Bromophenol blue is a dye and a pH indicator. It is yellow below pH 3 and blue above pH 4.6. At pH 3.6 it gives a green-red colour. So I think, what you are seeing is a change in the pH of the solution.

Is the colour of the bromophenol blue changing when you add it to the extract, or after running it on the gel? If the first case is true, then your extract has an acidic pH, and you need to check if this is causing any degradation of the proteins. If the latter case is true, then either the gel itself or the running buffer has an acidic pH, which shouldn't be the case in a standard SDS-PAGE (stacking gel pH 6.8, resolving gel pH 8.8, and running buffer pH 8.3). I don't think you can check the pH of the gel, but you can measure the pH of the running buffer before and after your run.

I have never faced such a phenomenon but while bromophenol blue is an acid base ondicator and is bighly correlatedwith phenol phetalein its color is changed in response to acid base changes of the buffer. When the ph raises rhe color might probably change while the color turns into yellow when the ph decreases. I think you should check the ph of your beffers and make new buffers according to the protocoles. 

Hope you success

Bromophenol blue is a dye and a pH indicator. It is yellow below pH 3 and blue above pH 4.6. At pH 3.6 it gives a green-red colour. So I think, what you are seeing is a change in the pH of the solution.

Is the colour of the bromophenol blue changing when you add it to the extract, or after running it on the gel? If the first case is true, then your extract has an acidic pH, and you need to check if this is causing any degradation of the proteins. If the latter case is true, then either the gel itself or the running buffer has an acidic pH, which shouldn't be the case in a standard SDS-PAGE (stacking gel pH 6.8, resolving gel pH 8.8, and running buffer pH 8.3). I don't think you can check the pH of the gel, but you can measure the pH of the running buffer before and after your run.

If it's changing as the gel runs, then relax: this happens all the time, and I wouldn't worry about it. Shouldn't affect the running of your proteins.

As Naji answered, your buffers may be in the wrong pH. Please check your buffer components for casting resolving- and stacking-gel. They should be at 8,8 and 6,8, respectively.. In our lab the dye never changed the colour while running the gel! In that point I disagree with John (sorry).

When your sample becoming red before you load them on the SDS-page, than you should ad one or two µl of concentrated TRIS to your sample-loading-dye and the sample. This adjust the pH to the right one!

I hope you already got your answer from previous posts. I would also suggest you to check the pH of your loading dye as well as extraction buffer (Buffer you have used to extract/finally dissolve your protein). You can try adjusting the pH of your loading dye with 1M Tris-Cl

I just noticed that there is a dual colour protein gel loading buffer called "ProSieve ProTrack Dual Color Loading Buffer", that gives a violet band along with a blue band. The bands are so close to each other, similar to the picture you have. I have never used it myself but it seems to be beneficial during blotting & the preparation of the protein sample! This seems to be a new product (at least to me), so many researchers may not know about it!

So I would suggest that before you do any tests, just check if this is the gel loading buffer you are using or not. If this is the case, then there is no need to do anything about it because this is what this buffer does!

It could also be that you're using a buffer that has two dyes and they're separating as you run it. A lot of commercial buffers do this.

But anyway, in my experience (and I've run a ton of gels), a slight reddening of the very very front of the dyefront, while the gel is running, is not unusual. And it has no effect on protein separation or subsequent blotting or whatever. I've always assumed it was either a multiple-dye scenario, or down to the charge differences of the ion front as the choride and glycine move through the gel, but either way it's stuff happening way ahead of all but the tiniest proteins (BPB dyefronts tend to run ahead of anything larger than 1-5kDa), and as long as your gel is still running, it's fine.

As everyone else has noted, if you're getting a colour change when you prepare your samples (i.e. before loading) this is more problematic, and you'll need to buffer it back to blue.

the red color could be remnant from the phenol red of ur culture media. wash with pbs 2-3 times before adding ur lysis buffer