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.
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.
I attended my wife’s graduation ceremony or her completion of her Masters of Arts in Education.
Her mom, dad, and grandma all came to Davis to join in the celebration.
And during the speech given by the university chancellor, the fire alarm went off!
We all had to slowly file out of the building while my mother-in-law helped my grandmother-in-law down the stairs.
We caught up to my wife, her friend, and her friend’s family and hung out with them, taking some “mid-graduation” photos.
After heading back inside we found the seats had shuffled around a little bit and another family was sitting where we’d been sitting before.
I got to sit next to a very well-dressed woman who quietly disapproved of me coming to a graduation ceremony in the same clothes I’d worn to work. Tight scheduling had forced me to do that, but she didn’t know that. Just a little frown out of her though. It was actually kind of funny.
My wife had decorated her graduation hat and we got to see her march on stage and get her apron draped over her or whatever it is.
There were a few more speeches besides the chancellor’s as well. All the usual stuff about moving forward and making the world a better place. The recipient of the faculty award had some interesting stuff to say about the necessity of being bilingual in California that I liked, but everything else was fairly typical for a graduation ceremony for teachers.
After leaving they gave us one of those little cards if you ever want to grab the official photographer’s photos of the events (Never done it. Way too expensive when we have our own photos).
After the ceremony we went back to our house for pizza and cake. My wife loved the cake that I picked out!
I know! Field trips in a Master’s of Science program? How ridiculous!
It was awesome. We went to the Institute of Regenerative Cures in Sacramento.
I arrived early and waited out front with some classmates. Our tour guide arrived and we waited out front a little longer til everyone showed up.
While waiting the tour guide, who had designed the building we were about to go into, told us about his hobby, early television history!
After the primer on early television we entered the building and got a tour of one of the best facilities for practicing biology in existence right now.
The building itself was actually built a long time ago for the California state fair. It was the “women’s building.”
The brick exterior and columnaic entrance have stayed the same since the building was constructed to maintain the historical site. The interior has been heavily modified.
The building had no roof back in the day and was just an enclosure for a bunch of different events that you usually see at state fairs.
The building was sold to the University of California system. They slapped a roof on it, and used it to store records.
Our tour guide said that he was called in to turn it into a biology facility later on. Half the building is used for bio research while the other half is rented out to other companies.
The researchers in the Institute are working on a number of things. They researched a treatment for the “bubble boy disease” there. They’re working on using umbilical cords to create bone marrow for transplants, using Tal proteins to treat Huntington’s, creating HIV resistant cells, and helping people who can’t swallow to swallow are just a few of the things they work on there.
The tour guide also showed us the section that he was most proud of as he had designed it. A set of rooms for making the actual drugs and proteins to export to hospitals. Making the drugs requires extremely sterile technique to prevent giving someone who is already sick something that will make them worse. The rooms are designed to be extremely sterile.
To enter the rooms you pass through an airlock where you are required to cover every inch of your body in a disposable gown.
The airlock goes to a hallway with access to three separate clean rooms.
There is “negative pressure” in the rooms. That means that air is constantly entering the room from the top and going out the bottom. This is so that if any cells that are worked with in the rooms get into the air, they will be redirected to teh ground and sucked out through a grate in the wall instead of ending up in someone’s medicine.
The air is cleaned excessively to about 3000 times more clean than average air before entering the facility.
There is a lot of electrical equipment in the rooms that will require replacing eventually. To prevent electricians from having to gown up just to replace a lightbulb, all the eletricals are accessible from panels on the second story of the building.
It was pretty cool for a scientist like me to see the best possible place to do research in. The tour guide mentioned that he does tours of the interior of the super clean rooms for smaller groups. I might take him up on that at a later time!
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.
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.
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.
I wanted to write about two things today, but I’ve only got space for one.
My wife had her graduation ceremony for getting her California teaching credential yesterday.
But today the World Cup started!
I decided I’d write about my wife because I am married to her not to soccer.
My wife’s teaching program has several different groups within it.
There are the doctoral students with their PhDs and EdDs.
There are a few people who got their credentials already and are coming back to school to get a Master’s.
Most of the people are getting a Master’s and a teaching credential within the same program.
The program takes two years to complete. The first year ends with a teaching credential, the second ends with a Master’s of Arts in education.
The teaching credential allows you to teach children in California. The MA gives you a pay raise.
The program thus has two groups, one getting their credentials at the graduation ceremony and one getting their MAs.
Those two groups are split once again based on whether they are studying to teach multiple subjects in elementary school or single subjects in middle school or high school.
My wife got her credential in multiple subjects and will be teaching children on her own next year at a elementary school a few blocks from our apartment.
She said that despite the graduation ceremony she doesn’t feel “graduated” yet because she still has another year of school left to get her Master’s (Saturday school as she will now be teaching fulltime).
Her family came into town for the ceremony. We sat through the speeches and clapped when she went up on stage to have her honor cord placed on her shoulders.
Afterwards we went out to eat at a great Mexican restaurant and had to wait super long because everyone else had the same idea.
My grandma-in-law got to meet our new cat and see our apartment too!
It was a pretty cool day, but its sad to say goodbye to that part of your life as well.