Senior Mohamed F. had high hopes for last spring’s Microbiology intensive. “One of the selling points for me was that by the end of the course, I would be able to perform labs with minimal teacher assistance or guidance, becoming a more independent and experiential learner,” he said. 

For Science Teacher Thanh Beedle, that was exactly the type of learning experience she had in mind when she designed the course two years ago. During the first week, students learned about the structures of viruses, bacteria, and other microbes, and were introduced to a range of lab techniques, including aseptic technique, spot tests, streak assays, plaque assays, and enrichment. 

Then students were tasked with attempting to find and isolate bacteriophages, which are viruses that infect bacteria, from soil samples collected by the students. Soil samples contain many phages, and phages have many uses, a key one being creating personalized therapeutics for individuals who are resistant to antibiotics.

To make the project applicable to the real world, Thanh researched local institutions conducting this type of research and learned about the work of the Coler Lab at Seattle Children’s Research Institute. The lab, led by Dr. Rhea Coler, a research scientist and University of Washington faculty member, focuses on vaccine development against epidemic and pandemic diseases, including tuberculosis.

Thanh reached out to the Coler Lab to inquire about a possible partnership and Research Scientist Dr. Sasha Akins responded enthusiastically. “Many of our own lab members fell in love with science in middle or high school and we wanted to provide those same opportunities for UPrep’s students,” she said.

Dr. Akins and two research technicians visited the Microbiology intensive and demonstrated for the students a plaque assay, a procedure for measuring the amount of phages. This research technique allows researchers to see individual colonies of the viruses, as opposed to all of the viruses on top of each other and determine their morphology to assess if they have found a new type of virus that has yet to be identified.

Following Dr. Akins’ demonstration, UPrep students conducted their own plaque assay. First, they shook the soil samples in a liquid that allowed the phages to run loose from the soil particles. They then infected the bacteria that they were interested in finding phages for with the liquid that they isolated from the soil sample. 

“If there are viruses there that infect this bacterium, we run tests that allow us to see what I call, zones of death,” Thanh said, “because the viruses basically kill the bacteria in those areas.” 

Students look for the zones of death where they have grown these bacteria to see if they've identified bacterial killers, or bacteria eaters, which are bacteriophages, a virus that infects and replicates within bacteria.  

Following multiple class visits, Dr. Akins and her team took the UPrep samples to a high throughput robot that allows them to screen 96 samples at one time compared to the individual processing that was happening at UPrep. This allowed Dr. Atkins and her team to validate the students’ positive results. From there, the students grew their phages in high concentrations and took a field trip to the Microscopy Center at the Fred Hutch where they met the Director Theo Humphreys and the Electron Microscopy Lead Steve MacFarlane, who are strong supporters of science education. They kindly provided a tour of the lab and imaged the samples the class collected.

Following the processing, seven viruses (phages) were isolated from the samples, much to the excitement of the students and their teachers. Dr. Akins’ lab will continue to test and verify the data to confirm if the viruses are lytic, meaning they will kill the bacteria outright, or if they will remain inactive within the host. The plan is to eventually test the samples against tuberculosis.

“Our mission was for the students to experience real microbiology bench work and show them exactly how we do our own phage hunting in the Coler Lab,” Dr. Akins said. “We wanted them to think critically about their results and come up with alternative plans if and when their results were difficult to interpret and implement new tests to find out which hypothesis was correct.” 

Dr. Akins also wanted students to understand how new phage discoveries can lead to translational therapies. The Coler Lab collaborates with the Hatfull Lab at the University of Pittsburgh, who are the real experts in phage discovery courses and run a national program called SEAPHAGES. This collaboration with UPrep was modeled after the Hatfull Lab’s university class model.

Reflecting on the class and their partnership with the Coler Lab, teachers Thanh and Karen Slon were effusive in their gratitude. “For the students, it just felt so authentic and real,” Karen said. The students were contributing to someone’s data in a real lab that is looking at alternative therapies to antibiotics. Seattle Children’s also provided lab supplies and testing equipment that was used during the intensive.

“For us as teachers, it was so helpful to have the expertise of Dr. Akins who works with phages every day to help us troubleshoot and act on it immediately,” Karen said. “We grew as teachers.” 

Looking back on the class, sophomore Cole S. reports being surprised by the variety of microbes (trillions!) that he learned about during the class. “It has given me a deeper view into another field of science,” he said. 

For Mohamed, the class helped him develop a new perspective. “The diversity and beauty of the microbiological world fascinated me and gave me a new perspective of the living things I interact with every day, whether I recognize it or not,” he said.  

Read more articles about academics at UPrep.