Molecular biology grade water

Manufactured by Corning

Sourced in United States

Molecular biology grade water is a high-purity, laboratory-grade water intended for use in molecular biology applications. It is produced through a multi-stage purification process to remove contaminants, ions, and organic matter, ensuring consistent quality and suitability for sensitive experiments and procedures.

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Lab products found in correlation

Nanodrop, by Thermo Fisher Scientific (8 mentions) Fast sybr green master mix, by Thermo Fisher Scientific (4 mentions) Quantstudio 7 flex system, by Thermo Fisher Scientific (4 mentions) High capacity cdna reverse transcription kit, by Thermo Fisher Scientific (4 mentions) Trizol, by Thermo Fisher Scientific (3 mentions) Sodium sulfide na2s, by Tokyo Chemical Industry (2 mentions) Qubit fluorometer, by Thermo Fisher Scientific (2 mentions) Cell counting kit 8 cck 8, by Dojindo Laboratories (1 mentions) Imagequant las 500 system, by GE Healthcare (1 mentions) Collagen type 1 from rat tail, by Corning (1 mentions) Phosphate buffered saline (pbs), by Lonza (1 mentions) Sodium hydroxide (naoh), by Merck Group (1 mentions) Growth factor reduced matrigel, by Corning (1 mentions) Glutamine, by Agilent Technologies (1 mentions) Pyruvate, by Agilent Technologies (1 mentions) Agilent seahorse xf cell mito stress test kit, by Agilent Technologies (1 mentions) Seahorse xf cell culture microplate, by Agilent Technologies (1 mentions) Agilent seahorse xf dmem medium, by Agilent Technologies (1 mentions) Xfe96 analyzer, by Agilent Technologies (1 mentions) Glucose, by Agilent Technologies (1 mentions)

20 protocols using molecular biology grade water

DNA Extraction from Epidermal Samples

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DNA samples from the primary cohort were extracted using Purelink TM Genomic DNA mini kit (Invitrogen, USA). Epidermal samples were digested using Proteinase K at 55°C heating block overnight following the manufacturers recommendations. For the extended cohort of samples, skin biopsies were similarly digested using Proteinase K and DNA was purified with phenolchloroform extraction and ethanol precipitation. DNA was eluted with 28 μL of Molecular Biology Grade Water (Corning, USA) for 1 and 2 mm punches or 36 μL of Molecular Biology Grade Water for 3, 4, and 6 mm punches. The isolated genomic DNA was stored at -20°C and the DNA concentration of each extraction was measured using a Qubit fluorometer or Quanti-iT PicoGreen kit (Invitrogen, USA).
(which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this preprint this version posted June 29, 2020. ; https://doi.org/10.1101/2020.01.10.902098 doi: bioRxiv preprint

Wei L., Christensen S.R., Fitzgerald M., Graham J., Hutson N., Zhang C., Huang Z., Hu Q., Zhan F., Xie J., Zhang J., Liu S., Remenyik É., Gellén E., Colegio O.R., Bax M.J., Xu J., Lin H., Huss W.J., Foster B.A., & Paragh G. (2020). Ultra-deep sequencing differentiates patterns of skin clonal mutations associated with sun-exposure status and skin cancer burden.

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Synthesis and Characterization of H2S Donors

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Sodium sulfide (Na₂S) was purchased from TCI chemicals. Cell Counting Kit-8 (CCK-8) was purchased from Dojindo Molecular Technologies, Inc. All other chemicals were purchased from Sigma Aldrich. H₂S donor 1 and RSSH donors 2 and 3 were synthesized following reported procedures [24 (link)]. N-acetyl-O-ethyl cysteine trisulfide (4) was synthesized as shown in Scheme S1 (Supplementary Materials) [25 (link),26 (link)]. Na₂S (10 mM) stock solution was freshly prepared by dissolving it in molecular biology grade water (Corning). Stock solution of RSSH donors 2 and 3, and sulfane sulfur donor trisulfide 4 were prepared in DMSO:Water (<0.001%) and diluted fresh each day before administration.

Pharoah B.M., Khodade V.S., Eremiev A., Bao E., Liu T., O’Rourke B., Paolocci N, & Toscano J.P. (2022). Hydropersulfides (RSSH) Outperform Post-Conditioning and Other Reactive Sulfur Species in Limiting Ischemia–Reperfusion Injury in the Isolated Mouse Heart. Antioxidants, 11(5), 1010.

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Paper-Based Protein Quantification

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First,
1–100 μg/mL IgG-HRP antibody diluted with molecular biology
grade water (Corning, Corning, NY) was loaded on the piezo printhead
printer and printed on printing paper or PVDF and nitrocellulose membranes.
IgG-HRP printed paper-based platforms were then cut into 1.5 ×
10 cm strips. Finally, 1 mL of ECL western blotting detection reagents
and the ImageQuant LAS 500 system (GE Healthcare) were used to record
chemiluminescence intensity from printed IgG-HRP (intensity from 0.8
cm diameter circular dot).

Koh B, & Kim K.R. (2019). Long-Term Stability Monitoring of Printed Proteins on Paper-Based Membranes. ACS Omega, 4(12), 15134-15138.

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Engineered Muscle Tissue Formation

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For all tissue seeding procedures, ECM solution is prepared on ice by first neutralizing type I collagen from rat tail (Corning) with 1 M sodium hydroxide (Sigma), 10× PBS (Lonza), and molecular biology grade water (Corning) and then mixing neutralized collagen thoroughly with growth factor reduced Matrigel (Corning) (28 (link)). Collagen and Matrigel are used at final concentrations of 2 mg/mL each. To form muscle rings, C2C12 cells are suspended in ECM solution at a density of 2.5 × 10⁶ cells/mL. Cell–ECM mixtures are seeded into sterile PDMS molds by pipetting and are polymerized at room temperature for 30 min. Samples are then inundated in growth medium and incubated for 2 d while they compacted the ECM gel and form muscle rings.

Li Z., Seo Y., Aydin O., Elhebeary M., Kamm R.D., Kong H, & Saif M.T. (2019). Biohybrid valveless pump-bot powered by engineered skeletal muscle. Proceedings of the National Academy of Sciences of the United States of America, 116(5), 1543-1548.

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Seahorse Assay to Measure Mitochondrial Function

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The Seahorse assay was conducted using Agilent Seahorse XF Cell Mito Stress Test Kit (#103015-100, Agilent) and Seahorse XFe96 Analyzer following the manufacturer's instructions. Briefly, 10,000 cells were seeded onto the Seahorse XF Cell Culture Microplate (#101085-004, Agilent) two days before assaying. One day before the assay, cells were treated with cholesterol and 58035 for 24 h while the microplate cartridge was hydrated by 200 μl Molecular Biology Grade Water (#46-000-CI, Corning) overnight at 37 °C. At the day of assay, the water in microplate cartridge was replaced by prewarmed XF Calibrant (#100840-000, Agilent) followed by incubation in 37 °C non-CO₂ incubator for 1 h. Then, 20 μl of 100 μM oligomycin, 22 μl of 100 μl 100 μM FCCP, and 25 μl of 50 μM Rotenone/AA was added to the port A, B, C of the sensor cartridge, respectively. For the cell culture microplate, the medium was replaced by Agilent Seahorse XF DMEM Medium (#103575-100, Agilent) supplemented with 1 mM pyruvate (#103578-100, Agilent), 2 mM glutamine (#103579-100, Agilent), and 10 mM glucose (#103577-100, Agilent), followed by 1 h incubation in a 37 °C non-CO₂ incubator. An XF cell mito stress-test template was used to measure oxygen consumption rate of cells. The data was normalized to protein concentration in Wave 2.6.1 software.

Chen L., Li Y., Sottas C., Lazaris A., Petrillo S.K., Metrakos P., Li L., Ishida Y., Saito T., Garza S, & Papadopoulos V. (2022). Loss of mitochondrial ATPase ATAD3A contributes to nonalcoholic fatty liver disease through accumulation of lipids and damaged mitochondria. The Journal of Biological Chemistry, 298(6), 102008.

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Preparation and Characterization of PAH Standards

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Standard reference materials DB[a,i]P and DB[e,l]P were purchased from Toronto Research Chemicals, Ontario, Canada; certified reference materials DB[a,e]P, DB[a,l]P, and DB[a,h]P were purchased from the European Commission Joint Research Centre, Institute for Reference Materials and Measurements, Community Bureau of Reference, Geel, Belgium. Analytical grade B[a]P was obtained from Millipore Sigma, St. Louis, Missouri. HPLC‐grade solvents and trace‐metal‐grade acids were purchased from Fisher Scientific, Hampton, New Hampshire. Molecular biology grade water was obtained from Corning, Corning, New York.
PAH standards were prepared in dimethylsulfoxide (DMSO) at concentrations appropriate to their solubility and working conditions. Each standard was filter‐sterilized with a 0.2 µm polytetrafluoroethylene (PTFE) syringe filter before use.

Lewis C.G, & Beazley M.J. (2020). Impacts of dibenzopyrenes on bacterial community isolated from Gulf of Mexico sediment. MicrobiologyOpen, 9(7), e1039.

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CRISPR-Cas9 Ribonucleoprotein Mediated Mutant Construction

Cited 1 time

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Mutants were constructed as previously described by Grahl et al. using an expression-free ribonucleoprotein CRISPR-Cas9 method (63 (link)). Briefly, 1 to 2 μg of DNA for gene knockout constructs generated by PCR or 2 μg of digested plasmid, purified, and concentrated with a final elution in molecular biology-grade water (Corning) was used per transformation. Plasmids containing complementation and knockout constructs and resulting strains are listed in Table S3 and CRISPR RNAs (crRNAs; IDT) are listed in Table S4. Transformants were selected on YPD agar containing 200 μg/ml nourseothricin or 600 μg/ml hygromycin B.

Demers E.G., Stajich J.E., Ashare A., Occhipinti P, & Hogan D.A. (2021). Balancing Positive and Negative Selection: In Vivo Evolution of Candida lusitaniae MRR1. mBio, 12(2), e03328-20.

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Quantifying Cytokine Gene Expression

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RNA from cells was extracted using TRIzol (Life Technologies) according to the manufacturer’s described protocol. The thus obtained RNA was quantified using NanoDrop (Thermo Fisher Scientific, USA) and equilibrated for all samples with Molecular Biology Grade water (Corning, USA) before they were reverse-transcribed into complementary DNA (cDNA) using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Foster City, CA). Equal amounts of cDNA were analyzed via real-time quantitative PCR using Fast SYBR Green Master Mix on QuantStudio 7 Flex system (Applied Biosystems). The primers used in this study were as follows: GAPDH forward, 5′-TCCACTGGCGTCTTCACC-3′; GAPDH reverse, 5′-GGCAGAGATGATGACCCTTTT-3′; IFN-α forward, 5′-GATGGCAACCAGTTCCAGAAG-3′; IFN-α reverse, 5′-AAAGAGGTTGAAGATCTGCTGGAT-3′; IFN-β forward, 5′-CTCCACTACAGCTCTTTCCAT-3′; IFN-β reverse, 5′-GTCAAAGTTCATCCTGTCCTT-3′; TNF-α forward, 5′-AGCCCATGTTGTAGCAAACCC-3′; TNF-α reverse, 5′-GGACCTGGGAGTAGATGAGGT-3′.

Yadavalli T., Ames J., Agelidis A., Suryawanshi R., Jaishankar D., Hopkins J., Thakkar N., Koujah L, & Shukla D. (2019). Drug-encapsulated carbon (DECON): A novel platform for enhanced drug delivery. Science Advances, 5(8), eaax0780.

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Hydrogen Sulfide Donor Synthesis and Evaluation

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Sodium sulfide (Na₂S) was purchased from TCI chemicals. N-acetyl cysteine was purchased from Sigma Aldrich. Dexrazoxane was obtained from Cayman Chemical. Doxorubicin was purchased from Astatech Inc. H₂S donor 1 [39 (link)], RSSH donor AST [40 (link)], and N-acetyl-O-ethyl cysteine trisulfide (Cys-S₃) [38 (link)] were synthesized following reported procedures. Na₂S (10 mM) and Na₂S₃ (10 mM) stock solutions were freshly prepared in molecular biology-grade water (Corning). The stock solutions of AST and Cys-S₃ were prepared in DMSO:Water (<0.001%) and diluted fresh each day before administration.

Pharoah B.M., Zhang C., Khodade V.S., Keceli G., McGinity C., Paolocci N, & Toscano J.P. (2023). Hydropersulfides (RSSH) attenuate doxorubicin-induced cardiotoxicity while boosting its anticancer action. Redox Biology, 60, 102625.

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Isolation of P. mirabilis RNA from Urine

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Overnight cultures of P. mirabilis HI4320 and the nickel transport mutants were diluted 1:100 into 5 ml of filter-sterilized human urine and incubated for 4 hours at 37°C with shaking at 225 rpm. Four 1-ml aliquots were then removed, centrifuged to pellet, and resuspended in 1 ml of RNA STAT-60 (Tel-Test, Inc). 0.2 ml chloroform: iso-amyl alcohol 24:1 (Calbiochem) was added to each aliquot, microfuge tubes were inverted several times to mix, and centrifuged at 18,000 × g for 30 minutes at 4°C. The aqueous layer was removed and transferred to a new microfuge tube, to which 0.5 mL isopropanol was added (Fischer Scientific), mixed by inversion, and incubated overnight at −20°C to precipitate RNA. The next day, samples were centrifuged at 18×000 × g for 30 minutes at 4°C, supernatants were discarded, and the nucleic acid pellet was washed three times with 1 mL 75% ethanol and centrifuged at 18×000 × g each wash for 10 minutes. After the final wash, the supernatant was carefully removed and the pellet was air-dried, then dissolved in 50 μL of molecular biology grade water (Corning). Nucleic acid concentration was measured by Nanodrop and adjusted to 200 ng/μL in 50 μL total volume with water. DNA was removed via the Invitrogen DNA Free Kit, according to manufacturer’s protocol. DNAse-treated RNA was frozen at −20°C until use.

Brauer A.L., Learman B.S, & Armbruster C.E. (2020). Ynt is the primary nickel import system used by Proteus mirabilis and specifically contributes to fitness by supplying nickel for urease activity. Molecular microbiology, 114(2), 185-199.

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