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S cerevisiae

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S. cerevisiae is a type of yeast commonly used in laboratory settings. It is a single-celled eukaryotic microorganism that belongs to the fungus kingdom. S. cerevisiae is a widely studied model organism and has a well-characterized genome, making it a valuable tool for various research applications.

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Lab products found in correlation

E coli, by Merck Group (2 mentions) Guava easycyte 8ht flow cytometer, by Merck Group (2 mentions) Vitrobot mark 4, by Thermo Fisher Scientific (2 mentions) Epu software package, by Thermo Fisher Scientific (1 mentions) Titan krios g3 electron microscope, by Thermo Fisher Scientific (1 mentions) Infinite m200 microplate reader, by Tecan (1 mentions) No 4 filter, by Cytiva (1 mentions)

10 protocols using s cerevisiae

1

Characterizing Probiotic Strains and Enzymes for Fermentation

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B. subtilis CW4 (NCBI accession no. MH885533) was obtained from a traditional fermented food (pickled vegetables) and was selected by using a soybean antigenic protein screening plate. E. faecium CWEF (NCBI accession no. MN038173) was isolated from the gut of a healthy pig. Both B. subtilis and E. faecium are government-authorized probiotics in China.
S. cerevisiae (CGMCC 2.3973), L. plantarum (CGMCC 1.16089), Lactobacillus casei (CGMCC 1.8727), and neutral protease from Bacillus spp. (P3111; Sigma-Aldrich Corp., St. Louis, MO, USA) were purchased to compare their effects on protein degradation and LA production during different fermentation processes.
Wang C., Shi C., Su W., Jin M., Xu B., Hao L., Zhang Y., Lu Z., Wang F., Wang Y, & Du H. (2020). Dynamics of the Physicochemical Characteristics, Microbiota, and Metabolic Functions of Soybean Meal and Corn Mixed Substrates during Two-Stage Solid-State Fermentation. mSystems, 5(1), e00501-19.
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2

Agglutination Assay with Chromone Derivatives

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The agglutination assay was studied using chromone derivatives as the earlier procedure (Sethupathy et al., 2020 (link)). V. parahaemolyticus overnight grown cultures (1:100) dilution were treated with chromone derivatives for 24 h at 30°C kept at 250 rpm. The cell pellets were adjusted to an approximate optical density of 0.5 OD, and 400 µL of the mixture was progressed to 14 mL tubes containing 1500 µL phosphate buffer solution and 500 µL concentration of 2% newly prepared S. cerevisiae (Sigma–Aldrich, St. Louis, USA). After gentle vortexing of the mixture for 5 s, the initial OD was measured at 600 nm using a UV-spectrophotometer (Optizen 2120UV, Korea). Subsequently, 25 min of incubation was kept at ambient temperature, 100 µL of the translucent supernatant was transferred into 96-well plates, and OD600 were measured. The following formula calculation showed agglutination as percentage: 100 × (1 − (OD600before/(OD600after)).
Sathiyamoorthi E., Lee J.H., Tan Y, & Lee J. (2023). Antimicrobial and antibiofilm activities of formylchromones against Vibrio parahaemolyticus and Vibrio harveyi. Frontiers in Cellular and Infection Microbiology, 13, 1234668.
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3

Yeast-derived Beta-Glucan Protocol

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The β-glucan utilized was the glucan from baker’s yeast S. cerevisiae (Sigma-Aldrich; St. Louis, MO), with a purity of 98%. Sterilized deionized water was used as the vehicle for β-glucan dilution.
Silva V.D., Pereira L.J, & Murata R.M. (2017). Oral microbe-host interactions: influence of β-glucans on gene expression of inflammatory cytokines and metabolome profile. BMC Microbiology, 17, 53.
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4

Phagocytosis Assay Using Flow Cytometry

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Alexa fluor 488 labelled bacteria (E. coli, Sigma-Aldrich) and yeast (S. cerevisiae, Sigma-Aldrich) were used as phagocytosis targets. After 1 h and 3 h of incubation with bacteria and yeast respectively, macrophages from four individuals were analyzed using Guava® easyCyte™ 8HT Flow Cytometer (Merck Millipore) to measure phagocytosis. Flow cytometry assessment of the cell population demonstrated homogeneity (92%) and was gated for further functional assays (gate R1 in Figures 1A, B).
Jin X., Morro B., Tørresen O.K., Moiche V., Solbakken M.H., Jakobsen K.S., Jentoft S, & MacKenzie S. (2020). Innovation in Nucleotide-Binding Oligomerization-Like Receptor and Toll-Like Receptor Sensing Drives the Major Histocompatibility Complex-II Free Atlantic Cod Immune System. Frontiers in Immunology, 11, 609456.
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5

Cryo-EM Structural Determination of Respiratory Supercomplexes

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Purified supercomplexes (3 µL) at a concentration of ~8 mg mL–1, supplemented with S. cerevisiae cyt. c (Sigma-Aldrich; aerobically grown S. cerevisiae contains 95% isoform-1 cyt. c) (83 (link)) at a ∼1:12 molar ratio, was applied to holey carbon film coated copper EM grids (C flat 2/2 3C T50) that had been glow-discharged in air (120 s, 20 mA using PELCO easiGlow). Grids were blotted for 3 s at 4 °C and 100% humidity before rapid freezing in liquid ethane with a Vitrobot Mark IV (Thermo Fisher Scientific). Cryo-EM data were collected using a Titan Krios G3 electron microscope (Thermo Fisher Scientific) operated at 300 kV, equipped with a Gatan BioQuantum energy filter and a K3 Summit direct electron detector (AMETEK). Automated data collection was done with the EPU software package (Thermo Fisher Scientific). A dataset of 10,347 movies, each consisting of 40 exposure fractions was collected at a nominal magnification of 105,000×, corresponding to a calibrated pixel size of 0.85 Å. The camera exposure rate and the total exposure of the specimen were 15.2 e–/pixel/s and ~41 e–/Å2, respectively (SI Appendix, Table S1).
Moe A., Dimogkioka A.R., Rapaport D., Öjemyr L.N, & Brzezinski P. (2023). Structure and function of the S. pombe III–IV–cyt c supercomplex. Proceedings of the National Academy of Sciences of the United States of America, 120(46), e2307697120.
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6

Simultaneous ATP and ADP Quantification

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Briefly as described previously (Yegutkin et al. 2003 (link)), 10 µL aliquots of EDTA plasma were transferred into two parallel wells of a white non-phosphorescent 96-well microplate containing 100 µL of PBS with (A) or without (B) a solution of 200 µM UTP and 5 U/mL NDP kinase from baker’s yeast S. cerevisiae (Sigma). Following the addition of 50 µL of ATP-monitoring reagent, sample luminescence was measured using a Tecan Infinite M200 microplate reader (Salzburg, Austria). The difference in luminescence signals between well “A” (ATP + ADP) and “B” (only ATP) enabled the quantification of ADP concentration, which was converted into ATP through an NDP kinase-mediated reaction in the presence of exogenous UTP. This approach allows simultaneous measurement of both ATP and ADP content within the same sample.
Jalkanen J., Maksimow M., Jalkanen S, & Hakovirta H. (2016). Hypoxia-induced inflammation and purinergic signaling in cross clamping the human aorta. SpringerPlus, 5, 2.
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7

α-Glucosidase Inhibition Assay

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Aliquots of 10 μL of acarbose or test compounds in the concentration range of 0.2 to 2 mg/mL (in triplicate) were incubated for 5 min with 20 μL of the enzyme stock solution: 0.9 units/mL of α-D-glucosidase (EC 3.2.1.20) from S. cerevisiae (Sigma-Aldrich, St. Louis, MO, USA) and 100 μM solution of sodium phosphate buffer. After incubation, 10 μL of substrate [p-nitrophenyl-α-D-glucopyranoside, 5 mM in 0.1 M sodium phosphate buffer] was added and incubated for 35 min at 37 °C; then, the absorbances were determined. Regression analysis was used to calculate the concentration required to inhibit the enzyme activity by 50% (IC50), using the equation V = (A100)/[1 + (I/IC50)S, where V is the percentage of inhibition, A100 is the maximum inhibition, I is the inhibitor concentration, IC50 is the concentration required to inhibit the activity of the enzyme by 50%, and S is the cooperative degree [11 (link),11 (link)].
Rosas-Ramírez D., Arreguín-Espinosa R., Escandón-Rivera S., Andrade-Cetto A., Mata-Torres G, & Pérez-Solís R. (2024). Identification of Hypoglycemic Glycolipids from Ipomoea murucoides by Affinity-Directed Fractionation, In Vitro, In Silico and Dynamic Light Scattering Analysis. Plants, 13(5), 644.
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8

Quantification of Inorganic Pyrophosphate and Polyphosphate in Trypanosoma cruzi

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Cells in log phase were harvested and washed twice with Buffer A. The PPi, and short-chain polyP were extracted using 0.5 M perchloric acid (HClO4) (Ruiz et al., 2001 (link)), and the long-chain polyP was extracted using glass milk (Molecular Probes) as described by Ault-Riche et al. (Ault-Riche et al., 1998 (link)). PPi was determined by measuring the amount of Pi released upon treatment with S. cerevisiae (Sigma) or Thermoccocus litoralis (New England Biolabs) inorganic pyrophosphatase. Extracts were incubated with 5 units/ml of yeast inorganic pyrophosphatase in 50 mM Tris-HCl, pH 7.5, and 6 mM MgCl2, at 30°C for 30 min, and the released Pi was measured using malachite green as described before (Ruiz et al., 2001 (link)). PolyP was determined by the amount of Pi released upon treatment with an excess of S. cerevisiae exopolyphosphatase 1 (ScPPX1), freshly purified in our laboratory (Ruiz et al., 2001 (link)). The concentration of PPi, and polyP in T. cruzi epimastigotes was expressed per mg of protein used to perform the extractions. Protein concentration was measured by BCA method following the manufacturer protocol (Pierce). Results correspond to 6 independent experiments.
Jimenez V, & Docampo R. (2015). TcPho91 is a contractile vacuole phosphate sodium symporter that regulates phosphate and polyphosphate metabolism in Trypanosoma cruzi. Molecular microbiology, 97(5), 911-925.
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9

Phagocytosis Assay of Bacteria and Yeast

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Alexa fluor 488 labelled bacteria (E. coli, Sigma-Aldrich) and yeast (S. cerevisiae, Sigma-Aldrich) were used as phagocytosis targets. After 1 hour and 3 hours of incubation with bacteria and yeast respectively, macrophages from four individuals were analysed using Guava® easyCyte™ 8HT Flow Cytometer (Merck Millipore) to measure phagocytosis. Flow cytometry assessment of the cell population demonstrated homogeneity (92%) and was gated for further functional assays (gate R1 in Fig. 1 A-B).
Jin X., Morro B., Tørresen O.K., Moiche V., Solbakken M.H., Jakobsen K.S., Jentoft S., & Mackenzie S. (2020). Innovation in NLR and TLR sensing drives the MHC-II free Atlantic cod immune system.
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10

Yeast Treatment of Goat Colostrum

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Yeast treatment was carried out as described by Ruiz-Aceituno et al., (2013) . Goat colostrum and lactose control samples, obtained after incubation with -galactosidase (0.68 U.mL -1 ) for 15 min, were treated with 1% (w/v) S. cerevisiae (Sigma-Aldrich) at 37 ºC under stirring for 30 h. All assays were done in triplicate. Aliquots were taken just before yeast addition (time 0) and at 10 min, 2, 4, 6, 24 and 30 h of treatment. Then, they were centrifuged at 4,400 × g at 10 ºC for 10 min and filtered through Whatman No. 4 filters to remove yeast, and kept at -20 ºC until analysis.
Martín-Ortiz A., Moreno F.J., Ruiz-Matute A.I, & Sanz M.L. (2019). Selective biotechnological fractionation of goat milk carbohydrates. International dairy journal, 94.
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