Rickey Yada: Professor at , UBC Faculty of Land and Food Systems

Professor

Faculty of Land and Food Systems

Research Classification

Enzymes (including kinetics and mechanisms, and biocatalyst)

Other biological sciences

Research Interests

Food science

Food protein chemistry

Structure-function relationships

Enzymes

aspartic proteases

Relevant Thesis-Based Degree Programs

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Affiliations to Research Centres, Institutes & Clusters

BC Diabetes Research Network

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.

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Research Methodology

Circular dichroism spectroscopy

Micro-calorimeter

Small angle neutron scattering

Ultracentrifugation

Enzyme kinetics

Recruitment

Looking to recruit:

Master's students

Doctoral students

Postdoctoral Fellows

Desired start dates: Any time / year round

Potential research project areas:

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.

Other options:

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.

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Supervision Enquiry

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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.

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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
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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.

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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.

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