Rice Genomics

My lab bench at the rice genetics lab I work in.
My lab bench at the rice genetics lab I work in.

One of my jobs is working with introns in C. elegans and the other is working on rice genetics.

Above is a picture of my lab bench in the rice genetics lab where I do most of my work.

The rice are kept in three separate greenhouses spread around the western fringes of the college campus. The furthest greenhouse is a little over a mile from the lab.

The technology and staff at the greenhouse complex essentially takes care of the rice for me. They’re checked on once a week by someone in the lab.

About once a month we collect leaves from the rice plants.

I grind the leaves up and extract the DNA from them.

The DNA then gets sent to the Joint Genome Institute to be sequenced.

Sequencing is when the genetic code is read in its entirety to see each letter within it.

The entirety of an organism’s genetic code is called the organism’s genome.

JGI reads the rice genome, then uploads it to the internet for researchers around the world to use.

The rice genome has already been sequenced, so why are we doing it again?

The first time the rice genome was sequenced there were a lot of errors in it. Rereading the sequence now will hopefully rectify those errors.

There’s another project going on at the same time as that though.

I am not isolating DNA from “vanilla” rice, but over 2500 different mutant varieties that were created in my lab.

The sequencing will find a bunch of little errors within the rice genome.

Researchers who are interested in specific errors can then ask my lab to send them some rice seed of that particular mutant variety.

Those researchers get what they want easily and my lab gets a little bit of money for selling the seed.

The mutant varieties don’t “taint” the overall sequence because they only contain errors in a few places. The consensus sequence between them will remain the same.

I’m just a little part in that sequencing project that’s taken almost a decade at this point. I won’t be the one to finish it either, but I’m moving the ball closer to the finish line!

-Mister Ed

Good and Bad

I had a strange amount of ups and downs today.

I started off by trying to install some child locks on our bathroom cabinets. Our new cat has been trying to sneak in and we think it’d be best if she doesn’t have access to all the toilet paper at once or all the chemicals that could hurt her under the sink.

Child locks come in two parts, the part you have to push to open it and the part the pushy part inserts into to keep the door locks. I’d glued the holdy part onto the cabinets on Monday.

I checked the glue today and was a bit rough in handling one of the holdy parts. It popped off in my hand. I sighed and reglued it on.

I glued on the pushy part and found it was very difficult to align it correctly with the holdy part. Fearing that I did it wrong, I only glued in one of the pushy parts today to see how it looks tomorrow.

After that frustration I went out to fix the flat in my bike. The flat had happened on Friday and I got new tubes on Monday.

I put the first tube in and it immediately popped. Figuring they can occasionally be duds, I pulled it out and put a second one in. It seemed fine and I biked off to work. It popped just before I got onto campus. I sighed and walked the rest of the way to my job.

I figured I was too pissed off to immediately get to work at lab, so I decided to make a quick appointment with an optometrist in town.

The optometrist informed me that I needed to know the exact amount of coverage my health insurance gave me for vision before I could get an appointment. On to calling the health insurance company then!

I called my health insurance and was put on hold (typical). I waited and zoned out not listening to the recorded message. Then the message said, “Goodbye,” and it hung up. I have no clue what led up to it saying goodbye, but I’m pretty sure it wasn’t the usual hold music.

I called again and avoided the previous menu options that had resulted in the robot disconnecting me. I ended up waiting an hour on hold before I got to talk to a human person.

The whole time it faked me out by switching up which robot voices were telling me about the health insurance website. Each time the voice changed I thought I had finally reached a real person only to have my hopes destroyed.

I eventually got the health insurance and the optometrist appointment set up.

After that my day improved. I stained some worms to see if they turn blue over the next two days. I checked some injected worms to see if the DNA I injected into them had successfully integrated into their genomes. IT HAD! WOOHOO!

I called my wife to come pick up my bike during the afternoon so I wouldn’t have to walk it home. She came by and put it in the car and reminded me why I love her.

At the end of the day my wife came home with two cupcakes for me.

A good day in the end despite the rocky start! 🙂

-Mister Ed