James and the Giant Corn Genetics: Studying the Source Code of Nature

Has anyone been trying to comment and instead getting a message that they appear to be a spam bot? (I’ve turned off all my SPAM defenses temporarily so you should be able to get through to tell me now.) I was setting up another blog and it appears the plug-in I was using was throwing out a lot of legitimate comments.

I should have waited before I posted the previous xkcd, while fun, it can not compare to the total awesomeness that is the cuttlefish!

Unfortunately for me I didn’t start messing with Perl until four years later (my junior year of college).

Now I have a sleeping bag which is wonderfully warm, and which I’ve owned since elementary school. Between my amazing sleeping bag, my pre-existing comforter, my sweatpants over pajama pants, plaid shirt over t-shirt, stocking cap over Iowa State Agronomy Club hat, and my delightfully warm corn socks, I may look ridiculous but I anticipate I’ll get a relaxing night’s sleep.

…which is good since tomorrow I have an oral exam over everything we’ve covered this semester, and graduate students are expected to receive A’s…

It’s currently 43 degrees and raining in Berkeley, CA. This would not be a problem except for two errors on my part. Firstly, my apartment is, so far as we can tell, unheated. Secondly, seduced by the image of California in popular culture and those still fantastical palm trees, I moved out here without a single item from the large collection of polar fleece clothing I’d accumulated in my life up to that point.

I’ve been at work since 8:20 am PST on Thursday the 11th. New entries will be inserted at the top of the post. (Expect most of this to be boring lab stuff.)

1:34 Home safe and sound from my 28 hour work day. Now I just want to do some laundry, eat a frozen pizza and catch up on the daily show.

8:10 I managed to get through most of the night without resorting to caffeine but now I’m leaning heavily on my mints to make it through the finals stretch of daytime. In four more hours my sampling will be complete.

12:11 AM – Officially Friday. My routine is simple. Get liquid nitrogen. Harvest tissue in the dark using green flashlight. Store tissue in -80 C freezer. Watch a couple of stargate episodes. Repeat. 

9:21 – Check out my phylogenetic tree!

The red genes are arabidopsis, the green is corn, the yellow is rice, and the black ones are the new genes I’ve been finding in brachy tonight. These genes are involved in regulating flowering and, while they were first discovered in arabidopsis, as you can see the story is a LOT more complicated in grasses like corn and rice.

8:02 – Just collected my second set of samples. I’m now four hours and three tasty and nutritious honey and peanut butter sandwiches into the sampling run.

6:45 – I’m alone in the lab now. Working on building a gene tree so I’ll have something graphical to show for all my work today. The qPCR machine is busy until 7:30, but I’m considering putting a second set of reactions in. After all, I’ve got all night.

4:11 – Well the qPCR results show no circadian changes in gene expression. The numbers are so similar for all three genes that I think the reactions might now have worked after all. I’ve spent most of the past four hours locating brachy genes. Sequence analysis, especially when you can listen to music, is one of the most fun/relaxing things I’ve ever gotten paid to do. Too bad one of these days a budding young computation biologist will write a program that does a better job of predicting genes than a human sitting at a keyboard. It’s already close.

12:33 – Well the qPCR reaction at least produced data, which puts me ahead of the other rotation student who used it this week. Whether it’s good data remains to be seen, analysis is going to take a while. In case anyone is interested by what I meant by annotating brachy genes, here’s a screenshot.

The brachypodium genome is currently in draft format, which means, among other things, there are no good gene models. Since we need to look at genes from brachy to compare to my work in maize I need to find those genes, and pull them out of the genomic sequence. The top orange bars show computationally predicted genes, the middle grey ones are areas that look sort of like known genes in other species, and the bottom colored areas show BLAST hits that I found using by searching the whole brachy genome with for sequences that look like the genes I’m studying.

10:38 – Ok, qPCR reaction just went in. I’ll find out if it worked in about two hours. Now time to build some brachy gene models…

9:13 – I’ve been at work just under an hour which I’ve spent setting up for a qPCR reaction, and moving the BLAST server from it’s temporary home under a desk to a location where it won’t constantly be in the way and getting kicked. I’m somewhat anxious as I contemplate the hours that lie between me and the end of work tomorrow afternoon, but I’ve pulled all nighters before (and usually for far worse reasons). When I woke up this morning I realized I’d forgotten that I’d need food between now and tomorrow, but fortunately I was able to remedy that situation:

Peanutbutter and honey sandwiches. The poor grad student’s powerbar. Ok, back to work now.

Visited a delicious burger restaurant in Berkeley today after class. They server beef, veggie, chicken and turkey burgers… to which my reaction was “No pork?” Seriously though it was very tasty, I was pleasant surprised.

Life is still really busy. I went in both days of this weekend to keep running reactions. I’ve also set up a local blast server for the lab.* I got to build the computer from left over parts from two computers that another grad student had inherited when a friend upgraded his LAN gaming set up. So the new lab blast server lives in a giant gaming case, with clear plastic sides and glowing blue lights.

After mixing and matching pieces it was just a matter of installing Ubuntu, setting up the webserver and blast server programs, and installing databases like the brachypodium and maize genomes. I’ve been accumulating this skill set for two and a half years, since Monty first showed me how to build a desktop computer and I got a summer job that got be started using the command line a perl scripts. It was really fun to put all the pieces together and go from two broken computers and an internet connection to a functioning piece of equipment of measurable benefit for the whole lab.

*Some context, BLAST is a program used to search for other genes related to the one you’re interested in, which can help apply knowledge gained from studying one organism to others. Along with PCR probably the most universal mainstays of a modern molecular biology lab.

The BBC has announced they’ll be releasing a new version of Day of the Triffids next year!

“Set in 2011, millions of people are blinded when they observe a meteor shower, leading to a breakdown in civilisation. The Triffids, an oil-producing plant crop, escape captivity and begin to breed rapidly and attack people. It is up to Dr Bill Masen to fight against them to prevent the end of humankind.”

Flesh eating biofuel plants, what’s not to enjoy? Hopeful it’ll be Dr. Bill Masen PhD. I’m not sure how having an MD would be relevant to a fight against murderous plants, but you never know.

After work today I moved this blog to a new website. It was actually surprisingly complicated to copy the SQL database over, but now everything seems to be working successfully. Drop a comment if you notice any broken features on the site.

These guys think there’s a 75% chance that the author of this blog (me) is male.