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8 protocols using b rker chamber

1

PBMC Isolation from Venous Blood

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Ten ml venous blood was collected into a heparinized tube from CCs and TB patients at baseline and 2 months follow-up. The blood samples were transported within two hours to the laboratory for PBMCs isolation. The blood was diluted with an equal volume of normal saline solution, layered on the top of LymphoPrep density gradient solution (Serumwerk, Bernburg AG, Oslo, Norway), and centrifuged at 800g for 30 minutes at 20°C with zero brake. After centrifugation, the interphase ring consisting of a mixture of mononuclear cells formed above the Lymphoprep solution and underneath the plasma. The plasma was stored at -80°C for cytokine analysis. The PBMCs were isolated as described previously [38 (link)], and counted using a Bürker chamber with 0.4% trypan blue solution (Sigma-Aldrich, Munich, Germany). All included samples had a cell viability above 75%, which was the cutoff point for the sample to be included for further cell stimulation.
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2

Evaluating Inflammatory Response in Rat CSF

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Eight-day-old rats were injected intraperitoneally with 1 mg/kg PAM3CSK4 (P3C, Merck Millipore France), or 0.9% saline. CSF was sampled 14 h later [5 (link)], and total leukocytes and polymorphonuclear neutrophiles (PMNs) were counted in a Bürker chamber after staining with Türk’s solution (Sigma-Aldrich). The phenotypic analysis of whole blood immune cells was performed by immunocytochemistry following red blood cell lysis as previously described [26 ].
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3

Curcumin and Copper Toxicity in HepG2 Cells

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HepG2 cells were grown on Poly-l-Lysine-coated (Boster Biological Technology, Pleasanton, CA, USA) glass coverslips in MEM cell culture medium supplemented with 10% FCS, glutamine (2 mM), penicillin and streptomycin (all from Thermo Scientific, Waltham, MA, USA) until they reached 90% confluence. After that, they were pre-treated with 25 µM or 5 µM curcumin (Dr. Elmenstofer GmbH, Ammerbuch-Entringen, Germany) for 24 h and then incubated with 20 µM or 100 µM CuCl2 (Alfa Aesan, Karlsruhe, Germany) for 4 h before immunostaining (protocol adapted from Zhang et al. [32 (link)]).
For copper measurements, cells were cultured in 25 cm2 flasks (BD Falcon, San Jose, CA, USA) until 90% confluence, then treated with 25 µM or 5 µM curcumin for 24 h and then incubated with 100 µM or 20 µM CuCl2 for additional 24 h, respectively. After that, cells were washed with PBS and fresh MEM medium added. Samples for atomic absorption spectrometry measurements were collected after 1.5, 3, 4.5, 6, 7.5 and 9 h and cells counted using Bürker chamber and standard Trypan Blue (Sigma Aldrich, Steinheim, Germany) staining for evaluation of dead cell proportion at the end of the experiment. Before temporary freezing, medium samples were centrifuged to remove cell debris.
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4

Isolation and Differentiation of Murine Th17 Cells

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The spleens were rubbed through a nylon sieve (70 μm, BD Falcon, Corning, NY, USA) and washed with PBS. The resulting cell suspensions were centrifuged for 10 min at 350× g (4 °C). The splenocytes were resuspended in 5 mL of red blood cell lysis buffer and kept for 5 min on ice before being washed with PBS and centrifuged at 350× g for 10 min at 4 °C. To obtain mouse CD4+ cells, magnetic separation was performed using a CD4+ T Cell Isolation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany), according to the manufacturer’s protocol. Cell number and viability were determined using trypan blue (Sigma-Aldrich, USA) staining and counting in a Bürker chamber (Sigma-Aldrich, St. Louis, MO, USA) under a light microscope. Th17 cells were obtained from collected CD4+ T cells using the Flow Cellect Mouse Th17 Differentiation Tool Kit (Millipore Merck, Darmstadt, Germany) according to the manufacturer’s protocol. Detailed assay instructions certify to gain complete Th17 cell generation in 6 days. After seeding 2 × 105 CD4+ cells on day 1 into each well of the kit’s plate, on day 6 the total number of differentiated cells were approximately 1–5 × 106. All cell types were stained with trypan blue solution and counted in a Bürker chamber under a light microscope.
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5

Flow Cytometric Analysis of 4T1 Cell Binding

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4T1 cells were cultured in the logarithmic phase to 70% confluency on a tissue culture Petri dish. The supernatant was aspirated, and the cells were washed with 5 mL of PBS (Merck) and detached using 3 mL of Accutase (Thermo Fisher Scientific) at room temperature for 5 min. The cells were harvested by adding 7 mL of PBS and then counted using a Bürker chamber and trypan blue excision dye (Merck). In total, 2 × 105 4T1 cells were incubated with plasma and then 5× diluted in 100 µL of IFB at 4 °C for 1 h. The cells were washed with 1 mL of IFB and centrifuged at 1500 rpm for 5 min. The cells were resuspended in 100 µL of IFB containing goat-anti-mouse anti-IgG Alexa FluorTM 488 (Thermo Fisher Scientific, A-11001 400× diluted), and then incubated at 4 °C for 30 min. The cells were washed with 1 mL of IFB and then centrifuged at 1500 rpm for 5 min. The cells were resuspended in 300 µL of IFB, and 10 µg/mL of propidium iodide was added (3 µL from 1 mg/mL stock) right before acquisition to gate on viable cells. In total, 10,000 events per sample were detected using an FACSCalibur cytofluorimeter, and data analyses were performed using the CellQuestTM software.
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6

Counting and Visualizing A. castellanii-V. cholerae Interactions

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A. castellanii cells, in the absence and presence of bacteria were counted in a Bürker chamber (Merck Eurolab, Sweden) under a light microscope (Carl Zeiss, Sweden). Eosin staining was used to detect dead amoeba cells, which were stained red, in contrast to the viable amoeba cells, which remained unstained.
The intracellular localisations of V. cholerae were analysed by electron microscope, for which 5-mL samples from culture flasks containing the amoeba in the presence of bacteria were centrifuged for 10 min at 300 g in a Labofuge GL centrifuge (VWR International). The resulting pellets were washed with PBS. Each pellet of infected amoeba was fixed in 2.5% glutaraldehyde in 0.1 M sodium cacodylate buffer pH 7.3, with 0.1 M sucrose and 3 mM CaCl2, for 30 min at room temperature. Samples were then washed in sodium cacodylate buffer and post-fixed in 2% osmium tetroxide in the same buffer for 1 h. The samples were centrifuged and the pellets were dehydrated and embedded in epoxy resin, LX-112. The embedded samples were cut into ultra-thin sections, placed on grids, and stained with uranyl acetate and lead citrate. Sections were examined with a transmission electron microscope (SEM, Philips 420).
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7

Quantifying Algae and Bacteria in Water

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Algae found in water samples after the 9-day experiment were identified mostly to the genus level in accordance with professional manuals [43 ,44 ]. The abundance of bacterial and algal cells was estimated by direct microscopic counting (Zeiss Primo Star, Monument, PA, USA) of cells in the Bürker chamber (Merck Eurolab, Stockholm, Sweden). This is a simple manual method for enumeration of average cell number by counting cells in squares; each square for bacteria counting has an area of 1/400 mm2 and sample volume of 1/4,000,000 mL, whereas for algal cells, the area was 1/25 mm2 and the sample volume was 1/250,000 mL. For each sample, counting was performed in triplicates and in 20 squares of the counting grid each time.
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8

Isolation of CNS Mononuclear Cells

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After being collected from an animal, the CNS (brain and spinal cord) was placed in ice-cold PBS and forced through 70 µm cell strainers (BD Bioscience, Bedford, MA, USA) for a single cell suspension and then centrifuged for 10 min at 350 × γ (4°C). The CNS mononuclear cells were resuspended in 40% percoll (Sigma, Poznan, Poland) and diluted with white Hank’s buffered salt solution (HBSS) (Lonza, Basel, Switzerland). Then, the suspension of cells was carefully overlayered on top of the 70% percoll, diluted with red HBSS. CNS mononuclear cells were isolated by centrifugation for 40 min at 700 × γ (4°C) with slow acceleration without a break. Cells were then collected from the 40%/70% interface, washed and resuspended in PBS [30 (link)]. In the next step, the CNS cells were stained with trypan blue solution 0.4% (Sigma, Poznan, Poland) and counted in the Bürker chamber (Merck, Warsaw, Poland) under a light microscope objective 10x (Carl Zeiss, Axio Observer.A1, Poznan, Poland) and prepared for flow cytometry.
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