AUGUST 2023
Jasper's Blog
Jasper McCutcheon, undergraduate student
1 August 2023
Hello again,
I am still over here in Delaware, but I'll be returning to Bellingham in a couple of weeks with the conclusion of my research here. I am very excited to get to see mountains again, have less humidity, and return to 70˚ F weather. I'm also looking forward to managing the Log Pond project in person instead of from across the country.
This July has been a busy one for my team of research assistants, with more and more seals being spotted at the Waterfront and Log Pond. Beyond the obvious benefit of getting to see more cute seal heads popping up, this increase in sightings means more data points are being collected for both the long-term project and my own! We have been getting great data in terms of how long seals are spending surfaced at lower noise levels and I am hoping that as the summer progresses, we will be able to gather data for higher noise levels as well.
During my time here in Delaware, my weeks have been filled with field days spent capturing and marking as many fish as we can, totaling out at 1,700 fish! As I have been analyzing the data we collected, two main patterns have jumped out to me. One: that we consistently caught more fish at the sites further downstream than those upstream, which could be related to a culvert that breaks the study area in two (With two sites below it and two above). And two: the number of Fundulus heteroclitus (mummichogs, or as I call them “Chogs”) caught appears not to be impacted by the environmental factors (dissolved oxygen, salinity, and temperature) that we have gathered. We anticipate that this pattern is related to the tolerance this species possesses for anoxic environments, large swings in salinity, and extreme temperatures. With that said, I need to dive into my data further before I can draw any firm conclusions.
By my next blog I will have finished my project in Delaware (and will update you all on what I find) and will have returned to Washington.
Until next time,
Jasper
Victoria's Blog
Victoria Vinecke, graduate student
1 August 2023
Hi all!
July has been quite a busy month, to say the least. This month included a continuation of tweaking potential sequencing primers and attending courses at the summer institute in statistical genetics at UW! The summer weather in Bellingham has been gorgeous, and I am soaking up as much sun as possible when I am not working!
I have had some success with primer tweaking and am ready to move on to the next step, finding a sweet spot for the PCR annealing temperature. Finding the sweet spot is important because if the temperature is too low, it can allow for the amplification of non-targeted DNA; if the temperature is too high, it may exclude target DNA. I am excited to find an appropriate annealing temperature and hopefully move on to sequencing my samples! My big goal for the summer is to receive my sequencing data so I can start bioinformatics before the fall quarter begins and I am inching closer to that goal every day!
SISG courses at UW were an absolute blast! I had the opportunity to learn from various professors who have made large contributions to the statistical genetics sector of biology. It was phenomenal hearing about their paths and learning foundational ideas that can be directly applied to my research. I am very grateful to have had this opportunity and I look forward to applying my new knowledge to current/future research! Being in Seattle for a week and a half called for nighttime adventures after class got out. Alex and I found a waterfront spot to swim at about a block away from where we were staying which helped us relax after a long day of class! Below is the view from the dock, notice you can see the space needle!
That is all I have for July's update! Wish me luck on future PCR success!
Until next time,
Victoria
Photo of Lake Union, Seattle, WA. Photo by V. Vinecke.
Alexandrea's Blog
Alexandra Otto, graduate student
1 August 2023
Hello there,
The ebbs and flows of graduate school and life surely still go on. As for this past month, I’ve been learning in-depth about population genetics and code (Python, WSL, Bash, you name it). I’m still chipping away on the project SNP selection code. It has been a whole new insight into the project I wasn’t sure I’d be able to see for myself. Working with RAD-Seq data, VCF files, and SNP metrics has been fun to explore and learn so far. It’s certainly been cool being able to work with data from a previous graduate student of the MMEL’s Nathaniel Guilford. It’s certainly cool being part of a bigger lab long-term and over time, where we are able to build off each other’s work for the conservation of the local system. Dr. Erin D'Agnese continues to be a huge mentor in the coding aspects and this project too.
Timing couldn’t have been better to attend the Summer Institute of Statistical Genetics (SISG) in Seattle this past month as well. I attended three modules (classes) over Fundamentals of Population Genetics, Applications of Population Genetics, and Statistical Genetics. The first class was extremely helpful gaining the foundational background knowledge on genetic models and has already proven helpful for tackling some of the project SNP selection code. I know a thing or two regarding minor allele frequency and linkage disequilibrium now! The second class was more hands-on with simulations and coding from scratch some population analyses similar to STRUCURE. I’ll certainly be referring back to my notes on those analyses in a short, few months! The last module was definitely special as well considering it was co-instructed by Dr. Bruce Weir the director of SISG, who is also retiring this year. It was very neat to listen to an instructor who wrote some of the foundational books in the field! Also, it was very nice to be able to pick up some of Dr. Weir’s donated books from his collection over the years of his career. On top of this rewarding workshop, I got to meet some cool people and students in other fields and share the whole experience with my lab partner, Victoria! Plus, we got free mugs (which in graduate student world is a huge bonus)!
Till next month,
Alexandrea