Chemical Biology – Aman’s Research Showcase

Hello everyone! 

My name is Aman Galymov. I graduated from TRU with a bachelor’s degree in Chemical Biology. I am very excited to share my research experience with you and share some tips I have acquired throughout my research journey. I will talk about my first “taste” of research and how a small pilot project led to several, more substantial research opportunities. 

When did you start considering doing research? 

I started thinking about doing research at the end of my second year in 2020. I had some minor exposure to academic research through my university course load and a collaborative educational project between TRU and school district 73 that I was invited to be a part of. Unfortunately, the latter never worked out for me; however, to this day, I am very grateful to have had the opportunity to write my very first official application for a Mitacs Research Training award because of that collaborative project, which would have allowed me to conduct research over the summer of 2020 (I did not receive the award). 

Bacteriophage Project:

Fast forward to Winter 2021, I submitted my application for the Undergraduate Research Experience Award Program (UREAP) with Dr. Naowarat Cheeptham (Ann) as my supervisor. 

In March 2021, my project titled “Phage Therapy: Screening Sewage Water Samples for the Presence of Bacteriophages Effective against Various Strains of Antibiotic-Resistant Bacteria” was selected for funding! I was very happy and excited to start working on my own project, which later turned into a collaborative work between Cave Microbiology lab, the City of Kamloops, and Royal Inland Hospital. My study evaluated if bacteriophages specific to clinically relevant multidrug-resistant (MDR) bacteria could be isolated and characterized from municipal sewage samples as a potential alternative that could be used alone in monotherapy or in combination therapy with other commonly used antibiotics. The Royal Inland Hospital kindly provided the clinical bacterial samples isolated from patients with the help of Dr. Muhammad Rehan and Laura Smith. I then collected sewage samples from Kamloops (hospital and city sewage), Vernon (city sewage), and Kelowna (hospital and city sewage). Hospital sewage sample collection in Kamloops was done with the help of the City of Kamloops and the “OG COVID” Cave Microbiology team: Keilin Gorman and Sara Lawrence (Figure 1). Eventually, I was able to isolate three strains of bacteriophages effective against two clinical MDR strains of E. coli from the municipal and hospital sewage of two locations: Kamloops and Kelowna. 

The whole research project went on from May 2021 until August 2021. I spent a reasonable amount of time familiarizing and perfecting the phage isolation procedure and general microbiology skills such as media making, antibiotic stock solution preparation, etc. TRU’s amazing microbiology technician Kathy Baethke played a huge role and taught me the essential microbiology lab skills I still use today. I was also very lucky to shadow Kathy during her regular work days before starting my research project. This small pilot research project allowed me to learn the basics of bacteriophage microbiology research and increased my interest in the field of medical and diagnostic microbiology. I acquired essential lab skills and techniques that I honed and utilized in my future research projects. 

In the Winter of 2022, the work received additional funding and I completed two more research terms developing a protocol for structural phage proteomics on MALDI-TOF-MS under the supervision of Dr. Naowarat Cheeptham (Ann) and Dr. Kingsley Donkor. Additionally, we sequenced the phage samples at the Integrated Microbiome Resource and performed transmission electron microscopy imaging at the UBC Bioimaging facility to further characterize the bacteriophages.

 I was incredibly lucky to meet and talk with so many amazing individuals from different companies and to disseminate the findings of my project at the 2022 TRU Undergraduate Research Conference, 2022 Annual Medical Microbiology and Infectious Disease Conference (AMMI 2022), 2022 Canadian Society of Microbiologists conference and 2022 Phage Canada Virtual Symposia. The 2022 Annual Medical Microbiology and Infectious Disease Conference will forever have a special place in my heart. It was such a memorable conference. I traveled with my lovely supervisor Dr. Naowarat Cheeptham (Ann), Keilin Gorman, and Marissa Yoneda. 

Biofilm Project: 

I became very invested and interested in research that studied the alternatives to antibiotics and their efficiency against multidrug-resistant bacteria. At that point, I had only worked with planktonic bacteria (free-living bacteria). In 2022, I received an Undergraduate Research Apprenticeship Award and was invited to work on another project under the supervision of Dr. Naowarat Cheeptham (Ann) and Dr. Joanna Urban with another researcher (Marissa Yoneda). As a part of a research team, I investigated the synergistic effect of cannabinoids and commonly used antibiotics on biofilms formed by the clinical multidrug-resistant strains of MRSA in a double-dose response assay. Bacteria, when found in communities (biofilms), tend to be more resistant to conventional antibiotic treatments due to their physical structure, something we call a “non-genetically encoded transient resistance” on top of their antibiotic-resistant phenotype and the upregulated expression of biofilm-specific genes. The biofilms were grown on the “pegs” of specialized biofilm incubators. The biofilms were then exposed to micro dilutions of the two antimicrobials; the respective MICs were determined with a plate reader and a viable count of cells recovered from the biofilms post double dose treatment. Fractional Inhibitory Indices (FICs) were calculated to determine whether a synergy was observed at different micro dilutions of the antimicrobials. The findings of the project were presented at the 2023 Annual Medical Microbiology and Infectious Disease Conference in Toronto, Ontario (AMMI 2023). This project further expanded my research toolkit as an undergraduate researcher and allowed me to build more appreciation towards medical microbiology. 

Uric Acid Project: 

I assisted with another exciting project led by Nicky Sigouin that studied the constitution of the oral microbial community in patients with a percutaneous endoscopic gastrostomy or gastrostomy-jejunostomy in the Interior Health region. The project also studied the chemical composition of saliva in these patients, specifically uric acid as one of the antimicrobial and antioxidant compounds present in human saliva. I developed and carried out the preliminary detection and quantification of uric acid in human saliva samples using capillary electrophoresis under the supervision of Dr. Kingsley Donkor. I viewed this research project as an incredible opportunity to apply my analytical chemistry skills and be a part of a community-based medical research team. 

What did research give me? 

My research experience has opened up so many doors for me during my undergraduate student career. I became more confident with conveying and presenting information to a wide range of audiences. This further inspired me to continue working as an undergraduate teaching assistant. I had an opportunity to TA in chemistry, biology, anatomy and physiology (I and II), and microbiology. I was able to make friends and long-lasting connections with incredible people that made my research experience unforgettable. I have shadowed laboratory medical professionals to learn firsthand the instrumental techniques that I later applied in my own research. Additionally, I was lucky to mentor and train new undergraduate research students and a very talented high school student. 

What are the tips you can share with others?

1. My biggest and most cliche tip is to not be afraid to reach out to supervisors that are working in the field of research that you find interesting in order to get started.
2. Definitely prepare to learn and practice lab techniques on your own after training, as that is an essential part of working autonomously on your research project in a lab. 
3. If you are working with a commercial lab item (DNA extraction kit, biofilm incubator, and so on), remember that you can always ask for technical advice by directly contacting the company behind the product. There is always a team of researchers willing to answer your questions. You will also learn a lot from them. 
4. Learn to see what your data tells you (thank you, Dr. Don). I still get a little nervous when a research project goes sideways, and you get unexpected or no results. Remember that it is a part of research and is totally normal. This is also where your troubleshooting skills will come in handy. 
5. Don’t be afraid to be creative. There were numerous occasions where I had to be resourceful and creative with the equipment to carry out the procedures specific to the projects without compromising the results. 
6. Do an inventory check early to make sure you have all the necessary reagents and products for your project. Sometimes stuff takes forever to get delivered and will push your research project end date further than you planned initially. 
7. Plan and document your experiments. This may not work for everyone; however, I find it hard to work without a set experiment plan for the day, so I always tried to have an outline of what I was doing. Later I would also document all the results from my work for future reference either digitally or in a lab notebook. 
8. Keep your lab workspace tidy! Remember that a clean lab is a happy lab!

Acknowledgments: 

I would like to express my immense gratitude to my incredible supervisor Dr. Naowarat Cheeptham (Ann), without whom my research journey would never exist. Thank you for seeing the potential in me and my research project ideas.

 I would like to thank Dr. Kingsley Donkor for being my co-supervisor and allowing me to work in his lab. Thank you, Kathy Baethke, for guiding me and always answering my microbiology lab-related questions. I also want to thank Dr. Joanna Urban, Dr. Eric Bottos, Dr. Jessica Goose, Dr. Alexander Hynes, Dr. Don Nelson, Dr. Mark Rakobowchuk, Dr. Mohammad Rehan, and Laura Smith (I have learned so much from you guys). 

Thank you CURN and Lauren Okano for inviting me to write about my research experience at TRU. 

Lastly, I would like to thank TRU for having such great research opportunities for undergraduate students.