Late Nights in the Lab

Posted on by

Eat breakfast, go to lab; eat lunch, go to lab, eat dinner, go back to lab. You see the pattern? Going out to the field, late hours in the lab, getting my experiment ready, getting pumped for whale watching or going out on the Centennial is all just another week in the Friday Harbor Labs (FHL). When this is the same schedule twenty others share with you it doesn’t seem as hard of a schedule. Especially when the sun doesn’t go down until ten at night, you get used to the work hard and play hard cycle that everyone seems to adopt when they come here.

My name is Deanna and I’m one of three students working with Molly this summer. My project is on Botrylloides violaceus which is an invasive here in the United States on both coasts. It originally came over from Japan and was first spotted in the 70’s here in the San Juan Islands. These sea squirts are a member of the fouling community and are pretty abundant at several harbors here in Washington. We went collecting on Tuesday last week and we found a lot at Roche Harbor (RH) and Fisherman’s Bay (FB) which are two of my field sites. We also saw a small colony of them at Cattle Point in the tide pools when we went one weekend. What I’m looking at with these guys is to see if they have any acclimation to local environmental conditions. This is important to look at because this invader is not found in some harbors (like the FHL docks) but is very abundant at others (FB). It would be interesting to find out which conditions they favor in order to see which harbors might be at greater risk of getting invaded.

This last week was really exciting as we prepped petri dishes containing juvenile Botrylloides violaceus for the field. After all the little guys were settled on the dishes we attached them to pvc trays submerged in 12°C seawater . . . while the plates were upside down. That was challenging and Molly and I worked late into the night/morning getting everything ready for deployment the next day.

With six hours or so of sleep we started up again later in the morning. We took the Coot (one of the four motor boats available for research) out to Fisherman’s Bay and hung the first of three of my contraptions. It was actually really good conditions for deployment because it was overcast. You would think that having a sunny day would make it better, but with the clouds it kept the trays cool while we assembled them in the field.

After hanging the one out at FB we headed back to the labs for lunch. In the afternoon we hung one off of the FHL docks and then took our sweet Ford Truck out to RH to hang the third and final tray. So now, my experiment has officially begun and we’ll be checking on it this Friday!

That’s all for now guys. We’ll be sure to keep you updated!

Dicty Dancing

Posted on by

Hello everyone! My name is Kirsten Bickford and I am doing summer research with Catherine O’Keeffe and Dr. Parrish. We are using the amoeba Dictyostelium discoideum to eventually isolate putative mRNA decapping enzymes. These enzymes, termed Nudix enzymes, are found in large viruses all the way up to humans so being able to isolate and define the function of these enzymes is very exciting.

In order to do our experiments, we need a constant stock of healthy cells. We grow the Dicty cells on plates and in a flask and usually pass them about 3 times a week, so as to diminish genomic mutations. So far we have isolated genomic DNA, and are starting the process of doing a gene knockout. Currently, we are ligating and transforming parts of the gene into bacterial cells, but this is just the beginning of the process.

Compared to working in class laboratory settings, summer research is much more independent. Although I have learned sterile technique previously, there is much more pressure to do it properly as our cells will become contaminated otherwise. Many of the molecular techniques are new to me but with Dr. Parrish’s supervision, I have been able to learn how to do them properly and on my own. Pipetting is a huge factor and my technique has definitely improved since the start of the summer.

Hopefully our research will continue to go as planned, without equipment failures or major contamination. We will definitely be busy for the next 5 weeks, but another blog post is coming soon!

Driving Miss Dicty

Posted on by

We are currently in our fourth week of research here at the McDaniel Dicty Lab. Dr. Parrish, Kirsten Bickford, and I (Catherine O’Keeffe) are studying the social amoeba Dictyostelium discoideum, also known as a slime mold. We are interested in looking at two particular genes that code for possible mRNA decapping enzymes.  We started this project at the very beginning, which means had had to grow the amoeba cells from stocks. Since our first days in late May we have been growing and passing cells. Luckily, the cells have been healthy and we only had one unfortunate case of fungal contamination. We have been mastering many molecular techniques such as DNA extraction, PCR, gel electrophoresis, ligation, and transformation.

One thing that surprised me about working here is the amount of independence we have. Before this summer, I was not too confident in my lab skills. However, now I am much more self-assured and feel motivated to work on my own initiative. One of my favorite things to do is troubleshoot (even though this means that something went wrong). Though we are just undergraduate students, Dr. Parrish asks us what we think needs to be changed and has us research to figure out how to fix the experiment.  We look at the protocols, search online, and talk together to figure out a solution.

Working in the lab is also a lot of fun! We listen to music, have glar dates together, and joke around. Enjoy these pictures:

A homecoming

Posted on by

We’ll be blogging about all the research and the cool organisms we’re working with in the coming weeks, so stay tuned for that, but first I (Molly, a.k.a. Dr. Jacobs) wanted to give you some background: Friday Harbor Labs (FHL) is a field station run by the University of Washington, and it is located in the San Juan Islands, which are a couple hour drive and a 1.5 hr ferry ride northwest of Seattle.  The Canadian border runs along Haro Strait, which separates San Juan Island (our home) from Vancouver Island.  The water is cold, the weather is cool, and the shores are rocky and steep!  Here’s a photo of the FHL dock – this is the view from right outside our lab space.

FHL is a special place for me.  I first came here as an undergraduate doing a summer research project, and this is where I really got hooked on marine science.  I came back as a graduate student, and lived and worked here for almost seven years while doing my dissertation research.  I think of this as paradise on earth, and not just because of the scenery – what really makes this place special is the scientific community.

In the summer, researchers come from all over the world to work here, and even though some of the people are very famous, the atmosphere is egalitarian: everyone from the lab director to the most junior undergraduate goes by his or her first name, and is treated as a scientific peer.  The level of science is high, and people work hard into the night, but it feels like we’re all at summer camp together.

I’m thrilled to be here with three McDaniel students!  We’ve been working hard, but on Saturday we took a break to go tidepooling in one of my favorite places on the island, Cattle Point (on the southern tip).  In this picture, rising junior Joe Odierno is standing in the low intertidal – behind him is the strait of Juan de Fuca, and behind that are the Olympic mountains!

Here’s another view of Cattle Point, this one looking a little more to the east.  The land mass in the background is another of the San Juan Islands (Lopez).  Rising senior Deanna Campbell is in the foreground; if you squint, you can see Joe and another student down on the shore:

Finally, here’s one of my favorite critters: the starfish Pycnopodia helianthoides.  These voracious predators can be more than 3 feet in diameter (!), making them the largest known starfish.  The really big ones are subtidal, though – this low intertidal specimen was much smaller.

 

First week at Friday Harbor Labs

Posted on by

It has been a full week already and it flew by. Everything about Friday Harbor Labs is awesome. The ferry ride to the island is one of the most scenic things I have ever experienced. There are big rocky cliffs everywhere dropping off into the cold blue waters of the Puget Sound. In the distance you can see Mount Baker in one direction and the Olympic Mountains to the other. Both are huge snowy peaks poking up through the clouds. Giant pine trees tower above the entire lab campus. The wildlife is also spectacular. There are so many birds everywhere, a true bird watchers dream. My favorites are the quails, which are a common and very charismatic ground bird. There is actually a Rufus hummingbird buzzing around me right now. The deer here are like squirrels they are everywhere and don’t care. You walk right by them and they pay you no real attention. However, by far the most amazing thing about this place is the marine ecosystems. A quick stroll on the shore about you will see giant bull kelp, starfish, polychaetes, crabs, isopods, seals, fish, and the list goes on and on.

The people here with me are also great. It’s only been a week but we are already like a family. There are 19 or so of us I think. Basically we all work very hard from after breakfast to dinner in our labs and then we all kick back together at night. It has been a great time every night so far. I am pretty sure I have made some friends for life and future colleagues. It is so nice to be in the company of other aspiring scientists like myself. All of actual scientists here are great too. They have all been very friendly. Everyone is on a first name basis. We are all working on our own projects and at the end of the summer we will be giving a presentation about our work. Hopefully at least some of us will be able to publish; I know I would be very siked if I could.

My research is investigating the decorating behavior in the last larval stage and very young graceful decorating crabs, Oregonia gracilis. I will also be characterizing their early ontogeny as it has not been done before. One of the most exciting things to me is I have managed to incorporate the electron microscope into my work. I have always wanted to use one. Well that is all for now enjoy the pictures.