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

December 11, 2008

Liveblogging my marathon workday (Finished)

Filed under: Uncategorized — James @ 10:19 am

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.

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