1μm) was placed on the adhesive layer (Fig. S1, step 3). The device was cured under UV-light for 2 minutes (365nm 20W LED, Shenzen Yonton Opto). The membrane covered 9 drilled holes, thus leaving 2 holes uncovered, which will serve as inlets. A circular Polydimethylsiloxane (PDMS) stamp of 150μm thickness and 20 mm diameter was prepared using a metal mold of the same dimensions. The PDMS stamp was placed on a 24x24 mm2 coverslip (Fig. S1, Step 4). The UV-curable adhesive was flown between the coverslip and PDMS by capillary, thus forming a spacer of thickness 150μm (Fig. S1, Step 5). The spacer was half-cured by UV-exposure, and the PDMS was pealed off (Fig. S1, Step 6).
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9

Extraction and Purification of Bacterial Membrane

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Example 2

M. smegmatis (strain mc2 155) was grown in Middlebrook 7H9 broth with the addition of a 10% (vol/vol) FD019 supplement at 37° C. with aeration and shaking. Cells were harvested at an OD600 of around 3, collected with a 4000 G centrifuge, and washed twice with distilled water.

The bacterial membrane was extracted as follow. A ˜2 g bacteria pellet was dispersed in 40 mL Tris HCl buffer (20 mM, pH 8.0) containing 15 mg/mL lysozyme. It was incubated in a 37° C. shaker for 3 h. After adding 400 mg SDS, the cells were further broken down with a probe sonicator in an ice bath for 10 min and then lyophilized. The dried bacteria lysate was suspended in a chloroform-methanol-water solution (CMW; 30:15:1, v/v/v), placed on a shaker at 37° C. for 1 h, and then filtered by Millipore HVLP Durapore® membrane (0.45 gun). The residue was extracted by CMW two more times and then the filtrate was combined and dried under vacuum. The bacterial membrane was dispersed in PBS and the protein concentration was determined using the BCA test. The membrane was extruded using a mini extruder (Avanti Polar Lipids Inc., Alabaster, Ala., USA) through a 0.4 μm polycarbonate membrane filter (Whatman® Nuclepore™ Track-Etched Membranes) 21 times before use.

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10

In Vitro Heat Shock on Neonatal Ovaries

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For in vitro HS treatment, neonatal ovaries were isolated from 2 dpp pups in cold Dulbecco’s Modified Eagle’s Medium (DMEM; Sigma). Ovaries were subjected to HS treatment (43°C for 10 min) in a 0.2-ml thin-walled PCR tube, as described previously [9 (link)]. After HS treatment, all samples were cultured on Nuclepore Track-Etched Membranes (Whatman) in DMEM containing 10% fetal bovine serum at 37°C for 9 h before fixation in 4% paraformaldehyde (PFA) in phosphate buffered saline (PBS).
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