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

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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

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

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

My Lab Meeting

Here's a picture of one of my PowerPoint slides from today's lab presentation.
Here’s a picture of one of my PowerPoint slides from today’s lab presentation.

I presented the progress on my research at lab meeting today.

I haven’t gotten as far as I wanted to since my last lab meeting, but I did get as far as I expected to.

By the end of the summer I was expecting to have 5 of the 6 constructs successfully injected and integrated into C. elegans strains.

I’ve gotten 4 out of the 6 and the summer isn’t over yet. I’m on track to finish.

Otherwise, I’ve had a problem with the worms not staining like the ones of the person who used to work on this project.

His worms stained extremely dark. There’s so much blue color that the picture of them looks black.

My worms don’t look like that, but we aren’t sure why.

I’m going to tweak some things to try and make my strains look that way.

If the tweaks don’t work… I’ll have to check using a more complicated method to ensure that I injected the worms correctly.

That’s the gist of what I presented at the meeting.

The meeting went pretty well.

Today’s meeting was between my lab and the lab adjacent to us.

Our lab meetings are always joint meetings. The neighboring lab works on similar stuff. Both of us are small labs as well so it makes a lot of sense for us to meet together.

The professor from the other lab always asks the presenter tough questions.

I felt like I fielded everyone of his questions really well.

I felt prepared, I had answers to most of his questions.

I’m going to look for answers to the questions I don’t know in research papers.

I haven’t gotten around to describing more about what I do in lab, which might have made this post a little confusing.

I’ll try and upload a post that goes in more depth for my lab meeting presentation in the future.

That’s all for tonight.

-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