Current Research Blogs
Jasper McCutcheon, undergraduate student
1 February 2024
Welcome to Winter Quarter! It has been a funky start due to the holidays and snow days, but I am finally starting to settle into a routine, and I hope everyone else is too. It’s been nice being back on campus and seeing familiar faces. Just a few days ago I got to catch up with Alex and Vic (the lab’s graduate students) and my fellow project managers (Jack and Maya).
Having school in session also means that my schedule has filled up once again, but I am making sure to set aside time so that I can keep working on my independent project. So far, observations are going well which makes me hopeful that my methods have finally been ironed out. Now that I finally have my research questions and methods figured out, it is time to start looking at the data that has been collected already. As I have mentioned before, I am starting data analysis. So far this has mostly consisted of researching the best models for the variables I have. I have been in contact with past MMEL undergraduate students (Kyra Bankhead and Holland Conwell) who have done similar projects to mine. With their help, I am hoping to be able to start making a dent in my analyses. Currently, I’m thinking that I’ll be using either a GLM (generalized linear model), GLMM (generalized linear mixed model), or GAM (generalized additive model). These models are more complex than anything I have dealt with before, so I have been doing a lot of Googling and will likely be continuing to do so for the foreseeable future. My goal for this quarter is to get most of my code for data analysis written so that as I am getting more data, I can just keep adding it in.
Hopefully the next several blogs will track my progress through the scary world of data analysis.
Until next time,
Maya Mijares, undergraduate student
1 February 2024
This month has definitely been an adjustment while getting back into the groove of school. It was a slow start since the first two weeks of school were interrupted by Holidays and TWO snow days! I don’t think that I have ever seen that much snow in Bellingham, and it made for a fun few days of playing in the snow!
The Whatcom Creek project has been pretty quiet so far this quarter. Since there are no salmon in the creek right now, the seals have been pretty scarce. I, unfortunately, haven’t seen any seals in the creek during the few observations I have been on so far, but I do know that one of the observation teams saw at least one seal over this past weekend! Due to the decrease in seal activity during the winter, there are going to be fewer observations this quarter than in the fall. However, this allows extra time for photo work, which is good because we have a huge backlog of photos from fall quarter to ID and crop!
The mtDNA project is also moving along smoothly! Alex recently showed Isabel and I how to Qubit, which essentially means measuring the concentration of DNA in our extraction samples. It is important to make sure that the concentration of DNA is not too high or low before we perform PCR (polymerase chain reaction) to trim the samples for sequencing. Alex is officially training Isabel and I on PCR protocol and how to run gels (a way to make sure that the PCR was successful) this weekend! We are going to run PCR on 4 samples, using two different primers on each sample. The primers we are testing are an older primer that others in the lab have used before and one that Victoria designed for her eDNA project. After running PCR on the samples, we are going to send them in for sequencing to see which primer will yield better data. I am excited to start doing some more molecular lab work this quarter and getting our samples ready for sequencing!
Alex, Isabel, and I are also going to be helping at an outreach event for college students interested in research! Next week, we will walk the students through a tour of the lab, as well as explain a little about general ecological and molecular research and specifically what our lab does. I am excited about this event, as I believe outreach and education events are a vital part of being a researcher, as well as just being super fun!
That is about it for January! I am looking forward to reporting how PCR and sequencing go in my blog next month!
Isabel Shier, undergraduate student
1 February 2024
Winter quarter has officially started, and it’s great to be back!
I spent most of the break back home with my parents in Pullman WA, which was nice and relaxing. Then my whole family went down to California for a week to visit my older sister. One highlight of that trip was going to the Aquarium of the Pacific and getting to see some seals and sea lions! (Don’t get me wrong, I obviously love all marine mammals, but I’m a pinniped girl through and through.)
California sea lion at the Aquarium of the Pacific, Long Beach, CA. Photo by I. Shier.
It is good to be back though, and I’m excited to hit the ground running on some lab work this quarter! Maya and I have been working with Alex to finish up DNA extractions and qubiting. This has been some good housekeeping while we set up for our next step, which is running PCR’s on the DNA extracts, running gels, and sending the products off for Sanger Sequencing.
Alex is going to train Maya and me on PCR and gel electrophoresis this weekend, which I’m stoked for! We actually got to run a PCR and gel in my Methods in Molec lab recently. I really enjoyed the process in class, and it’s going to be even cooler knowing the samples being run are working towards our project!
After that, we’re planning to send off a couple of our PCR products to be sequenced. This will just be a test run to see that everything is working as it should be, and to help us choose which of the two sets of primers we have access to works the best. (Big thanks to Vic for letting us use her primers!)
That's all for now, but more news to come!
P.S. I’ve had the joke: “Is your agarose gel running? Then you’d better go catch it!” stuck in my head for days.
I don’t think it will ever leave.
Jack Mezzone, undergraduate student
1 February 2024
My name is Jack Mezzone and I am the new co-manager for the Whatcom Creek Project alongside Maya. I am a senior working towards a general emphasis biology major and a minor in chemistry. I have had an amazing time in the lab since joining! Being a part of such a motivated, dedicated, and fun group of people has made for a strong highlight of my college experience.
I had the opportunity to be a part of Madison Gard’s Smolt Project last Spring as an observation lead in which harbor seal predation pre and post to the Bellingham Technical College’s smolt release was examined. I am excited to announce that I will be taking on this research in the MMEL and furthering the data we have on harbor seal predation surrounding smolt release. Maddie and I will be continuing this project with the goal of a manuscript in the future. Maddie graduated last Spring and will be working on the project remotely while I am on campus and on site. Thus far, we have been discussing the setup for the second year such as how many research assistants are ideal for a project with so many observations and moving parts.
In other news, the MMEL is bringing on more undergraduate research assistants for Spring and future quarters. The managers have been working together on getting the word out and developing/updating the hiring process. For those interested, this is a for credit or volunteer opportunity with applications due February 29th. We are super excited about meeting the applicants and welcoming enthusiastic individuals into the lab as undergraduate research assistants!
Updates to come on the Smolt Project as Spring gets closer and more details are finalized!
Until next time,
Maren Duffy, undergraduate student
1 February 2024
Hello! My name is Maren Duffy and I am currently a junior at Western, studying Biology with Marine Emphasis and working on a minor in the Honors College. This winter I am starting my third quarter with MMEL, since joining the Whatcom Creek Project in spring. It has been a really exciting opportunity to become a part of the marine mammal community here at Western and to apply my interests to research and my education! Outside of school, I work during the summers on a whale-watching boat in Anacortes, WA, as a deckhand and naturalist. This has allowed me to get some excellent on-the-water experience and has absolutely motivated me to work in an environment such as MMEL.
These past three quarters have been very exciting for me at MMEL, filled with projects that have provided plenty of chances to really dig deep into pinniped research. Alongside assisting with Whatcom Creek observations, photo-cropping and starting to learn to photo ID, I started this Fall quarter with assisting Erin D'Agnese with her harbor seal diet study. Working with a group of my MMEL peers, we homogenize fish in the lab on a weekly basis. I am looking forward to continuing to help with the project and get trained on extractions in the next coming weeks. I have also recently gotten an opportunity to work with Haley Recob on an independent project looking at harbor seal haul out sites and their sex ratios, examining differences in boldness levels and availability of prey. This is something I am very excited to expand on in the next couple quarters. We are currently in the beginning stages, working on our concept maps and outlines, along with reading as many related papers as we can. This quarter has a lot in store and I am thrilled to be a part of it.
Haley Recob, undergraduate student
1 February 2024
My name is Haley Recob (she/her) and am currently a junior at Western Washington University majoring in General Biology with a minor in Environmental Science. My journey as a Marine Mammal Ecology Lab student started last March when I joined the Whatcom Creek project as a research assistant. Since then, I’ve helped numerous of my lab-mates take field observations, extract DNA, and collect data for their individual projects. I am very appreciative of the opportunities the MMEL has given me and all the support from my peers. The fall quarter was spent working on photo ID folders and collecting a ton of data on the harbor seals at Whatcom Creek during the salmon spawning season. I also obtained a position at the Nooksack Salmon Enhancement Association as a Community Programs Intern doing riparian habitat restoration and community outreach.
As of winter quarter, I have been appointed the MMEL Photo ID Lead for the Whatcom Creek project. I’ve been getting used to my new position as being on the leadership side of the lab has been exciting. I hope that the new assistants we hire in the spring will be interested in photo ID as well and ask to be trained! I also have eagerly started an independent project with Maren Duffy. Our project examines the factors that may explain sex ratios across harbor seal haul-out sites in the Salish Sea. We’re specifically looking into the impacts of prey availability and boldness levels. So far, we have been brainstorming ideas and creating concept maps to look at the big picture within our research, including different ways we can collect data. We hope to come up with a complete outline soon! In the coming months, I hope to continue balancing my responsibilities of my course work, lab work, and work-work.
I am excited to start sharing my monthly updates with you all. Thank you so much to Alejandro, Maren, Alex, and all my peers who have supported me up until this point!
Until next time,
Olivia Balaban, undergraduate student
1 February 2024
I started this project just this quarter, so this is my first blog. For this project I am recreating data from a master’s thesis by Jonathan Blubaugh. My job is to create and R program that will calculate the weighted average of the trophic impact of harbor seal prey on male and female harbor seals by using biomass. So far this quarter I have mostly been making sure I have all the data I need, and I know where to get it. Last week everything was officially prepared so I made a map of how each prey category would be organized. All that’s left is to start coding. I’ve started practicing pulling all the data I need into a program from excel but there is still a lot to do. I’m looking forward to getting into the weeds.
Thanks for reading!
Alexandrea Otto, graduate student
1 February 2024
It was a very entertaining start to the first week of labs this past month. From double “snow days” (not in the same context to Nebraskan snow days I am use to) and falling victim to the occasional dubious dining choices that led to my demise and case of food poisoning. Today, I’m glad to be past all the chaos and grateful for my health during this busy time as a graduate student!
I don’t have many particularly new updates this time, but nevertheless updates! I received data from the fifth optimization run and am currently mining through the data again to narrow down our SNP markers. It seems in this last round of optimization there are some more SNP primers than last time that are not playing well with one another in primer interactions. To those SNP primers, we remove one of the culprits in hopes to lessen the reads being eaten up by just one SNP and gain better resolution in our SNP panel overall. I am definitely getting more comfortable handling massive amounts of data and coding through each optimization run.
I’m excited to start lab work with Maya and Isabel during their mtDNA project this quarter! We are going to do some PCR and gel electrophoresis this weekend. This different type of lab work will be refreshing while at the same time a flashback to my eDNA project and work as a technician. In addition, the MMEL is selecting more research assistants this quarter and I am beyond stoked to meet all the new exciting and inspiring applicants again!
Victoria and I just received news that we were awarded student travel grants to attend and present at the 2nd EPMOHC (Eastern Pacific Marine One Health Coalition) Workshop coming up in the end of February! We will be presenting 15-minute talks at the workshop, which can be a little nerve wracking and intimidating as a student. In times like this though, I just try to remind myself some science and the fun fact that excitement and nerves are just the same physiological response in the body! I am super excited to have this opportunity to get a realistic perspective and understanding of what science looks like past academia! I am especially interested to get a sneak peek “behind the scenes” in discussions and collaborations between different working groups that workshops like this foster and develop. I will also be presenting a 30-minute thesis presentation soon for class. By the next blog post, hopefully I will have whipped up two thesis talks by then!
Till next month,
Victoria Vinecke, graduate student
1 February 2024
How is it already February?! Winter quarter has been a whirlwind so far with lots of surprising events such as unexpected snow days and last-minute funding application opportunities!
This quarter I have stepped into a “Super-TA” position along with being the Lead-TA for Biology 206 lab. As a Super-TA I am in charge of organizing materials, updating reading chapters, assisting other graduate TAs, and conducting behind-the-scenes dissections! It is nice to have time set aside to help with the organization of materials and learning dissections done outside of lab. Organization of materials takes quite a bit of time but I know it will make future TAs and instructors lives easier!
Bellingham received multiple inches of snow during the second week of classes which resulted in two snow days! It was nice spending time in the snow with my dog while taking breaks from working! With 206 missing two full lab days it was all hands on deck figuring out how to get our students up to speed. But with a collaborative effort, we were able to come up with alternatives!
Lastly, Alex and I were notified of a funding opportunity to attend a marine ecosystem health workshop for professionals! We were able to submit the funding application in time and were notified shortly after we both received the funding! We are extremely excited to take part in the workshop, present our current research, and spend time networking!
Overall, it has been a fun but very busy month! I am eager to share my experiences from the workshop next month along with other exciting updates!