HCl Spill in the Lab

I had an interesting day in the lab. I spilled a large amount of concentrated HCl on the floor!

I would’ve taken a picture of the damage zone, but my first thought was, “Oh shit!” not, “This would look good on my blog.”

HCl is the strongest acid used in most labs. If you’re familiar with the pH scale it goes from 1-14. Water is 7. Orange juice is 3 and stomach acid is 1.

Concentrated HCl is -1. the pH scale is a log scale so that means concentrated HCl is 100 times stronger than stomach acid.

HCl is used all the time in lab work, but often in a more dilute form. I had the concentrated stuff out so I could dilute a small amount of it in a large bottle of water.

I got the amount I needed and then I dropped the large bottle on the floor as I was putting it away. SPLOOSH! CRACK! Glass and acid everywhere!

It started eating away at the floor immediately, BUT WAIT! THERE’S MORE!

HCl is composed of Hydrogen (H) and Chlorine (Cl) in water. In concentrated HCl the acid is so smooshed together that it starts falling apart into its component parts of Hydrogen and Chlorine gas.

Chlorine is a deadly gas! Hurray! -_-

I closed off the room and put a warning sign on it before rushing upstairs to contact my PI (boss).

He came down and we agreed that we needed to call Environmental, Health, and Safety (EH&S). They’re the guys who handle spills in the lab that my labmates and I can’t deal with.

EH&S didn’t come by themselves though!

First five firemen came up. Two cops as well, but they left after I told them I wasn’t injured. Some of the acid got on my shoe but nothing serious.

The firefighters stuck around until EH&S arrived. Three people from EH&S came to assess the situation and after doing so they sent two more people to do the actual cleanup work.

So a small spill of a nasty chemical attracted a dozen emergency response personnel.

Meanwhile I took off my shoe just to be safe and am now wearing a bootie for the rest of the day.

The bike ride of shame awaits me when I go home. EVERYONE WILL KNOW!!!
The bike ride of shame awaits me when I go home. EVERYONE WILL KNOW!!!

The cleanup crew removed all the broken glass and chlorine gas as well as most of the acid that was still on the ground.

Supply cart. The crew is inside cleaning up my mistakes.
Supply cart. The crew is inside cleaning up my mistakes.

After they finished up I came in with Sodium Carbonate (grainy baking soda) to clean up the rest of the acid.

I still managed to work with the dilute acid I made, but what a day!

-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

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

Abandoned Lab

Two shelves I filled up with pipette tips.
Two shelves I filled up with pipette tips.

Last week the rice research lab I work in was all but abandoned due to a local conference on plant pathogens.

I didn’t go to the conference as I’ll soon be changing to working entirely on C. elegans.

Spending the lab’s money on me learning more about a topic that I probably won’t encounter again would’ve made me feel guilty.

I was left in the lab with a few people who stayed behind or came back early.

I finished all my usual duties in the lab like taking care of plants and setting up stuff for next week, but I still had a lot of extra time before the end of the day.

I cleaned up the lab a bit and… FILLED TIPS.

I filled two entire shelves with boxes of tips.

You might be wondering what are tips and what are they used for?

Biological research often requires very small amounts of liquid to be measured.

For comparison, in the science we usually measure volumes of liquids in liters.

Most people are familiar with liters in the form of those two liter soda bottles that are used for parties.

A milliliter is equal to one thousandth of a liter, or two thousandths of a soda bottle.

A milliliter is still rather big though. It’s about the size of the last joint on your pinky finger.

The research I perform measures liquids in microliters, which are one thousandth of a milliliter (or two millionths of a soda bottle).

A microliter is about as big as a period.

So how is something that small measured?

With a pipette!

A pipette is essentially a mechanical suction device, similar to a straw.

A pipette tip is added on to the sharp end of the device you see above.

The button on top is pressed down, expelling a specific volume of air from the pipette.

When the button is released the pipette sucks that volume back up into the pipette tip.

Pretty much the same principle as using a straw to drink a two-liter bottle of soda.

The amount of air expelled from a pipette allows researchers like me to work with extremely small volumes. Some pipettes can even measure volumes as small as a thousandth of a micoliter (Another name for that is a nanoliter).

When working with small volumes like this its even more important to be clean.

Any small contaminant on the pipette tip would be a large contaminant in a mixture of only a few microliters.

So the tips are put into those boxes in the first picture and then autoclaved to sterilize them.

Oh and here’s a closeup of a pipette tip!

-Mister Ed

Liquid Nitrogen in the Lab

A thermos with some bubbling liquid nitrogen at the bottom.
A thermos with some bubbling liquid nitrogen at the bottom.

Liquid nitrogen is used pretty much everyday by someone in my lab.

Liquid nitrogen is an extremely cold liquid coming in at close to -200°C (-330°F).

Nitrogen’s natural phase is a gas. Its a fairly common gas to, making up 78% of the Earth’s air.

When it nitrogen is condensed as a liquid it is essentially always at boiling temperature.

I tried to capture the vapor coming off the bubbling liquid nitrogen in the picture above, but its difficult to convey what liquid nitrogen is like in a photo.

Liquid nitrogen looks exactly like boiling water. If you put liquid nitrogen into a pot it would look just like a boiling pot of water ready for spaghetti to be added.

But liquid nitrogen is not boiling water. It won’t scald your hand if you touch it.

Liquid nitrogen is the coldest thing you will ever touch and can instantly freeze burn your hand.

Even things that come out of liquid nitrogen are painful to touch with you hands. I can’t do it for more than a second.

Using gloves to handle liquid nitrogen has another problem attached to it.

When you wear gloves a natural layer of sweat and oil occurs between your hand and the inside of the glove.

If your gloved hand is in the liquid nitrogen for too long, the sweat freezes.

That’s just ice though. It’s happened to me plenty of times. I just yank my hand out of the nitrogen and my bodyheat melts the ice back into sweat right away.

So if its so dangerous, why do we use it in the lab?

Liquid nitrogen is useful because it stops all biological activity. That’s why its dangerous and why its useful at the same time.

When working with a dead specimen its best to prevent bacterial decay. Bacteria can’t survive at liquid nitrogen temperatures, so its used for that.

Liquid nitrogen is also used to isolate RNA from a specimen.

Every cell has RNA inside of it, but RNA is also what many viruses are made out of.

Cells quickly learn to distinguish RNA inside the cell as good and RNA outside of the cell as bad virus RNA.

Cells have defense mechanisms to destroy RNA called RNases.

RNases can’t work at liquid nitrogen temperatures though!

I was using liquid nitrogen for a third purpose today, just to quickly freeze some worms.

More on why I need to freeze worms another day!

-Mister Ed

Rice Husks and Video Games

I was dehusking some rice seeds today in order to sterilize them.
I was dehusking some rice seeds today in order to sterilize them.

Rice seeds grow with a husk around them. After the husk is removed they look like the rice you buy in a store.

Sometimes the seeds from a particular strain don’t grow right.

The lack of growth often happens because a fungus infected the seed from the start.

The fungus is removed by washing the seed.

The husk needs to be removed first to ensure the seed is fully cleaned, just like you have to take off all of your clothes to ensure your body is fully cleaned when you shower or bathe.

While I was washing the seeds in diluted bleach I talked with one of my friends in the lab about streaming Hearthstone.

The oldest member of the lab besides the professor (I sometimes call him the lab fossil) overheard us and was curious about what streaming was.

We described it to him and he was a little surprised that people would want to watch others play video games.

He’s seen his son play first person shooter (FPS) games and he dislikes them, but not for the usual reasons.

The lab fossil dislikes FPS games because they don’t match reality.

He feels they teach people that if you die/fail you can just get a do-over where you try again.

The real world and the real battlefield doesn’t work that way. If you die in real life, you’re dead.

You can’t respawn, you can’t start over from the beginning. It’s over.

He told us about when he was in the army for two years.

All the time they would do drills and the drills were about staying alive.

Not about shooting and killing others no matter the consequences to yourself like in FPS games.

One of the first things the lab fossil learned is that if you hear gunfire, you should immediately drop to the ground (something people in gang neighborhoods already know).

He told us that the way you survive a battle is by finding cover, not shooting your gun.

He said bullets are heavy, you don’t want to waste them, you might need them later to survive.

My past experience with army veterans is that they never want to talk about their experiences.

Out of respect, I’ve never asked them to recall memories that might be painful for them.

This was one of the first times I actually got to talk about war with a soldier, even if he’d never been actively deployed.

It was a good learning experience.

-Mister Ed

Which Lab for Grad School?

This is the microscope I use to inject DNA into nematode worms.
This is the microscope I use to inject DNA into nematode worms.

I’ve been doing some thinking lately about which lab I should work in for grad school.

As it turns out I get to choose among a few different options.

The folks at Sacramento State are okay with me doing my research at either of my labs in Davis.

I’ve been with the rice lab for almost three years now and feel I’ve gotten what I wanted to out of it.

I’ve already written some goodbye/thank you letters, but have yet to hand them out. I’m just ready to leave the rice lab.

Yesterday I looked up some information on what exactly I’d be doing if I joined the new professor’s lab at Sac State.

The professors old students finished their theses which are then stored in the school library.

Recently the library has started putting digital copies of the theses online. I read a few of the more recent ones that were uploaded.

While the research is interesting, there was nothing that I wanted to do more than the intron research I do currently.

Part of it was the occupational hazard of working with food pathogens. Most food pathogens are collected from raw food samples or from poop.

The idea of having to collect poop samples and work with them… Let’s say its not on my bucket list and leave it at that.

Continuing my intron research would be awesome though. The project has room for expansion and it fits better with what I want to do on a grander scale.

I want to create tools for people to use in other laboratories. Enhancing introns could be used in any laboratory to fine-tune the expression of a gene to the exact level required for an experiment.

I want to create tools like that when I get an official job as a researcher, so it would be best if I did my Master’s Thesis on the same topic.

So it looks like I will be attending Sac State next year but performing my research at UC Davis on introns!

-Mister Ed

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

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