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pH - Science topic

Explore the latest questions and answers in pH, and find pH experts.
Questions related to pH
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I have a novel compound that is insoluble in water. I have tried cyclodextrines and varying pHs. I have also tried to presolubilize in a wide variety of solvents (hexane, ACN, alcohols, DMSO, chloroform, acetone, xylene, etc) and found it is only slowly soluble in toluene. Is there a standard way to prepare a salt I should try? I also welcome other suggestions.
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Dear Wayne Briner,
you can prepare salt with organic or inorganic acids,
just dissolve your compound in the solvent as you mention your compound is soluble in toluene, then add organic or inorganic acid to it in drop wise manner, and stir it for 30-45 min to precipitate out. then either you can filter it in inert atmosphere or directly distilled off your solvent and you will get your compound in salt form.
if still can not solve the problem, then try some formulation solvent for the formulation in mixture,
currently we are using DMSO, EtOH, cremophore, PEG, Tween 80, glucose, water, PBS, saline....so on,
hope this is helpful to you...
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15 answers
I have a problem with ACSF, the pH of this solution dramatically changes from 7.3 to 8.8. It happens if they stay 2 days in fridge. I always test pH at RT. And as a result mice hippocampal slices are almost dead (pyramidal neurons are all dead, astrocytes look alive). What can I do to prevent this changing of pH?
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I agree with Tim and would suggest making your aCSF fresh every day from a 10x aCSF stock solution (don't include CaCl2 or glucose in the stock - add when you dilute).
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I have gama-Fe2O3/carbon nanotube nanohybride and I need to know the pH at which the surface charge is zero. This can be achieved using zeta potential but I wanted to know if there is any chemical procedure like acid-base titration to measure that pH?
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Thank you very much.I read the thesis and I found it great. it was of great help Mike Bender.
That is so kind of you Mr Haghi for helping me through this problem
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I incubate my cells with a specific stimulant for a certain duration then I take an aliquot of the cell culture supernatant to measure the oxidative stress induced by my stimulant. I assume that the pH in my solution is different depending on the condition. However, I assume also that processing my samples for oxidative stress measurement will yield a similar final pH (acid) in all my samples. Still, I am not sure of the exact final pH in each sample. Could fluctuations of pH in my samples be affecting my results? Can anyone help or have similar experience?
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Dear Zeina,
There are reports available showing pH dependence of reactive oxygen species production (Shu Z et al, Am J Physiol. 1997 Nov;273(5 Pt 1):G1118-26.). The authors had shown that the extracellular pH influences NO and hydroxyl radical (OH) production in hepatocytes. Acidification (pH 7.0) of the medium revealed a significant increase (P < 0.05) of OH-like radicals, enhanced hepatocellular damage, and a sharp drop in cellular glutathione (GSH) content compared with levels measured at physiological or alkaline pH conditions. Furthermore, inhibition of NO synthesis at all pH conditions resulted in decreased NO production and cellular GSH levels but a simultaneous increase of OH-like radicals and hepatocellular damage with a maximum seen at pH 7.0. Our results suggest that hepatocellular damage is in part regulated by the surrounding pH and that inhibition of NO synthesis at acidic conditions (e.g., in sepsis) leads to increased reactive oxygen-mediated cell injury.
I myself did some ROS assay under the treatment of NO donor, SNP and performed all experiments at pH 7.4 (physiological).
For further reading I am sharing these two papers as s single pdf file.
Hope that helps.
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I'm doing western blot and am looking for the reasons why I can not get bands. Various literature sources say it can be adjusted with acids, while others say this is not recommended, what is the truth?
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It depends on what you want. For Tris-Gly buffer, you control pH by varying the Tris:Gly ratio (keeping the amount of Tris constant). Of course you can change pH by adding HCl, but then it will not be exactly Tris-Gly buffer anymore, ionic strength will increase and so will conductance, etc (whether this will have an effect on your results or not depends on the specifics of the downstream application).
In any case, my impression is that you are asking the wrong question. What do you mean by "I can not get bands"? Have you stained the membrane with something like Pounceau red to ensure that transfer was successful? Do you have a positive control?
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Please could you give me an idea of how to measure pH in a volume ~100 µl if I don't have an appropriate pH meter?
I had an idea to use fluorescent ph-sensitive tags.
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Vasily, have you tried finally in your experiments some fluorophores? What is your opinion to use them for pH measurements of microvolumes?
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Organellar pH measurement.
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For lysosomal pH measures currently in the literature there are several dyes that you can use without affecting cellular function. I recomend the two that are used in the paper that I am sending you. At least in my hand they have worked fine. All depends is you need a qualitative assay or a quantitative one.
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Volume weighted mean pH<5.6 whereas mean or median (pH>5.8).
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The pH is less than 5.6 for "the non-polluted site" because of the presence of natural souces of sulfur and nitrogen in the atmosphere. Much work was done in the 1980's-1990's on identfying a non-anthropogenic influenced pH of rain and cloud water. We report on this and other work we did with clouds in a manuscript from a few years ago. See: Atmospheric Environment 45 (2011) 6669-6673
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DI water + nitric acid, pH 3, after adding NaCl to make a 1 m NaCl solution, pH is exactly same. As NaCl decrease the activity coefficients, pH should move toward 7.
Can anyone explain why? I used thermo scientific Ag/AgCl electrode.
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I'm not sure about the relationship between activity coefficient and pH, but there are a couple things to consider:
1. At pH 3 with nitric acid, your solution is unbuffered. I would not expect it to read "exactly" the same over time.
2. A pH meter like the one you are using is itself somewhat sensitive to salt concentration, at least on the order of 0.1 to 0.2 pH units going from 0 to 1 M salt. It could be that the change in pH measurement (due to salt's effect on the meter) is cancelling out any change in the "true" pH of the solution due to adding salt.
To test this out, you can try adding the same amount of salt to a weakly buffered solution of something like acetate, and see how much that affects the measured pH.
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2 answers
I am using arsenic transformng bacteria for reducing arsenate (V) to arsenite (III) in a soil sample. The soil sample is treated with water for one month. After one month I am analyzing the pH, electrical conductivity and oxidation reduction potential of the soil sample. I would like to know whether these three properties will increase or decrease after reduction of arsenate to arsenite after one month.
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So, this is a very complicated system that you're looking at, particularly depending on the composition of the soils that you're using. If you're not controlling some of the factors in some way (i.e. - using a buffer to control pH), then one of those factors could be inter-related with the others.
The observed redox potential of a simple system where you're looking at just one metal (in your case, arsenate and arsenite) is dependent on the concentrations of the two and the equilibrium between them, which is also related back to the standard reduction potential of the system through the Nernst equation. In your case, if you were just looking at arsenate and arsenite, as you increase the arsenite concentration (and increase the ratio of reduced to oxidized), the redox potential would become more negative. In addition, if any of the equilibria that are present in the system involve protic species (which is also true for arsenate and arsenite), then protonation constants would come into play in the redox equilibria. There have been a number of studies that have looked at the relationship between Eh (system redox potential) and pH in the past, and they have produced detailed plots of the system speciation when both Eh and pH are varied. These plots are called either Pourbaix diagrams or just "Eh vs pH" diagrams.
Your system may also be slightly more complex since you will have all of the soil components, many of which can have an effect on all three of the system characteristics that you mentioned in your question.
I hope this was helpful!
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If there is only pH value, how to assess the ion concentration of CO2 system in natural seawater under different pH conditions?
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You need to also know either the alkalinity or dissolved inorganic C. You can approximate the alkalinity if you know the salinity and temperature. For example:
If you know the pH and can estimate the alkalinity from salinity and temperature, then you can use CO2SYS to solve for the pCO2 and other properties of the CO2 system. Here is a link to download CO2SYS:
Here is a link with another Excel version of CO2SYS:
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It seems that golgi pH could only be increased by small molecular such as Bafilomycin A1; moreover, there are lots of inhibitors that could regulate intracellular pH, but not that of golgi.
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Nice question. Ammonia and chloroquin can change Golgi pH but maybe not in the direction that you are looking for.
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At what pH will Au in HAuCl4 start precipitating and at what pH complete precipitation takes place?
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Dear Shah
You have need to do the experiment for pH variation from 1.5 - 8.0 and will see the effect of pH conc in UV-vis studies, may be lower conc is best for growth.
Regards
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Is there any reliable free software to draw the acid dissociate vs. pH plot? For example, in the case of citric acid at pH=7, the portion of the ions in the solution?
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I like the HySS program. It's pretty good for drawing equilibrium speciation plots of protonation reactions, complexation reactions, etc. It's not too hard to use and is free of charge. You can also export the data into Excel format for plotting for manuscripts and presentations.
(Interesting thing to note, that citric acid is one of the systems that is included when you download the program, so all you have to do is change the concentration to match your system and you're good to go for your example.)
As a side-note, they also sell a program, Hyperquad, which helps to determine protonation constants and complex formation constants from spectrophotometric or potentiometric experimental data.
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I was just wondering what your thoughts were on storage of purified PCR products - fridge or freezer temperature?
I always elute purified products using the buffer provided with the purification kit I'm using, so this is usually TE or some sort of buffered solution that will keep the DNA stable by maintaining the pH. I realize that I have some purified products frozen and some refrigerated so wanted to have a reasoning for one storage method over the other and keep to this. I didn't think repeated freeze-thawing would be good for purified PCR product?
Thanks
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pH of pure DPG is around 4-5, DIW around 5.50, but when both are mixed together in 9 part DIW with 1 part vol DPG the pH drops to 3.49. What could be the explanation for this observed change in pH?
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Is DPG Dipropylene glycol? If so, how do you know the pH in this liquid.
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As correctly mentioned by Manoj, DMSO is aprotic. In fact, the pH concept does not apply to such solvents, because it is applicable only for H2O; hence, we know of super-acids like H[PF6] and such. Thus, you cannot talk about a pH of a pure anhydrous DMSO whatsoever. Compounds dissolved in pure DMSO will have wildly different pKa values than when dissolved in H2O, thus if you measure pH, which based on water, the measurements may be very different than expected. Literature is abundant on this topic.
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Do all types of cancer cells bear acidic pH within? Does the change in endogenous pH in cancer cells contribute to the anticancer effect?
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Many of the tumors exhibit acidosis with an acidic cytoplasm. It could be effectively used for designing pH sensitive drug releasing particles. Many such particles with Doxorubicin are still in trial.
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Far UV CD, tryptophan fluorescence and SEC was used to confirm the results.
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Carbonic Anhydrase has been reported to be quite stable over a wide range of pH: between pH 4.0 and pH 11.0 - although not as low as pH 2.0. Its thermal stability and folding has been studied in some detail by a Swedish group.
Martin Karlsson, Lars-Göran Mårtensson, Bengt-Harald Jonsson, and Uno Carlsson.
You may want to read some of their publications.
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Can you help me understand the chemistry of chlorinated swimming pools? When the pH is tested and found off balance, usually an alkaline power is first added and then some acid a few hours later.
Why?
Why not just add less of the acid only or less of the alkaline only? Does anyone know theory of the chemistry behind swimming pools?
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I thing this question fits to the chemistry.stackexchange.com well.
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I want to measure cytoplasmic ph, in E.coli, under several conditions in-vivo. To this end I would like to use cells expressing a plasmid harboring PH-sensitive GFP variant.
Does anyone have a plasmid like that and is willing to send it to my lab?
alternatively, can anyone please point me to a plasmid repository (other than 'addgene') that might have something like that in stock?
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Hi Daniel,
you may try to write to Paulo Magalhaes from prof. Pozzan's lab in Padua Uni/Italy
maybe you can try directly thorugh their lab's page http://www.pozzanlab.org/group.php.
As I can recall correctly, Paulo was working on some pH-sensitiv GFP mutants. He is a very nice guy, and if it is possible he will help you.
Good luck
Roman
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I am trying to do patch clamp (whole cell) electrophysiology on astrocytes in culture (namely, primary human fetal astrocytes). It seems for astrocytes, an external solution of pH 7.2 is often used, instead of pH 7.4. Is there a reason for this? this seems awfully acidic - but it may be helping me patch. Also, it seems people tend to use very high internal EGTA to remove Ca++ (e.g. papers I've seen use 5 and 10 mM). Is this needed? This could create a problem for us.
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I've experience in patching cultured astrocytes (Podda MV et al, Glia 2012) obtained from brain cortex and never had problems with standard internal or external solution commonly used for neurons. Astrocytes tend to be quite flat in culture and therefore you have less probability to do good seals with "the first shot".
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8 answers
Why lowering the pH increases the corrosion rates? lowering the pH increases the rates of cathodic reduction, so how this increases the rates of anodic reactions?
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Metals typically develop a passivation layer in moderately alkaline (high pH) solutions, which lowers the corrosion rate as compared to acidic (low pH) solutions. The passivation layer provides a measure of immunity to further corrosion (e.g. Ti, Ta).
However, the corrosion rates can be expected to be comparable in the transpassive region (i.e. highly alkaline versus highly acidic)
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Has someone directly measured it?
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I'm working with acidophilic archaea, which grow at pH 1.2. Their intracellular pH has been measured to be in the range 4.6-7.0. They maintain this higher intracellular pH due to the composition of the cellular membrane, which has a very low permeability for protons. On the other hand, studies on cloned enzymes showed that they have an optimum pH lower that the intracellular one (e.g. functioning in the pH range 1.0-4.0), indicating that there might be sub-cellular compartmentalization of the pH distribution, with some compartments more acidic than the others.
I'm fixing the cells by adding formaldehyde and formaldehyde directly to their growth media (pH 1.2).
The question is: after removing the fixative, the storing buffer should have a pH of 1.2 (as the culture media) or in between of 4.6-7.0 (as their intracellular pH)? How long can I store the cells until electron microscopy?
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Hi Cristina,
prior to give an answer, please give us (The answerers) some infos about your pH buffer (e.g. how prepared or bought)  of 1,2. On other part I need some infos about your formaldehyde (quality (purity),  how % are used) solution.
This aspect is important because the commercial formaldehyde solution is 10 % formalin but in fact  3,7 % formaldehyde and 1 % methanol in water. The undiluted commercial solution contains 10 % methanol and acts as 2 phases fixative e.g. at first fixation phase with methanol and crosslinking phase with aldehyde.
If your formaldehyde is not entirely removed , it oxidizes to formic acid when stored for a long time..
Please give us the protocoll of fixation.(%, time, washing....) too.
JRG
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I have prepared the pH sensitive nanoparticles and want to check their pH sensitivity.
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For pH sensitivity first chose appropriate buffer like HEPEs and vary pH by using acid/base. Then measure its zeta potential for stability. By using stable nanoaprticle solution at particular pH you can measure their sensitivity towards different analytes.
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A process was carried on with Hg/HgO as a reference and with a continuous passage of CO2, and the CV was recorded before and after passage of CO2 (pH changes from 13 to 8). Also, in both the cases a fresh RHE was prepared and potential of reference vs RHE was measured, so that findings could be reported as per vs RHE instead of  vs Hg/HgO, but then I am confused because the RHE reference itself changes with pH. So is it sufficient to just ignore RHE shift because of pH changes or does it need to be considered, because with RHE shift considered, observation is quite correct and with RHE shift ignored, the observation is meaningless.
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It is difficult to know whether you have a problem without knowing your experimental setup. However, before worrying about the RHE you should maybe consider if you should use Hg/HgO in the first place. You are using it in an environment where pH changes considerably, and also the potential of the Hg/HgO electrode is pH dependant.
I d second Qijin Chi 's suggestion and use a SCE or Ag/AgCl which, besides being  widespread, are not affected by changes in pH and can therefore act as a real reference.
What are the responses to PH-homeostasis of gram positive bacteria and archaea?
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How does the pH of the periplasmic space of gram positive bacteria and archaea respond to environmental pH lower than the optimal cytoplasmic pH? Thank you in advance for your answers, Florian
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In the paper I linked before, they mention the case of H. pylori as an special case capable of controling the periplasmic pH through the activity of urease and carbonic anhydrase enzymes. But it seems it is an special case. Stingl, K., Uhlemann, E.M., Deckers-Hebestreit, G., Schmid, R., Bakker, E.P. and Altendorf, K. (2001) Prolonged survival and cytoplasmic pH homeostasis of Helicobacter pylori at pH 1. Infect. Immun. 69, 1178–1180. Stingl, K., Uhlemann, E.M., Schmid, R., Altendorf, K. and Bakker, E.P. (2002) Energetics of Helicobacter pylori and its implications for the mechanism of urease-dependent acid tolerance at pH 1. J. Bacteriol. 184, 3053–3060. Sachs, G., Kraut, J.A., Wen, Y., Feng, J. and Scott, D.R. (2006) Urea transport in bacteria: acid acclimation by gastric Helicobacter spp. J. Membr. Biol. 212, 71–82. Sachs, G., Weeks, D.L., Wen, Y., Marcus, E.A., Scott, D.R. and Melchers, K. (2005) Acid acclimation by Helicobacter pylori. Physiology 20, 429–438.
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We took a mixture of span and sds for our surfactant system (microemulsions) and the observed that the trend is similar to that of ph sensitive surfactants.
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No, SDS is a strong electrolyte and it must not be pH sensitive. This is true, however, only at constant ionic strength and only if the background electrolyte is of much higher concentration than the buffer you use.
So what are your conditions? If you don't keep ionic strength constant, you will get a trend similar to pH sensitive surfactants (but it would be only due to Gouy equation). If you keep IS constant but your counterion-to-H+ ratio changes significantly, you will get a Hofmeister effect (not quite like pH-sensitive surfactant, but yet there will be a pH sensitivity).
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Dear all,
I want to prepare a 0.4 M Acetate Buffer Solution with pH=3.0.
I don't know what the appropriate amount of acetic acid and sodium acetate are. How can I adjust the pH?
Thank you very much in advance.
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Dear Parham, dear Rastislav,
both of you are right (at least in part)....  Problems I have with your suggestions:
(not to teach you!)
1) @Parham: if you have diluted your original mixture (as you wrote: "and after adding more than 5L [NB: 5 LITERS!!] of acetic acid 0.4 M solution to 80 ml of sodium acetate 0.4, the acetate buffer with the pH of 3 was achieved!" ) this way to end up with a pH of 3, you missed your goal to have a 0.4M buffer solution.
2) The principal premise of a buffer is "to exert buffer capacity over a certain range of pH", and therfore there are buffer solutions with different composition (ingredients) to achieve such: e.g.:
Range of common buffer systems
Buffering system                                                   Useful buffering pH range @ 25°C
Hydrochloric acid/ Potassium chloride                               1.0 - 2.2
Glycine/ Hydrochloric acid                                                     2.2 - 3.6
Potassium hydrogen phthalate/ Hydrochloric acid           2.2 - 4.0
Citric acid/ Sodium citrate                                                      3.0 - 6.2
Sodium acetate/ Acetic acid                                                   3.7 - 5.6
and so on. 
3) as you can see, usually Sodium acetate/acetic acid buffer system is ideally when buffering range is within 3.7 to 5.6.
4) therefore Rastislav is right in two ways: i) for a "functional buffer solution at pH 3.0" one better uses perhaps a citric acid/sodium citrate buffer and ii) perhaps also concerning the molarity of the buffer solution (dissociation).
5) Nevertheless there exist some recipes (or at least one) for Acetate buffer solution(s) (Sodium acetate/Acetic acid) for pH 3.0, unfortunately only for Molarity = 0.1 M or 0.2 M. I do not know whether one can use "similar" volumetric calculations if using 0.3 M stock solutions:
Acetate buffer solutions pH 3 - 6 ³
Make up the following solutions (1) 0.1M acetic acid (2) 0.1M sodium acetate (tri-hydrate) (13.6g / l) Mix in the following proportions to get the required ph
pH                        vol. of 0.1M acetic acid            vol. of 0.1M sodium acetate
3                                 982.3 mls                                         17.7 mls
4                                 847.0 mls                                         153.0 mls
5                                 357.0 mls                                         643.0 mls
6                                 52.2 mls                                           947.8 mls
or:
SODIUM ACETATE; PH 3.6–5.6, PKA = 4.76
Combine the following proportions of 0.1N acetic acid and 0.1N sodium acetate (Pearse, 1980).
 acetic acid   sodium acetate   pH
185              15                       3.6
176              24                       3.8
164              36                       4.0
147              53                       4.2
126              74                       4.4
102              98                       4.6
80                120                     4.8
59                141                     5.0
42                158                     5.2
29                171                     5.4
19                181                     5.6
or:
Acetate Buffer (only down to a pH of 3.6, this also in concordance with Rastislavs suggestion)
Stock Solutions:
A: 0.2 M solution of acetic acid (11.55 ml in 100 ml of distilled water)
B: 0.2 M solution of sodium acetate (16.4 g of C2H3O2Na   or 27.2 g of C2H3O2Na·3H2O   in 1000 ml of distilled water)
x ml of A plus y ml of B       and diluted to a total of 100 ml with distilled water:
x                      y                      pH
46.3                3.7                  3.6
41.0                9.0                  4.0
30.5                19.5                4.4
20.0                30.0                4.8
14.8                35.2                5.0
10.5                39.5                5.2
4.8                  45.2                5.6 .
Lower pH buffer systems eg.
CITRATE BUFFER; PH 3.0–6.2, PKA = 6.40 Citrate buffer (Gomori, 1955)  or GLYCINE–HCL; PH 2.2–3.6, PKA = 2.35 (Dawson, et al., 1969)    or PHOSPHATE–CITRATE BUFFER; PH 2.2–8.0, PKA = 7.20/6.40 (Pearse 1980)
certainly would be an option, but unfortunately we do not know about the real purpose of nedding and/or using <0.4M!> Acetate Buffer pH 3.0.
I wave downvoting the question or even the reply of Parham (because the attempt really is of no value at all)  since the matter really is too important to be deleted from the topic "buffers" and/or buffer preparation.
Sources I have included, others from web-files (I would have to dig for their original URL).
Regards,
Wolfgang
NB: if those columns will get chaotic after adding my answer here, I should post another reply including an attached pdf to this thread)
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Observed during Amylase-Starch assay at various pH.
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Verify that you have the apropriate blank at each condition, pay particular attention to solution turbidity in blank and test solutions
Use matching cuvettes for blank and test solutions
Finally, if you are measuring enzyme activity, the specific value of absorbace is often not so important as you have to work with the slope of the linear portion of the time course. I hope this helps.
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We use to prepare 1.5M tris pH 8.8 and 1 Mtris ph 6.8 for SDS and we keep it at room temperature. After few days I could see there is a increase in pH
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I would like to do a native gel on a small (9 kDa) basic (pI-9.5) protein, and we will be looking to resolve different isoforms that have different PTM's.  These PTM's will alter the pI significantly (by 1-2 pH units), so we would need an electrophoresis system that covers a range of pH's, like 6-9. I read that acetic-acid urea gels are good for basic proteins, but could that be used in this case?  Any ideas would be appreciated!
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Thanks for your help everyone!  I will give this a try.  Vivek, my email is carabevj@njms.rutgers.edu.  I'd like to see which protocol you use.
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I would like to ask about the preparation of Tris - Base buffer 0.4M 8.9 pH. The reagents I already have are Trizma hydrochloride (T3253 from sigma) and Trisma base (T1503 from sigma). 
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Hi, based on previous experience in preparing a buffer and adjusting the pH, I would recommend you make up the Tris base to a concentration of 0.4M and then use concentrated acid and base (maybe HCl and NaOH?? I am not sure) to adjust the pH. That way, the concentration won't change from the addition of the acid or base because you would only need a few drops. 
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i.e a way off speeding up the process for the residue to reach pH 7?
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increase the water volume,
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I try to make HOAGLAND Solution, but when i set the pH of solution it became precipitate and there was any substitute for ferric tartrate?
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Hello Jignesh
Process of making hoagland solution is not so simple first of all you need to prepare all the nutrient solutions as stock solutions for example
stock A: KNO3 solution
Stock B: calcium nitrate
stock C: ammonium hydrogen phosphate
stock D: Magnesium Sulfate
stock E: micronutrients
prepare 100X stocks of all and mix them into a working solution in the precise sequence. Moreover, micronutrient sequence shall be strictly adhered to. Now after you have added everything add IRON EDTA in a concentration of 40 mg/L in the final working solution. Don't prepare solution of iron edta use it as fresh addition and it will work just fine and will suffice your requirements. Hope you find the information useful and all the best for you experimentation
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In our lab we induce acute colitis in mice by dissolving DSS in the animals drinking water. After purification by reverce osmosis, the animal house supplies water at pH of 3.5 to 4, as a precaution against bacterial contaminations. However, there is another tap that can supply water at pH 7 to 7.4, this too after reverse osmosis. Does the pH of the water alter the activity of DSS.
Furthermore, should experiments conducted using the drinking water at pH 7 be repeated using the drinking water at pH 3.5, or are these experiments comparable?
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Interesting questions. We used the water supplied by the Animal Facility but never commented in publications about the pH. Isn't it conceivable that a lower pH if anything would increase the effect of DSS treatment. We changed DSS concentration but not water if we weren't happy with the resulting colitis. If in doubt, it would be an easy experiment to conduct comparing the two different pH levels. 
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I have a physical mixture of PLGA and 1,4-diaminobutane in DCM. PLGA is completely insoluble in water while diaminobutane is completely miscible in it. I'm not sure whether PLGA and DAB are making any bond (H-bond, hydrophilic bond, ionic bond) or not.
I tried to perform liq-liq extraction with water having 3 different pHs. The lower pH (HCl, 2.3) didn't give any separation. Neutral and basic pH (7.3 & 10) separated after a while however, the bottom DCM part doesn't have any PLGA now; all of the PLGA is somehow in the aqueous phase now making semisolid mass.
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First, please note that solubility of PLGA in chloroform decreases with the increase of the average lengths of the glycolic acid units. Secondly, there is thermal stability of PLGA if e.g. a temperature is selected below 100 oC as the attached article indicates.
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What pH do lecanicillium like to grow in?
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most fungi grow well at acidic pH.
  Lactic acid is used to correct the pH of mycological media, and have seen it grow to  media ,however, the lactic acid concentration should be considered
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My problem is related to microbial nitrogen cycle.  
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check out chapter 5 (section B) of the first edition of the Handbook of soil science, chapter on Redox Phenomenon by BR James and RJ Bartlett (I am not sure if this same chapter and its contents are in the second edition). 
parts of the handbook are available in google books 
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If I open with Jmol and select model A or C, both have hydrogen bonding with the oxygen. Should this hydrogen being there?
From the 3NIR document this is the method used
60% ethanol in water, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
thanks
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In case somebody else is having the same question this is a document talking about mistakes in the databank.
And pdb files can be checked from here.
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If plant leaves are extracted with just PBS buffer (pH 6.9), what ingredients are collected in the supernatant from leaves?
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Have the samples been disrupted (ground or cut) in any way?  If you grind plant leaves in this solution then centrifuge in a table top microcentrifuge the solution will contain most of the DNA, RNA and proteins with pellet of mostly cell walls and non-broken cells.  What are you hoping to extract?
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It is observed that as the Si/Al ratio increases, acidity decreases. This indicates that aluminium genarates acidity. Due to its valency, there is an overall negative charge (due to oxygen) on the zeolite which is balanced by a cation. If it is a proton, the zeolite acts a bronsted acid.
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When aluminum substitutes for silicon in a tetrahedral zeolite framework, a cation is required to satisfy the Al tetrahedron. If this cation is a proton (which is quite often the case), the proton is a strong Bronsted acid. Thus, increasing the Al/Si ratio (or decreasing the Si/Al ratio) in the zeolite framework increases the number of acid sites if all the cation sites are populated by protons. However, each acid site becomes a somewhat weaker Bronsted site as the population of protons increases. This is due to proton crowding in the zeolite pores.
Lewis acidity due to aluminum in a zeolite generally results from extra-framework aluminum. Extra-framework aluminum is aluminum which is not tetrahedrally bound in the framework. You could think of this as islands of Al2O3 often dispersed in the zeolite pore structure, but it can also appear on the exterior of the zeolite crystals or even at the pore mouths. Extra-framework aluminum is often an artifact of the synthesis process whereby excess aluminum in the synthesis mixture does not get incorporated into the zeolite crystals. Extra-framework aluminum can also be created by purposely steaming a zeolite to remove Al from the framework. This process is used to increase the Si/Al ratio of zeolite-Y for cracking catalysts.
Generally, Lewis acidity is much weaker in zeolites than Bronsted acidity if the zeolites are in their form.
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To our knowledge, endosomal pH is ranging from 5.0~6.5. However, is it possible to detect the pH of different cells and is there a difference for the endosomal pH between tumor cells and normal cells.
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Dear Wenyu,
This is a great question, and I can imagine will bring some interesting discussion. Detection of pH within cells is a relatively easy process through the use of specific pharmaco reagents that use pH reactive dyes, and also directly through the use of electrophysiology. The technology is certainly out there to measure pH of cells and of intra-cellular compartments.
To be totally honest I dont know if the pH of endosomes varies between tumor cells and normal cells, as I have not tested this or read about this. Considering tumor cells can be either benign or activated that would suggest a change in state of the endomembrane system (system that encompasses endosomes, lysosomes, autophagosomes...etc) between tumor cells. My reasoning is that activity greatly depends on the rate of turnover of the cytoskeleton, the energy required for that turnover, and an excess of available membrane, all of which are interconnected with the endomembrane system.
The endomembrane system itself is an active trafficking process requiring energy, cytoskeleton and membrane. But the processes itself are required to produce excess ATP, free membrane, directional deposition of membrane...etc. The regulation of pH is key as pH change through ion transfer across membranes is a crucial mechanical control over the whole process. Relating this back to tumor cells, I would imagine that pH change occurs faster (possibly due to less regulation or even greater regulation??) to push for faster turnover in other intra-cellular systems. But this would be for an activated tumor cell, what would be the state for benign tumor cells and how does a tumor cell control this change?
As you can see, there are lots of questions that stem from your own. I understand that I havent answered your questions, simply added to them. I apologise if this has added any confusion but this is a great topic for debate and addition of ideas, which I wanted to add to. Thank you for asking your questions, its great to see other researchers asking similar things! I hope there is someone out there who can give you the best answers.
Best regards,
Chris
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See above
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Dear sinan, thanks for your comment. I use MWCNTs suspension in various pHs for LBL thin films. the related articles  did not mention the specific buffer or salt for this purpose. 
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I have crystalline TiO2 colloids in PH 7. When I added 0.1 M HCL little by little, the colloid became unstable. I know the isoelectric point of Tio2 is about PH 4 to 5.5 but I need TiO2 aqueous solution in PH3!
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Mdm. Maryam Anjidani
For a moment-
Did you try the QUANTITATIVE addition of the buffer ON or BEFORE the isoelectric point ?
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Measuring the pH of an onion after diluting it in deionized water may not reflect the real pH of the onion. I need other alternatives.
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How about cutting the onion in half and layering on a strip of narrow range pH paper?
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We are trying to optimize the dissolution media for lornoxicam.
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Choosing the suitable buffer is based on the route of administration rather than the drug pKa. For instance, we use pH 1.2 buffer to simulate stomach environment i.e. the dosage form is taken orally.
After selecting the buffer, you might need to adjust or enhance the drug solubility in it to ensure sink condition by adding a surfactant for example.
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For pH stability experiments by NMR, I need to change the pH of PBS from 7.4 to 8 and to 11. Has anybody done something similar?
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You firstly should note the composition of your PBS solution, since it may change. There is a possibility of changing the pH by using Handerson-Hasselbach equations, but since solution would also have NaCl, KCl like salts, it would change the ionic strength of solution, and the results obtained from Handerson Hasselbach may not be the same. But nevertheless, let me put it into words:
You would have to use Handerson-Hasselbach equation:
pKas of Phosphoric acid are 2.3, 7.2, 12.35.
Looking at these values, any pH between 7.2 and 12.35 would require you to use monoprotic (HPO4--) and diprotic (H2PO4-) salts (Na or K salts). Now, what you need to do is to get Handerson-Hasselbach equation, which is
pH = pKa + log ([A-]/[HA])
Now, for A- you put HPO4-- concentration, and for HA you put H2PO4 concentration.
For example, for pH=8, you need:
8 = 7.2 + log(A/HA)
log(A/HA)=0.8
A/HA = 6.31
So, now you know the fold difference between these salts, and the Molarity of the solution would be given to you, and you can calculate the required amount. For example, if molarity is 0.5M:
H+A=0.5
H/A=6.31
from here you can calculate the concentration of each salt, but be careful, don't forget to add the weight of K or Na to your salts while calculating the mass of each salt required to be added.
I wish the calculations are clear, same things are valid for ph=11, where A/HA would be 6309, which is pushing the limits, but still plausable.
But, if these steps would not give the required pH for you, you still can work by having your stock solution, which would be around pH=8. And then, by dropwise addition of high molar NaOH (for ex 10M), you can change the pH of the solution, but still maintain its buffering capability.
Measurements can be done by pH-meter, that gives you instantaneous pH value of solution, not with pH papers.
I wish it was helpful.
Good luck
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I want to know whether there is any proton transfer in excited states because spectroscopically I'm not able to justify it.
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The pKa of a given functional group may change in the electronically excited state, compared to the value in the ground state. Check Chap. 7 of Lakowicz's Principles of Fluorescence Spectroscopy.
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I have flat combination electrode and pH-meter. As I understood, electrode should be immersed into drop of water on analysing surface, but are the volume and contact surface important in this case? It's slightly difficult for me to extrapolate the knowledge about pH onto solid surfaces.
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I would suggest to try using contact angle measurements:
I believe that these and related publications should be reproduced in your system. I thin that a kind of "surface titaration" based on caontact angle measurements would be highyl relevant to your potential applications.
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pI of my protein is 8.2 and it is in Tris buffer of pH 11.
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first of all, you should never make Tris-buffer at pH 11, because that's far outside the buffer range of Tris. For such high pH's you should use either Sodium bicarbonate/Sodium hydroxide or Sodium hydrogen orthophosphate/Sodium hydroxide (see this link: http://delloyd.50megs.com/moreinfo/buffers2.html). Why do you need to have your protein in pH 11 anyway?? This way it will be negatively charged, but you might as well get it into buffer at pH 6 (where it will be positively charged) and then use a cation-exchanger. Is there a specific reason why you want to run a pH-gradient (more complicated) and not a salt-gradient to get your protein out?
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I have a protein that I've purified from a His column. I've noticed that when I do a buffer exchange of the eluted fractions into PBS (pH 7.3) and then concentrate the fractions, the solution gets cloudy and appears to have small precipitates. The isoelectric point of my protein is 8.4, so I should be far enough away from the PI for it to be soluble. I measure the concentration of the concentrated fractions on a nanodrop, but as you can imagine, the results vary quite a bit depending on whether the "precipitates" are resuspended or spun down. I've used the concentrated protein in several in vitro assays already, so despite the cloudiness of the protein in PBS, the protein still performs quite well. So, should I be using a different buffer for buffer exchange, and if so, how does one decide on which one to use? Should I go up or down with pH to get it more soluble?
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Finding the right buffer to keep a protein in solution and obtain optimal activity is definitely a trial-and-process. First, I would not assume that you are far enough away from the pI is ensure solubility. Second, you should try a number of standard buffers such as sodium phosphate, HEPES, and many others that can be found in the literature and in classical works such as Methods in Enzymology. Third, don't forget that ionic strength can be critical. Many proteins like a "salty" buffer, such as 100-500 mM NaCl. Fourth, your buffer exchange may have removed a critical metal ion that is essential to maintain structure. You are fortunate in being able to measure activity. Use that to determine which combination of buffer component and salts give the best activity and optimal solubility. Good Luck!
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I have done soil testing of black soil of mainly clay texture. But when SAR(>13) and ESP ( is estimated to mark it as saline-sodic (high EC value) , the pH seldom falls above 8.5. Why pH is not going above 8.5
Here is sample data, check sr. 1 to 6
The formula for SAR= Na/ Sqrt((Ca+Mg)/2) and ESP=Na/(Ca+Mg)*100. All ions meq/L extracted from 1:2 dilution.
Am I making mistake in calculation of ion concentrations.
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Hi sachin,
i guess the formula you used for the calclation of ESP may be worng. ESp can be calculated as ESP= 100* Na / ( Ca+ Mg+Na+ K). You  can ignore Al and H  as your soil is alkaline. 
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I am looking for software (for Mac or Linux) which will allow me to simulate DNA structure at varying pH values. In particular i want to know what happens to H-bonds.
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As far as I know, the "pH value" is transformed into "protonation state" in a simulation. That is to say, the difference of pH = 5 and pH =7 in simulation is HIS or HIP(histidine has different protonation state, for example). I guess there is no software which has the absolute concentration of [H] into consideration?
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Using ordinary pH glass electrodes, one encounters problems in pH measurement when the solution pH is about 1 or above 12. In such cases, acid and alkali errors come on the way. A few electrodes of specific make will work in such solutions. Hence one should know how to choose or design pH electrodes which do not cause any problems for pH measurement at pH 1or less than 1 and at pH 12 or above.
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For sure a Hydrogen / Hydrogen Electrode combination will work.
We produce now for 2 decades Hydrogen reference electrodes. They do work in concentrated 50% hot NaOH as well as in 50% Sulfuric acid. As the hydrogen Potential is the origin of the pH Scale, this electrode will give you the right pH value in any case.
Unfortunately until now you just have to build your own pH electrode out of two hydrogen reference electrodes.
We are at the beginning to produce and sell such kind of pH meter
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We are preparing ferrites ( NiZnFe2O4, MgZnFe2O4, etc.,). After preparing solution we are adding NaOH to get precipitation. Could someone please explain the chemistry behind it? When I took EDS spectra for the sample I did not find Na or H elements - where do these elements go?
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solutions get precipitated when the repulsion between the solutes is decreased or vanished. pH play very important role in precipitating solution as with pH the charge on the solute changes. sometimes solute makes stable insoluble or less soluble compounds upon gain of hydrogen or hydroxyl ions.
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Before storing the DMEM (sigma high glucose) at 4°C. I set the pH 7.2, and next day I checked the pH of the medium. After warming up at 37°C the pH rose to 7.8. What could be the reason and will it effect the growth of my cell line? I am using ACHN and A498 (renal cell carcinoma cell line).
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Dear Kathryn & Wolfgang
I have done tissue culture since 1972, and have previously established departmental media mass-production facilities. I understand bicarbonate buffer chemistry quite well, as well as all the other ways in which media is buffered. Moreover, my first hand experience over many years has taught me more than any theory can explain. However I'll try to elaborate further.
The earth's atmospheric CO2 concentration is only 0.04%. In contrast, CO2 incubators are generally set at 5-10% depending on the buffer system. The average humidity over land is quite low, whilst humidity inside the incubator must always be 100% saturation. Opening incubator doors too often thus allows humidity to escape, and consequently vented culture vessels will dry out until humidity is reestablished. This means the salt concentration of the media in which your cells are growing increases, which can kill cells. Even leaving the outer insulating doors open for too long allows the inner glass doors to act as a condenser, and the humidity will drop even though the temperture will remain constant. Because of the relatively high CO2 concentration inside the incubator, this humidity is more like acid rain (carbonic acid). In this regard humidity acts like a CO2 sink to maintain stable CO2 levels, so loss of humidity also means you waste CO2.
CO2 is more soluble in cold water, which is why highly carbonated drinks go flat when warm and open to the air. CO2 gas dissolves in water to produce carbonic acid, and sets up a bicarbonate-carbonate equilibrium that determines dissolved CO2 concentration at a given temperature. Cold drives the reaction to the right, warmth drives it to the left.
CO2 + H2O ↔ H2CO3 ↔ H+1 + HCO3-1 ↔ 2H+1 + CO3-2
carbonic acid bicarbonate carbonate
Carbonic acid is a weak acid and doesn't dissociate its protons easily. Most dissolved CO2 remains as undissociated carbonic acid, or exchanges with atmospheric CO2. Despite warmth, the incubator's CO2 concentration drives the reaction to the right. Culture media formulations are optimised for given CO2 settings (usually 5%) and temperatures (usually 37C). However the humidity must always be 100%, because water is an essential part of the above reaction. I used to grow tumor cells in tightly capped bottles, in a warm room (no CO2 incubator required). After passaging cells, the media would turn alkaline. Over the next few days lactic acid and CO2 produced by the rapidly growing cells would bring the pH back down, at which point the monolayer was confluent and the cells were ready for passage again.
In sodium bicarbonate-buffered media, the bicarbonate concentration is in vast excess of what would occur from dissolved atmospheric CO2. As long as the system is closed (sealed bottle) and CO2 cannot escape, the original pH is maintained. Inside the CO2 incubator, the pH equilibrium is maintained because that's the way it's been formulated. However when open to the air, excess bicarbonate drives this equilibrium reaction to the left and CO2 gas escapes (media goes flat). The result is is a loss of protons (acidity), so the media goes alkaline. Phenol red in DMEM is a sensitive indicator in the pH 6-9 range (orange-purple).
Because tissue culture media contain sodium bicarbonate, there is a new equilibrium reaction established which modifies (buffers) the above reaction.
2 NaHCO3 → 2 Na+1 + 2 HCO3-1 ↔ 2 Na+1 + CO3-2 + CO2 + H2O
The presence of both sodium and bicarbonate ions means that when CO2 escapes, the reaction is driven to the right and sodium carbonate is produced. When CO2 dissolves in media, the reaction is driven to the left. Once the correct amount of bicarbonate has been added, the pH of flat alkaline media should only be adjusted by bubbling CO2 gas through it, not by addition of HCl.
While it is true that bicarbonate ions may be lost, as they are composed of just CO2 and H2O, all sodium ions remain in solution. The buffering ability of sodium bicarbonate allows for dissolved CO2 to be gained (carbonic acid) or lost (sodium carbonate). Carbonate solutions are more basic than bicarbonate on a mole for mole basis. Carbonate ions can neutralize two protons, whilst bicarbonate can only neutralize one. Besides, it's really not this simple, as there are other buffers including serum which stabilize the pH.
To understand bicarbonate buffers is to understand global warming. The earth's oceans are full of insoluble calcium carbonate - think sea shells and coral reefs. As increased atmospheric CO2 drives formation of acidic oceans, this carbonate sink will be dissolved as it becomes bicarbonate. Whales migrate to cold waters to feed because there is more dissolved CO2 to support photosynthesis by phytoplankton, the base of the food chain. And so on, and so on.
What is the smallest pH autotitrator that can be purchased or made easily?
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I am studying the effects of pH on a self-assembled system (micelles and liposomes) in water. I have done some pH microtitrations by hand, but I would prefer to have an automated method. To conserve material, I'd also like to use a relatively small volume of initial sample (~1 mL or less) and titrant.
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Metrohm (www.metrohm.com/com and www.metrohmusa.com/ - United States) is a manufacturer that has available very nice, smart and feasible titrators for very small volumes. I hope that you can find a satisfactory solution with them. Best regards from Madrid, M. Antonia Martín
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Conformational aptamers
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You may get degradation of the aptamer at low pH's
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To calculate mean pH, you have to convert first to ion concentration, but the std. dev. you get cannot be converted back into pH (or at least isn't a logical number).
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yes it is possible to calculate standard deviationf or pH...why u have to convert it into ion concentration...? calculate it directly...
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When we use a pH meter to test the pH, the meter indicates both the pH and temperature of the solution. I want to know the correction factors for the right pH value of the solution.
Example : pH 7.82 and temp 28.4°C - what would the pH of this solution be?
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Hi Bhupender,
the correction factor I haven't but I found a table / chart with divergences value for difference temperature by difference pH-values (see at pages 11 at www.jumo.net/attachments/JUMO/attachmentdownload?id=12013)
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This protocol is reported in a journal written by Paolucci-Jeanjean et al. (2000).
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Sometimes with SDS, one has to boil the sample to completely denature. I would recommend hIgh concentrations of acid or base for instant quenching. Or add proteinase K to the SDS as Jovencio mentioned.
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I am trying to work out a protocol for measuring sodium hydrogen exchange activity by using a pH sensitive dye BCECF-AM, I am planning on using the BMB NOVOSTAR plate reader for measuring the flourecenceof BCECF-AM. I was wondering if anyone would be willing to share ther protocol as well as the settings on the BMG NOVOSTAR plate reader for intarcelluar pH measurement using BCECF-AM
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I also want to know.
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A pH adjustment <2 is generally prescribed for water samples applied in trace metal analyses to stop metals from precipitating. If the pH was not adjusted and some of the metals potentially precipitated, will those metals move back into solution if the pH is adjusted <2 weeks later, providing a realistic view of the metal content in the sample upon collection?
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In order to fully answer the question, more information is needed I think. Like others have already asked:
What will you analyze for? How will you analyze it? What kind of samples are these (seawater, groundwater etc.) as well as what characteristics do your samples have (e.g. for river waters, colloid-rich or not)? Are the samples to be filtered?
Please provide some more information so that you can get a more detailed response from the community.
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Cu-doped TiO2 nanoparticles for photocatalytic disinfection of bacteria under visible light
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The sol-gel method,transition from a liquid into a solid.Thus, in the case of silicon alkoxides, a change of surface charge can be easily carried out by changing pH using acid or alkaline catalyst to increase the hydrolysis and condensation reactions.
The pH also affects the dissolution and reprecipitation of metal.for e.g,at high pH values maintained ,more porous structures was obtained.the generaly,some metal oxide forming in particular pH value.
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As most pulications reported, STF was made using NaCl 0.67 g, NaHCO3 0.20 g, CaCl2 2H2O 0.008 g and distilled, deionized water to 100 g. And the pH of STF in publications was often adjusted to 7.4 with HCl.
However, I found the pH changes to 8.3 within 1 hour when it was used to evaluate in vitro release in 35-37 degrees centigrade.
So how to keep the pH of STF stabilized for a longer time, such as 6 hours?
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Dear Zhongya Chen,
Addition of sodium bicarbonate in modified simulated body fluid ends to pH enhancement. besides, we should add NaHCO3 exactly before using the simulated fluid. if we add this material in stock solution, sedimentation of salts will be happened during less than 1 hour. I am not sure about my answer. but May be simulated tear fluid changes by the time because of above same happening.  
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When we use the sol gel method to synthesize nano particles which stage of synthesis determines whether the final product is nano or not? Also how does the pH value become an important factor for the crystallite size?
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I would like to synthesize 20 to 30 nm of Fe3O4.. My material is not reaching that size. I am following acetate route sol gel method. As I am very new to sol gel method I have no idea how the parameters you mentioned are affecting the synthesis. If i control only one parameter like hydrolysis rate ,then can I achieve the size what I am expecting or I should control many parameters together to achieve the goal? In general I would like to know what each parameter does so that I can understand how to control the parameters.
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How to prepare a buffer of NH3-NH4Cl with pH 10 for a titration between Zn2+ and EDTA?
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Dear aastha
This buffer is also called Ammoniacal Buffer, Dissolve 90 g of ammonium chloride in 375 mL of 28–30% ammonium hydroxide, and dilute to 500 mL with water. (The pH of a 1 + 10 dilution with water should be about 10.)
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I am working on generating an artificial tongue system. Thus, I need to know more details about tastes. What is the pH for bitter tastes or sweet tastes, etc. Can anyone share more details?
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Thanks Karl
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My P. acnes culture with soda lime glass balls have a problem: after an OD of 0.4 bacteria were dying. The ph is 6.4. I guess that something of my media (Brain heart infusion broth) interacts with the glass balls and inhibit the growth of my bacteria. Could you give me some idea for trouble shooting?
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To determine the amount of growth in a culture with both planktonic and biofilm-associated cells, you need to use a different method other than OD - as you have re-discovered! If you can afford to sacrifice a replicate culture, you could e.g. extract the protein as a proxy for biomass. There are plenty of other biomass-estimation methods - see Collin's & Lynes "Microbiological Methods" book.
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Sometimes I see people adjust the pH of the mobile phase in TLC. How does this help in separation?
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Sometimes organic acids or bases are added in small amounts to the developing solvent (in TLC the term mobile phase is inappropriate). You normally adjust the pH if you get bad tailing of your bands, but pH can also be a strong tool to fine tune the retention of the compounds on the stationary phase. For example, carboxylic acids often have pKa in the range 3-5 and are ionized at neutral conditions. This can cause poor retention of these analytes on RP TLC plates, but adding an acid to the developing solvent renders the analytes neutral, therefore you should get better retention. Additionally, low pH also minimizes silanol interactions with your basic analytes. Silica is by nature slightly acidic and at higher pH values the silanol groups can interact with your ionized basic analytes via ion exchange interactions. To avoid this phenomenon, again, a small amount of acid is usually added to the developing solvent to suppres the silanol interactions. Basic additives to the developing solvent have an analogous function.
Hope this helps...
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I have two pH meters with the same brand but with significantly different results. Why is this and how should I solve this problem?
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They need to be calibrated.
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The level of activity of this enzyme varies according to age, species and muscle, potentially making it one of the explanatory factors behind the variation in pH decline between different muscles and animals
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http://www.ncbi.nlm.nih.gov › NCBI › Literature › PubMed Central (PMC)
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How to measure pH in tumors and the tumor micro-environment of animals during the experiment?
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Next ...
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We have two solutions with known volume and pH. We want to mix them together and then adjust its pH to a specific value using 1M HCl which also has a known pH. Without any trial we want to exactly know the required volume of HCl for pH adjustment. Theoretically we can find the total concentration of H+ in the mixture that shows its pH. But will it be exactly the pH which would be obtained if measured? Actually I want to know that if the theoretical pH and actual one are equal to each other.
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Do you mean that you want to prepare buffer solution or you are doing acid-base reaction or you are mixing salts.But any way the most accurate way is to use pH meter
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When I analyze the Al content in groundwater, I found that there is a relation between Al-pH. When pH low Al3+ is solube very high, then increasing pH Al3+ decrease, but it increases again when pH is above 6. From lab test, I found a hyperbol relation between Al3+ and pH (2,8-6). I don't care type of pH yet. Do you know some published references relate to this topic?
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Dear Tu,
You rediscovered something well known. Aluminium is amphoteric - that is, it is soluble in low pH solutions and in high pH solutions, but pretty insoluble at intermediate pH. Any chemistry textbook should show a graph of the solubility of Al as a function of pH. If it doesn't, buy a better textbook.
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What is the relation between pH and conductivity? Is there any mathematical formula that can be used to correlate both ? Is it possible to calculate pH from conductivity or vice-versa for water?
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Yes, there is a relation between the pH and the electrical current flow [the conductivity] of a solution, but there are other factors that affect the conductivity. This topic, the conductivity of solutions, takes up a full chapter in a textbook on physical chemistry with many graphs and numerical tables. But I will try to keep it simple, basic, non-mathematical, - and short. When an electrical current passes through a wire, what actually moves and carries the curent is ELECTRONS. But in solutions, the current is carried by IONS: positively charged CATIONS [+]such as H+ , Na+, Mg+, etc. and negative ANIONS [-]such as OH-, Cl-, Acetate-, etc. [The + and - should be superscripts, but this computer cant show this [maybe it can, but I cant]. The conductivity of a solution depends on the concentration of ALL the ions present, the greater their concentrations, the greater the conductivity, These ions all have the electrical unit charges shown by their symbols, but they move at different velocities [mobilities] through the solution, so they contribute differently to the conductivity. An analogy would be a line of persons carrying water to a tank, they all have the same size bucket, but some walk faster than others [i.e. have greater mobility]so they contribute more. These relative mobilities have been measured and are listed in many chemistry texts and reference books. Of the common ions, the most mobile CATION is the Hydrogen ion [H+] with a value of 350 units, and the most mobile ANION is the Hydroxyl ion [OH-], 199 units. The other common ions have values ranging between 40 and 80 units. So you se that strongly acidic [or strongly basic] solution will have high conductivity Since the pH is a measure of the concentration of the Hydrogen [and the Hydroxyl] ions, for an acidic solutin, the lower the pH [i.e. the higher the H+ concentration,] the greater the conductivity will be. Remember, the conductivity is the sum of the contribution of ALL the ions present in the solution I hope this brief discussion helps you. For more detailed information, I suggest bellow reference for further detail information.
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Generally glass pH electrode is considered as most suitable electrode for accurate determination of pH. But it cannot be used when solution temperature exceeds 80 deg.C. I am looking for a suitable electrode for online measurement in industrial setup where temperature of sample exceeds 100 deg.C with high pressure. Which electrode can be the best choice?
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pH-ISFET we advice follows a Nernst linearity (that is 55mV/ pH) over a large pH range. It can be used beyond 100°C . Combine with a miniature Ag/AgCl Ref Electrode the system a solid state device and can also be used at high pressure. For more information and datasheets please ask by e-mail : alain.grisel@microsens.ch and info@microsens.ch
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I'm looking for values of pH of amine solutions during neutralization with CO2. Such information, presented as graph, is shown in Kohl's "Gas Purification": http://books.google.pl/books?id=rpzrIZW-OcEC&lpg=PP1&hl=pl&pg=PA47#v=onepage&q&f=false
Do you know any other sources of similar data?
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May be this paper can help you
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I prepared DPBS (pH 7.4) and filter sterilized it using a 0.2 micron membrane filter. When I checked the pH of filtered buffer, it raised to 7.79.
What could be the reason behind this?
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Yes it does, even for preparing media for tissue culture, a decimal digit difference is often kept as a margin when steralization is done using filter emmbranes.
Water comes first from the membrane as it has the minimal molecular size thus, initially the solution becomes near neutrility first and then shifts to respective pH but it never reaches to the same as unfiltered one as some of teh left over also trapps some hydronium ions with it as for its own aqueous ionization.
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Distilled water is known to be acidic due to atmospheric CO2 absorption. how can one measure the degree of acidity in water due to CO2 absorption ? Distilled water in our labratory has pH ~ 5.8-6.4. How can I know that this change in pH is due to CO2 absorption ? Might I be measuring the concentration of HCO3- ion in water?
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Dear Jenish,
The pH can be measured by a standard (well calibrated) pH electrode. Pure water at 25 Celsius in equilibrium with the standard atmosphere (air) has a pH of 5.67, say 5.70 according hydro chemical equilibrium calculations (e.g. using Phreeqc model). Of course, cooling, heating, shaking water, can modify some gas equilibria and induce some fluctuations, as indicated by you. Pure distilled water is in fact rather unstable, and a few micromol change of CO2 gas absorption from e.g. air or depletion, change the bicarbonate equilibrium and pH. You can measure bicarbonate or the alkalinity (TIC or total inorganic carbon) using a titration. For pure water, a special accurate titration method (as described in Stumm and Morgan , Aquatic Chemistry) is recommended.
All analytical work on aqueous solutions in contact with the air, will have to deal with CO2 from atmosphere, although it are micro-molar transfers, and not that important (in general). Most other electrolytes (dissolved salts) or soluble organic compounds (with acid-base action) will override the atmospheric CO2 effect quickly. Therefore, I wouldn't bother that much.
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Anaerobic reactor.
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Even if the pH is 4.5, depending on the methanogenic consortia and the temperature of operation (thermophilc), the pH can increase and reach a stable value around 7. further increase can occur because of presence of alkanity, when methanogenic as well as acid producing bacteria are directly affected by increase in pH and thus are not able to decrease the pH. Incrase in pH up to8.5 is also seen when formate has been the main interspecies electron transfer and/or used as a substrate. But in this case the methanogenic activity should also be active.
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Could anybody suggest some good literature references on the concept of "operational pH" in non-aqueous media possibly including a discussion of justified or not justified utilization of conventional pH electrodes for measuring meaningful values?
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Dear Roman:
The following textbook reference is not up to date but still gives a particularly clear introduction to this subject: Herbert A. Laitinen & Walter E. Harris, “Chemical Analysis ─ An Advanced Text and Reference”, 2nd ed., McGraw-Hill Kogakusha, International Student Edition, 1975, cf. section 4-10: "pH measurements in nonaqueous solvents", pp. 85-88 & 94.
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I am having hard time making agar plates at pH 3.0. Any help will be appreciated.
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if it necessary to use agar media at such low pH , then try to prepare your medium at double strength and the agar at double strength as well, and sterilized them separately and mix them just before use
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Most of the glass electrodes recommended for pH measurement do not work well while measuring pH of high purity water. They work well in buffer solutions and other aqueous solutions not for high purity water. Hence why it is so and which electrodes can be exclusively used for pH measurement of high purity water
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It all depends how you define "high purity water" In the absence of air contamination, the ion concentrations should all be below 10-6 M, and the pH will be between 6 and 8, and their should be no reason to know it exactly, because once it comes in contact with anything (metal surfaces) the pH will change as it becomes contaminated. For pure water open to the atmosphere, there is enough carbonate in the water that an accurate pH measurement can be made with a pH electrode, but you need a good one. For this purpose the key is to use an combination electrode (or reference electrode) that has a more porous frit. The typical glass frit (electrolyte junction between the outer filling solution and the aqueous sample) has a flow rate of 8 microliters per hour. Good pH probes (and it really is the reference probe), like Thermo-Orion's Ross electrodes (about $400 USD), have glass fiber junctions that have flow rates of 120 microliters per hour. Hence the total electochemical cell has better electrical properties, and a stable reading is achieved quickly. These combination pH probes have double junction reference probes. I think, even for systems with very low ion concentrations, getting one of these probes is the best way to go. Because flow of the outer filling solution into our sample occurs (and the rate mentioned above, it is best to use a large sample size, and discard the sample once the reading has been made, since it now has some contamination from the filling solution.
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I tried many buffers in achieving my protein in soluble fraction, fortunately I am successful at pH1. Moreover, I have not used any buffer for pH1: its just milliq adjusted to pH1 using conc HCL. My question is: will I be able to do further studies on this protein with affecting its solubility? Now, it is in the state of impure fraction. My proteins pI is 5.78. So, which purification method is suggested?
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Dear Venkat,
The HCl could serve as an "buffer" you equilibrate Superdex column, thus size-exclusion in this weird situation is the first hit I'm finding. Did it many times with HCl, seems to work for proteins like low pH. Anyway I'm afraid your protein could be slightly aggregated, just make sure before loading on the column you spin it down at highest G possible.
Keep fingers cross - Jan
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I purified some proteins by E.coli. Proteins conjugated with 6x-His, I purified with Ni-NTA (qiagen) and use buffer which is written in the qiagen expressionist.
In the protocol, qiagen buffer pH was pH=8.0
I have a question in this step. Some researchers use various pH buffer. PI value of protein is related with protein purification?
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Hi! The answer is YES! To purify the protein of your interest you should always use a buffer with a pH that will make your protein "happy" which usually will be a pH that is not very close to the pI of your protein, since when the pH=pI the protein could aggregate and misbehave. Usually I would use something around 7.5 just to be close to the physiological conditions. If using a His-tag you should also take into account that the buffer's pH should be over 6.5 because that's the pKa of histidine, below this pH binding to nickel is weaker and, as Barbara said, it can be used as a method to elute your protein.
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In many instances a small amount (5-30 ML.) of blood from the external surface of body is let out. In the process of homeostasis, some chemical parameters might change. I wish to know- what are the changes in the biochemistry of blood that take place eg. pH and after how much time does the compensatory mechanism stop?
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Small amount like 5-30 ml don't have significant role in changing any parameter within human body . 
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For example if a pH increases, the conductivity will increase, too.
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Relationships exist, but not one single relatiosnhip. Conductivity is related to ionic mobility, which is higher if the ion is smaller. For example, the highest conductivity is given by H3O+. So the lower the pH, the higher the conductivity. But when pH increases above 7, this is often due to the addition of NaOH used as base. The conductivity of Na+ is high but not as much as that of H3O+. Therefore, the conductivity also increases when the pH increases, but slower. And there is a conductivity minimum at neutral pH. This is the reason why pH titration can be done by conductimetry.
Alain
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A colleage of mine says it is OK to put HEPES-buffered media in the CO2-incubator. I have serious doubts about this because I think the pH might drop. Does anyone have any experience with this?
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HEPES, MOPS and DIPSO are buffers which are to be used out of the presence of CO2, you'll have to select the buffer with the pKa as close the the internal pH(i) of the cells you want to culture. If you put a HEPES buffer solution in a CO2 atmosphere yourmedium will become extremely acid. Cell culture media contain in general 2.1 g/l Bicarbonate to have a pH between 7.25 and 7.45 you will have to work with CO2 between 8 and 4.5 % . If you want to combine Hepes and Bicarnonate then you must work at very low levels of CO2 . Culturing cell in the presence of Hepes is subject to the generation of free radicals which are very deleterious for cell cultures....if you want to learn more about you can join the webinars ( on line seminars ) I organize go to www.quartec or contact me.
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Does anyone know what is the best buffer to keep on the pH on a medium (complete and KH) with Nigericin and Monensin to permeabilize our fibroblasts and detect through FITC-dextran their intralysosomal pH by flow cytometry? We need keep constant pH to realize our calibration line.
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Dear Maria,
It might be not easy to find a short and 100% correct answer to your interesting but complex question.
Perhaps if someone works in this your field he/she will have an reliable opinion and perhaps can / will tell you his or her “optimum buffer system”.
Until there will be a sufficient, valuable and reliable reply by a colleague involved in cell culture experiments of this type I only honestly can guess that it might be a good idea to go through the references I posted below (which I will not comment on here and only provide the URLS which either end up with a pdf – free access- or at least at an abstract page, if the article is available only by PPV = pay per view)
Hopefully you will find – at least rudimentary - an answer or solution for your complex experimental setup,
with my best regards and wishes, Wolfgang
References:
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For bicarbonate/CO2 buffered (HEPES free) DMEM media being stored in the fridge, the immediate CO2 environment is just atmospheric CO2 concentrations (i.e. low). Because of this, the bicarbonate should pick up H+, form carbonic acid, dissociate into H2O + CO2 and release CO2 into the air in the bottle.
This results in the media becoming more alkaline over time, but would it not also result in a reduction in the moles of bicarbonate present in the media? So over time, the concentration of bicarbonate in the media would decrease?
Would this then have the effect of reducing the overall buffering capacity of the media over time?
Based on this, if you then used aged media in cell culture at 5% CO2, would aged media acidify more under these elevated CO2 conditions than media that had been made up fresh, having lost some of its buffering capacity? (All else held constant.)
So could the media become more acidic over time?
I have done the same experiment several times and it seems like the pH of the media (even when in the incubator) was changing over time. It would make more sense with my results if it was becoming more acidic. Could the mechanism described above explain this phenomenon?
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Hello Kathryn, I regularly use carbonate buffers in the lab and can confirm that they become a lot more alkaline over time. I often observe a very significant pH change from 8.0 to 8.5/9.0 within a week or so. I never tried it, but base on these numbers it should be possible to estimate how much of the carbonate evaporates as CO2. Regarding acidification by the absorption of CO2 from the air, I have noticed that double-distilled water quickly acidifies in the lab. However, pure water has no buffering capacity, so I don't expect cultures that are grown in 5% CO2 will change in pH dramatically.
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There are now several open ocean time series stations but it is not so for coastal zones.Most of the coastal records I know of are of relatively low precision or are very short.
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It's start from January 1985 for some other sations
What are the factors responsible for high pH of fly ash?
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I am wondering about the factors for high pH of fly ash.
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Ca- & Mg- carbonate; High concentration of Al etc. That is why, in a weathered fly ash pH becomes neutral to slightly acidic due to leaching of ca & Ma ions, Na & K etc.
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I have a 10mg/ml concentration CuCl2.2H2O solution and this solution's pH is 4.0. I want this solution's pH to be 8.0. I tried 1N NaOH and KOH but something were precipitated and I do not want precipitate.
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Probably, you have to add a chelating agent as EDTA to avoid Cu(OH)2 precipitation, other option could be the use of NH4OH solution to increase the pH, but in solution you will have Cu-NH3 complexes. The problem is the possible interferences of NH3 or chelating agent in the use of this solution.
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In want to know if bacteriophage can survive in higly acidic medium.
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Indeed, phages are able to survive at low pHs, a clear evidence is bacteriophages of lactic bacteria. We have in our lab, bacteria that can grow at pH 0.5 !!!! I am almost sure that they have specific phages able to infect those bacteria. From my own experience, E.coli phages (Coliphages) can survive for a while at pH 3.5-4.0...
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What may be the difference in the pH of distilled water and deionized water? Does deionized water have a greater pH value than distilled water?
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Deionizing systems use a mixture of cation and anion exchange resins (usually in a mixed bed). These resins exchange cations and anions in the source water for H+ and OH-, respectively. The H+ and OH- combine to form H2O, leaving only the residual H+ and OH- produced by autodissociation (autoprotolysis), H2O = H+ + OH-; the equilibrium constant of this reaction = 1 x 10^-14 at 25 °C. So the pH of deionized (DI) water is close to 7 **at delivery** and the electrolytic conductivity is about 0.055 µS/cm (corresponds to resistivity ~18 MΩ cm, hence the - technically incorrect, as the units are incorrect - term "18 megohm" water). However, this is true only if the DI water **has not** been in contact with atmospheric CO2. If it is in equilibrium with atmospheric CO2, the conductivity is on the order of 1 µS/cm (resistivity ~1 MΩ cm) and the pH is ~5,6 , both owing to dissociation of the dissolved CO2 to H+ and HCO3-. DI (or any other CO2-free-) water avidly takes up atmospheric CO2 and rapidly approaches the equilibrated values of pH and conductivity. For this reason, conductivity sensors in DI systems are located immediately following the last resin bed (column) and the water is continuously circulated, so that the conductivity value is obtained before the water has a chance to take up any CO2.
Distillation relies on phase separation to eliminate the dissolved ions (which remain in the pot). However, the steam is in contact with the atmosphere, and distilled water generally has electrolytic conductivity and pH values simliar to those of DI water that has equilibrated with the atmosphere (i.e., pH 5.6 and conductivity 1 µS/cm). Distillation systems can only remove CO2 if elaborate measures are taken to avoid contact with the atmosphere (e.g., flushing with pure N2 and blanketing the product H2O with N2).
DI systems do not remove molecular species (e.g. sugar, most other organics) from the product water. However, many commercial systems include an activated charcoal (or similar) column that removes many organics. Distillation will remove nonvolatile molecular species, but not volatile ones (they distill over with the steam).
Note that DI systems do not remove dissolved O2, as it is a molecular species.
The same dissociation reactions occur in both distilled and DI water. DI resins can "bleed" organics, although many of these will be taken up by the activated charcoal.
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During an experiment by increasing salinity levels in calcareous soil, I faced PH reduction, but i do not know what the reason for it might be.
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I guess that base saturation is close to 100% in Ali's soil and if pH really dropped from 8 to 7.6 it seems unlikely to me that other buffer mechanisms than carbonates are involved. By using NaCl solution Ali exchanged Ca (and likely Mg) by Na, which should not alter pH, since NaCl and CaCl2 (MgCl2) are neutral salts.
But maybe the observed drop in pH is an effect of high Na concentrations on the pH electrode? I am aware that typically this Na-effect occurs at higher pH values, but anyway I would recommend to check this, for example by adding NaCl to the pH calibration buffers. Just to make sure it is not an electrode problem.
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I was following a discussion on how lower pH (acidification) causes demineralization of tooth enamel, increasing risk for caries. This ties together with Bardow, A. et al (2000) - Archives of Oral Biology, where they found that an unstimulated low salivary flow rate was the best variable for predicting demineralization (bicarbonate, calcium, phosphate).
Therefore, low pH and low salivary flow -> demineralization -> leading to increased caries risk. 
So what is causing the change in pH and the change in salivary flow?
I have been looking if stress, critical illness, hospitalization may affect the salivary pH. And in turn, this would increase the bacterial colonization and microorganisms that could lead to a hospital acquired aspiration pneumonia. There is a lot of info out there on oral flora changing in critically ill and oral flora associated with ventilator acquired pneumonia, but I want to know more about how and when the pH is affected. Is a change in pH the first causal factor that gets the ball rolling?
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Your question is difficult to answer because it raises at lot more questions. First of all. Measuring salivary pH is a critical matter. It should be done within the oral cavity, as it changes under experimental conditions outside the oral cavity. Secondly salivary pH varies consideably is is dependent from a lot of different factors such as CO2, bicarbonate, protein concentration and last not least from the physiological contition of the individdum (see. also Naumova et a. Sci Rep. 4:4884). Bacterial colonization and distribution in the oral cavity is not equal. It is different in different niches. Most bacteria are found on the tongue surface. Very little are fount on the mouth floor. We are just about to study the physiological differences of the bacterial colonization in different areas of the oral cavity.