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54 protocols using guanine

1

Evaluating Yeast Growth Conditions

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Yeast cells with BY4741 genetic background (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0) were grown in 10 mL CSM minimal media containing 2% glucose. Four different treatment/growth conditions were used: minimal media containing (i) 10 µM DMSO (American Bio AB00435), (ii) 10 µM DMSO and 10 µM mycophenolic acid (Sigma M5255), (iii) 10 µM DMSO and 10 µM guanine (Sigma–Aldrich G11950) and 10 µM mycophenolic acid, (iv) 10 µM guanine. Cells were grown for 18 h to a final density (OD600) between 0.1 and 0.25. Cells were then diluted to 50 cells/μL for the final yeastDrop-Seq cell-collection using the microfluidic chip.
Doubling time of cells in each treatment condition was calculated as follows: ODf=ODi×2Δttdlog2ODfODi=Δttdtd=Δtlog2ODfODi where: ODf=OD600final
ODi = OD600 initial
Δt  = elapsed culture time (18 h)
td  = calculated doubling time
Based on two-point cell density measurements, we found that the doubling time for MPA-treated cells was 187.8 min, for DMSO-treated cells was 130 min, for guanine-treated cells was 130 min, and for GM-treated cells was 158.9 min.
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2

Simultaneous Detection of Diverse Compounds

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The neurotransmitters and metabolites tested were acetamidophenol, catechol, L-DOPA, dopamine, vanillylamine, homovanillic acid, norepinephrine, resorcinol, vanillic acid (all from Aldrich Chemical, Milwaukee, WI, USA), and uric acid (Fisher Scientific). The working solution was prepared in universal buffer with a concentration of 1.12–2.04 ppm (approximately 1 × 10−5 M) for each of the 10 compounds listed above.
The second class of analytes was nucleic acids and heterocyclic bases including adenine, adenosine, cytidine, cytosine, guanine, guanosine, thymidine, and uridine (all from Aldrich Chemical, Milwaukee, WI, USA). The working solution was prepared in universal buffer with a concentration of 56–204 ppm (approximately 5.00 × 10−4 M) for each of the eight analytes in this group.
The capsaicinoids used were capsaicin, dihyrocapsaicin, and N-vanillylnonanamide (VANA) (all from Sigma Chemical, St. Louis, MO, USA). The working solution was prepared in acetonitrile with a concentration of 148–152 ppm (approximately 5.00 × 10−4 M) for each of the three analytes listed above.
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3

Synthesis and Characterization of Nucleobases

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Silver nitrate (anhydrous, 99.999%), sodium borohydride (powder, ≥98.0%), adenine, guanine, thymine, cytosine, sodium hydroxide and poly(ethylene glycol) (average Mn 3,350, powder), avidin, rhodamine B, ninhydrin and glycine were purchased from Aldrich and used without further purification. 12mer polycytosine was obtained from Integrated DNA Technologies. Fisherfinest™ Premium Cover Glasses were purchased from Fisher Scientific and used without further treatment. TEM grids (Carbon Grid Type-A, 300Mesh, Cu) were purchased from TedPella. Ultrapure (Nanopure system) filtered water with a resistivity 18.2 MΩ cm was used in all experiments.
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4

Synthesis of Adenosine Derivatives

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Adenine (> 99%) and D‐(−)‐ribose (analytical grade) were purchased from TCI EUROPE N.V., and Serva, respectively. Adenosine, D‐(+)‐glucose, cytosine, cytidine, guanine, and guanosine were purchased from Aldrich. Calcium chloride‐dihydrate (≥ 99%) was purchased from Fisher Chemicals. Iron (III)‐acetylacetonate (99+%) and nickel (II)‐acetylacetonate (96%) were from Acros, respectively. Nafion (5 wt. % in a mixture of lower aliphatic alcohols and water, containing 45% water) was from Aldrich. The chemicals were all used as received. The RuO2 and IrO2 were purchased from Aldrich, 99.9%
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5

Solubility of Nucleobases Characterization

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6-N-hydroxylaminopurine (MP Biomedicals) and 6-thioGuanine (Sigma-Aldrich) was dissolved in dimethyl sulfoxide (DMSO). Guanine and 6-mercaptopurine (Sigma-Aldrich) was dissolved in 1M NaOH, and 2-aminopurine (Sigma Aldrich) was dissolved in phosphate buffered saline, respectively. Adenine (Sigma-Aldrich), cytosine (Sigma-Aldrich) and thymine (Sigma-Aldrich) were dissolved in 0.5 M HCl, H2O and 1 M NaOH, respectively. All chemicals were stored at 4°C.
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6

Depurination Analysis of Nucleic Acids

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All ODNs used in this study were ordered from Integrated DNA Technologies, Inc. (Coralville, IA, USA) and dissolved in sterile Milli-Q water to 100 µM for stock. M13mp18 single-stranded DNA (M13 ssDNA, 250 µg/mL), M13mp18 RF I DNA (M13 dsDNA, 100 µg/mL) and Lambda DNA (300 µg/mL) were purchased from New England Biolabs, Inc. (Beverly, MA, USA). Salmon sperm DNA (Sigma-Aldrich, WI, USA) was dissolved in sterile Milli-Q water to 300 µg/mL and used as the substrate for depurination. Nucleotide bases, including adenine, guanine, thymine, cytosine and uracil (Sigma-Aldrich, WI, USA) were used as the standard substances for HPLC analysis. They were dissolved in sterile Milli-Q water to 200 µg/mL, respectively, and diluted to the final concentration of 20 µg/mL in mixed samples.
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7

Characterization of Klebsiella and Pseudomonas Strains

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The strains used in this study are described in Table 1. For general maintenance, K. pneumoniae and P. aeruginosa were grown at 37°C overnight in Hy-Soy (HS) bacteriological media (5 g/L sodium chloride, 10 g/L soytone [Teknova, CA], 5 g/L Hy-yest [Sigma Aldrich, MO]) at 37°C. 1.5% bacteriological agar (AmericanBio, MA) was added to HS for solid media preparations. Fully chemically defined medium (CDM) used for growth of KP in fermentation cultures and to assess guanine auxotrophy has been described previously [19 (link)]. 0.004%-0.025% guanine (Sigma Aldrich, MO) was added for the growth of CVD 3001 to supplement the guaBA mutation. O types were determined by PCR with extracted genomic DNA as described [14 (link)]. K types were determined by sequencing of the wzi or wzc genes, or multiplex PCR [20 (link)–22 (link)].
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8

Drosophila Dietary Modulators Protocol

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Flies were raised on standard lab food (corn meal/agar medium). For conditional expression using tubGal80ts, flies were grown at 18 °C until eclosion, maintained at 18 °C for an additional 2d, and then shifted to 29 °C to induce expression. The concentration of chemicals mixed in the fly food was based on previously published reports21 (link),23 (link). The Super CitriMax Garcinia Cambogia extract (Swanson) contains 60% hydroxycitric acid and was purchased from Amazon. Fly food was melted and mixed with a final concentration of 30 mg/ml Garcinia Cambogia extract23 (link). For NaOx feeding, a final concentration of 5 mg/ml sodium oxalate was mixed into melted fly food23 (link). The high purine food contains 20 mM adenine (Sigma-Aldrich, # A8626) and 20 mM guanine (Sigma-Aldrich, # G11950)21 (link).
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9

Bacterial Strain Cultivation and Reagents

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Bacterial strains used for this study are shown in the Table 2. Shigella strains were grown on tryptic soy broth or on tryptic soy media containing agar (TSA) (BD Difco, Franklin Lakes, NJ, USA). CVD 1233, CVD 1233-SP, and CVD 1233-SP::CS2-CS3 were grown in the presence of guanine 0.005% (w/v) (Sigma-Aldrich, St. Louis, MO, USA). Congo red (Sigma, St. Louis, MO, USA) was added to TSA media at a final concentration of 0.01% (w/v) to make CR-TSA plates. Escherichia coli strains were grown on lysogeny broth (LB, Invitrogen) or solid media containing 1.5% (w/v) agar (Oxoid). Antibiotics were used, when necessary, at the following concentrations: chloramphenicol, 20 μg/mL; carbenicillin, 100 μg/mL.
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10

Quantification of Purine Compounds in Lentinula edodes

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Raw lentinus edodes and dried lentinus edodes were collected from Logistics Service Center of South China University of Technology and stored at 4 °C. Purine standards (guanine, adenine, hypoxanthine and xanthine, purity ≥ 99%) were obtained from Sigma-Aldrich Co. Ltd (St. Louis, MO, USA) and stored at 4 °C. HPLC-grade acetonitrile and methanol were obtained from Tianjin Damao Chemical Reagent Factory Co., Ltd. (Tianjin, China). Analytical Reagents (AR) monopotassium phosphate, sodium 1-pentanesulfonate, phosphoric acid, formic acid and trifluoroacetic acid were purchased from Tianjin Kermel Chemical Reagent Co., Ltd. (Tianjin, China). PCA was gained from Cangzhou xinyuanquan Chemical Co., Ltd (Cangzhou, China). Ultrapure water was obtained using a Milli-Q Direct system (Millipore, USA).
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