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

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.
wpid-20150617_140515.jpg
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

Institute of Regenerative Cures

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

150508_002
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.

150508_001
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

An Interlude to TAing

I enjoyed TAing a lot last semester, but due to a scheduling hiccup I won’t be able to this semester.

Hopefully I can pick it up again over the summer or next semester. I love teaching people and getting paid to do something you love is always appealing.

Since there won’t be any posts this semester about me TAing I have prepared this glorious selection of photos from the Vertebrate Museum at Sac State.

The Vertebrate Museum has hundreds of taxidermied animals and skeletons in it. The animals are from zoos or people who donated their own collections.

Last semester my class got to go on a “field trip” to the museum to examine different evolutionary traits. I say field trip in quotation marks as the museum was literally across the hall from the normal classroom.

So without further delay, here are some photos!

Chimpanzee Skeleton
A baby chimp skeleton.

 

Snake Skeletons
Snake skeletons. There’s supposed to be tiny toes near the back end of the tail.
Moose Head
Moose Head!
Undergraduates
The students comparing the different birds.
At least I think this one was a goat?
I think this one was a goat? Maybe a pig.
They're in love!
They’re in love!
All the deer!
All the deer!

-GoCorral

 

 

 

Gurutama Timeline Revising Part 22

Previous: Gurutama Timeline Revising Part 21

This post sees the start of the Shanties around Hykma. The Shanties are similar to suburbs or slums, depending on what neighborhood you’re in. We also see the start of the Merfolk Blockade that influences a lot of subsequent events in the third age of our Dawn of Worlds campaign. Everyone is going to start scrambling to get around the Blockade to continue the profitable trade with Hearthland. And of course the Grez continue to expand and no one does anything about it.

704 NA: The Grez animated the frozen corpses of the humans in the north. To lead their new undead army, the Grez reanimated the Hero. The world shuddered at the still foreboding presence in the arctic.

705 NA: The splendor and draw of the glowing city of Hykma continued – incredible wealth resided in the city and the Elven Gardens were hailed as one of the great wonders of the modern world. The government began to solidify as the old blood princes and their merchant counterparts established themselves as proper lords. A new order was formed and a new constitution written. The Revered Administration now ruled over the Hykman League.

Meanwhile, the poor and disenfranchised in Hykma were slowly forced out through zoning and vagrancy restrictions. The Elves sheepishly closed the gates of Rotandean, apologizing yet refusing to accept the flow of refugees. The masses turned east, heading down the river toward Pulchrito, Domicilius, and The Hearth. The Rana were gracious hosts, but unable to host the numbers in either of their own cities. With the help of the Monks of the Gossamer Waves and the “gracious charity” of the Hykman Administration, shanty towns popped up all along the rivers, spreading from the base of the mountains at Hykma to the Tonsil Lake, and then more stretching from Domicilius to The Hearth. Impoverished at first, soon wealth began to trickle down from Hykma and The Hearth as merchants saw consumers and laborers in the Shanties. The Shanties grew in splendor. Festivals were common along the rivers and colored lanterns and lights adorned the long stretches of water and cobblestone roads.

709 NA: Profits in the Maw soared. Peace bred wealth, new power, and an influx of new blood into the old aristocracies of Najar, the Hykman League, and the pirate princes of Balkus.  Tensions rise. The seas were not as safe as they once were and piracy was rampant. Merchants begged their governments for protection and demanded action. The cities of Hykma, Cynelle, Alixria, Alrdia, and Balkus each raised a “defensive” fleet and begin to patrol their waters.

710 NA: The Grez froze the area connecting Glacierstone, the Upper Maw, and Hearthland. Reesrevo used his godly power to animate the entirety of the frozen Najar people as a new race of people. An undead race entered the world as servants of the Grez. The world was shocked and horrified, but no one would take action against the Grez. Commanders feared that while their army was away fighting the Grez, another city-state in the Upper Maw would attack their home city.

711 NA: The Merfolk, frustrated by the latest threat to their naval supremacy, unveiled new advances in the craft of shipbuilding and naval patrolling. New fleets were constructed in Drolfo’s Cove, New Tortuga, and Cyflenwi. The Merfolk flexed their new naval muscles by setting up a blockade across the Mouth of the Maw from the ruins of Nanatok to Cynelle. The people of Drolfo demanded reasonable tariffs for passage in and out of the Maw. This blockade was in response to the raising of Proaxium by the Dwarves. The blockade would end only if Proaxium was returned to Merfolk custody. The Merfolk blockade sent chaotic ripples through the Human trade networks. Dwarven goods were in high demand and prices soared. The Mouth of the Maw had always been the only free and safe route to Dwarven lands. Where would the Humans get their fine Dwarven luxuries now?

-Mister Ed

Next: Gurutama Timeline Revising Part 23

NorCal Preview Gymnastics Meet

My wife and I went to the NorCal Preview Gymnastics Meet this weekend. The meet was held at UC Davis between the women’s gymnastics teams of UC Davis, Sac State, San Jose State, Stanford, and UC Berkeley.

Cal (UC Berkeley) won the meet. My wife and I had a lot of fun watching the different competitors. She recognized a few people that she knew previously from her time at SJSU and UC Davis. I thought I recognized one of the Sac State gymnasts as one of the people I’d taught last semester, but I ended up being wrong about that.

Here are some pictures from the floor and beam events. Vault pictures don’t look that amazing and we sat too far away from the bar event to get good pictures of that. I hope you enjoy stills of close to Olympic level gymnasts! Stanford is on beam and Cal is on floor.

IMG_2651

 

IMG_2652

IMG_2653

IMG_2654

IMG_2659

IMG_2660

IMG_2664

-Mister Ed

TAing at Sac State

One of the lab benches of the room I teach in.
One of the lab benches of the room I teach in.

For the past few months I have been assisting in teaching a introductory biology lab at Sac State.

I TA Bio 15L which is a general education course for non-science majors. The course uses interactive labs to go over all the basics of biology, like ecology, speciation, DNA, genes, and that good stuff.

The class has been a lot of fun for me for a lot of different reasons.

I like helping out the students. Its nice to see some of them so interested in biology even if it is nowhere near what their major is. One of them is even considering switching her major.

It’s nice to go over all the material again. I learned it all years ago and everything is easy for me now. Obviously I should know the material in a class that I teach, but its still fun to know that I could get any of the questions in the class right if the teacher called on me, even when I am the teacher.

The experience of being on the other side of a class is also interesting. I have to deal with making quizzes, grading, student absences, and preventing cheating.

Student absences is probably the hardest part. This is a college level class, so they’re free to not show up if they don’t want to. Its just inevitable that the ones who don’t show up do poorly on the quizzes that cover the material they missed or they miss the quizzes entirely. And this is college so there are no makeup quizzes.

There’s nothing I can really do about absences, but I’d like to be able to tech the students that do come to class so that they can all understand the material and use it in their own lives later on.

Learning biology is important for a number of reasons. How can you be an informed voter on GMO issues if you don’t properly understand what GMOs are? How can you vote on global warming initiatives without knowing more about that? And wouldn’t you like to know how genetics work when you start planning a family to see what genetic risks your potential child could have?

I try to teach the students that sort of stuff. I feel like I’m just learning how the labs work this semester. I know I’ll do way better next semester when I can focus more on directing what we are trying to learn with the labs and giving the students more specific strategies for learning.

Also, I can hopefully be more enthusiastic when I give lectures. The mid-semester student evaluations indicated that the only place I really needed to improve was in how enthusiastic my voice sounded when I was presenting the material.

-Mister Ed

First Day of Graduate School

Woo! Yesterday I had my first day of graduate school and it was amazing!

For awhile I’d been worried that I wouldn’t like going back to school once the semester started. All of those worries went away once I stepped out of my car onto campus.

I unfortunately arrived late to my first class. I live in Davis and driving to Sacramento has never taken this long in the past.

I thought I’d budgeted enough for rush hour traffic. I guessed the time accurately except for the time to leave the freeway.

Everyone and their mother wanted to get off the freeway at the Howe Ave exit right by Sacramento State.

Next time I go in the morning I’ll get off at an earlier exit and dodge all that traffic. Hopefully that will get me to school with time to spare.

Anyways! I got approved to be a TA in a lab course which meets Tuesday mornings. This semester I’m in training, but in the future I’ll be paid.

The lab class is a GE fulfilling course, so its filled with students who are not biology majors.

The course is also taught by my graduate adviser, which is a huge plus. We’ll get to know more about each through teaching together which will help a lot later in the graduate school process.

I assisted the students with a simple discussion lab which tried to define what life is.

After the discussion each student took a sterile swabbed and rubbed it on something before rubbing it on a petri dish. Whatever they rubbed onto it will grow over the week and we can take a look at it next Tuesday.

When the lab finished I walked around campus. I found the bookstore, the activities fair (no I don’t want to join a fraternity), the student union, and the library. I at my lunch on the quad and then went to read in the library til my next class.

I have two other classes on Tuesday. The first was about how to be a better TA. I met the other students and the teacher told us a little bit about herself, her teaching style, and some resources we could use to improve ourselves as teachers.

My last class, Molecular Biology, was in the same room as the class on how to be a TA. I was surprised when the teacher walked in because I recognized him!

The teacher for my Molecular Biology class is also the post-doc who works in the same worm lab as me at Davis!

It was a pretty cool coincidence. Apparently he had already known for awhile, but hadn’t told me yet.

I was unfortunately the only person who consistently raised my hand to answer questions in his class. I’m hoping that will change in the future. Maybe everyone else was just shy because they hadn’t met the instructor yet.

At the end of the day the instructor and I discussed carpooling together.

Turns out that won’t work because he lives in Sacramento and I live in Davis. At the end of the day we want to be in different places.

Altogether it was a great day. I loved being back on campus as a student and as a teacher. I love learning and helping other people learn. I’m looking forward to the next two or three years at Sac State!

-Mister Ed