Sunday, October 18, 2009

Oh, the microbial world...

I am taking a class by the great microbiologist, Norm Pace, this semester. Turns out we literally cannot escape all the microbial life around us, regardless of the amount of hand washing we do, and that 10^4 cells/mL of microbes in drinking water is really doing very good as far as sanitation goes. Also, oxygen is actually fairly toxic to life, but this guy, who grew on a plate in the refrigerator, seems to be doing fine with it:

A pretty shiny orange button! That's kanamycin resistant...

I was told that if you get orange stuff, its salmonella. Of course, having Salmonella infect random things in your lab is slightly scary, seeing as how one of our people got sick with Salmonella within the past year. Whoops.

Tuesday, June 16, 2009

Oh, beautiful dirt...

Hooray! I am most pleased to be a part of this little blog and plan to mostly post about beautiful contamination, because my other failures are all pretty boring and routine. Soon I will upload a picture of the mold that started it all, a lovely little orange shiny button, which was growing on an LB-Kan plate of mine.


Behold, something appears to be crystallizing... nearly 30 microns across, you say? Oh but look! They are bicolor... And they are not birefringent. Blasted contaiminating dirt in the crystallography screen getting us all excited for nothing. Ah well.

As you might guess, I am in a protein crystallography lab, and so most of what I will post are from failed adventures in protein expression, purification, and crystallization.

Glossary for the uninitiated:
LB: Luria Burtani broth - a liquid chop full of nutrients for growing up E. coli
Kan: Kanamycin - an antibiotic commonly used in labs to select for the bacteria they want
Plates: It's like making jello out of the LB broth, so that bacteria can grow on the surface
Microns: micrometer, 1/1000,000 of meter, 1/1000 of a millimeter
Birefringent: If something is arrayed in a regular matrix, like in a crystal, and has directionality to it (like is a large blobby protein), it can bend light. Therefore, if youre shining polarized light at it, and look at it through a polarized lens, it will light up when the rest of the light is canceled out by the polarization...
Crystallography: this is when us biochemists try to crystallize things like large biomolecules to make crystals, not unlike salt or rock crystals. The molecules are arranged in giant regular arrays and make crystals, which are actually very fragile. Then we can shine x-rays on them, and from the light patterns that result, determine a three-dimensional structure of the protein. The idea is that if there are LOTS of protein molecules all arranged the same, their composite signal will be MUCH stronger than if there were just one protein bouncing light around.
Protein expression and purification: We enslave bacteria to grow protein for us, and then we kill them and take all their protein through extensive purification processes so that we only have the one kind of protein we want left. Things need to be especially pure for crystallography purposes because we don't want impurities in our crystals. PERFECTION!

Permiscuous Cells

Here are some of the stem cells that I culture (they are stained for Alkaline Phosphatase, which is what happy healthy cells produce). The one on the right is running into the one on the left, which is having a total disaster. Look at that colony dispersing wildly. Complete chaos. What are you supposed to do when your cells don't listen to you?

When Good Science Goes Bad

Hi everyone! This is my second attempt at creating a science blog. My first one was too serious and I got bored with it. This is going to be about science disasters! Everybody in grad school has serious disasters once in a while. My worst disaster happens to be centered around a really old centrifuge...but perhaps in another post. I'll try to share stories about terrible science mistakes and hopefully include some cool art of contamination, etc etc. Share your own, or suggest ideas. Interaction is key here on the interwebs!