Pipes

Manufactured by Merck Group

Sourced in United States, Italy, Australia, Germany, United Kingdom, Canada

PIPES is a laboratory buffer solution used to maintain a stable pH in various biochemical applications. It functions as a buffering agent to help maintain the desired pH environment for experiments and reactions.

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Lab products found in correlation

Ethylene glycol tetraacetic acid (egta), by Merck Group (26 mentions) Hepes, by Merck Group (15 mentions) Mgcl2, by Merck Group (14 mentions) Triton x 100, by Merck Group (10 mentions) Mgso4, by Merck Group (10 mentions) Bovine serum albumin (bsa), by Merck Group (7 mentions) Paraformaldehyde (pfa), by Merck Group (6 mentions) Percoll, by Merck Group (6 mentions) Hoechst 33342, by Thermo Fisher Scientific (6 mentions) Sodium chloride (nacl), by Merck Group (5 mentions) Sucrose, by Merck Group (5 mentions) Fetal bovine serum (fbs), by Thermo Fisher Scientific (5 mentions) Dulbecco phosphate buffered saline (dpbs), by Thermo Fisher Scientific (4 mentions) Phenol red, by Merck Group (4 mentions) Calcein am live stain dye, by Thermo Fisher Scientific (4 mentions) Antibiotic antimycotic, by Thermo Fisher Scientific (4 mentions) Dnase, by Worthington (4 mentions) Gentamicin, by Thermo Fisher Scientific (4 mentions) Potassium chloride (kcl), by Merck Group (3 mentions) 4 6 diamidino 2 phenylindole (dapi), by Thermo Fisher Scientific (3 mentions)

Close spelling variants of this product

PIPES buffer (13 citations) Piperazine-N,N′-bis(2-ethanesulfonic acid) (PIPES), (5 citations) Piperazine (PiP) (3 citations) PIPES-KOH (2 citations) Paraformaldehyde/PIPES (2 citations) K-PIPES (2 citations) D/l-Pip (2 citations) PIP strips (2 citations) DL-2-piperidine-d9 carboxylic acid (D9-Pip; (2 citations) Piperacillin (PIP) (2 citations)

99 protocols using pipes

Purification and Characterization of Coagulation Factors

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Human fibrinogen (plasminogen,
von Willebrand
Factor, and fibronectin depleted) and α-thrombin were obtained
(in powder form in 20 mM sodium citrate-HCl, pH 7.4) from Enzyme Research
Laboratories (Swansea, UK), dissolved in water, aliquoted to single-use
volumes, and stored at −80 °C. Ancrod, a thrombin-like
enzyme derived from the venom of the Mayalan pit viper, was obtained
from the National Institute for Biological Standards and Control (Hertfordshire,
UK), dissolved in water, and stored in single-use aliquots at −80
°C. Platelet-poor plasma (PPP) was obtained by two-step centrifugation
of porcine blood freshly obtained from a local slaughterhouse near
Eindhoven (The Netherlands) as described previously.^{45 (link)} Buffer compounds HEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic
acid), PIPES (piperazine-N,N′-bis(2-ethanesulfonic
acid)), BHEP (1,4-bis(2-hydroxyethyl)piperazine), Tris (2-amino-2-hydroxymethylpropane-1,3-diol),
and sodium bicarbonate were obtained from Sigma-Aldrich (Zwijndrecht,
The Netherlands), dissolved in water, adjusted to achieve pH 7.4 by
titration with 1 M NaOH (HEPES and PIPES) or 1 M HCl (BHEP, Tris,
and bicarbonate), and stored at a concentration of 1 M. At pH 7.4
and 37 °C, the fractions of buffer protonation are 45% for HEPES,
15% for PIPES, 56% for BHEP, and 67% for Tris.⁴⁶

Kurniawan N.A., van Kempen T.H., Sonneveld S., Rosalina T.T., Vos B.E., Jansen K.A., Peters G.W., van de Vosse F.N, & Koenderink G.H. (2017). Buffers Strongly Modulate Fibrin Self-Assembly into Fibrous Networks. Langmuir, 33(25), 6342-6352.

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Purification of Porcine Brain Tubulin

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Tubulin was purified from porcine brains using a concentrated 1,4-piperazinediethanesulfonate (PIPES) (Sigma-Aldrich, USA) buffer according to the protocol established in previous work [30 (link)]. In brief, food grade porcine brains were purchased from a local slaughterhouse, conserved before use in ice-cold PBS (phosphate buffer saline) prepared by mixing 137 mM NaCl, 8.1 nM Na₂HPO₄, 2.68 mM KOH and 1.47 mM KH₂PO₄ (all reagents from WAKO Pure Chemical Corporation, Japan). High-concentration PIPES buffer and Brinkley BR buffer 1980 (BRB80) were prepared using the dipotassium salt of PIPES (Sigma-Aldrich, USA), and the pH was adjusted to 6.8 using KOH (WAKO Pure Chemical Corporation, Japan). The purity of tubulin was confirmed to be ~98–99% from the result of sodium dodecyl sulfate/polyacrylamide (WAKO Pure Chemical Corporation, Japan) electrophoresis [30 (link)].

Keya J.J., Kudoh H., Kabir A.M., Inoue D., Miyamoto N., Tani T., Kakugo A, & Shikinaka K. (2020). Radial alignment of microtubules through tubulin polymerization in an evaporating droplet. PLoS ONE, 15(4), e0231352.

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Ultrastructural Analysis of Nodule and Root Cells

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Plants were grown as described for infection thread experiments. Large wild-type nodules (3–4 mm), the largest na-1 nodules (1–2 mm), and na-1 roots containing bacterial accumulations were fixed and stored in 2.5% glutaraldehyde in buffer (100 mM sodium phosphate at pH 7, 10 mM KCl, and 1 mM MgCl₂·6H₂O), washed twice in 0.1 M PIPES (Sigma Australia) buffer (pH 7), treated with 1% osmium tetroxide in 0.1 M PIPES buffer (pH 7) for 2 h, then washed twice and stored in 0.1 M PIPES buffer. Samples were then treated with 5% uranyl acetate (ProSciTech Pty Ltd, Australia) in 50% ethanol for 30 min, dehydrated through graded ethanol and propylene oxide, and embedded in Procure 812 resin (ProSciTech Pty Ltd) according to the manufacturer’s instructions. Sections 70 nm thick were cut with a Reichert Ultracut S Ultramicrotome, and images of cross-sections captured with an Olympus BX50 microscope (Supplementary Fig. S2). The sections were then collected onto copper grids, and stained with uranyl acetate and Reynolds Lead citrate, then imaged with a Hitachi HT7700 transmission electron microscope at 80 kV at ×1000–×15 000 magnification.

McAdam E.L., Reid J.B, & Foo E. (2018). Gibberellins promote nodule organogenesis but inhibit the infection stages of nodulation. Journal of Experimental Botany, 69(8), 2117-2130.

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Profiling V-SVZ and Olfactory Bulb Cells

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Whole-mounts of the lateral and septal walls of the V-SVZ were dissected as previously described (Mirzadeh et al., 2010 ; Mizrak et al., 2019 (link)), and combined prior to dissociation. Olfactory bulb (OB) was also removed to profile V-SVZ and OB from the same animal. For scRNA-seq experiments, sex and age of each animal, and the number of single cells analyzed are indicated in the Figure S1. Dissected whole mounts were dissociated as described previously (Mizrak et al., 2019 (link)). Briefly, minced V-SVZ pieces were digested with papain (Worthington, 6 mg per sample, 10 min at 37°C) in PIPES solution (120 mM NaCl, 5 mM KCl, 20 mM PIPES (Sigma), 0.45% glucose, 1× Antibiotic/Antimycotic (GIBCO), and phenol red (Sigma) in water; pH adjusted to 7.6). After trituration to single cells in DMEM/F12 containing ovomucoid (Worthington, 0.7 mg/ml) and DNase (Worthington, 0.5 mg/ml), the cell suspension was layered on top of 22% Percoll (Sigma) and centrifuged for 10 mins at 4°C without brakes to remove debris and myelin. The single cell suspension was washed by two rounds of centrifugation (1300 rpm at 4°C) and resuspended in 1× Tris Buffered Saline. Cells were stained with Calcein AM live stain dye (Fisher, 1:500) on ice for 30 minutes, and were passed through a 40 μm cell strainer (Fisher) to remove any cell clumps before loading.

Mizrak D., Bayin N.S., Yuan J., Liu Z., Suciu R.M., Niphakis M.J., Ngo N., Lum K.M., Cravatt B.F., Joyner A.L, & Sims P.A. (2020). Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator. Cell reports, 31(12), 107805.

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Profiling V-SVZ and Olfactory Bulb Cells

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Synthesis and Handling of Thiol Probes

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Piperazine-N,N′-bis(2-ethanesulfonic acid)
(PIPES, Aldrich) and KCl (99.999%, Aldrich) were used to prepare buffered
solutions (50 mM PIPES, 100 mM KCl, pH 7.0) with Millipore water.
Buffered solutions were deoxygenated by vigorous sparging with nitrogen
for at least 2 h. Samples for all spectroscopic measurements were
prepared in an Innovative Technology N₂-filled glovebox
with O₂ levels less than 1.0 ppm. Anhydrous sodium hydrogen
sulfide (NaSH) was purchased from Strem Chemicals and handled under
nitrogen. Thiol labeling reagents 1 and 2 were obtained from TCI, 4 from Sigma-Aldrich, 5 from Echelon Biosciences, and 3 and 6 were prepared as described in the literature.^{41 (link),49 −51 (link)} GYY4137 was prepared according to the published procedure.^{52 (link)} Stock solutions of the different thiol probes
were prepared in deoxygenated DMSO and stored in aliquots at −25
°C under nitrogen until immediately prior to use.

Montoya L.A, & Pluth M.D. (2014). Hydrogen Sulfide Deactivates Common Nitrobenzofurazan-Based Fluorescent Thiol Labeling Reagents. Analytical Chemistry, 86(12), 6032-6039.

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Fluorescent Probes for Hydrogen Sulfide Detection

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Piperazine-N,N′-bis(2-ethanesulfonic acid)
(PIPES, Aldrich) and potassium chloride (99.999%, Aldrich) were used
to make buffered solutions (50 mM PIPES, 100 mM KCl, pH 7.4) in Millipore
water. Anhydrous sodium hydrosulfide (NaHS) was purchased from Strem
Chemicals and handled under nitrogen. Angeli’s salt and DEA
NONOate were purchased from Cayman and used to generate HNO and NO,
respectively. Stock solutions of NBD-Coum in DMSO were
prepared in an N₂-filled glovebox and stored at −25
°C until immediately prior to use. Stock solutions of l-cysteine, homocysteine, glutathione, serine, lysine, threonine,
H₂O₂, Na₂SO₃, Na₂SO₄, and Na₂S₂O₃ in buffer
and tyrosine in 0.1 M NaOH were freshly prepared in a glovebox. Stock
solutions of NaHS in degassed buffer, and Angeli’s salt and
DEA NONOate in degassed 0.01 M NaOH, and l-cystine in degassed
1 M HCl were prepared under nitrogen immediately prior to use. All
absorption and fluorescence measurements were made under anaerobic
conditions, and cuvette solutions were prepared under an inert atmosphere
in septum-sealed cuvettes obtained from Starna Scientific.

Hammers M.D, & Pluth M.D. (2014). Ratiometric Measurement of Hydrogen Sulfide and Cysteine/Homocysteine Ratios Using a Dual-Fluorophore Fragmentation Strategy. Analytical Chemistry, 86(14), 7135-7140.

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Transmission Electron Microscopy Sample Preparation

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For transmission electron microscopy, the samples were fixed in 2.5% glutaraldehyde (Ted Pella INC, Redding, CA, USA) + 1% paraformaldehyde (Merck, Darmstadt, Germany) in PIPES (Merck, Darmstadt, Germany) pH 7.4, and stored at 4 °C until further processed. Samples were rinsed with 0.1 M phosphate buffer for 10 min prior to 1 h incubation in 1% osmium tetroxide (TAAB, Aldermaston, England) in 0.1 M phosphate buffer. After rinsing in 0.1 M phosphate buffer, samples were dehydrated by incubation in increasing concentrations of ethanol (50%, 70%, 95% and 99.9%) for 10 min each, followed by 5 min incubation in propylene oxide (TAAB, Aldermaston, England). The tissue samples were thereafter placed in a mixture of Epon Resin (Ted Pella INC, Redding, CA, USA) and propylene oxide (1:1) for 1 h, followed by 100% resin, and left over night. Subsequently, the samples were embedded in capsules in newly prepared Epon Resin, left for 1–2 h, and then polymerized at 60 °C for 48 h.

Stenberg H., Hellman S., Lindström L., Jacobson M., Fossum C., Hayer J, & Malmberg M. (2022). Congenital tremor and splay leg in piglets – insights into the virome, local cytokine response, and histology. BMC Veterinary Research, 18, 348.

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Cell Viability Assessment by Live/Dead Staining

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Cell viability was determined by performing a LIVE/DEAD staining assay as described previously [55 (link)]. After 7 days, cells were stained using calcein acetoxymethyl ester (Calcein AM, LIVE) (Invitrogen^TM, Molecular probes by Life technologies^TM, USA) and propidium iodide (PI, DEAD) (InvitrogenTM, Molecular probes by Life technologies^TM, USA), to indicate viable and dead/apoptotic cells, respectively. BaTiO₃/BG samples were washed with phosphate-buffered saline (DPBS, Thermo Fisher, USA) and incubated with 1 ml of DPBS stock solution containing 4 μl/ml Calcein AM and 5 μl/ml PI for 45min. Samples were washed (DPBS) and fixed using 500 μl of fixation solution (0.1 M PIPES (Piperazine-N,N′- bis(2-ethanesulfonic acid), Merck, Germany), 1 mM EGTA (Ethylene glycol tetraacetic acid, Merck, Germany), 4% (w/v) polyethyleneglycol, 3.7% (w/v) paraformaldehyde (all Sigma Aldrich, Germany) in Hank's balanced salt solution (HBSS)).

Polley C., Distler T., Scheufler C., Detsch R., Lund H., Springer A., Schneidereit D., Friedrich O., Boccaccini A.R, & Seitz H. (2023). 3D printing of piezoelectric and bioactive barium titanate-bioactive glass scaffolds for bone tissue engineering. Materials Today Bio, 21, 100719.

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Evaluating 3D Scaffold Cytotoxicity

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To determine the cellular viability on the 3D printed disk, a live/dead staining assay was performed. Viable cells were stained by calcein acetoxymethyl ester (Calcein AM), while apoptotic and necrotic cells were stained by propidium iodide (PI) (both Invitrogen™, Molecular probes by Life technologies™, USA), corresponding to live and dead cells, respectively. The samples were washed with phosphate buffered saline (DPBS, Thermo Fisher, USA) and incubated with 1 ml of DPBS stock solution containing 4 μl.ml⁻¹ Calcein AM and 5 μl.ml⁻¹ PI for 45 min. After incubation, the samples were washed with DPBS and fixed using 500 μl of fixing solution containing 0.1 M PIPES (Piperazine-N,N′-bis(2-ethanesulfonic acid), Merck, Germany), 1 mM EGTA (Ethylene glycol tetraacetic acid, Merck, Germany), 4% (w/v) polyethyleneglycol, and 3.7% (w/v) paraformaldehyde (all Sigma Aldrich, Germany), dissolved in HBSS. After 5 min of fixing, the samples were washed with DPBS and examined using a fluorescence microscope (FM) (Scope.A1, Carl Zeiss, Germany). Cell nuclei of fixed cells on 3D printed scaffolds were stained using Hank's buffered salt solution (HBSS) containing 1 μl.ml⁻¹ DAPI (4′,6-diamidino-2-phenylindole, Invitrogen™, USA) for 5 min.

Distler T., Fournier N., Grünewald A., Polley C., Seitz H., Detsch R, & Boccaccini A.R. (2020). Polymer-Bioactive Glass Composite Filaments for 3D Scaffold Manufacturing by Fused Deposition Modeling: Fabrication and Characterization. Frontiers in Bioengineering and Biotechnology, 8, 552.

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