THE FIRST DAY IN THE LAB - September 12

We traveled back to Beijing on Sunday, September 11, after visiting the Terra Cotta Soldiers that morning.  We took that evening off (which I used to post the previous text for the blogs) and rest up after four harrowing days of travel.

On Monday, which was actually a holiday - the mid-Autumn Festival - we spent the great bulk of the morning putting together all the solutions that would be used throughout the rest of the extraction procedures.  I should say I'm using the word "we" loosely, as I didn't do much but catch up on data entry while "they" put together the solutions.

But, for those who are interested, here is a list of a few things "they" made up on Monday morning:

DEPC Water (actually made up before we left)

1 M Tris (pH 8) (100 ml) FW: 121.14
0.5 M EDTA (pH 8) (100 ml)
4 M NaCl (200 ml) FW: 58.44
CTAB for RNA (200ml) (need ~ 100 ml)

Just to name a few.  How much fun is THAT!!  It's a lot of fun, that's how much!
After all the solutions were made, we went out to lunch while the autoclave sterilized everything (for about 2 hours).

When we got back, we could finally get down to business.  The hardest part was grinding the samples.  For those of you who have never tried to grind small pieces of wood into a fine powder using liquid nitrogen and a mortar and pestle, well, my friend, you just haven't lived!  Actually, you can easily simulate the process by putting on leather gloves, and grinding a short piece of cinder block into concrete for about 15 minutes, and putting a couple of bags of ice around you.  Oh, but only use one arm for the grinding.  Repeat that six times.  How much fun is THAT!  Too much fun, right there.

After the samples were ground, it was mostly just a lot of waiting.  For those who have never done any sort of extractions, the majority of it involves a lot of pipetting, pouring, loading of centrifuges, and waiting.  The DNA extraction protocol actually involves a total of 4 hours of waiting (if you follow the entire protocol).  So, by the time we got all of our samples ground, it was about 3pm.  We were in the lab until about 7:30 that night.

We got through six of our 18 samples on the first day, because those were the ones we were going to use for DNA extraction.  Then, both those and the rest were going to be for RNA extraction.  The RNA folks finished their protocol, and Katie and I stopped our DNA protocol at the iso-propanol precipitation step, where the solutions could be left to sit overnight at -20C (they should be left for at least 1 hour).

All our samples, floating piece-fully (ha!) in RNALater.  The stem samples are on the left.  The leaf samples on the right were only taken from the healthy trees.  We would grind those on Wednesday to use as backups for DNA extractions from the stem tissue.

Andy pours some things and lets some stuff mix up and junk.

Two finches, the labs mascots.  They were actually quite nice to have in the lab.  At first, I thought it was something electronic, but they were very real.  And cute!

Kathleen and Amelia label microcentrifuge tubes.  The DNA extractions alone take 42 tubes for he first six samples.  Having them pre-labeled helps the process go much more smoothly.  I believe Amelia is doing the DNA tubes and Kathleen is prepping the ones for RNA.

Bill and Andy work on grinding samples.  It's definitely the most difficult part of the process.  The dewer of liquid nitrogen is in the middle.

Frozen lab bench, frozen mortar, and frozen stem powder.  This is the product after the stem grinding process.  A small amount was used for RNA extractions, another small bit for the DNA extractions, and then a final small amount for some metabolomics that Amelia was working on.  We only used about 3/4 of the powder that was made.