updates cause I left you hanging

So after the scare last week when the electricity went out while all of my DNA was sitting in a gel, all was well. One sample didn't work very well. But my ridiculous streak of good luck with these samples continued-the sample that didn't work was one that I still had DNA left and it worked when I repeated the proceedure. So now I have 50-75% of my major lab work successfully completed (the range is because we're trying to get approval to run more samples). All the hard work figuring out what the data mean hasn't even begun, but at least the stage where a little bad luck or moment of inattention or both can completely ruin a sample is nearly done.



I'm heading back out to sea Tuesday. The turn around between the June cruise and this Aug cruise is crazy short. Too short for me to have worked up much excitement about going out again, but hopefully that will come once we get everything packed and organized.



Our collaborators have contributed to my near-dread of the coming cruise, we've been bending over backwards trying to help this lab get samples (they don't have any money for sampling). But they keep demanding more and more samples-we're taking 3 people this time because just 2 of us last time was too punishing AND we dropped several of our planned samples. The work that they are supposed to do will be interesting (providing that they can get their methods to work) but they are increasingly difficult to deal with. The collaborator lab is headed by a very young investigator who doesn't seem to realize that we aren't working for them-we're working with them. And we don't need them, there is a lab in our building that does the same type of work with slightly older methods (as in proven methods). However, collaborator lab can't get these samples without us. Yet they still thought that my sampling plan was somehow a negotiation position, that they could just come back with their demands and we'd drop some of our samples (again) in favor of theirs. There were some veiled threats that they may walk if they don't get there way. then they reconsidered. We'll see if that turns out to be good-saving the collaboration-or bad-prolonging the pain of a doomed relationship.



I think that we all realize that ultimatums are not a good way to go. Professional ultimatums probably are going to backfire. Professional ultimatums when you have nothing to leverage are just stupid.

It was all going so well...

Lab work has been going really well on the samples that I collected last cruise, starting with getting lots of DNA because we filtered lots of water. I've made fosmid libraries for 8 of the 12 samples that we wanted from that cruise and started the last 4 last night. The I go to school this morning to start the 12+ hours of processing the sample today, only to find that the building has been shut down due to a blown electrical transformer. So, right now all of my precious DNA is sitting in the size selection gel degrading as the lab gets hotter and hotter. No electricity means that our beautiful building with it's huge glass windows and skylights is now a giant greenhouse. AAACCCCCKKKKKK

Very very clean DNA

Alright, lab work is finally going well-based on field work having gone well last month. I didn't sleep much during the cruise but at least I got good samples. Here's a picture of that DNA-each tube has DNA from one of the depths at one station. The DNA is the bright band about 2/3 of the way down the tube.

I love contour plots

Thairo and I went over to the island for the past 2 days. I hung out in a dark room watching presentations from a chunk of people that work on the same transect. It was really interesting and I learned tons. I also found that we really are doing something new, working on the bacteria and archaea. And I have to say, contour plots are cool.
Here's a nice one showing oxygen in the Pacific. The y axis is depth. x is latitude so south on the left, north on the right. Yellow is low oxygen and blue is high oxygen. Pretty graph.

old vs new

Subtitle to this post is: Change, EEEKKKKKK. I'm extracting DNA which is something that I can nearly do while sleeping, but it's an case in point of the issues that I'm having changing from phd lab to postdoc lab. Everyone is very nice and the equipment and lab space is wonderful, but there are lots of things that I've done for a long time that now I'm having to tweak to fit in with new lab group. I'm sure this is something that everyone who changes jobs goes through but I haven't changed jobs for quite a while. Settling in is taking some time and I want to be settled already.

Anyway, back to the DNA. New lab uses a similar protocol for the
extraction but a fancydancy filter system for cleaning and concentrating the DNA. Old lab uses the cheap (but in my mind, just as good if not better) alcohol precipitation. I'm testing out the difference between the two methods using samples from the most recent cruise. We don't have all of the depths for this particular station because the weather got bad before our second cast of the rosette, therefore these are fairly safe samples to test methods on. They wouldn't be used for the big analysis anyway.

Any bets? Fancy filter or cheap alcohol which will yield more and/or cleaner DNA. I'm betting alcohol.