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.

-GoCorral

My Master’s Project

All labwork is overseen by the disembodied head of Muppet lab assistant, Beaker.
All labwork is overseen by the disembodied head of Muppet lab assistant, Beaker.

I have begun my Master’s project in earnest and the goal is slightly different than what I’d been doing before.

First, I’ll repeat myself. I’m a biologist and I work with introns in C. elegans. C. elegans is a type of nematode worm that naturally lives in soil or on rotting vegetables. It is also one of the most widely used model organisms for biological research.

Worms! Ew! Gross!
Worms! Ew! Gross!

Introns are unused sections of genes. You’re probably aware that DNA is in our cells and contains the instructions for how an organism functions. The human genome contains around 25,000 genes and those genes are split into two parts, introns and exons.

Exons are the part of that gene that are actually used to produce things in your cells, while introns are spliced out and removed. So why are introns on there at all if they’re removed?

Well it turns out that some introns increase expression of the genes they’re in. My project looks at how placement of those enhancing introns affects expression.

Experiments in plants have shown that an enhancing intron works best when it is placed near the start of a gene. Experiments in C. elegans have suggested that, but no experiment has outright proved it. My project will hopefully do that.

I’m measuring the expression of genes according to how introns affect them, so I get to pick which gene to use. When picking a gene like this scientists often pick what are called reporter genes. The expression of these types of genes is easy to measure, often because they have produce light or fluorescence of some kind. The light tells you whether the gene is on, but also at what level it is turned on based on how bright the cell is.

Previously I was using a reporter gene called GUS. GUS is an enzyme that digests a specially prepared sugar, releasing a blue chemical that was attached to that sugar. The blue chemical is then visible to the naked eye.

There were a number of problems with that experiment though. First, adding the sugar chemical to the worms was a pain, taking about three days to set up and look at. Plus, the blue color was difficult to measure precisely because most of the machines in the lab are set up to measure red or green colors, not blue. Finally, GUS is traditionally a reporter gene for plants, not C. elegans. This could’ve been introducing other problems that we couldn’t easily identify. Thus the use of the GUS reporter gene has been scrapped in favor of another reporter gene.

I’ll be using Green Fluorescent Protein (GFP) as my reporter gene now. GFP is widely used in C. elegans and many other organisms. The protein created by the GFP gene glows green when you shine a red light on it. Very easy to see and measure. None of that three day procedure for GUS. I just pop the worms under the light and take a look.

Why weren’t we using this procedure before if it’s so easy? Two reasons!

Reason number one: C. elegans won’t express GFP without introns in the gene. So does that mean we proceed and hope one intron is enough or do we add the standard amount of introns to get expression? I’ve decided to see what the GFP looks like with the standard introns scientists put in it for C. elegans and without them. I’ll also be testing with an added intron. The whole thing is a little complicated so here’s a diagram to explain.

Here are the constructs I've been creating. The wide parts are exons and the thing parts are introns. The green bands are the GFP which will glow green in the worms. The white bands are a scaffold which allow the worms to express GFP
Here are the constructs I’ve been creating. The wide parts are exons and the thing parts are introns. The green bands are the GFP which will glow green in the worms. The white bands are a scaffold which allow the worms to express GFP.

There are eight different constructs I’m making. They are a combination of three different features that are present or not. Are there introns in the first GFP? Yes or no? The second GFP? And is the Unc54 intron there? This allows us to control for the positional effect the standard introns in C. elegans GFP.

Reason number two: Those eight constructs above? Those aren’t made yet! All the GUS constructs were made when I started the project. I’ve been working on making the new constructs for a few months. It could take a few more months to finish.

So my project is to make those constructs, put them into worms, and then see what the worms look like. As I perform these steps I’ll make more posts about what work I’m doing in lab and why its so cool.

-Mister Ed

Public Persona

EEEEEEE! Gretchen Rubin emailed me! *faints*
EEEEEEE! Gretchen Rubin emailed me! *faints*

Previously I wrote about my reluctance to go public with my real name.

I ended up emailing Gretchen Rubin, the author of The Happiness Project. Reading that book was what gave me the idea to start this blog.

And I got a reply! Hurray!

The emails are in the picture above and I’ll repeat them in the text here. First, the email I initially sent to Gretchen.

“Dear Gretchen,

My wife got me The Happiness Project last year and I’ve enjoyed reading it slowly and applying your advice to my own life. One of your happiness projects was starting a blog. I liked the idea so much that I’ve started my own. The blog is called GoCorral and you can find it at gocorral.wordpress.com if you’re interested. Now that I’ve gotten into a rhythm of sorts with the blog I wanted to ask for a little help from you.

So far I’ve been running my blog and associated sites anonymously. I was worried about unwanted attention in my personal life if my blog ever took off to epic proportions like yours has. By maintaining anonymity I’ve kept the option open of disappearing in the future, but I fear I’m also alienating my audience by doing so. All the serious bloggers I’ve heard of use their real names. I get the feeling that personal identification naturally improves a blog because so much of the content is about the author’s personal life, thoughts, and experiences.

I wanted to get your opinion on using your real name and your family’s names in your writing.  I’m interested in the positives and the negatives. Do you ever feel uncomfortable using your real name instead of a pseudonym? How do your children and your husband feel about it? Have there ever been any real problems associated with having a public persona that you’ve encountered or heard of? What are some of the good things about going public with your name?

I’d appreciate anything you can tell me!

-Mister Ed”
And the reply I got back:
“Terrific!
I use my name online, but don’t use my family members’ names (though I do use those in my books).
I didn’t really ponder this, because I wanted my work to be associated with my name. Everything I write is with the expectation that it’s public.
I’ve never experienced a negative with it, nor has my family.
Good luck!”
And then my thank you note:
“Gretchen,

Wow! Thanks for your reply! I think I will go public with my name then. I appreciate your help.
-Isaac Shaker (Mister Ed)”
And now I am public on my blog!
For most of the people reading the blog this will mean almost nothing. My family and friends already know I’m writing this and access my blog through Facebook or Google+.
For everyone else? Still almost nothing. I’m still the same person and I’ll still write the same stuff. I’ll even keep writing Mister Ed at the end of each post.
The About Me section of the site is pretty much the only thing that’ll change.
That’s pretty much it. I’m no longer worried about any negative consequences. I’ve looked for them and they just don’t seem to be there. Steven King’s Misery really is as fictional as it seems.
-Mister Ed

Last Day of Work

No More Work Keys
My keychain has four fewer keys on it now.

On Friday I had my last day of work at my old job in the rice lab.

It was a bit anticlimactic to leave because a lot of the people I wanted to say goodbye to weren’t there on my last day.

Still, my two supervisors were there. We went out for coffee and talked about my future plans.

It was kind of nice to talk to them as friends. I heard about their families and what their lives are like. I’d like to be in their place in a few years, minus the Chinese immigrant status.

I packed up all my stuff from my job: computer, lab pants, old cords, and old notebook.

I had to leave behind a few things as well like my keys, my new notebook, and a few data sheets that are probably irrelevant at this point.

The last few weeks at work have been a little boring.

I was originally hired to sequence the genome of rice leaves, but that project got passed on to other people.

I was then put on a project of organizing the huge database of rice seeds in the storage room (probably over 10,000 varieties of rice all thrown into cardboard boxes).

I finished that project in June.

For the past two months I’ve been keeping an eye on the rice plants in the greenhouse and doing regular maintenance stuff in the lab.

It wasn’t anything fancy, but it wasn’t particularly challenging either.

I started at my Master’s program today and I felt a lot better almost the instant I stepped on campus. I get to learn things again! I’m so excited!

While it was sad to leave my old job and even sadder that I left it with a whisper instead of a party, I’m psyched for what’s coming in the future!

-Mister Ed

Solar Freaking Roadways

My wife showed me this cool new technology called Solar Roadways this morning.

She showed me with a Youtube video you can look at here.

The technology is a new type of pavement made out of solar panels.

The video describes it quite well in a funny way (Solar Freaking Roadways!).

Solar panels cover the road. On top of the panels are a few LED lights and then a strong shield of glass.

The glass can support up to 250,000 pound (113,000kg) trucks. The inventor of Solar Roadways, Scott Brusaw, chose that researched weight because the transportation of oil refinery equipment is done at weights of around 230,000 pounds (104,000kg).

The LEDs are used to create lane lines or for other necessary road paint (Pedestrian Xing, Slow Down, etc.).

If every paved surface in the USA were covered with these panels they would generate three times the current energy consumption of the USA.

Other energy sources would still be needed as solar panels don’t operate at night.

The panels can also heat themselves to melt snow and prevent dangerous driving conditions in colder states.

Two underground channels are planned to run along side the Roadway. One will hold water runoff. The other will hold electrical wires.

The wires carry the electricity off the solar panels to consumers.

The channel could also hold telephone lines, fiberoptic internet cables, etc. By placing them underground, storms are less likely to cause outages.

Mr. Brusaw, pictured above in a tractor on the prototype driveway of Solar Roadways, seemed particularly proud of the traction of Solar Roadways.

Some people worry that cars won’t be able to stop on glass, but Solar Roadways glass panels are textured in a way that cars going 80mph (130kph) on a wet panel could stop just as fast as on wet asphalt.

My worry upon seeing the giant textured panels was that bikes would not be able to go on them.

Fortunately, Mr. Brusaw has an answer for that too. Another variety of the panels has a smoother texture that bikes can ride over comfortably.

The smoother texture allows cars to stop in times similar to wet asphalt at speeds of only 40mph (65kph) though. You can’t have everything.

It would be easy enough to build a bike lane out of the smoother panels next to a road made of the textured panels to accommodate both types of vehicles.

If you’re interested in learning more about Solar Roadways you can check out their website or fund them using Indiegogo. The fundraiser is until June 20th 2014.

-Mister Ed