My lab works with tuberculosis, which requires BioSafety Level 3 (BSL-3) containment. You know what else needs BSL-3 containment? COVID-19!
BSL-3 lab spaces have a lot of specialized safety features that make them expensive to construct. To save money different labs at UC Davis often share the same BSL-3 space and just schedule their time in that lab space to not get in each other’s way.
Because of that, when researchers started working on COVID-19 at UC Davis they needed a place to do it. My boss’s space was volunteered, so now another lab researching COVID works in the same space as us.
Besides the safety features, the BSL-3 also requires biohazard suits and respirators. Additionally anyone working in the room within 24 hours of COVID being used in the room has to do temperature checks for two weeks afterwards. Our safety protocols have been successful and no one working in the space has contracted COVID-19.
But working in that space puts our lab into a high risk factor, just like healthcare workers. As such, I got contacted by my HR supervisor at UC Davis Health that I’d been approved for being one of the first people to get one of the COVID vaccines.
So here’s what that was like!
I scheduled an appointment for 8:30am on the first day of distribution. I got there at 8:25, checked in, and promptly waited for an hour in line.
NASA made an interesting announcement, they’re looking for new astronauts!
This came as a surprise to me as I’d thought NASA had discontinued all manned missions.
As far as I know the halt on manned missions happened for two reasons, funding is tight and NASA is an obvious thing to cut and we already did the man on the moon thing so why go again?
As to the funding, I’m not sure what’s going on there. Regardless, the missions NASA is planning are scheduled ten years out so the funding situation could be entirely different then.
But what are the new missions?
Not going to Mars like Mark Watney in The Martian, but almost as good!
NASA will be landing an astronaut on an asteroid.
There are a group of asteroids called “near-Earth asteroids” that have orbits around the sun pretty similar to Earth’s orbit.
A couple of the near-Earth asteroids are as big two kilometers across (about a mile).
Before landing a person on an asteroid, NASA plans to land a rover like what they did with the Rosetta space probe on a comet. Then a manned mission will commence in 2025.
I don’t know which asteroid NASA will be landing an astronaut on, there are a whole bunch to choose from. Regardless, this appears to be the next step in manned space exploration.
NASA hopes this will be a stepping stone to manned missions on Mars.
In addition to the work on the asteroids, astronauts are spending longer amounts of time on the ISS. They’re doing this so we can see what precautions need to be taken when someone is in space for years at a time.
A mission to Mars would take a year or two, so we need to be prepared for how someone’s mind and body reacts to being in space for that long.
So enough about why NASA is hiring astronauts, how do I get the job?
If you’re like me, upon hearing the news that NASA is hiring you immediately looked up the qualifications they’re looking for.
They want someone with at least a Master’s degree in science or engineering. I’m working on that, so good so far.
The next big qualification is 1,000 hours of logged jet plane fight time.
If you’re paying for lessons and rental time on a plane that amount of logged time would cost upwards of $50,000. So you either have to be really serious about flying jets recreationally, a commercial flyer, or a member of the airforce.
There are a few other qualifications, but nothing as big as those two.
Obviously I don’t meet that requirement, but maybe some kid is reading this and is thinking, “If I get a Master’s in physics and learn to fly a jet then I’d be ready to apply to be an astronaut by the time NASA starts doing missions to Mars.”
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!
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.
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.
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!
Another movie I saw with my wife! Can you tell who my favorite person to go to the movies with is?
Age of Adaline tells the story of a woman who acquires immortality during a car accident. The movie has a pseudoscience explanation for how she becomes immortal that my wife and I laughed at.
Adaline was born in 1908. The movie hops around a little bit, but most of the story takes place in 2015.
Adaline fell in love and had a family back in the day. She obviously outlives her husband, but her daughter remains a character throughout the movie, aging into a granny by 2015.
At some point the FBI figure out that Adaline is immortal and they move to arrest her because she’s suspected of communism or something (this part wasn’t clear to me).
Adaline goes on the run. Every ten years she changes her name and moves to a new place, keeping the same youthful appearance of Blake Lively wherever she goes.
In 2015 Adaline falls in love with Ellis, a rich socialite who spends his time learning about the local history of San Francisco, something Adaline is intimately familiar with.
I suppose the viewer is meant to feel that the love between Adaline and Ellis is something wonderful and worth preserving, but frankly it feels creepy.
First of all, Ellis pursues her in the most stalker-like fashion possible. She sternly tells him she’s not interested at a party. Next he shows up at her work and hits on her there. They go on a date and then she calls it off. After that he figures out where she lives and waits for her outside her apartment.
Like I said, I think the audience is supposed to feel that his love is earnest, but he seems more like a rich boy who can’t have what he wants and starts freaking out about it. A normal person would start considering a restraining order at this point.
Of course Adaline doesn’t do that, she takes him back and agrees to go on a weekend trip to his parents’ house!
When she meets Ellis’s parents Adaline discovers that she used to date his dad after her husband died and was considering marrying him. The plot ensues and I don’t want to ruin the rest of it for you if you plan on seeing it.
The romance of the movie is terrible. There’s the issue with Ellis being a stalker, but the additional problem of Adaline being a little bit of a cougar. After all she is dating someone who is a quarter of her age.
That said, the science fiction parts of the story are interesting. How does an immortal person’s life work amongst mortals? Is she still sad when her pets die? How do friendships work for her? What does she do with all her time? Does she “retire” every couple of years or keep working? Those are all interesting questions that the movie answers well without even focusing on them.
I wouldn’t recommend seeing this movie in theaters, but if you like little science fiction stories about immortality (I do!) then I’d recommend renting Age of Adaline once it comes out on DVD.
A week after moving into our new home my wife and I had some of our friends over to celebrate my birthday.
We went out to eat and then saw the Dreamworks movie, Home.
The movie is about an alien race that invades Earth and takes over everything.
The trailer didn’t talk about this much, but the invading race, the Boov, are running away from another alien race, the Gorg.
The Boov move all the humans on Earth to Australia and deposit them in a prefabricated idyllic suburban complete with ice cream and amusement park rides for everyone (nevermind that most of the world wouldn’t consider this a paradise but a horrible alien environment).
The Boov overlook one human in the abduction process, Tip.
Tip and her cat, Pig, soon hookup with an outcast Boov, Oh. Oh is as socially awkward as someone can be and also accidentally sent an email to everyone in the galaxy, inviting them to a housewarming party on Earth. Everyone in the galaxy also includes the Gorg who will be coming soon to blow up the Earth.
The rest of the Boov are looking for Oh. Oh is running away from them with Tip, but to get her cooperation he has to help find her mother who was moved to Australia.
The trailer can probably tell you the rest of what you can expect from the movie. Oh doesn’t understand human culture and Tip teaches him about it.
I liked the movie a lot. It is a traditional kid’s movie where everyone gets a happy ending with no consequences, but that’s fine.
The acting is well done by Rihanna and Jim Parsons. They aren’t playing characters that are significantly different from what they’ve done before. A little typecasting never hurt anybody.
The movie has great coloration as well. I don’t often expect movies to be that visually pleasing.
The Boov have all sorts of colors for their technology, going all over Earth presents tons of different landscapes and colors, and most important of all the Boov themselves have tons of colors to represent their different emotions (blue for neutral, red for anger, yellow for scared, green for lying, etc.).
The movie had the ever present issue of “Why does everyone speak English in space?” but that’s something you get over after watching and reading tons of science fiction stuff.
It was the perfect movie for my loosely space themed birthday party! We had a cake with stars and a moon on it after the movie of course.
I have begun my Master’s project in earnest and the goal is slightly different than what I’d been doing before.
First, I’ll repeat myself. I’m a biologist and I work with introns in C. elegans. C. elegans is a type of nematode worm that naturally lives in soil or on rotting vegetables. It is also one of the most widely used model organisms for biological research.
Introns are unused sections of genes. You’re probably aware that DNA is in our cells and contains the instructions for how an organism functions. The human genome contains around 25,000 genes and those genes are split into two parts, introns and exons.
Exons are the part of that gene that are actually used to produce things in your cells, while introns are spliced out and removed. So why are introns on there at all if they’re removed?
Well it turns out that some introns increase expression of the genes they’re in. My project looks at how placement of those enhancing introns affects expression.
Experiments in plants have shown that an enhancing intron works best when it is placed near the start of a gene. Experiments in C. elegans have suggested that, but no experiment has outright proved it. My project will hopefully do that.
I’m measuring the expression of genes according to how introns affect them, so I get to pick which gene to use. When picking a gene like this scientists often pick what are called reporter genes. The expression of these types of genes is easy to measure, often because they have produce light or fluorescence of some kind. The light tells you whether the gene is on, but also at what level it is turned on based on how bright the cell is.
Previously I was using a reporter gene called GUS. GUS is an enzyme that digests a specially prepared sugar, releasing a blue chemical that was attached to that sugar. The blue chemical is then visible to the naked eye.
There were a number of problems with that experiment though. First, adding the sugar chemical to the worms was a pain, taking about three days to set up and look at. Plus, the blue color was difficult to measure precisely because most of the machines in the lab are set up to measure red or green colors, not blue. Finally, GUS is traditionally a reporter gene for plants, not C. elegans. This could’ve been introducing other problems that we couldn’t easily identify. Thus the use of the GUS reporter gene has been scrapped in favor of another reporter gene.
I’ll be using Green Fluorescent Protein (GFP) as my reporter gene now. GFP is widely used in C. elegans and many other organisms. The protein created by the GFP gene glows green when you shine a red light on it. Very easy to see and measure. None of that three day procedure for GUS. I just pop the worms under the light and take a look.
Why weren’t we using this procedure before if it’s so easy? Two reasons!
Reason number one: C. elegans won’t express GFP without introns in the gene. So does that mean we proceed and hope one intron is enough or do we add the standard amount of introns to get expression? I’ve decided to see what the GFP looks like with the standard introns scientists put in it for C. elegans and without them. I’ll also be testing with an added intron. The whole thing is a little complicated so here’s a diagram to explain.
There are eight different constructs I’m making. They are a combination of three different features that are present or not. Are there introns in the first GFP? Yes or no? The second GFP? And is the Unc54 intron there? This allows us to control for the positional effect the standard introns in C. elegans GFP.
Reason number two: Those eight constructs above? Those aren’t made yet! All the GUS constructs were made when I started the project. I’ve been working on making the new constructs for a few months. It could take a few more months to finish.
So my project is to make those constructs, put them into worms, and then see what the worms look like. As I perform these steps I’ll make more posts about what work I’m doing in lab and why its so cool.
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!
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.