INTRODUCTION

Hi, my name is Maria Alejandra Rojas Rivero a 5th year chemical biology student and my research journey began with small class projects like one under Dr. Kingsley supervision, where I analyzed heavy metal contamination in cocoa powder using ICP-MS after microwave-assisted digestion. While this experience introduced me to analytical chemistry and instrumental techniques, my true engagement in research deepened during my directed studies term with Dr. Cheeptham, where I focused on bacteriophage research.

In this project, I worked with bacteriophages from sewage that specifically target E. coli, working with phage lysate preparation, protein digestion using trypsin, and SDS-PAGE analysis for protein characterization. Additionally, I developed expertise in data analysis using Mascot software to interpret mass spectrometry results. This research has the potential to contribute to novel biofilm treatments, and I am refining it further for possible publication or patenting.

Presenting my bacteriophage research at the TRU Undergraduate Conference allowed me to effectively communicate my findings and gain valuable feedback from faculty and peers. Through this experience, I enhanced my ability to convey complex scientific concepts while refining my research approach based on expert insights.

Beyond laboratory research, I have cultivated leadership and teamwork skills as president of both the TRUSU Pre-Medical Society and the TRUSU Baking Club. These roles have strengthened my ability to organize projects, mentor students, and foster collaboration within academic and extracurricular settings.

By integrating microbiology, molecular biology, and analytical techniques into my research, I have developed a strong foundation in scientific inquiry. My experiences align with the Undergraduate Research Certificate’s objectives, demonstrating my ability to conduct independent research, analyze data, and communicate findings effectively.

THE STANDARDS

Understanding the Research Process

Students analyze and discuss examples of writing from scientific and technical literature to improve their communication skills for lay and scientific audiences. Students learn to identify and produce writing styles and formats appropriate for science-based contexts and audiences, as well as develop skills in writing and documenting research documents on science and technology topics.

Students are introduced to statistical procedures for biological research. Topics include the nature of data, probability, hypothesis testing, goodness of fit, analysis of variance, correlation, and regression. The computer lab laboratory provides students with hands-on computer experience in graphical and statistical analysis.

Students are introduced to the physiochemical basis for cellular activity, with emphasis on energy relationships, functions of cell parts, integration and internal control of cellular activities, and the mechanisms of influence of external factors. Laboratory work provides hands-on experience with the techniques and apparatus used to study cell function.

This is a laboratory course designed to give students practical hands-on experience with the instrumentation discussed in CHEM 3100: Instrumental Analysis. Students focus on the needs of chemical biologists while performing a variety of chemical analyses and gaining independent experience in analytical experimental design and method application to real samples.

This course is designed to allow students to undertake an investigation on a specific topic as agreed upon by the faculty member and the student.

Directed Studies Research Proposal: Sample Preparation Methodology for Detection of Bacteriophage Structural Proteins Using MALDI-TOF-MS

This research proposal outlines my directed studies project under the supervision of Dr. Naowarat Cheeptham and Dr. Kingsley Donkor. The study aims to develop a methodology for identifying bacteriophage structural proteins using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS).

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This course will focus on analytical method development, including sampling and sample handling, extraction, determination, and data acquisition. The analysis of organic and inorganic compounds in a variety of matrices will be discussed. Case studies from the literature will illustrate typical applications.

Lectures and seminars examine the interface of chemistry and biology, and practical laboratory experience introduces students to advanced chemical biology techniques. The emphasis is on providing the knowledge and theory behind biological systems from a chemical perspective, while exposing students to the modern laboratory techniques that are of current value in the biotechnology and pharmaceutical industries. These industries require professionals who have a strong background in organic chemistry, molecular biology and genomics. Current journal articles are incorporated into a problem-based learning approach that has students researching background material in order to complete an assigned project experiment.

Evaluating existing research

Literature Review: Bioremediation and the Application of Bacteria in Combating Anthropogenic Oil Spill Pollution

This literature review examines the role of bacterial bioremediation in addressing oil spill pollution, focusing on its effectiveness compared to conventional cleanup methods. Oil spills pose significant environmental threats, with past disasters such as the BP Deepwater Horizon and Exxon Valdez spills demonstrating the limitations of chemical dispersants, mechanical extraction, and burning techniques. Bioremediation offers a promising alternative by utilizing oil-degrading bacteria to naturally break down hydrocarbons, reducing environmental harm while maintaining ecosystem balance.

For this project, I was responsible for writing the introduction and discussion sections. In the introduction, I outlined the severity of oil spills, the challenges posed by crude oil’s complex hydrocarbon composition, and the need for innovative, eco-friendly remediation methods. The discussion section analyzed the potential of bioremediation, exploring different bacterial strains, their metabolic pathways, and the environmental factors influencing their effectiveness. Additionally, I evaluated the advantages and limitations of bioremediation, emphasizing the need for further research on biodegradation rates in real-world conditions.

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Research Project: Weather Impact on Mental Well-Being in Canadian and Latin American Students Living in Canada

As part of this course research project, I contributed to investigating how seasonal weather changes affect the mental well-being of international Latin American students compared to domestic Canadian students under the supervision of Dr. Emily Studd. My primary responsibilities included data collection, ensuring accuracy and consistency in responses. Additionally, I authored the introduction and methodology and discussion sections of the research paper, providing a structured foundation for the study by outlining its purpose, significance, and experimental approach.

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Research Project: The Effect of pH on the Proliferation of Endothelial Cells

As part of a team-based course research project, I contributed to the investigation of how pH variations influence endothelial cell proliferation under the supervision of Dr.Joanna Urban . My primary responsibilities included preparing the cell culture media, ensuring consistent feeding of the endothelial cells, performing sub-culturing techniques, and conducting the scratch assay to assess cell migration. Additionally, I was responsible for drafting the methodology section of the research paper, detailing the experimental procedures with precision and clarity.

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Research Project: Determination of Heavy Metals in Cocoa Powder by ICP-MS Method after Microwave-Assisted Digestion

This course study aimed to determine the concentration of trace heavy metals in four different cocoa powder brands using Inductively Coupled Plasma Mass Spectrometry (ICP-MS) under the supervision of Dr.Kingsley Donkor. Samples were digested with concentrated nitric acid in a microwave digestion system before being analyzed for metal content. The results provided insight into the presence of potentially harmful heavy metals in commonly consumed cocoa products.

For this project, I was responsible for the results section, data analysis, discussion, and conclusion. My role involved interpreting ICP-MS data, identifying trends in heavy metal concentrations, and assessing potential health implications. I conducted statistical analyses to ensure data reliability, discussed findings in the context of existing literature. Additionally, I synthesized the key outcomes in the conclusion, highlighting their significance and suggesting directions for future research.

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Applying research methods

Statistical Analysis using R Studio

During my research on “Weather Impact on Mental Well-Being in Canadian and Latin American Students Living in Canada“, I utilized R Studio for data visualization, which proved to be an invaluable tool for analyzing and presenting my results. R Studio offers a comprehensive environment for statistical computing, and its vast array of libraries enabled me to create clear, informative, and visually compelling graphs.

One of the key advantages of R Studio is its ability to handle large datasets efficiently. Using the tidyverse package, I was able to clean and manipulate survey and weather data seamlessly before visualization. ggplot2, in particular, allowed me to generate comparative time series plots, histograms, and scatterplots that effectively captured differences in responses between international and domestic students.

The attached file is the result sections of my report for this research project, the figures were created using R studio based on data obtained

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Excel for data organization

For my direct studies project “Sample Preparation Methodology for Detection of Bacteriophage Structural Proteins using MALDI-TOF-MS“, I use Excel to organize and analyze data from Mascot software, which helps with protein identification from mass spectrometry results. By structuring the data in Excel, I can efficiently sort peptide matches, filter significant results, and visualize trends that may be relevant to my research.

Using Excel’s functions, such as conditional formatting, pivot tables, and statistical tools, allows me to streamline data interpretation and ensure accuracy in identifying key proteins. This organization is crucial for comparing different bacteriophage lysates, detecting patterns, and ultimately drawing meaningful conclusions about protein composition. Proper data management not only enhances the reliability of my research but also facilitates collaboration and future analysis.

The attached Data-on-excel file is a example on how I organized my results during my direct studies research project, the data on excel are the proteins detected and analyzed by MASCOT server. I used excel for better visualization and interpretation of this data.

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Bacteriophage project

This study employed a series of biochemical and analytical techniques to identify bacteriophage structural proteins using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF-MS). Bacteriophage strains (EC1KELCTY, EC1KELHOS, and EC3KAMCTY) were propagated, and phage lysates were prepared to isolate structural proteins. Protein separation was performed using SDS-PAGE, followed by in-gel trypsin digestion to generate peptides suitable for mass spectrometric analysis. The digested samples were analyzed using MALDI-TOF-MS, and peptide mass fingerprints were processed through the MASCOT search engine for protein identification.

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Effect of pH on the Proliferation of Endothelial Cells

This study investigated the effects of pH changes on epithelial cells by preparing media at different pH levels and assessing cell proliferation through a scratch test. Media preparation involved formulating Leibovitz’s L-15 supplemented with fetal bovine serum (FBS) and antibiotics, with pH adjustments using 1.0 M HCl or NaOH to create acidic (pH 6.9), control (pH 7.4), and alkaline (pH 7.9) conditions. Cells were maintained in T-25 flasks and sub-cultured upon reaching 80% confluency. The scratch test was performed by introducing a uniform scratch in well plates containing cells at ~66% confluency, followed by exposure to the different pH conditions. Healing was monitored over three days, with images taken to measure scratch width and assess cell proliferation under each condition.

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Detection of heavy metals in cocoa powder

This study aimed to determine the presence of heavy metals in cocoa powder samples using Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Five calibration standards of varying concentrations were prepared by diluting a 200-ppb stock solution in a mixture of 2% HNO₃ and 0.5% HCl. A blank sample was also prepared for baseline measurements.

Four cocoa powder samples—Hershey’s Natural Unsweetened Cocoa Powder, PC Organics Organic Cocoa Powder, Cocoa Camino Organic Cocoa Powder, and Fry’s Cocoa Premium Cocoa—were analyzed. Approximately 0.50 g of each sample was weighed into microwave digestion cells, followed by the addition of 5 mL of concentrated nitric acid. The samples were digested using an Anton Paar Multiwave GO Digestor for 35 minutes. After cooling, the digested solutions were filtered into 50-mL centrifuge tubes, diluted to volume with the 200-ppb stock solution, and analyzed using ICP-MS to quantify heavy metal concentrations.

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Analyzing and drawing conclusions

Sample Preparation Methodology for Detection of Bacteriophage Structural Proteins using MALDI-TOF-MS

This study aimed to develop a methodology for the preparation of bacteriophage structural protein samples for MALDI-TOF MS identification, using three bacteriophage strains (EC1KELCTY, EC1KELHOS and EC3KAMCTY). The bacteriophages were propagated on plate lysates using their respective bacterial hosts. For the protein gel, the phage lysates were treated with 1X SDS sample buffer and analyzed on a 10% SDS-PAGE gel. Individual protein bands were excised for in-gel trypsin digestion to extract peptides for MALDI-TOF MS analysis. Mass spectra were acquired using FlexControl software, with a range of 1 kDa to 9 kDa. Data analysis performed using the MASCOT search engine indicated limitations in the methodology, as the BSA control was not accurately identified. While peptide fragments corresponding to structural proteins of the bacteriophages were recognized, their reliability is uncertain due to potential methodological inconsistencies. Incorporation of desalting columns to the sample preparation procedure prior to mass spectra acquisition with MALDI is required to remove salts that may interfere with mass spectrometry results.

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Sample Preparation Methodology for Detection of Bacteriophage Structural Proteins using MALDI-TOF-MS

The academic poster served as a visual and concise representation of my research on bacteriophage structural protein detection using MALDI-TOF-MS. It provided an overview of key methods, including phage lysate preparation, SDS-PAGE separation, in-gel trypsin digestion, and mass spectrometry analysis, allowing for clear communication of complex procedures. The poster was instrumental in presenting my findings at conferences, facilitating discussions with researchers, receiving feedback, and networking with professionals in microbiology and mass spectrometry. Additionally, it helped refine my ability to convey scientific concepts visually, using structured layouts, data visualizations, and concise text to engage both experts and general audiences.

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Engaging in knowledge mobilization

Click blue bottom to hear interview

Interview with CBC news

CBC News visited Dr. Cheeptham’s Cave Microbiology Lab to highlight the groundbreaking research being conducted by our team, including my work on bacteriophages. During the visit, I had the opportunity to be interviewed about my research on bacteriophage structural proteins and their potential applications in combating bacterial infections. My project focuses on optimizing methodologies for identifying bacteriophage proteins using MALDI-TOF-MS, which could contribute to advancements in microbial diagnostics and biofilm treatment. Being featured by CBC was an incredible opportunity to share my research with a broader audience and emphasize the importance of bacteriophage studies in the fight against antibiotic-resistant bacteria.

TRU Undergraduate Research Conference 2025

At the TRU Undergraduate Conference, I had the opportunity to present my bacteriophage project, showcasing my research on isolating bacteriophages from sewage that target E. coli and their potential applications in biofilm treatment. I discussed my methodology, including phage lysate preparation, protein digestion for SDS-PAGE analysis, and data organization using Mascot software. Engaging with fellow researchers and faculty allowed me to refine my ideas and gain valuable feedback on optimizing my approach. This experience not only strengthened my presentation skills but also reinforced my commitment to advancing bacteriophage-based solutions for antimicrobial resistance.

Academic poster for direct studies research

Poster presented at the TRU Undergraduate Conference 2025 for direct studies project

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REFLECTIVE ESSAY

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