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

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Cool Stuff from Last Semester

I did some cool stuff last semester in my science classes that I’d like to show you guys.

The gist of it is… This picture:


This is a picture taken by my lab group in my basic lab technique class last semester of a mouse fibroblast cell moving into a simulated wound on a glass slide.

Fibroblast cells are kind of like the contractors of your body when you get a scratch or wound. There are your first responders to the “disaster,” your immune system, and then fibroblasts go in to start the process of rebuilding your tissue by laying the foundation for other cells to move in.

A lot of scientists are interested in wound healing. How can we make it faster? How can we make it better so people don’t have lingering problems after the superficial injury has healed? How can we prevent infection? How can we prevent scarring?

Those questions are tested with a variety of experiments but one of the msot common is the scratch assay.

A bunch of fibroblasts are grown on a glass slide until they practically cover it. Then the slide is scratched.

The fibroblasts move into the scratch, thinking it is a wound. Their movement into the scratch is measured in a couple different ways and those measurements can tell us a little bit more about how wounds heal.

Which brings me back to the picture my lab group took. Obviously its got a lot of color and is very prety, but what are all those colors? What’s going on in that picture?

My lab group scratched the space above the big cell in teh picture. The cell is now moving into the scratch.

The red lines are called actin. Actin is the support structure of your cells. Cells move by extending actin filaments where they want to go and breaking them down behind them.

The green parts are called vinculin. Vinculin is spread throughout the cell and localizes into spots where the cell is attached to a surface to assist in adhereing to that surface. All those bright green spots are where the vinculin is helping the cell hold onto the glass slide.

The blue parts are cell nuclei. Each cell has one nucleus and I’ll bet you can pick out the one that belongs to all the actin and vinculin in the middle of this picture.

I did a lot more stuff on scratch assays in this class and leaarned a few new techniques, but the best part was definitely getting this picture.

Oh and apologies to any color blind people. I have no idea how to spearatae out the red and green things for you. Enjoy!

-GoCorral

Graduated Student Tour

While letting myself into my lab a woman approached me and said, “Hi!”

She had just graduated UC Davis and was looking around all the buildings she hadn’t been in much.

She was a Landscape Architecture major (didn’t even know you could major in that). My building is for biological sciences, so its understandable that she had probably never set foot in it before.

My lab’s building, Briggs Hall, is interesting from an architecture perspective (but maybe not landscape architecture).

The building was built in 1971 when there were a lot of campus demonstrations (still are! Pepper Spray Cop was at UC Davis).

A method of cutting down on demonstrations was giving students no places to gather indoors. Thus Briggs Hall’s layout is amazing confusing and even I get lost in it after working in the building for several years.

Briggs also doesn’t have any staircases inside. All of the stairs are on the exterior of the building. Don’t ask me what lunatic decided that was a good idea for a four story building.

Anyways, the recently graduated student asked if there was anything interesting in Briggs.

I showed her my lab. She glanced around in it, but not being a biologist she didn’t really understand anything in the lab.

I showed her the -80°C (-112°F) freezer which she did like as summer is starting in Davis.
I also showed her my favorite part of Briggs, the back exit by the police station.
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The back exit is where all the old equipment is put that no one wants anymore. These are the pieces that are too big to just throw in the trash.
There’s old computers, old centrifuges, old heating blocks, old incubators. Tons of cool science equipment.
It’s this sort of industrial wasteland and NO ONE EVER GOES THERE.
My lab is super peaceful, but if something ever got too stressful and I needed to go outside, this is where I’d go.
Why does industrial junk calm me down? I had an air filter going in my room constantly when I was a kid. That constant hum while I slept made me associate industrial hums and old appliances with peaceful rest.
So now places like this always calm me down.
Course, the graduated student didn’t get any of that business. Shook her hand and congratulated her on graduating after I showed her the junk pile before going back inside to my lab.
-GoCorral

Education Graduation

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.

Bedazzled with tons of stickers, tape, and paint adhesive to keep it all on.
Bedazzled with tons of stickers, tape, and paint adhesive to keep it all on.

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).

See! My camera is just fine...
See! My camera is just fine…

After the ceremony we went back to our house for pizza and cake. My wife loved the cake that I picked out!

-GoCorral

Pitch Perfect 2

We saw Pitch Perfect 2 and sadly it suffered from sequelitis.

That’s when the sequel to a movie just isn’t as good as the original and probably wouldn’t have been made if it didn’t already have an established fanbase.

It’s still a decent movie and if you enjoyed the first movie you’ll most likely enjoy the second, but I wouldn’t recommend it to anyone who hasn’t seen the first Pitch Perfect.

So what was weaker in this movie than the first? Gosh… Where to start?

The two announcer characters got a lot more racy and offensive. They were already a little bad in the first movie, but it was cringeworthy in the second.

I listened to a few interviews of the production staff as well and apparently most of the announcer scenes were adlibbed. I don’t know if that makes the racy parts better or worse, but they’re there.

The romantic plot between Beca and Jesse is essentially absent in the second movie. Their relationship is stable and off-camera. Their romantic sub-plot is replaced with Fat Amy and Benji’s two love interests. While those sub-plots are interesting they don’t really compare to the entertainment provided by Jesse cracking open Beca’s shell in the first movie.

The other thing that’s absent is Beca’s dad. I really liked his role in the first movie.

It makes some sense to phase out parental figures as the characters get older. And the whole sub-plot of Beca getting over her parents’ divorce is absent in Pitch Perfect 2 means that her dad doesn’t have much to do. I still missed his presence though. He’s somewhat replaced by the mother of a new freshman member of the Bellas, but the new relationship isn’t nearly as interesting as the old.

The villains in the second movie, Das Sound Machine, aren’t nearly as likeable as the Treblemakers.

Now why would you want to like your villains? Well I just wrote about that in a previous post. Go read that one and come back if you need an answer to this question.

Das Sound Machine are portrayed as just evil which makes them a little boring.

The movie also portrays them as hyper competent. While that’s definitely true, their performances are still a little boring. Their first performance is Uprising by Muse, one of my favorite songs. They do a great job, probably as good as they could do, but the song just sounds awful in acapella. I could barely understand the lyrics over the background music imitations.

The musical performances do really suffer compared to the original movie.

There are good reasons for this. The Bellas as a whole suffer some sort of identity crisis that comes out in their performances not being as good, but that also means that the first half of the movie has unsatisfying performances by the Bellas.

The first movie had this as well, but it covered it with humor. Aubrey throwing up pulls you into the hilarity of the movie right away. Aubrey’s tongue lashing after the poor performance at the fraternity party is great character development for her.

How does the Bellas excess use of props enhance the other plots in the movie?

It doesn’t.

I felt the songs picked for numbers were in general worse than the original as well. I didn’t know as many this time around and that hampered my enjoyment.

And there’s just a few other things that the second movie just missed. Lily’s little whispers aren’t as terrifying as the first movie. Beca’s odd sexual attraction to Das Sound Machine’s leader isn’t explored further by having Jesse find out. The inclusion of the new freshman in the Bellas felt like an excuse to have an original song in the moive so they could sell something with fewer royalties attached. If the international competition is for college groups, why are people out of college allowed to compete?

Just tons of small stuff like that.

Like I said, its not a good movie for people who haven’t seen the original. For those who enjoyed the original, there’s still plenty of stuff like it in the new movie. The songs are still catchy and Fat Amy is still hilarious.

-GoCorral

Institute of Regenerative Cures

My class got to go on a field trip last week.

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All the joys of barely being able to see the tour guide when you’re at the back of the group.

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.

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The entrance hallway with pictures of the cooler discoveries at the Institute.

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.

Where all the research is done!
Where all the research is done!

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!

-GoCorral

The Longest Ride Movie Review

Another movie that my wife and I saw together (Oh my God! He never writes movie reviews!).

Unlike Cinderella this movie had the level of passion I’ve come to expect from romance movies.

The Longest Ride is another Nicholas Sparks book turned to a movie. It seems like he and Stephen King get every single one of their books optioned into a movie script.

If you’ve seen The Notebook this is more of what that movie offered. It even has a story within a story like The Notebook.

The Longest Ride starts by establishing a budding relationship between Sophia, aspiring art student, and Luke, professional bull rider.

On the way home from their first date at a secluded lake Luke and Sophia spot a crashed car off the side of the road. They pull an old man from the wreckage. He’s a bit out of it, but he has enough sense to ask them to save a box from the backseat of the car.

They rush him to the hospital. Somewhere in there Sophia tells Luke that she’s moving to New York for an art internship in two months and she’s not sure she wants a serious relationship.

They get the man to the hospital and Luke leaves. Sophia stays and opens the box to find dozens of letters written by the rescued man, Ira, to his wife, Ruth.

When Ira awakes, Sophia tells him she read one of the letters and he asks her to read the rest to him as his eyesight no longer allows him to read them to himself (Ruth is dead and can’t read them to him either).

From there the movie tells two parallel storylines of the romance between Ira and Ruth and the romance between Luke and Sophia.

Luke and Sophia have the drama of Sophia’s plan to move to New York, Luke’s persistence in bull riding even after a serious injury, and the culture clash between their two worlds.

Ira and Ruth are two Jews that escaped Nazi Europe and fall in love in the USA. Ira joins the army to fight the Nazis and sustains an injury that sterilizes him. The main conflict in that story is Ira’s inability to have children and Ruth’s desire to fill that void anyway she can.

Both the stories are fun in their own way and while one segment is going on I started to develop a thirst to find out what was happening in the other segment.

If you’ve seen one Nicholas Sparks movie you’ve seen them all. You probably already know exactly what’s going to happen in this movie. My wife and I happen to like Nicholas Sparks movies, so I’d definitely recommend this to anyone else who enjoyed other adaptions of his work.

-GoCorral