Thesis Proposal and Homework

Some of you may be asking, “Where, oh where, has GoCorral gone? Where is the weekly update of his blog? There hasn’t even been a picture of his toenails to tell us he’s still alive!”

Well, I am still alive, I’ve just been rather busy with school these last few days.

Among my many responsibilities I have had:
1. A massive final project on homologous genes to the C. elegans myosin gene, unc-54, that is rapidly approaching 50 pages in length.
2. A final paper on intron retention being the first sign of speciation.
3. Scheduling and preparing my thesis proposal presentation.
4. Grading essays for the basic biology class I am teaching this semester.
5. All the usual stuff I have to do.

I’m keeping a good handle on #1 and #5. #4 is a slow truck that keeps on going.

Due to all the other stuff I’ve been doing #2 did not turn out as good as I would’ve liked. I loved the thesis of that paper, but I wish I’d used more time to find additional supporting evidence and described the supporting evidence in a better fashion.

#3 is the most exciting one! My thesis proposal presentation happened on Friday and was probably the most important moment in my career up to this point.

I got super nervous before giving the presentation and made a few mistakes in the preparation and delivery, but it still went quite well.

Every presentation should have at least one picture of a confused panda.
Every presentation should have at least one picture of a confused panda.

I passed the proposal which means I can continue on with my project! Woohoo! I do have to update my abstract to reflect my definite research goals which were outlined in the meeting.

That’s what I’ve been up to. There’s still more to do! I predict I’ll be done with most of it by the end of next week. After that, regular blog updates will resume.



Abandoned Lab

Two shelves I filled up with pipette tips.
Two shelves I filled up with pipette tips.

Last week the rice research lab I work in was all but abandoned due to a local conference on plant pathogens.

I didn’t go to the conference as I’ll soon be changing to working entirely on C. elegans.

Spending the lab’s money on me learning more about a topic that I probably won’t encounter again would’ve made me feel guilty.

I was left in the lab with a few people who stayed behind or came back early.

I finished all my usual duties in the lab like taking care of plants and setting up stuff for next week, but I still had a lot of extra time before the end of the day.

I cleaned up the lab a bit and… FILLED TIPS.

I filled two entire shelves with boxes of tips.

You might be wondering what are tips and what are they used for?

Biological research often requires very small amounts of liquid to be measured.

For comparison, in the science we usually measure volumes of liquids in liters.

Most people are familiar with liters in the form of those two liter soda bottles that are used for parties.

A milliliter is equal to one thousandth of a liter, or two thousandths of a soda bottle.

A milliliter is still rather big though. It’s about the size of the last joint on your pinky finger.

The research I perform measures liquids in microliters, which are one thousandth of a milliliter (or two millionths of a soda bottle).

A microliter is about as big as a period.

So how is something that small measured?

With a pipette!

A pipette is essentially a mechanical suction device, similar to a straw.

A pipette tip is added on to the sharp end of the device you see above.

The button on top is pressed down, expelling a specific volume of air from the pipette.

When the button is released the pipette sucks that volume back up into the pipette tip.

Pretty much the same principle as using a straw to drink a two-liter bottle of soda.

The amount of air expelled from a pipette allows researchers like me to work with extremely small volumes. Some pipettes can even measure volumes as small as a thousandth of a micoliter (Another name for that is a nanoliter).

When working with small volumes like this its even more important to be clean.

Any small contaminant on the pipette tip would be a large contaminant in a mixture of only a few microliters.

So the tips are put into those boxes in the first picture and then autoclaved to sterilize them.

Oh and here’s a closeup of a pipette tip!

-Mister Ed

My Lab Meeting

Here's a picture of one of my PowerPoint slides from today's lab presentation.
Here’s a picture of one of my PowerPoint slides from today’s lab presentation.

I presented the progress on my research at lab meeting today.

I haven’t gotten as far as I wanted to since my last lab meeting, but I did get as far as I expected to.

By the end of the summer I was expecting to have 5 of the 6 constructs successfully injected and integrated into C. elegans strains.

I’ve gotten 4 out of the 6 and the summer isn’t over yet. I’m on track to finish.

Otherwise, I’ve had a problem with the worms not staining like the ones of the person who used to work on this project.

His worms stained extremely dark. There’s so much blue color that the picture of them looks black.

My worms don’t look like that, but we aren’t sure why.

I’m going to tweak some things to try and make my strains look that way.

If the tweaks don’t work… I’ll have to check using a more complicated method to ensure that I injected the worms correctly.

That’s the gist of what I presented at the meeting.

The meeting went pretty well.

Today’s meeting was between my lab and the lab adjacent to us.

Our lab meetings are always joint meetings. The neighboring lab works on similar stuff. Both of us are small labs as well so it makes a lot of sense for us to meet together.

The professor from the other lab always asks the presenter tough questions.

I felt like I fielded everyone of his questions really well.

I felt prepared, I had answers to most of his questions.

I’m going to look for answers to the questions I don’t know in research papers.

I haven’t gotten around to describing more about what I do in lab, which might have made this post a little confusing.

I’ll try and upload a post that goes in more depth for my lab meeting presentation in the future.

That’s all for tonight.

-Mister Ed

Injecting Worms

This is what my computer captures under my microscope when I inject a worm.
This is what my computer captures under my microscope when I inject a worm.

I gave an extra post about one of my jobs. It seems fair to cover the other job as well at some point!

I study introns in C. elegans worms, but how do I get the specific introns in the worms?

I need introns in specific placements in specific genes in order to study them with scientific accuracy.

The gene we are studying is simple. If the worms are put in a solution called X-gluc, they turn blue.

Based on where our enhancing intron is in the worm we expect it to turn more blue if the intron is closer to the start of the gene or less blue if it is near the end.

So I have these genes that I’m putting into the worm. They get in by injecting them like you see in the picture.

The needle of DNA is aimed at the gonad of the worm.

C. elegans worms are hermaphrodites. They contain sperm and eggs and they self-fertilize.

The worms are “male” at first, producing a bunch of sperm.

Later on they produce eggs and then they fertilize their own eggs with the sperm stored in their body.

Since they contain both genitalia the whole area is referred to as the gonad.

I aim my injection at the gonad, hoping that the DNA I’m injecting will get into the fertilized eggs.

Then the injected worm is put on a plate with lots of food and I hope that its babies will have the injected DNA.

But I don’t test for “blueness” immediately.

When a worm is first injected, the DNA is inside its cells, but not necessarily integrated into the cell’s chromosomes. I need the DNA to be a part of the chromosomes.

There are only two genes in the mix of injected DNA that will integrate. One gene is the blue gene, called GUS. The other gene is called unc119.

Unc119 is to “recover” the worms.

The worms I inject lack unc119, which is a normal gene for worms.

In a natural wild-type worm unc119 aids the development of the worm’s neural network. Without it, the worm has poor neural connections and has a lot of trouble even moving around and eating.

So the first way I test a successful injection is by looking to see if the babies of the injected worm are moving around normally or flopping around.

The normally moving ones were successful and now have unc119. They are “recovered” back to their natural wild-type state.

The floppy crippled ones did not have a successful injection. Either I missed the gonad, I didn’t inject enough DNA, or the eggs that got my injection didn’t fully germinate.

There are other markers I use to see if an injection was successful, but I’ll get to those later!

-Mister Ed

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

Worms and Introns


I have two jobs right now. One of them is an internship working on introns.

Introns are part of your genes, but they’re a strange part.

Imagine your genes are like a TV show. There are parts you watch and there are the commercials that you mute or ignore.

When the TV show comes out on DVD or Netflix the commercials are removed.

Genes are split up into watchable parts and commercials too. The watchable parts are called exons and the commercials are called introns.

When DNA makes RNA the introns are removed from the code, just like when a TV show is released on DVD the commercials are removed.

For a while scientists thought that introns did nothing for the genetic code of an organism. Introns were just useless DNA trash.

That changed in the late 1980s when some introns were found to enhance the expression of genes.

Some genes have what are called enhancing introns that increase the expression of that gene. This is called intron mediated enhancement (IME).

If you take an enhancing intron from one gene and put it into another, then the other gene will create more RNA and thus more proteins as well.

So enhancing introns increase expression of a gene, but not much is known about why. The lab I work in is one of the few that studies this process to try and figure out the specifics.

Most intron research right now is done in plants. I’m trying to extend that research to animals by using worms.

The worms I use are called C. elegans. They’re only 1mm long and are commonly used for research projects around the globe.

My lab previously discovered that enhancing introns in plants work best near the beginning of a gene.

My project is to see if the same holds true for C. elegans.

I’ll also be looking at whether an intron that is enhancing in plants is also enhancing when out into a gene in C. elegans.

That’s all for now!

-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