For the analysis of L. rhamnosus K3 and L. johnsonii K4 CFUs, 1 g of the puree mixtures with probiotics was added to 9 mL of sterile peptone water and homogenized with a stomacher at medium speed for 2 min. Seven-fold serial dilutions were prepared from the homogenized samples with peptone (Sigma-Aldrich, Poznań, Poland) water. Appropriate dilutions were inoculated onto MRS agar (pH 6.8 ± 7.2, Merck-110,660, Darmstadt, Germany), and Petri plates were incubated at 37 °C for 48 h. After the digestion in the gastric and intestinal phases, an aliquot of the digested sample was decimally diluted with peptone water and plated onto MRS agar plates at 37 °C for 48 h. Colony counts were calculated as CFU/g of mixtures, and the obtained means of the data were transformed to log10 CFU/g.
Peptone
Manufactured by Merck Group
Sourced in United States, Germany, Italy, United Kingdom, China, Hungary, Netherlands, Australia, Spain
Peptone is a laboratory-grade nutrient product manufactured by Merck Group. It is a complex mixture of peptides and amino acids derived from the enzymatic hydrolysis of proteins. Peptone serves as a source of nitrogen, carbon, and other essential nutrients to support the growth and cultivation of various microorganisms in microbiological media and cell culture applications.
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Lab products found in correlation
Yeast extract, by Merck Group (86 mentions)
Glucose, by Merck Group (61 mentions)
Agar, by Merck Group (23 mentions)
Sodium chloride (nacl), by Merck Group (21 mentions)
Sodium hydroxide (naoh), by Merck Group (16 mentions)
Hydrochloric acid (hcl), by Merck Group (15 mentions)
Dextrose, by Merck Group (13 mentions)
Glycerol, by Merck Group (11 mentions)
Yeast extract, by Thermo Fisher Scientific (10 mentions)
Tween 80, by Merck Group (9 mentions)
Malt extract, by Merck Group (9 mentions)
Methanol, by Merck Group (9 mentions)
Calcium chloride, by Merck Group (8 mentions)
Citric acid monohydrate, by Merck Group (8 mentions)
Acetic acid, by Merck Group (8 mentions)
Beef extract, by Merck Group (8 mentions)
Kh2po4, by Merck Group (8 mentions)
K2hpo4, by Merck Group (7 mentions)
Bovine serum albumin (bsa), by Merck Group (7 mentions)
D glucose, by Merck Group (6 mentions)
200 protocols using peptone
1
Enumeration of Probiotic Lactobacillus Strains
2
Cultivation of Trichophyton rubrum Strain
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T. rubrum strain CBS 119892 (WT) was kindly donated by the CBS-KNAW Fungal Collection (Westerdijk Fungal Biodiversity Institute). T. rubrum culture was carried out in Malt Extract Agar (MEA, 2 % malt extract (w/v), 2% glucose (w/v), 0.1% peptone (w/v) – Sigma Aldrich) at 28 °C. Conidia were recovered by scraping the mycelium from 15-day MEA plates flooded with sterilized 0.9% NaCl, followed by vortexing and filtration through glass wool. After centrifugation, the microconidia concentration was estimated by counting on the Neubauer chamber. Other media used in this study were: Sabouraud Dextrose Agar (SDA - 2% dextrose (w/v), 1% peptone (w/v), pH 5.7), Minimal Medium (MM) pH 5.0 (Cove, 1966 (link)), Potato Dextrose Agar (PDA - 0.4% potato extract (w/v) (Sigma Aldrich), 2% dextrose (w/v), pH 5.7), and Keratin Medium (KM - 2.5 g/L keratin powder from hooves and horns - MP Biomedicals, pH 5.5). The solid medium contained 2% agar (w/v).
3
Antifungal Activity of Panomycocin
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W. anomalus from the National Collection of Yeast Cultures, UK (NCYC 434, K+) was used as the source of panomycocin and maintained on YEPD agar (yeast extract [Sigma-Aldrich Co., St Louis, MO, USA] 1% [w/v], peptone [Sigma-Aldrich Co.] 2% [w/v], dextrose [Sigma-Aldrich Co.] 2% [w/v], and agar [EMD Millipore, Billerica, MA, USA] 2% [w/v], pH 5.5). Candida strains (four in total; three C. albicans and one C. glabrata vaginal isolates) were from German Hospital, İstanbul, Turkey and maintained on Sabouraud dextrose agar (SDA) (peptone [Sigma-Aldrich Co.] 2% [w/v], dextrose [Sigma-Aldrich Co.] 2% [w/v], and agar [EMD Millipore] 2% [w/v], pH 5.6). The identity of all isolates was confirmed by MALDI-TOF mass spectroscopic species identification technique (MALDI Biotyper, Bruker Corporation, Billerica, MA, USA) according to the manufacturer’s instructions.
4
Evaluation of Novel Bacterial Growth Media
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Bacterial suspension was added (10%) to four different media three of which are newly synthesized media and the other is MRS broth. The new media compositions included SGSL: 1% tryptone (Difco, Le Ponte de Claix, France), 1% peptone, (Difco, Le Ponte de Claix, France), 1% yeast extract (Difco, Le Ponte de Claix, France), 5% glucose (Merck, Darmstadt, Germany), 0.05% ascorbic acid (R & M Chemicals, Essex, UK), 0.2% sodium citrate (Peking Chemical Works, Peking, China), 0.005% manganese(II) sulphate (BDH Chemicals Ltd, Poole, England), 0.025% magnesium sulphate (Halewood Chemical Ltd, Middlesex, England), 0.02% sodium chloride (John Kollin Corporation, USA) and 0.1% Tween 80 (Sigma-Aldrich, Missouri, USA), TPYGMA: 1% tryptone, 1% peptone, 1% yeast extract, 5% glucose, 1% 2-morpholinoethanesulphonic acid, MESA (Merck, Darmstadt, Germany) and 0.05% ascorbic acid, TPYGCaT80: 1% tryptone, 1% peptone, 1% yeast extract, 5% glucose, 0.1% CaCO3 and 0.1% Tween 80. Incubation at 37 °C was done after broth inoculation. OD was monitored over a period of 24 h. Fermencin SA715 production was determined by well diffusion assay using Micrococcus luteus as the bacterial target.
5
Yeast Auxotroph Strain Engineering
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The bacterial strains, plasmids, and
primers used in this study are
listed in the Supporting Information,Table S1 . Escherichia coli NEB5α high efficiency competent
cells were obtained from NEB (New England Biolabs Ipswich, MA). The
auxotrophic Y. lipolytica Po1g (Leu−) was
purchased from Yeastern Biotech Company (Taipei, Taiwan). Y. lipolytica XP1 harboring the plasmid pYaliA1-vioDCBAE
was stored in our lab.39 (link) YPD medium contains
20 g/L glucose (Sigma-Aldrich), 10 g/L yeast extract (Sigma-Aldrich),
and 20 g/L peptone (Sigma-Aldrich). YNB medium (C/N = 60, 80, 100,
120) contains 1.7 g/L yeast nitrogen base (without amino acids and
ammonium sulfate) (Difco), 1.1 g/L ammonium sulfate (Sigma-Aldrich),
0.69 g/L CSM-Leu (Sunrise Science Products, Inc.), and 30, 40, 50,
60 g/L glucose, respectively. YNB medium (pH 6.0, 6.5, 7.0, 7.5) contains
1.7 g/L yeast nitrogen base (without amino acids and ammonium sulfate)
(Difco), 1.1 g/L ammonium sulfate (Sigma-Aldrich), 0.69 g/L CSM-Leu
(Sunrise Science Products, Inc.), 30 g/L glucose, and was adjusted
to pH 6.0, 6.5, 7.0, 7.5, respectively, through Na2HPO4 and NaH2PO4. YNB medium with CaCO3 was made with YNB media supplemented with 10 g/L CaCO3. Selective YNB plates were made with YNB media supplemented
with 20 g/L Bacto agar (Difco).
primers used in this study are
listed in the Supporting Information,
cells were obtained from NEB (New England Biolabs Ipswich, MA). The
auxotrophic Y. lipolytica Po1g (Leu−) was
purchased from Yeastern Biotech Company (Taipei, Taiwan). Y. lipolytica XP1 harboring the plasmid pYaliA1-vioDCBAE
was stored in our lab.39 (link) YPD medium contains
20 g/L glucose (Sigma-Aldrich), 10 g/L yeast extract (Sigma-Aldrich),
and 20 g/L peptone (Sigma-Aldrich). YNB medium (C/N = 60, 80, 100,
120) contains 1.7 g/L yeast nitrogen base (without amino acids and
ammonium sulfate) (Difco), 1.1 g/L ammonium sulfate (Sigma-Aldrich),
0.69 g/L CSM-Leu (Sunrise Science Products, Inc.), and 30, 40, 50,
60 g/L glucose, respectively. YNB medium (pH 6.0, 6.5, 7.0, 7.5) contains
1.7 g/L yeast nitrogen base (without amino acids and ammonium sulfate)
(Difco), 1.1 g/L ammonium sulfate (Sigma-Aldrich), 0.69 g/L CSM-Leu
(Sunrise Science Products, Inc.), 30 g/L glucose, and was adjusted
to pH 6.0, 6.5, 7.0, 7.5, respectively, through Na2HPO4 and NaH2PO4. YNB medium with CaCO3 was made with YNB media supplemented with 10 g/L CaCO3. Selective YNB plates were made with YNB media supplemented
with 20 g/L Bacto agar (Difco).
6
Dietary Sugar Modulation of Drosophila Development
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Cultures were carried out on a modified Bloomington semi-defined medium (https://bdsc.indiana.edu/information/recipes/germanfood.html ), containing Sucrose (0.15 and 1.0 M in CD and HSD, respectively) as the only purified sugar source. Ingredients were obtained from; Agar (Fisher Scientific; BP2641-1), Brewer’s Yeast (MP Biomedicals; 903312, Lot: BCBN0171V), Yeast Extract (Sigma-Aldrich; 70161), Peptone (Sigma-Aldrich; 82303), Sucrose (Fisher Scientific; S/8560/63), Magnesium sulfate hexahydrate (Fluka; 00627), Calcium chloride dihydrate (Sigma-Aldrich; 223506), Propionic acid (Sigma-Aldrich; P1386), p-Hydroxy-benzoic acid methyl ester (Sigma-Aldrich; H5501). For dietary supplementation experiments, L-proline (Sigma-Aldrich; P5607), D-proline (Sigma-Aldrich; 858919), L-glycine (VWR Chemicals; 101196X), L-alanine (Sigma-Aldrich; 7627), L-tryptophan (Sigma-Aldrich; T0254), Indole-5-carboxylic acid (Sigma-Aldrich; I5400) and IPA (Sigma-Aldrich; 57400) were added to CD or HSD. Cultures were performed at 25 °C unless otherwise noted. HSD feeding led to a developmental delay in reaching the third-instar larval stage; all experiments were performed on late third-instar larvae at day 8 after egg laying (CD) and day 14 after egg laying (HSD) unless otherwise noted.
7
Simulated Gastrointestinal Digestion
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Pepsin from porcine stomach mucosa (250 U/mg), pancreatin (8 × USP) from porcine pancreas, porcine bile extract, mucin from porcine stomach-type II, albumin, resazurin, cysteine, peptone, yeast extract, pectin, xylan, gum arabic, potato starch, casein, glucose, and inulin were purchased from Sigma-Aldrich Chemical Co. (St. Louis, MO, USA). Phenolic compounds standards (2,4 dihydroxybenzoic, 3,4 dihydroxybenzoic, gallic, benzoic, caffeic, ferulic, p-coumaric, salicylic, rosmarinic, and 5-caffeoylquinic acids) were purchased from Sigma-Aldrich Chemical Co. All solvents were HPLC grade from Tedia (Fairfield, OH, USA). HPLC grade water (Milli-Q system, Millipore, Bedford, MA, USA) was used throughout the experiments.
8
Microbial Enzyme Production Substrate Screening
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Rhodamine B, nutrient broth, agar, peptone, yeast extract, 4-nitrophenyl-decanoate, gum Arabic and sodium taurocholate were purchased from Sigma, USA. NaCl, beef extract, Bradford, glucose, fructose, sucrose and malt extract, K2HPO4, KH2PO4, CaCl2, MgSO4.7-H2O and (NH4)2SO4 were supplied by Merck, Germany. Starch, molasses and glucose syrup, wheat bran, gluten, dried fish powder, gelatin, corn and soya bean were prepared from the market and or animal feed wholesale.
9
Bioreactor Cultivation and Analysis
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A stirred tank reactor-STR and SCBBR was bought from Bioengineering Inc, Germany. Spectrophotometer, GC column CP-WAX 58, Gas chromatography HP 5890 series II, where from Hewlett-Packard, Avondale, PA, USA. All other chemicals, including yeast extract nitrogen base without amino acid, ammonium acetate, amino acid mixture, sodium alginate, calcium chloride, sodium chloride, chitosan, hydrochloric acid, potassium sodium tartrate, dinitro salicylic acid (DNS), n-butanol, ethyl acetate, glucose, peptone, yeast extract, agar, sodium hydroxide were of analytical grades and purchased directly from Sigma (USA) and Applichem (Germany).
10
Yeast Haploid Strain Analysis
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The following Saccharomyces cerevisiae haploid strains were used in the present analysis: SC7K lys2-3, wild type SJR751 (MATa ade2-101 his3∆200 ura3∆Nco lys2∆Bgl CAN1), and the corresponding mutant strains: sml1 (MATa ade2-101 his3∆200 ura3∆Nco lys2∆Bgl CAN1 sml1∆::Kan) and sml1/mec1 (MATa ade2-101 his3∆200 ura3 ∆Ncolys2∆Bgl CAN1 sml1∆::Kan mec1∆::Hyg) (14 (link)).
Yeast cells were grown to exponential phase (N=1, 2×107 cells per mL) at 30°C with aeration by shaking, in liquid nutrient medium YPD (1% yeast extract, 2% peptone, and 2% glucose (Sigma-Aldrich, USA).
Yeast cells were grown to exponential phase (N=1, 2×107 cells per mL) at 30°C with aeration by shaking, in liquid nutrient medium YPD (1% yeast extract, 2% peptone, and 2% glucose (Sigma-Aldrich, USA).
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