SURP’s Up: Worms, pond scum and fruit flies make for interesting summer research
Summer at Western is usually a quiet time, with fewer in-person classes making for nearly empty buildings.
That’s one of the reasons why the Biology Department created the new Summer Undergraduate Research Program (SURP), led by seven faculty in the department. SURP cuts some of the isolation involved with summer research by holding research student meetings once a week, hosting field trips, and encouraging collaboration between labs.
“Part of the intention was to bring people out of their scientific silos– to interact and exchange ideas,” said Adrienne Wang, Assistant Biology Professor at WWU and one of the leaders of SURP.
Talking to other research students about different studies can help students sharpen their skills to communicate that science better, Wang said.
The weekly SURP meeting helps instruct the program’s members on important concepts like research ethics, poster design for presenting their research, and how to create a special kind of scientific resumé called a curriculum vitae (CV).
SURP field trips that took place throughout the summer included the Fred Hutchinson Cancer Research Center and the Allen Institute, where students got to tour research facilities, meet lab heads, and hear from WWU alumni doing research in the Seattle area, according to Suzanne Lee, Assistant Professor in Biology and one of the SURP faculty leaders.
Many of the labs in the SURP program study molecular and cellular phenomenon in a variety of different model systems, ranging from microscopic organisms, like yeast and ciliates, to larger organisms, like fruit flies and trees, to ultimately help shed light on how conserved biology relevant to the human body and human health works.
“We’re not doing medical research in our labs, but it’s a grassroots foundation of ‘how does this work?’” said Aidan Pintuff, an undergraduate research assistant in Assistant Professor Nick Galati’s lab. “If it works in one organism, it works the same if not similarly to humans.”
The studies that SURP program participants engaged in this year also included ecological and organismal research, including a study about harbor seal behavior in Bellingham Bay being conducted in Alejandro Acevedo-Gutierrez’s lab. A SURP trip to visit the Shannon Point Marine Center (SPMC) in Anacortes is planned for September.
In the early Fall, each of the labs presents their research and results during a poster session open to the Western community and donors who helped make this program possible, according to Wang.
Several students were supported by summer stipends this year in Biology, thanks in part to the generosity of Peter and Judith Hallson who established the Hallson Research Stipends in Biology, and the biotechnology company, Seagen. Additional support came from the Jarvis Memorial Summer Research Award, the Vehicle Research Institute Award, and the National Science Foundation.
Five of the seven Biology SURP labs are featured below.
Assistant Professor Adrienne Wang's Fruit Fly Lab:
The Wang lab spent the summer studying immune response in fruit flies. According to student research assistant Chiyo Aoki-Kramer, there are two kinds of immune responses: innate and adaptive. The innate immune system kicks in first and provides a first line of defense for cuts and other minor sources of potential infection. The adaptive immune system fights infections and sickness once they’ve taken hold, and it has a “memory” in order to build immunity.
Scientists know little about the innate immune system in humans, but a study on mice indicated that decreased mitochondrial DNA in mice improved their innate immune system’s response to sources of infection. Mitochondria are the powerhouses of cells that turn sugars into usable energy.
Fruit flies are ideal candidates to explore the discoveries of the mouse study further because they only have innate immune responses, so there’s no interference from an adaptive immune system in the data. What they find could help inform disease response in elderly and immunocompromised people who have low mitochondrial DNA, Wang said.
Assistant Professor Suzanne Lee’s “Pond Scum” (Tetrahymena) Lab:
The Lee Lab was hard at work all summer observing single-celled organisms shaped like tiny swimming avocados with hair-like projections called Tetrahymena thermophila, which are affectionately called “pond scum” because they normally reside in freshwater environments.
The Lee Lab currently studies how different factors in Tetrahymena play important roles in protecting the nuclei of cells from accumulating damage.
Nuclei are the brains of a cell – they contain most of the DNA and help run the (cellular) ship – and therefore, need to remain intact. However, under conditions where a cell fails to properly divide, extra DNA-containing bodies that are not normal nuclei will be generated; these are called extrusion bodies. In humans, the presence of extrusion bodies is correlated with cancer, according to undergraduate research student Lola Lang.
In one of the studies the Lee Lab has been conducting this summer, students have been examining which Tetrahymena mutant strains have extrusion bodies to better understand the cellular pathways that protect against production of these abnormal structures.
To make sure a cellular structure is an extrusion body, microscope images are taken in three different channels (types) of light: DIC (white light) to see what the overall cell looks like, DAPI (green) to highlight DNA structures including extrusion bodies and CHE (red) to view which cells are dividing, Lang said.
Associate Professor Lina Dahlberg’s Worm Lab:
Professor Dahlberg’s lab spent the summer studying stress responses in microscopic worms. Like humans and other multicellular organisms, worms have pathways that get rid of defective proteins. In humans, a buildup of these proteins can lead to diseases, including Alzheimer’s and Parkinson’s diseases, according to undergraduate research assistant Tessa Marks.
By manipulating these pathways using genetics and heat or drug treatments and studying how the worms respond, this lab strives to shed some light on how these pathways work–literally. They use a green fluorescent protein (GFP) as a “reporter” – the brighter and therefore more abundant the protein, the more stressed each worm is. The GFP can be observed and measured using microscopes and biochemical assays.
Associate Professor Dan Pollard’s Brewer’s Yeast Lab:
Bellingham is known as the beer capital of the world. Naturally, WWU has a lab working on brewer’s yeast, helping the city maintain its title.
One of the projects the Pollard Lab works on is what happens inside of cells as they age. It turns out that a big part of this is that old cells turn on every gene at full blast, making every type of protein at once. Young cells only turn on some of their cells at a given time, which allows the cells to maintain control of all of their tasks - like eating sugar and releasing CO2 and alcohol. Turning on all of the genes at once is like trying to have a conversation when everyone talks at the same time. Chaos ensues.
To figure out how early in the aging process cells start losing control and accidentally turning on genes that are supposed to be off, students in the Pollard lab are engineering yeasts to have fluorescent indicators attached to genes. Young cells will be dark. But as they age they will suddenly light up, revealing the chaos of aging is beginning. Part of the engineering process involves checking that the fluorescent indicators, which are made out of DNA, are ready to be added to the yeasts. This is done with a size-separating gel, that is like firm Jell-O with an electrical current running through it, according to Aidan Corbin, a student in the lab. Smaller strands of DNA move to the bottom of the gel more readily than longer strands, allowing them to count the number of base pairs and see if the gene for fluorescent indicators is complete.
Once the students get the fluorescent indicators set up they can watch the cells age over the course of a day. They hope that the discoveries they make in yeast will be helpful in understanding how all organisms age, including us.
Assistant Professor Nick Galati’s Cilia Lab:
If you’ve ever wondered how single-celled organisms move around, cilia – hair-like protrusions that help propel organisms through fluids – are often the answer. If you’ve ever wondered how cells communicate with each other in a multicellular organism like humans, cilia are also often the answer.
While mobile cilia beat back and forth to allow movement, signaling cilia act as antenna for cell-to-cell communication, according to Pintuff, introduced at the beginning.
Pintuff and his team spent the summer studying Tetrahymena cells, much like the Lee lab, only the Galati lab looked at how cilia are organized across the surface of cells. They do so by highlighting the cell structures with fluorescent antibodies for viewing under a microscope, Pintuff said.
Another team in the Galati Lab observed cells from mammals and adjusted calcium levels to see how calcium impacts the way that cilia communicate.
Signaling cilia require study because diseases, called ciliopathies, can result from a breakdown in cilia communication between cells in a human body, so understanding them better could help people in the future, Pintuff said.
Undergraduate Research Assistant Lola Demurger examines fruit flies for gender and phenotype (traits) to make sure they go in the right test tubes. Photo by Luke Hollister/WWU
Undergraduate researchers Tessa Marks (front) and Anna Byquist (rear) hard at work putting various strains of worms in the appropriate petri dishes and organizing them for storage. Photo by Jacob O'Donnell.
Professor Wang leads a brainstorming session on what to include in a CV during a weekly SURP meetings with Assistant Professor Matthew Zinkgraf and students. Photo by Jacob O'Donnell.