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

Advertisements

My Easter Weekend

I found this at the mall in Chico. Pretty cool!
I found this at the mall in Chico. Pretty cool!

I didn’t play D&D this weekend again due to the Easter holiday.

Instead I went to Chico to visit one of my wife’s friends who was a bridesmaid in our wedding.

She recently got engaged to her boyfriend, now her fiance.

I’ve been hanging out with her boyfriend a lot via the internet.

We’ve been playing Diablo 3 a lot together. Fun game to play with other people!

We went to the mall while in Chico.

The girls went clothes-shopping while the boys went looking for track pants for me.

There’s a new regulation at my job that requires pants to be worn at all times in the lab (no shorts).

The pants are so if you spill a dangerous chemical it gets on your pants instead of your legs.

Heavy pants are awful in the summer, so I wanted the lightness of track pants.

We found two at Dick’s Sporting Goods and then bummed around the mall for awhile.

The picture above was taken in Spencer’s.

Spencer’s is a strange shop. It sells a lot of cool stuff like Pikachu hats, Adventure Time belts, and Zelda shirts.

Spencer’s also has a sex section. It’s dominated by freaky bondage stuff and lots of “pecker” candy themed for bachelorette parties.

We laughed at a lot of the stuff there. We were looking for the Newlyweds party game for the four of us to play, but they didn’t have it.

The only Easter themed thing I did this weekend was eat a chocolate bunny.

I feel like Easter for nonreligious people like me is something you celebrate with children.

I’m in the midpoint of my life where I’m too old to be a child with my parents anymore and too young to have kids of myself.

Maybe in a few years I’ll have children, but for now Easter will remain a smaller holiday.

That’s all for tonight!

-Mister Ed

Lab Construction Work

The new shelves where rice seeds for the sequencing project I work on will be stored.
The new shelves where rice seeds for the sequencing project I work on will be stored.

Yesterday I got home pretty tired after work.

The picture above is what I did at work. I made some shelves and put some boxes on them. That took all day.

The shelves came in five different cardboard boxes.

The lab manager and I put the shelves together in the hallway because there isn’t enough room for it on the floor in this room. That took about an hour.

We pushed the shelves in after putting them together. Everyone laughed thinking that we couldn’t fit them through the door. SHOWED THEM DIDN’T WE?!?

The shelves are seven feet tall. They’ll be holding the thousands of different varieties of seed in those boxes on them.

Next, the lab manager wanted to construct another set of shelves for other lab storage.

This other shelf had to fit into a space taken up by even more shelves.

The lab manager, another lab guy, and I spent half an hour shoving the other shelves around until there was just enough room to squeeze the new set of shelves in.

The lab manager started putting together that other shelf while I and the other lab guy worked on those boxes you can see in the picture.

Each box holds more than a hundred varieties of seed. Some hold close to 600.

These seeds were stored in ordinary cardboard boxes previously. Like the kind that you pack your stuff in when you move.

This storage was pretty unorganized. Our job is to sort them out and put them into the new boxes which will be much more organized.

So I spent all day taking envelopes of rice seeds from one box, writing down what the envelopes said on an Excel sheet, and putting the envelope into a new box.

It is WAY more ordered now. Previously, it’d take 5 minutes to find a particular variety of seed. When we’re done it’ll take 5 seconds.

I worked my way through one cardboard moving box and was on my second when the day finished.

The other lab worker and I got through about 1,000 seed varieties each. Lots more boxes to go through though!

This taste of the more mundane side of lab life was brought to you by the talking horse.

-Mister Ed

Writing for Master’s

The guidelines for how to prove you are a competent writer for Sac State's Master's Program.
The guidelines for how to prove you are a competent writer for Sac State’s Master’s Program.

I ended up getting rejected from the other program I applied to so I accepted Sac State’s offer of admission last week.

Sac State has a typical biology Master’s program. I’m reading up more on the specifics lately.

One of the things I found is pictured above, a writing test.

Sac State wants to know that its Master’s students can write competently.

A competent writer reflects well on the college and honestly, they wouldn’t be doing their job if they didn’t make sure their graduates were good writers.

I like to think of myself as a good writer. I do this blog after all don’t I?

I’m published in a magazine too. I’m a successful amateur for sure!

But they have higher qualifications for themselves.

So I can resign myself to taking a class on writing at Sac State (not so bad actually) or I can try and waive myself out of it.

First way to get out, already have a Master’s or PhD. NOPE!

Second way, publish an article in a peer-reviewed journal. Nope.

Third way, have an undergraduate GPA of 3.7. I’ve got a 3.55. Not quite there.

Fourth way, get a 4.5 on the writing section of the GRE. I got a 4.0. I could retake it though!

Fifth way, teach a writing class at a college. No again.

The second way was the most intriguing to me. I’m already working on a paper for a peer-reviewed journal.

I mentioned in a post on Alexander the Great a while back that I’m writing a paper on him.

The paper is basically finished at this point. I’ve gone through a lot of edits over the past two years with a lot of advice from very helpful friends, family, and friends of family.

I actually already submitted the paper for publication once in the Journal of Popular Culture. It was turned down.

This is pretty typical scholarly journals. The paper is never quite what they’re looking for.

So I was turned down, but with a list of revisions I could make to resubmit.

I finally sat down finished the revisions given by them and a few other helpers that read the paper since my first submission.

Now my most persistent helper is my favorite Classics professor when I was taking Classics as an undergrad. He gave me a more difficult edit, to try restructuring the conclusion section.

Right now the conclusion section is separated into paragraphs based on which source on Alexander I’m talking about.

The professor wants to see how it looks when the conclusion is split based on which topic I’m talking about.

I’m doubtful that it’ll be better. The conclusion already looks so good! I’ll give it a try though.

So tonight I’m going to stay up later and rewrite two pages on Alexander the Great’s modern image. Hopefully this version will get published and then Sac State will have proof that I’m a good writer. Wish me luck!

-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

What Is My Profession?

20140405-071152.jpg
I’ve talked about how I work in a lab before, but haven’t gone into specifics.

There’s a bit of background knowledge needed before you can fully understand what I do at my job though.

I work in a research lab which means I’m a scientist. What type of scientist am I? A biologist!

Biology used to be all about plants and animals and stuff, but since the discovery of DNA that’s changed quite a bit.

Studying animals and plants is now referred to as zoology, botany, or ecology.

Biology now almost exclusively refers the study of DNA and other things related to DNA.

You probably remember learning about DNA in school where your teachers described it as the “instruction manual for your body” or something to that effect.

That’s essentially true. DNA does provide the instructions for building everything in your body. But how does it do that?

DNA is kept inside a protective bubble in your cells called the nucleus. When an invader like bacteria or viruses gets into your cells they are cut off from your DNA by the nucleus.

If invaders could get at your DNA they could alter it. These alterations are what make viruses so dangerous. Alterations can also cause cancer.

But with your DNA cut off from the rest of your cell how does it provide instructions?

DNA produces a copy of its instructions called RNA that leaves the nucleus.

RNA goes to something in your cells called a ribosome.

Ribosomes read the instructions from RNA and create proteins.

This is where I got a little confused in my biology classes. Aren’t proteins just one of those things on the nutrition facts labels?

Turns out proteins are responsible for almost all cellular activity your body performs.

Proteins make your cells move, send signals between cells, help your cells digest things, etc. They do everything.

So the whole process is DNA makes RNA which goes to ribosomes which make proteins. Proteins then go on to do everything else.

In both my labs I study the first step, the organization of DNA and how RNA is made from it.

I’ll tell more about each of my labs in a future post.

-Mister Ed

Acceptance Wall

Normally I’d post something about D&D on Monday, but this week I’ll be showing off something that came in the mail recently.

My first graduate school acceptance letter.
My first graduate school acceptance letter.

I got into graduate school! Hurray! Validation!

This year I only applied to local schools as my wife is in the first year of a two year program for her teaching credential.

I applied to two programs at the college I got my undergraduate degree from and a third program at a nearby CSU (Sac State).

I’ve been rejected from one of the programs and have yet to hear back from the other one, but Sac State has accepted me! Woohoo!

Assuming the other program doesn’t accept me, I will be driving to the capital every day to learn and research science stuff.

The professor I’ve been placed with studies salmonella. I haven’t read up a lot on it, but what I saw on the papers she’s published was interesting.

Salmonella typically hurt your body in many ways one of which is by attacking your macrophage cells. Macrophages are the part of your immune system that eats bacterial invaders.

The salmonella bacteria don’t like being eaten by macrophages though. They protect themselves by putting poisons into your macrophages.

The professor has helped discover how this process works and she is attempting to harness the power of salmonella for good, not evil!

You see, if salmonella are so good at invading macrophages and killing them, they can also be used to invade macrophages and help them.

We can modify salmonella to make it deliver medicine to macrophages. This could do a number of things.

It could protect against auto-immune diseases like HIV. It could also super charge the immune system to assist the fight against other bacterial infections. These two things are some of the most sought after effects in medicine right now.

HIV is a huge problem throughout the developing world, so the interest in that is obvious.

The second effect, of boosting the immune system is even more amazing in my opinion.

Bacterial infections such as tuberculosis, STIs, and many others are currently treated with antibiotics. But bacteria can evolve and become immune to these antibiotics.

Researchers can come up with new antibiotics, but in a few years the disease will have evolved immunity to it again.

But what if you treated the disease just by making the immune system better? The bacteria can still evolve past this, but it takes much longer to do that than to develop antibiotic resistance. Possibly long enough that the disease can be eradicated entirely? That would be astounding.

While my original goal was to get entrance into a PhD program, working on making people immune to disease doesn’t sound that bad either. I think I’ll be quite happy at Sac State.

That’s all for tonight!

-Mister Ed