Rickey Yada


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Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - Nov 2019)
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 (2010 - 2018)
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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