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Phosphate buffer saline (pbs)

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Phosphate buffer saline (PBS) is a commonly used buffer solution in biological research and laboratory applications. Its core function is to maintain a stable pH and ionic concentration, providing a physiologically compatible environment for various biological samples and experiments.

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255 protocols using phosphate buffer saline (pbs)

1

Gut Microbiome Analysis by Culture

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First, a direct inoculation of the stool was performed. To do so, one gram of stool sample was diluted in 1 ml of phosphate buffer saline (Thermo Fisher Scientific, Illkirch, France). Then, 100 μl was taken from the sample, deposited and then homogenized in a second tube containing 900 μl of phosphate buffer saline (Thermo Fisher Scientific, Illkirch, France). This step was carried out several times in order to perform a cascade dilution at 1/10th (from 10-2 to 10-10). Subsequently, 50 μl of each tube was deposited and spread homogeneously on YCFA modified agar (DSMZ : Deutsche Sammlung von Mikroorganismen und Zellkulturen, Germany) (https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium1611.pdf) + 0.5g/L of Na2S + 1 g/L of sodium acetate (Martín et al., 2017 (link)) + 100 mg/L of Vitamin K2 (Fenn et al., 2017 (link)) + 5% of sheep blood (BioMérieux, Marcy l’Etoile, France) and on Columbia agar plates + 5% of blood (Cos, Biomerieux, Marcy l’Etoile, France). The agar plates are then incubated at 37°C under anaerobic condition, mimicked with Zip bag (Oxoid, Dardilly, France) containing an anaerobic GasPak (Becton Dickinson, Le Pont de Claix, France) for 48 h.
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2

Microfluidic Device Fabrication and Bacterial Assay

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Microfluidic device fabrication was done by using a polydimethylsiloxane (PDMS) preparation set (Sylgard 184, Dow-corning, United States). The oil-soluble surfactant, polyglycerol polyricinoleate (PGPR) was obtained from Danisco (Denmark). Mineral oil, sodium chloride (NaCl) were from Fischer Scientific (United Kingdom) while Poly(allylamine hydrochloride) (Mw ≈ 17 500), poly(sodium 4-styrenesulfonate) (Mw ≈ 70 000) and water-soluble surfactant, polysorbate 80 (Tween 80) were purchased from Sigma Aldrich (United Kingdom). For bacterial study, the material used were nutrient agar, Luria Bertani broth (LB broth), tryptone, yeast extract and phosphate buffer saline (PBS) all by Oxoid Ltd. (United Kingdom). d(+)-glucose was purchased from Acros Organics (United Kingdom) and Nile red stain was purchased from Invitrogen™ (United Kingdom). Escherichia coli strain SCC1 (MG1655-GFP mutation) expressing green fluorescent protein (E. coli-GFP) stock culture was obtained from Biochemical Engineering Laboratory, University of Birmingham, United Kingdom.
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3

Microbial Quantification in Chicken Meat

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Standard plate count technique was used to determine the initial microbial concentration and the efficiency of the treatment in reducing the number of microorganisms on the surface of the sample. After each treatment, chicken meat samples were collected in sterile Falcon tubes, mixed with 9 mL of Phosphate Buffer Saline (PBS; 0.01 M, pH 7.4; Oxoid, UK), and homogenized at 35 Hz for 1 min (Stomacher 400; International P.B.I., Milan, Italy). The solution was serially diluted (1:10) in PBS; 100 µ L of the solution was plated in duplicate onto the selective media Chromatic Coli/Coliform Agar (Liofilchem, Italia) for E. coli, and on Rose Bengal (RB) (Microbiol, Cagliari, IT) for yeasts and molds, while 1 mL was pour-plated into Plate Count Agar (PCA, Sacco, Como, IT) for the determination of the total mesophilic count. The incubation temperature and time were 37°C and 24 h for E. coli, and 30 and 22°C for 3 to 5 D for PCA and RB plates, respectively. The inactivation degree was determined by evaluating the log(N/N0), where N0(CFU/g) is the number of colony forming units per mL initially present in the untreated sample, and N (CFU/g) is the number of survivors after the treatment. At least 3 independent experiments were carried out for each single treatment condition, and the results were expressed as mean and standard deviation. Each experiment was performed at least in triplicate.
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4

Biomarkers of Pathogen Infection in Fish

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Six fish were sampled (2 fish /tank) from each group at weeks 1, 2, and 3 post-infection and anesthetized with buffer tricaine (MS-222, FINQUEL®, ARGENT). Blood samples were collected via venipuncture by using a 3-cc syringe and (23gauge) needle and emptied into a plain centrifuge tube to clot at room temperature (24–25 °C) and then kept at 4 °C for 4 h before centrifugation at 1198 × g for 10 min to collect serum and stored in Eppendorf tubes at − 20 °C till analysis. Serum samples were analyzed for C-reactive protein (CRP) and IgM. Gill homogenate was prepared by adding 0.5 g of gills to 4.5 mL of ice-cold phosphate buffer saline (Oxoid) at pH 7.4; and homogenized by homogenizer (Sigma, UK). The homogenate was then centrifuged at 1198 × g for 15 min at 4 °C (Centrikon H-401 centrifuge), and the resultant supernatant was aliquoted and stored at − 80 °C for later oxidative stress and antioxidant enzyme assays. Gill tissues were collected in RNAlater® solution and kept at − 80 °C until gene expression analysis. Samples of skin and gills were excised from experimentally infected fish and placed in 10% neutral buffered formalin for histopathological examination.
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5

Bacterial Culture and Dilution Protocol

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Staphylococcus aureus (ATCC 25923) and Escherichia coli (ATCC 25922) were selected as model bacteria. The bacteria were maintained in TSA (Tryptone Soya Agar from Oxoid, England) slants at 4 °C for the bacterial test. Before each analysis, the bacteria were grown in fresh liquid TSB (Tryptone Soya Broth from Oxoid, England) and incubated overnight at 37 °C. The bacterial suspension was diluted in phosphate buffer saline (Oxoid, England) solution by 10-fold serial dilution until the final concentration of 1 × 10 3 and 1 × 10 5 colony forming units (cfu)/mL was obtained.
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6

Encapsulation of Probiotic Lactobacillus

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Lactobacillus plantarum NCIMB 8826 was obtained from the UK National Collection of Industrial and Marine Bacteria (NCIMB). MRS broth and agar and phosphate buffer saline (PBS) were obtained from Oxoid. Sodium alginate (19-40 kDa), dimethyldioctadecylammonium chloride (DDAC), hexadecyltrimethylammonium bromide (CTAB), benzalkonium chloride (BZK), ammonium lauryl sulphate (ALS), sodium dodecyl sulphate (SDS), Nile Red (for microscopy) and glycerol, pepsin (from porcine) and pancreatin lipase were purchased from Sigma-Aldrich. L-alphalecithin was purchased from ACROS Organics. Glacial acetic acid 96% (v/v), sodium chloride and sodium hydroxide were obtained from Fisher Scientific. Calcium chloride dihydrate was purchased from VWR International.
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7

Apoptosis Assay with Annexin V, PI, and Caspase-3

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Propidium iodide (PI), 7-aminoactinomycin D (7-AAD), Annexin V Apoptosis Detection Kit APC and isotype-matched negative control antibody were from Ebioscience (Paris, France). The Pan Caspase Inhibitor Z-VAD-FMK (1/1000) was from R and D system (Minneapolis, MN, USA). N-acetyl-L-cysteine (NAC), were purchased form Sigma Aldrich, St Louis, MO, USA). Rabbit anti human antibody specific for the cleaved (active) form of caspase-3, 3,3'-Dihexyloxacarbocyanine Iodide DiOC 6(3), Dylight 647 goat anti-rabbit IgG, Hoechst 33342, Accutase, penicillin, streptomycin, phosphate buffer saline, α and D Minimum Essential Medium (MEM) Glutamax, fetal calf serum and goat serum, were from Invitrogen (Carlsbad, CA, USA). Rabbit polyclonal anti-caspase-3 antibody was from Cell Signaling Technology (Danvers, MA, USA).
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8

Comprehensive DNA Extraction from Water

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Total DNA from water samples was extracted from the duplicate Sterivex filters using the Qiagen Allprep PowerViral DNA/RNA and DNeasy PowerLyzer PowerSoil kits with modifications as follows. The RNAlater was flushed out of the filters using a sterile syringe, and filters were rinsed with 2 mL of 1X sterile nuclease-free Phosphate Buffer Saline (PBS, pH 7.4, Invitrogen). Solution PV1 (1800 μL) and β-mercaptoethanol (18 μL) were added to the filter cartridge and incubated at 37 °C for 30 min. Next, 20 μL of proteinase K was added to the filter and digested at 55 °C for 1 h. The supernatant was flushed from the filter, and the protocol continued according to the manufacturer’s recommendations. DNA was purified from the entire total nucleic acid product and quantified using the methods described above.
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9

Apoptosis Induction and Inhibition in Immune Cells

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RPMI 1640 (Roswell Park Memorial Institute medium), l-glutamine, HEPES, Gentamicin, Phosphate buffer saline (PBS), and fetal bovine serum were purchased from Invitrogen (Carlsbad, CA). Concanavalin A (Con A), Methanol, DMSO, and 3,3′-Dihexyloxacarbocyanine Iodide (DIOC6) were purchased from Sigma-Aldrich (St-Louis, MO). TUNEL kits were obtained from Roche (Indianapolis, IN). Alexa Fluor 488 Annexin V/Dead cell Apoptosis Kits were procured from Invitrogen by Thermo Fisher Scientific. Lipopolysaccharide (LPS) was purchased from Invitrogen. Inhibitors against Caspase 8 (Z-IETD-FMK) and Caspase 9 (Z-LEHD-FMK) were purchased from R&D Systems (Minneapolis, MN). Plant extracts suspended in DMSO were used in the in vitro studies and DMSO was used as vehicle control.
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10

Antiseptic solutions for cell culture

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Tissue culture plasticware was obtained from BD (Germany). Culture medium, phosphate buffer saline (PBS), trypsin solution, fetal calf serum (FCS) and all other reagents were obtained from Invitrogen (Karlsruhe, Germany) and Sigma-Aldrich (Merck KGaA, Darmstadt, Germany).
Antiseptic solutions NaOCl (0.08% sodium hypochlorite, Lavanox®, Serag-Wiessner GmbH und Co. KG, Naila, Germany) and CHG (0.05% chlorhexidine gluconate, Irrisept®, Irrimax Corporation, Lawrenceville GA, USA) were purchased. Fresh dilutions were produced for each experiment. The products were used in their original concentration 1:1 and at 1:5 and 1:25 dilutions (CHG: 1:1 0.05%, 1:5 0.01%, 1:25 0.002%; NaOCl: 1:1 0.08%, 1:5 0.016%, 1:25 0.0032%).
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