Current Research Blogs
Jaspers's Blog
Jasper McCutcheon, undergraduate student
1 May 2024
Hey again everyone!
I cannot believe that it has already been a whole month since my last blog post! Time seems to be moving at warp speed and a snail’s pace all at the same time. Spring break is long gone, and Spring quarter is now well underway.
With April over, the Northwest Student Chapter of the Society for Marine Mammalogy (NWSSMM) conference is fast approaching. Fortunately, I have nearly completed the poster for my presentation - the only part I am missing is some real results. At the moment, I’m not liking my chances of finishing the statistical analysis in time for the conference. In lieu of a completed results section and the accompanying figures, I plan to discuss some preliminary results. While they are very (and I mean VERY) preliminary, they will still give my audience a good idea of how I am attempting to answer my research question. For my new readers (I like to imagine I have an ever-growing fan base who are sitting on the edge of their seat at the beginning of each month for a new post) my research question is to determine the influence of in-air noise on the number of harbor seals at the surface, how long they spend there, and the frequency of different surface behaviors. While my poster is not quite what I had imagined, I am proud of the work I have done (with the help of many others) and am excited to present it at the conference.
Additionally, I am hopeful that I may even meet some interested audience members who will have some advice for me about my statistical analysis. This sort of networking will be very new to me (my first large-scale opportunity to do so), but I am looking forward to it. From what my mentors have told me, networking is where a lot of great work begins.
All in all, this next month is going to be very busy, but will have a great starting point: the NWSSMM conference.
Until next time,
Jasper
Maren's Blog
Maren Duffy, undergraduate student
1 May 2024
Hello!
Spring quarter has absolutely come in full swing. Classes have picked up and they are certainly keeping me busy. Work in the lab is also picking up as Haley and I prepare for our poster presentation at the Northwest Student Chapter of the Society for Marine Mammalogy (NWSSMM) with the whole lab lead team, which is very exciting. It will be fun to head down for Seattle for the weekend and have the opportunity to attend the conference and hopefully meet some new people. I am also continuing assisting with Erin D’Agnese’s diet study project. We have mostly finished up our homogenized fish samples and are moving on to a massive amount of harbor seal scat samples to extract. The extraction process is less intimidating now and I am looking forward to continuing the work.
Looking ahead, Haley and I are now both funded for the summer which is super exciting! It is awesome to see the progress on the project, especially seeing a visual representation of it through our poster. Definitely a bit nerve wracking but it's great to have the lab as a resource for advice, so many knowledgeable folks around. It will also be fun to be working in Bellingham over the summer, as the past two summers I have either mostly been in Anacortes working whale watching boats, or home in Alaska. I know we are not quite mid-quarter yet but it feels like summer is going to come extremely quickly, as my weeks are so packed. This quarter is definitely my most intense one yet, but I feel confident I can keep it up to balance lab work, classes, hobbies and sleep until summer comes.
Until next month,
Maren
Maya's Blog
Maya Mijares, undergraduate student
1 May 2024
Hello everyone!
This month has been an absolute whirlwind of different lab projects! Between getting sequencing data back, preparing for the NWSSMM conference and Scholar’s Week, training all the new research assistants, and the start of smolt observations, everyone in the lab has been super busy!
Starting off the quarter with training the new research assistants was a really nice way to ease back into having more observations as we move out of winter. I’ve been lucky to have had really beautiful weather on most of my observations, so hanging out at the creek has been a nice break from schoolwork! It is also fun to get to chat with all of the new research assistants and get to know them better.
Smolt observations also started this month! Because there are two observations daily during smolt season on top of regular Whatcom Creek observations, this means that everyone in the lab has a lot on their plate right now. Luckily, the research assistants have been a HUGE help with all these extra observations, and we are so appreciative of them! Being down at the creek at dawn/dusk also means that we get to see some beautiful sunsets and sunrises, along with some cool new animals! Alex, Vic, and I had a pm observation at Whatcom Creek last weekend where we saw a beaver and a muskrat, which are animals that I’ve never seen at our observation site before.
Regarding the mtDNA project, we finally have sequencing data back for all 249 samples! Yay!! It has been a bit of a struggle to start our data analysis as we have been having some issues assembling the forward and reverse sequences, but I think we finally figured it out today. Luckily, this is right in time for the conference this weekend, so we will be able to have some preliminary results to share with other marine mammal researchers! All we’ve been able to detect so far is that there is definite variability between individual sequences, which is a good sign for future analysis! We are currently working on developing a haplotype network that will show us the different genetically distinct populations of harbor seals in Washington State.
The last exciting piece of news from this month is that I got a job at the Catalina Island Marine Institute (CIMI) as a Marine Science Instructor! I will be starting in August this summer, and get to live on Catalina island for a year. This job combines two of my biggest passions, marine science and working with kids, and I am so excited about this opportunity!
That’s all for April! I'm looking forward to updating everyone on how the conference and scholar's week went in my next blog!
Maya Mijares
Maya placing an electrophoresed gel loaded with PCR product in a UV lightbox to ensure PCR was successful. Photo by I. Shier.
Olivia's Blog
Olivia Balaban, undergraduate student
1 May 2024
Hi everybody!
Happy spring! I have had a very busy few weeks. My code is done but it is now a matter of double checking the math and debugging any issues related to that. This final part is taking a little longer than I thought but I need to work closely with Dietmar to make sure the data is correct before we send it off to Jonothan. The current issue I am working on is that the final proportions are not adding up to 1 for each predator. I am not sure where this issue is coming from since each species group is off by a different amount. I am closing in on the problem though because with the last few changes I have made there are some obvious patterns emerging.
Since the NWSSMM conference is this Saturday, I have also been working on my poster which has been fun but a little challenging to navigate without results. It has been especially difficult to summarize my final calculations. There is so much data I have had to tell R to condense the table into multiple tables. Despite the chaos of everything, I am looking forward to presenting the project and seeing everyone else’s posters! We got leave/receive comments on the MMEL posters the past 2 weeks, and they all look great! I am also really curious to see what other universities are doing work on.
Thanks for reading. I hope everyone does good on their midterms!
Olivia
Jack's Blog
Jack Mezzone undergraduate student
1 May 2024
Hey folks,
This last month has been a wild one! We ended up bringing on 27 new undergraduate research assistants (URA's) and had a meeting at the beginning of the quarter with new members to go over our projects and to welcome everyone. We started off the first couple of weeks by training almost everyone on Whatcom Creek protocol. A reason for so many folks being on training was that anyone who wanted to be on the Smolt project needed to be trained on Whatcom Creek or have already been a member of the lab. Training folks on Whatcom Creek was a great starting place since most protocols are the same on the Smolt project. This allowed URA's to be more prepared for Smolt training so they were only being refreshed on the protocols, allowing them to focus on the new items such as the 5-minute datasheet, head tilt behavior, and log pond site. I needed to get about 30 release forms filled out by folks due to our log pond location and gave people the option to fill it out online or in person. I made the mistake of not realizing that I was limited in my ability to scan documents, so I ended up scanning each of the 20 or so release forms page by page. You live and you learn... and you could say this was a case of learning.
The starting time of the Smolt project is dependent on the estimated Chinook smolt release date and so I was in contact with Bellingham Technical College's hatchery. After some discussion, I was told that the smolt could be released as early as May 1st but that they could be released at any point in the month due to the large number of variable factors that go into the release date decisions. Since the smolt could be released on May 1st, I needed to prepare as if they were going to be released on this date to be sure that we got a minimum of 5 days of prerelease data. This number is important as this was the amount of prerelease data that was recorded last year. This all meant that observations needed to start on April 26th and that training needed to be done ASAP.
Training was scheduled and done in 3 groups of about 10 people. Each training was two hours long and entailed going over safety, procedures and equipment in the lab. Then we traveled out to Whatcom Creek, went over protocol, and did practice data collection. Since seals weren't present in the creek, I had the great opportunity to make up seals and what they were doing so as for everyone to be able to practice collection. This was a lot of fun and allowed folks to mark behaviors that they otherwise may not see. Following Whatcom Creek, we traveled to Log Pond, walked the sites, went over protocol, and did another round of practice data collection. This repetition was incredibly useful and allowed for data collection to be more consistent and accurate in the future. Training finished on 4/24 with observations set to start on 4/26. In the blink of an eye, I was unlocking the Biology building door at 5:00 a.m. to let people in, pick up equipment, and go out to the sites.
For the foreseeable future and depending on smolt release, we will be doing observations at 5:30 and 18:00 at Whatcom Creek and Log Pond with 3 people on each site. This means that we have 12 people on observations/day. I have been and will continue to schedule myself on most observations which allows me to make sure procedures are being followed, be available for questions, and to lessen the workload on other folks. Observations have been incredible with the first AM observation spotting the first seal in Whatcom Creek during an observation since January. Some less than usual sighting have occurred with folks seeing a beaver, muskrat, and river otters! Most observations have been cold and wet, but everyone has done a great job about dressing warm and in waterproof clothes to reduce uncomfortableness.
On another note, the NWSSMM conference is coming up on 5/4 and Maddie and I will be presenting our poster on the Smolt Project. I am super excited to talk about the project and get to experience a conference for the first time as a participant! Scholars' week is also coming up this month which will be a great experience!
The next month is looking like a LOT of late nights and early mornings with a bunch of great people. I can't think of a better way to finish off my senior year!
Until next time,
Jack
Haley's Blog
Haley Recob, undergraduate student
1 May 2024
Hi everyone!
It is finally spring! The flowers are blooming all around Western Washington University’s campus and the days are warming up again. April has been a busy month as per usual. The start of spring quarter started off slow but is picking up the pace with deadlines and midterms approaching. On top of schoolwork, lab projects have been busy as well. The Whatcom Creek project has been fortunate enough to welcome some new lab assistants. It’s been great meeting everyone and introducing them to lab work. I hope to start training those who are interested in photo ID soon. I have also chosen to help collect data for the Smolt Project this season. Just today, during an observation for this project I saw a beaver and a nutria in Whatcom Creek! As the weather continues to get sunnier, I am excited for more field work.
So far with our independent project, Maren and I have been getting ready for the Northwest Student Chapter of the Society for Marine Mammalogy (NWSSMM) conference. We have been working on creating our poster to show off what we have been working on. Maren has done a beautiful job creating maps of the harbor seal haul-out sites in GIS. After getting some great feedback from the lab meeting, we have fine-tuned the poster and are almost ready to print. This is going to be my first conference and I am so excited to meet other scientists and travel with the MMEL folks! Also, I recently got awarded the Washington NASA Space Grant Consortium Summer 2024 Research Internship! This grant will provide funding to continue working on the independent project over the summer with Maren. I am excited to start working on our project full time and focus solely on research this summer!
Until next time,
Haley Recob
Isabel's Blog
Isabel Shier, undergraduate student
1 May 2024
Hi everyone,
Has it really been a month already? Things have been going by so fast! The NWSSMM conference and Scholar’s Week are coming up back-to-back. The conference is at UW in Seattle this weekend, and Scholar’s Week is next week. Maya and I will be doing a poster presentation at both events in addition to a collaborative presentation with Alejandro, Dietmar, and Alex at Scholar’s Week.
I’m super excited for the conference! It’s been off in the distance for such a long time and hasn’t felt real.
Maya and I just got our sequencing results back a little bit ago, and we’ve been racing to do data analysis and finish making our poster. We have an appointment to print it on Thursday, and I think once we have our poster printed things will feel much more real.
In other news, smolt observations have started again. I just had my first one today, which is exciting! The 5:30 am start time is pretty brutal, but watching the sunrise over the water is absolutely magical. This picture is from before observation, so pretty dark– but I thought it was really neat!
That’s it for now, but more updates soon!
Isabel
Sunset in Bellingham Washington. Photo by I. Shier.
Alexandra's Blog
Alexandrea Otto, graduate student
1 April 2024
Hi there,
We have received the data back from the last optimization run for the SNP panel! I currently am running the code analysis to see how well this last round of SNP primers worked and what SNPs should be included in the final panel with the 109 great SNP markers we have already found. This analysis involves running the GTseq genotyping success workflow of code. Just a year ago in genomic analysis class, I remember learning how to run this workflow of code and multiple scripts for the first time. It’s neat to almost have this “full circle” moment of a feeling as a year later now I have helped optimized the SNP panel and am rerunning the same code I once was so naïve to and just learning!
In addition to all thesis things, the MMEL is busier than ever right now! The smolt project is back up and running in full force with the help of our freshly introduced new lab members. Jack is doing a fantastic job continuing and leading this project from Maddie’s work a year ago. Leading the smolt project is no small task for just one lab member due to the nature of the project being such intense field work for only a short seasonal month. It has been great to see and observe harbor seals again in the field (along with some new beaver and muskrat friends at Whatcom Creek!)
Maya and Isabel have received their own sequencing data back as well and are also deep in sequence analysis! Victoria, myself, and eight other undergraduates in the lab are all finishing our posters/presentations and gearing up for this weekend’s NWSSMM conference in Seattle, WA! Victoria and I are over the moon excited to have helped receive funding from the Biology Department in order to support/fund both ourselves and the undergraduates to present at this conference this year. Oh how the lab has grown in just one year! I remember last year traveling to the NWSSMM conference with just myself, Victoria, and Holland. It is really something special to be going with such a big team from the lab this year now! For a majority of MMEL undergraduates coming, this will be their first conference their presenting at and I cannot wait to be right alongside them and support them during this memorable time in their research journeys!
Til next month,
Alexandrea
Victoria's Blog
Victoria Vinecke, graduate student
1 May 2024
Happy spring everyone! With the arrival of spring, Whatcom Creek has been quite lively! Along with the return of harbor seals to the creek there have also been sightings of a beaver and a muskrat! The second year of the smolt project is in full swing and I am quite excited to see the results at the end of the month!
Regarding my own project, after a couple of long weeks of lab work, I am happy to report that I will be able to include both field seasons sampling data in my poster for the upcoming Northwest Student Chapter of the Society for Marine Mammals (NWSSMM) conference! I have been hard at work compiling data from both field seasons, drawing conclusions from qPCR results, and linking sex to photo-id’ed harbor seals! I am excited to share my results with peers at the conference and hopefully get some helpful feedback!
Alexandrea and I spent some time this month working on a funding proposal to gain funding for the undergraduates along with ourselves to help with costs for the NWSSMM conference held is Seattle, WA this year. We were able to successfully get all seven undergrads and ourselves fully funded for travel and lodging! Being able to secure funding for everyone is a huge win for the lab! Having the ability to make this conference a fun learning experience without the worry of financial stress is a great success! We will be heading off on Friday to present at the conference on Saturday so wish us all luck!
Along with presenting a poster at NWSSMM I will also be presenting the same poster in WWU’s Scholars week this month! I am thankful for the opportunities like Scholar’s week and NWSSMM that allow me to share my research with people outside of my immediate research circle!
Lastly, I have a meeting with Dr. David Rosen to discuss collecting samples from the Vancouver aquarium harbor seals in a controlled setting to test the accuracy of my qPCR probes/primers. I plan on using these samples of harbor seals with known sex as a control to see how accurate the validated sex probes are at sexing individuals. I also plan on collecting some mixed samples to see what that looks like when run on qPCR as well!
I am eager to give updates on both poster presentations during my next blog post so be looking out for that!
Until next time,
Victoria