Duke University | Howard Hughes Undergraduate Program

 Haha, so for once I'm not going to put off my blog writing because I have something related to say... this blog is dedicated to my rant about how AWFUL of a day it was! I'm pretty sure the other people in my lab have developed a resilience to this already, since they just brushed it off with a "oh, typical Monday", but I was really frustrated. So, this is going to be my "woes of research" post, maybe I'll do another "joys of research" one, if I can fit them all in one post :)

So basically, our lab is cursed. It didn't used to be cursed, this is a recent development. You know why I think it's cursed? This morning, my mentor Jen was doing an extraction while I was doing a Fastseq reaction on some PCR products to prepare them for sequencing. We both screwed up in frustrating ways (or at least she seemed sort of frustrated... she was working with Kevin who described it using profanity and the word "fest". Like "profanityfest"). I ended up wasting way too much money's worth of bigdye (probably should've been reprimanded, but the people in my lab are too nice to yell at me, haha) and messing up the same simple reaction, basically just transferring stuff from one plate to another like a robot, two times. And there isn't that much PCR product. So I had to go back to my bacteria, pick colonies again, and redo a bunch of the PCRs, getting basically nothing done in the morning - SO aggravating! 

After lunch, I was feeling a lot better (I actually took an early lunch because I didn't think I could not screw up in that annoyed state). I finished my sequencing (which was now out of order due to the mishaps from this morning). Unfortunately, my frustration made my lab notes disorganized and barely legible. Not that my handwriting is ever that easily legible, haha! And I think I'm going to cut that short and say that the plates we submitted for sequencing were spliced up into chunks and fitted back together, and I'm so grateful that Lisa, who does the sequencing, was willing to deal with them. AND SHE'S ISABEL'S MOM. ISABEL, COMMENT ON THIS!!! Hahaha :D

So after I was done with the sequencing, I was pretty much "okay, so I'm going to do something that requires very little concentration and has very little potential for error - I know! I'll write my introduction!" This required logging out of someone else's account on the sexy mac and logging into Jen's. And the mac, which never freezes, froze. But you couldn't even tell, so we waited for what seemed like forever, and finally decided to switch to another computer (which wasn't as sexy, but easier to use for me because it was a PC). BUT THEN THE PC FROZE TOO. I fixed it, it wasn't as big of a deal, but seriously, when do 2 separate computers freeze within like half an hour?

Introduction: Sometimes, people screw up. Often, it's because they're having a bad day. Curses can sometimes cause people in a lab to have a bad day. In this particular study, we examine the effects of curses on a genetics lab.

Materials and Methods: Using a longitudinal analysis of the Willis Lab conducted between the dates of June 15th and July 13th, we estimated the ratio of work done to results obtained and assessed the qualitative effects on researchers' emotions (see fig. 1)

Conclusion: Based on the high ratio of work done to results obtained, the feeling of frustration present especially in the prone-to-overreaction novice researcher, and the prevalence of unfortunate incidences, we conclude that THE LAB IS CURSED.

Figures:

Fig. 1. An example of a common emotion felt in labs that are cursed

Been dreading this blog post - how are we supposed to summarize what our day is like when it's different every day? At worst, my days have been an entire day of doing the same time-consuming thing (like picking colonies of bacteria to use for DNA. SO. MANY. COLONIES). At best, they've been chock-full of only the exciting parts, like getting sequence back, or running gels, or PCR! Those are my favorite days. I love having a lot of different stuff to do and trying to work it into an efficient schedule, so my hands are always moving and I minimize my downtime; it always makes me feel so efficient :D

Since this is only one day in the life, I'll just give you want I'll be doing next time I'm in the lab! I just finished cloning a set of bacteria that had DNA from my plants in them, so now I need to make them sequenceable. Surprisingly, there isn't a red squiggly spell check line under sequenceable.

First thing - prepare the gels! I need 2 small gels and 2 large gels, since I have 200-something samples to run (yes, this was from my entire day of picking colonies). The lab doesn't have that many combs, so I'll make a large gel and a small gel first. These take like 20 minutes to set.

While I'm preparing gels, I can do quick tasks, like going to the refrigerator and checking how many plates I have prepared or going to the incubator to check if the E. coli grew and if the transformation worked. These are really really quickly, so sometimes I'll do them while I'm microwaving (they take less than 30 seconds, I swear!!). But if I'm feeling like a good person who listens perfectly to Kriti/Tanya/Chris's instructions, I'll stand by the microwave and check those things while the agarose is cooling (to cool-enough-to-add-SYBR-safe-dye) :D

If my plates worked, my next priority is picking colonies and lysing them (10 minutes in the PCR machines, which are hopefully open because I forgot to sign up for them yesterday). The plates that are in the incubator right now are re-dos which didn't work the first time. I plated the same transformants again, so they probably won't work this time either... if not, I'll retransform my ligation mix. I think the problem was that I added the SOC media too early, so by the end, my cells were starving and most of them died :(

Then, I need to run my first gel, which by now finished solidifying a long time ago. Filling the wells is going to take me forever, haha. About 15 minutes in, I'll take the lysed bacteria out of the PCR machine and put them back for Standard PCR, and then go back to loading and running the gel.

Then I need to run the first small gel, shouldn't take too long to load.

After I'm done loading and before I need to stop the large gel, I'll prepare my second 2 gels.

Then I take a picture of the large gel using the supercool picture taking machine. I don't really know what it's called... but it reminds me of a superpowered scanner.

Take a picture of the small gel if it's done

Load the other 2 gels

Plate the newly transformed bacteria, if I had to re-transform.

I'll probably get through about half of this list, unfortunately! Days at the lab go by so quickly, it's really not fair :(

OH I FORGOT ONE THING. I GET TO SORT THROUGH MORE SEQUENCES. Most satisfying feeling in the entire world, I love it!

Wow, this is kinda a late update… sorry! I had a hard time thinking of what to write – significance has always been something that’s hard to explain for me. It makes sense in my head that understanding things is important, but when I try to explain that to anyone else, it ends up sounding trifling and lame. But that’s okay. It seems that I’m not the only one who’s curious about how things work, as the entire goal of the Willis Lab is to understand how speciation works in the grand scheme of evolution (Oh man, did you see that smooth transition??). In particular, they investigate why and how new species form, and why/how they stay as reproductively isolated new species, using Mimulus as a model. Mimulus is a really good model because the generation time isn’t too long and the genus is really diverse.
My project deals with a tiny species of Mimulus called “haidensis”. It’s found only on Queen Charlotte Island in BC, and the only other species of Mimulus on the island is guttatus. Jen, the grad student I’m working with, has already figured out that haidensis is a tetraploid – its cells have 4 copies of all the chromosomes instead of the normal 2 copies. What she doesn’t know yet is whether the 2 sets of chromosomes came from the same species (autotetraploid) or different species (allotetraploid), how the 2 plants came to form the tetraploid (Which one was the “mom”?), and what the path of evolution was (Did they all come from one original tetraploid that self-pollinated or did the same tetraploid form multiple times?). You might think the first question is obvious – after all, the only other species on the island is guttatus, so the tetraploid must just have a doubled guttatus genome. However, the plant lives in higher altitudes that guttatus can usually tolerate, and shares a lot of characteristics with another high altitude species, tilingii. This means that there could’ve been tilingii in the area before, but then haidensis formed as an allotetraploid and outcompeted the tilingii, causing it to go extinct in the area. Or it could mean that there were never tilingii in the area and haidensis formed as an autotetraploid of guttatus, then adapted to the high altitudes by evolving similar traits to tilingii. Either way, the evolutionary path of haidensis could show us at least a little bit about the capabilities of plants to evolve and speciate, which could contribute to our long-term understanding of polyploidization as it contributes to evolution. This could be very significant, since polyploidization is likely the most common path to speciation (tetraploids are considered a separate species from their diploid parents, since their different genome numbers keep them from interbreeding). Goldblatt et al. and Masterson et al. estimated that 70% of all angiosperms evolved into their current forms by doubling their genome at some point (or at multiple points). Therefore, understanding the process behind polyploidization is pretty significant.
As for why the polyploids stay new species instead of just dying out, it’s assumed that they must have some kind of competitive advantage. One theory is that polyploids adapt more quickly and have less inbreeding depression because the extra set of genomes allows for more heterozygosity. In allotetraploids, all the plants are initially heterozygous, since their 2 sets of chromosomes are from 2 different species. This is why figuring out how many times haidensis formed is important. If the tetraploid only formed once, and there’s only 1 set of diploid parents, the genetic diversity of haidensis is severely limited. However, if there were many sets of diploid parents that formed allotetraploids, that’s a lot larger of a gene pool, which would increase haidensis’ competitive advantage, if the theory I just mentioned is true.
I get the feeling that a lot of this doesn’t make sense hahah, so ask questions in the comments!

 So today I sat down with my PI, John Willis, so I could ask him a couple random questions that he would have interesting anwers to. He's a really awesome guy, fun to talk to and almost as easily distracted as I am!  As proof of this quality, I've got all these unrelated terms scribbled down in the margins because I thought they were interesting and need to go look them up haha. So here's our superduperawesome conversation (I'm paraphrasing his replies, and brackets are side notes)

What made you want to pursue a career in plant evolutionary genomics?

I've always been interested in nature - ever since I was young, I liked to hike, go birdwatching, collect bugs, etc. In college, I took a comparative anatomy class that was really interesting. It made evolution seem so obvious [as in irrefutable], and that really got me started in studying evolution. 

What college did you get your undergraduate degree at?

Brown.

What were your favorite and least favorite classes?

I had so many favorite classes... uhm... I really liked genetics. My least favorite was organic chemistry. I got a 3 out of 100 on a test in that class once, but it was okay because the teacher dropped our lowest grade.

What was your favorite research project?

All of them, really. I think genetic mapping is fun. Sequencing the Mimulus genome was also really exciting - the genome is entirely sequenced now, but not available to the public yet. However, we have full access to it [how awesome is that?]

What was the hardest part about becoming a professor?

Nothing, it was all just fun. Writing grants stinks.

What was the most dangerous thing you've ever done in a lab?

They don't really let me into labs anymore... it's much safer if I stay away from the lab. I'm too distracted all the time. Maybe field work in risky places? [some Mimulus grow in high elevations]

Have you ever had any lab accidents?

Nah, nothing really bad. I spilled some radioactive material once, but it wasn't bad, we didn't have to evacuate or anything. I just wiped it up.

Do you have any advice for an aspiring scientist?

Oh sure. Find questions you're interested in. You can't study stuff you don't like. Definitely take lots of upper level classes, because those are usually more interesting and you can have better discussions in them. It's a good idea to ask professors for opportunities - just call them up and say "Hey, I'm really interested in this question and I noticed you were researching it, is there any room for me to come and work in your lab?"

Do you have any regrets, like classes you wish you had taken?

I wish I took more statistics classes, and I wish I worked more with computers, and I wish I studied more molecular biology.

Was your family sciency?

Hah, no, not at all. My dad was an English professor. My mom was a historian. Neither of my siblings went into science either.

If you weren't a scientist, what would you be?

I don't know, a cook maybe. I like to cook. 

Are you a good cook?

I'm good at eating...

If you could have any superpower, what would it be?

Teleportation, that would be neat. [cue long conversation about mind-reading and Facebook] I wouldn't want to read minds though, that would be too creepy. I like my privacy, so I wouldn't want people to read my mind, and I feel like if I don't want people to read my mind, then I shouldn't want to read other peoples' minds either.

Hi everyone! I'm Connie Wang, and I'm a rising senior at East Chapel Hill High School. In addition to participating in pretty much everything science related, I also spend a lot of time prepping for and competing in debate, my second love, as well as avoiding anything having to do with history. My summer's really hectic this year, but I always make time to watch So You Think You Can Dance and the occassional Food Network show :)

I'm completely psyched to be working in the Willis Lab for the next 6 weeks (the above cart label represents my thoughts pretty well), especially now that people are starting to return from their trips and the lab's starting to fill up. Everyone in the Willis Lab studies a genus of plants called Mimulus (monkeyflowers) in order to further understanding of evolution and speciation. Specifically, they work on a group of Mimulus species called the gutattus complex, which contains the most common monkeyflowers. Even within this group of closely related species, there are so many differences between the plants, in things as fundamental as whether the flowers are pollinated by bees or self-fertilized and whether they are perennial or annual. Plus the flowers are just so pretty, see?

This week, Carrie Wu and Jessica Selby have been showing me around the lab and getting me used to all the plants and building and lab equipment and whatnot. My favorite part is our workroom in the biology greenhouse - it smells SO GOOD. I thought it was just someone's perfume at first, but the smell has been there every day. It's like a nice apricot-y smell, I wish I could bottle it up and take it with me everyone I go haha. Strange part is, I smelled the flowers up close and they don't smell like anything. So I'm not sure what it is. Given the genetic diversity of Mimulus, I might've just smelled the wrong species or population or something, so it might actually be the flowers... if I get bored one day, I'll go around and sniff all of them and tell you guys where the smells coming from! Haha, trust me that was worth typing a paragraph about. Here are some nice pictures of Jessica (with Young Wha, another postdoc) at the computer and the biology greenhouse. I wish I could take a picture of the smell.

So this week was more of a learning week than one actually working on what my project will be - I planted seeds, transplanted tiny Mimulus sprouts, pruned plants, prepared primers, and collected samples from plants. I touched the plants a lot. Considering that I seem to be cursed with a black thumb (I managed to kill my aloe plant a couple years ago...) I really really hope that the plants are still okay... maybe by the end of the summer I'll get rid of that nasty curse. The first plant I buy will be another aloe. Even though I feel like I haven't done much constructive work on my project yet, I've learned a lot this week (and thought up a lot of questions that I'll probably forget about before I figure out the answer) from looking around. I noticed a lot of things about plants that I never would've noticed otherwise. The sprouts that I replanted were the cutest little things. While most of them had 2 cotyledons (Mimulus are dicots), there were a couple that had 3 and were triangle shaped. They were especially cute. I think they're like 4 leaf clovers, so I'm hoping they're lucky too. I took a picture of one, growing in slightly fungus-infested perlite, so maybe it'll bring you luck too:

This little baby Mimulus is the reason why the cuteness of plants is debateable. The "fuzzy" part is debatable because some of these things actually have slimy hair-like structures... so they look sorta fuzzy. 

I'll most likely be paired with Jen M. a graduate student who's working on polyploidism in one species of Mimulus. For that reason, I went on a textbook/internet scavenger hunt about polyploidism today. That was when it became painfully clear that I'm a huge science nerd who gets excited by plants and enjoys reading textbooks about biology. Young Wha explained to me some stuff about polyploidism and I'm sure my entire face lit up. Basically, you can create new species of plants in the lab with a chemical that duplicates the original plant's set of chromosomes - how cool is that?? Jen is trying to figure out whether one species of Mimulus is actually an allotetraploid hybrid of 2 other related species, and to be honest, I'm not really sure how that relates to anything yet. I just know that it's supercool that she's created polyploid Mimulus in lab before. Oh man I'm so excited, I hope I get to do that.

With all the fun I've had this week, there was one disappointment - monkeyflowers don't actually look anything like monkeys. Seriously, what were the namers thinking? However, the lab did have a whiteboard, on which someone posted a little cut-out picture, colored with a crayon, of a monkey flower that looks like a monkey. It's the only one.