Development and Application of Predictive Models for Survival, Growth, and Death of Enteric Pathogens in Leafy Greens Supply Chain

Leafy greens are essential part of a healthy diet. Because of their health benefits, production and consumption of leafy greens has increased considerably in the U.S. in the last few decades. However, leafy greens are also associated with a large number of foodborne disease outbreaks in the last few years. The overall goal of this dissertation was to use the current knowledge of predictive models and available data to understand the growth, survival, and death of enteric pathogens in leafy greens at pre- and post-harvest levels. Temperature plays a major role in the growth and death of bacteria in foods. A growth-death model was developed for Salmonella and Listeria monocytogenes in leafy greens for varying temperature conditions typically encountered during supply chain. The developed growth-death models were validated using experimental dynamic time-temperature profiles available in the literature. Furthermore, these growth-death models for Salmonella and Listeria monocytogenes and a similar model for E. coli O157:H7 were used to predict the growth of these pathogens in leafy greens during transportation without temperature control. Refrigeration of leafy greens meets the purposes of increasing their shelf-life and mitigating the bacterial growth, but at the same time, storage of foods at lower temperature increases the storage cost. Nonlinear programming was used to optimize the storage temperature of leafy greens during supply chain while minimizing the storage cost and maintaining the desired levels of sensory quality and microbial safety. Most of the outbreaks associated with consumption of leafy greens contaminated with E. coli O157:H7 have occurred during July-November in the U.S. A dynamic system model consisting of subsystems and inputs (soil, irrigation, cattle, wildlife, and rainfall) simulating a farm in a major leafy greens producing area in California was developed. The model was simulated incorporating the events of planting, irrigation, harvesting, ground preparation for the new crop, contamination of soil and plants, and survival of E. coli O157:H7. The predictions of this system model are in agreement with the seasonality of outbreaks. This dissertation utilized the growth, survival, and death models of enteric pathogens in leafy greens during production and supply chain.

THERMODYNAMICS AND APPLICATION OF A PAIR OF SYNTHETIC NUCLEOBASES FROM ARTIFICIALLY EXPANDED GENETIC INFORMATION SYSTEM

UV-melting experiments were performed on 9-mer duplexes containing a pair of synthetic nucleobases P·Z, two members of Expanded Genetic Information System (AEGIS), or P, Z containing mismatches. Enthalpy, entropy and free energy change were derived from simulation using two-state transition model. Nearest neighbor thermodynamic parameters of trimers or tetramers containing P·Z pair or P, Z containing mismatches were derived based on known nearest neighbor parameters. Proposed structures based on thermodynamic parameters are discussed. An application using P·Z pair as reverse selection tool of desired nucleic acid secondary structure is described.

Using a Combination of Phylogenetic Comparative and Paleobotanical Methods to Elucidate Patterns of Lineage Selection in Rosales (Plantae: Anthophyta)

An increasing focus in evolutionary biology is on the interplay between mesoscale ecological and evolutionary processes such as population demographics, habitat tolerance, and especially geographic distribution, as potential drivers responsible for patterns of diversification and extinction over geologic time. However, few studies to date connect organismal processes such as survival and reproduction through mesoscale patterns to long-term macroevolutionary trends. In my dissertation, I investigate how mechanism of seed dispersal, mediated through geographic range size, influences diversification rates in the Rosales (Plantae: Anthophyta). In my first chapter, I validate the phylogenetic comparative methods that I use in my second and third chapters. Available state speciation and extinction (SSE) models assumptions about evolution known to be false through fossil data. I show, however, that as long as net diversification rates remain positive – a condition likely true for the Rosales – these violations of SSE’s assumptions do not cause significantly biased results. With SSE methods validated, my second chapter reconstructs three associations that appear to increase diversification rate for Rosalean genera: (1) herbaceous habit; (2) a three-way interaction combining animal dispersal, high within-genus species richness, and geographic range on multiple continents; (3) a four-way interaction combining woody habit with the other three characteristics of (2). I suggest that the three- and four-way interactions represent colonization ability and resulting extinction resistance in the face of late Cenozoic climate change; however, there are other possibilities as well that I hope to investigate in future research. My third chapter reconstructs the phylogeographic history of the Rosales using both non-fossil-assisted SSE methods as well as fossil-informed traditional phylogeographic analysis. Ancestral state reconstructions indicate that the Rosaceae diversified in North America while the other Rosalean families diversified elsewhere, possibly in Eurasia. SSE is able to successfully identify groups of genera that were likely to have been ancestrally widespread, but has poorer taxonomic resolution than methods that use fossil data. In conclusion, these chapters together suggest several potential causal links between organismal, mesoscale, and geologic scale processes, but further work will be needed to test the hypotheses that I raise here.

THE ROLE OF RULES, EXAMPLES AND INDIVIDUAL DIFFERENCES IN THE ACQUISITION OF DECLARATIVE AND PROCEDURAL SECOND LANGUAGE KNOWLEDGE

The relevance of explicit instruction has been well documented in SLA research. Despite numerous positive findings, however, the issue continues to engage scholars worldwide. One issue that was largely neglected in previous empirical studies - and one that may be crucial for the effectiveness of explicit instruction - is the timing and integration of rules and practice. The present study investigated the extent to which grammar explanation (GE) before practice, grammar explanation during practice, and individual differences impact the acquisition of L2 declarative and procedural knowledge of two grammatical structures in Spanish. In this experiment, 128 English-speaking learners of Spanish were randomly assigned to four experimental treatments and completed comprehension-based task-essential practice for interpreting object-verb (OV) and ser/estar (SER) sentences in Spanish. Results confirmed the predicted importance of timing of GE: participants who received GE during practice were more likely to develop and retain their knowledge successfully. Results further revealed that the various combinations of rules and practice posed differential task demands on the learners and consequently drew on language aptitude and WM to a different extent. Since these correlations between individual differences and learning outcomes were the least observed in the conditions that received GE during practice, we argue that the suitable integration of rules and practice ameliorated task demands, reducing the burden on the learner, and accordingly mitigated the role of participants’ individual differences. Finally, some evidence also showed that the comprehension practice that participants received for the two structures was not sufficient for the formation of solid productive knowledge, but was more effective for the OV than for the SER construction.