Rickey Yada

Professor

Research Interests

Food science
Food protein chemistry
Structure-function relationships
Enzymes
aspartic proteases

Relevant Thesis-Based Degree Programs

Affiliations to Research Centres, Institutes & Clusters

Research Options

I am available and interested in collaborations (e.g. clusters, grants).
I am interested in and conduct interdisciplinary research.
I am interested in working with undergraduate students on research projects.
 
 

Research Methodology

Circular dichroism spectroscopy
Micro-calorimeter
Small angle neutron scattering
Ultracentrifugation
Enzyme kinetics

Recruitment

Master's students
Doctoral students
Postdoctoral Fellows
Any time / year round

Current research interests include: the structure-function relationships of food and non-food related enzymes using molecular biology and various physico-chemical techniques (eg. circular dichroism spectroscopy, micro-calorimeter, small angle neutron scattering, ultracentrifugation, enzyme kinetics, etc.), carbohydrate metabolism in potatoes as it related to process quality as well as various applications of food-related nanoscale science and technology.

I support public scholarship, e.g. through the Public Scholars Initiative, and am available to supervise students and Postdocs interested in collaborating with external partners as part of their research.
I support experiential learning experiences, such as internships and work placements, for my graduate students and Postdocs.
I am open to hosting Visiting International Research Students (non-degree, up to 12 months).
I am interested in hiring Co-op students for research placements.

Complete these steps before you reach out to a faculty member!

Check requirements
  • Familiarize yourself with program requirements. You want to learn as much as possible from the information available to you before you reach out to a faculty member. Be sure to visit the graduate degree program listing and program-specific websites.
  • Check whether the program requires you to seek commitment from a supervisor prior to submitting an application. For some programs this is an essential step while others match successful applicants with faculty members within the first year of study. This is either indicated in the program profile under "Admission Information & Requirements" - "Prepare Application" - "Supervision" or on the program website.
Focus your search
  • Identify specific faculty members who are conducting research in your specific area of interest.
  • Establish that your research interests align with the faculty member’s research interests.
    • Read up on the faculty members in the program and the research being conducted in the department.
    • Familiarize yourself with their work, read their recent publications and past theses/dissertations that they supervised. Be certain that their research is indeed what you are hoping to study.
Make a good impression
  • Compose an error-free and grammatically correct email addressed to your specifically targeted faculty member, and remember to use their correct titles.
    • Do not send non-specific, mass emails to everyone in the department hoping for a match.
    • Address the faculty members by name. Your contact should be genuine rather than generic.
  • Include a brief outline of your academic background, why you are interested in working with the faculty member, and what experience you could bring to the department. The supervision enquiry form guides you with targeted questions. Ensure to craft compelling answers to these questions.
  • Highlight your achievements and why you are a top student. Faculty members receive dozens of requests from prospective students and you may have less than 30 seconds to pique someone’s interest.
  • Demonstrate that you are familiar with their research:
    • Convey the specific ways you are a good fit for the program.
    • Convey the specific ways the program/lab/faculty member is a good fit for the research you are interested in/already conducting.
  • Be enthusiastic, but don’t overdo it.
Attend an information session

G+PS regularly provides virtual sessions that focus on admission requirements and procedures and tips how to improve your application.

 

ADVICE AND INSIGHTS FROM UBC FACULTY ON REACHING OUT TO SUPERVISORS

These videos contain some general advice from faculty across UBC on finding and reaching out to a potential thesis supervisor.

Graduate Student Supervision

Doctoral Student Supervision

Dissertations completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest dissertations.

In silico insights into the membrane binding mechanism and role of disulfide bridges in the Solanum tuberosum plant specific insert (2020)

The Solanum tuberosum plant specific insert (StPSI) has a defensive role in potato plants. The StPSI is expressed alongside an aspartic protease, which is targeted to the acidic central vacuole. It functions at an acidic pH and interacts with the anionic lipids of a membrane. The StPSI contains a set of three highly conserved disulfide bonds that bridge the protein’s helical domains, and their removal leads to enhanced membrane interactions. The present work examined several aspects of the StPSI in dimeric form, including the structure and membrane binding as a function of pH, and the effect of sequential removal of the disulfide bonds and their role in maintaining overall protein tertiary structure. Several glutamic and aspartic acid residues displayed highly perturbed pKa values, however, pH was found to have little, if any, effects on the secondary structure of the StPSI at pH 3.0 or 7.4. Coarse-grained modelling of the StPSI demonstrated poor affinity for neutral or anionic membranes at pH 7.4. Conversely, at pH 3.0, two binding modes were uncovered: Mode 1 (inactive binding) and Mode 2 (active binding). In Mode 2, N- and C-terminal residues of one monomer and numerous polar and basic residues on the second monomer interacted strongly with anionic membranes, accompanied by a re-orientation of the dimer to a more vertical position. These results offer the first examination, at near-atomic resolution, of residues mediating the StPSI-membrane interactions, and allow for the proposal of a possible fusion mechanism. Removal of disulfide bonds did not lead to destabilization of the tertiary structure at either pH 3.0 or 7.4. The StPSI possesses an extensive network of inter-monomer hydrophobic interactions and intra-monomer hydrogen bonds, which stabilize the local secondary structure, leading to a robust association between monomers, regardless of the disulfide bond state. Removal of disulfide bonds did not substantially impact secondary structure, however, they may play an important role in maintaining a less plastic structure within plant cells in order to regulate membrane affinity or targeting.

View record

Elucidation of novel physiological and genetic elements associated with the cold adaptability and survival of Listeria monocytogenes in the food processing continuum (2018)

Novel physiological and genetic factors associated with the survival of Listeria monocytogenes in the food-processing continuum were investigated, with an emphasis on its cold-growth ability. Food-related L. monocytogenes strains (n=166) were sequenced and subsequently evaluated on their ability to tolerate cold (4°C), salt (6% NaCl, 25°C), acid (pH 5, 25°C), and desiccation (33% RH, 20°C) stress. Stress tolerances were associated with serotype, clonal complex, full-length inlA profiles, and plasmid harbourage. Notably, strains possessing full length inlA (as opposed to a truncated version) exhibited significantly (p1,000-fold) of differentially expressed (e.g., >2-fold, p
View record

Master's Student Supervision

Theses completed in 2010 or later are listed below. Please note that there is a 6-12 month delay to add the latest theses.

Collective mindfulness within a food security non-profit organization during the COVID-19 crisis : a case study (2023)

This study focussed on how collective mindfulness contributes to resilience in non-profit organizations coping with crises, such as the COVID-19 pandemic. Taking a Vancouver B.C. non-profit organization’s emergency food security response as a case study, it examines the role that mindfulness plays in non-profit organizations’ adaptations to the COVID-19 pandemic through the lens of complexity science. Specifically, it identifies emergent mindfulness processes and their effects on organizational resilience within non-profit organizations. This qualitative research employs a responsive, phronetic-iterative approach to interviewing and analysis that is grounded in a post-structuralist paradigm; attempts to advance a complexity-based theory of collective mindfulness; and furthers complexity science as a comprehensive interpretive framework. Findings demonstrate that collective mindfulness may be enacted through interdependent processes of dynamic reflexivity, responsive self-organization, and flexible co-evolution, through which resilience may emerge.

View record

Mechanism of interaction between Solanum tuberosum plant specific insert with phospholipid membranes using NMR spectroscopy (2017)

Plants rely on their innate immunity as a first line of host defense against external pathogens. In potatoes, Solanum tuberosum, upon the infestation of the late blight disease causing pathogen, Phytophthora infestans, there is an increased expression of aspartic proteases. Most plant aspartic proteases are characterized by a hydrophobic signal peptide, a prosegment, and an N-terminal and C-terminal domain separated by a plant specific insert. Like saposins and various other members in this family, PSI of Solanum tuberosum was discovered to have antimicrobial and antifungal activities. PSI is active under acidic pH conditions by self-assembling into a dimer and it interacts with phospholipid membranes from pathogens to cause leakage activities. The objectives of this thesis were to elucidate the pH dependent protein monomer-dimer equilibrium and the backbone chemical shift assignments of PSI by solution NMR ,the dynamic properties of PSI by the NMR relaxation, PSI-membrane interaction by solid-state NMR, and the topology of PSI-membrane complex. A combination of solution state and solid-state NMR were used to study the characteristics of PSI in solution and PSI-membrane interactions at different pH conditions. Protein backbone assignments and dynamics characterization were performed on the PSI in solution. Protein-membrane interaction was examined through NMR titration, NMR based H/D exchange, and protein-lipid interactions by solid-state NMR. PSI monomer-dimer equilibrium occurred between pH 2.0 and 7.0. From dynamics studies, the average ¹⁵N longitudinal relaxation (T₁) times were 0.99 ± 0.18 s and 0.53 ± 0.03 s for pH 2.0 and 7.0, respectively, this demonstrated that PSI was a dimer at pH 2.0 and a monomer at pH 7.0. Comparison of the transverse relaxation (T₂) times of PSI at different pH values yielded the same conclusion. ¹H-¹⁵N heteronuclear NOE determined that PSI had rigid helical segments connected with flexible long loops. Solid-state NMR data suggested that protein-membrane interaction occurred on the phosphate head group and protein is embedded in the lipid environment after PSI-membrane interaction. These results contributed to protein dynamics and mechanisms of PSI and its interactions with phospholipid membrane, and therefore, a better mechanistic understanding of the innate natural plant host defense response against pathogen invasions.

View record

Publications

 
 

If this is your researcher profile you can log in to the Faculty & Staff portal to update your details and provide recruitment preferences.

 
 

Planning to do a research degree? Use our expert search to find a potential supervisor!