@article{burris_simmons_webb_moore_jaykus_zheng_reed_ferreira_brown_bell_2021, title={Salmonella enterica colonization and fitness in pre-harvest cantaloupe production}, volume={93}, ISSN={["1095-9998"]}, DOI={10.1016/j.fm.2020.103612}, abstractNote={Cantaloupes have emerged as significant vehicles of widespread foodborne illness outbreaks caused by bacterial pathogens, including Salmonella . The purpose of this study was to investigate the efficiency of Salmonella colonization and internalization in cantaloupes by relevant routes of contamination. Cantaloupe plants ( Cucumis melo ‘reticulatus’) from two cultivars ‘Athena’ (Eastern) and ‘Primo’ (Western) were grown from commercial seed. Plants were maintained in the NCSU BSL-3P phytotron greenhouse. Salmonella enterica (a cocktail of cantaloupe-associated outbreak serovars Javiana, Newport, Panama, Poona and Typhimurium) contamination was introduced via blossoms or soil at ca. 4.4 log 10 CFU/blossom or 8.4 log 10 CFU/root zone, respectively. Cantaloupes were analyzed for Salmonella by enrichment in accordance with modified FDA-BAM methods. Five randomly chosen colonies from each Salmonella -positive sample were typed using the Agilent 2100 bioanalyzer following multiplex PCR. Data were analyzed for prevalence of contamination and serovar predominance in fruit, stems and soil. Of the total cantaloupe fruit harvested from Salmonella -inoculated blossoms (n = 63), 89% (56/63) were externally contaminated and 73% (46/63) had Salmonella internalized into the fruit. Serovar Panama was the most commonly isolated from the surface of fruit while S. Panama and S. Poona were the most prevalent inside the fruit. When soil was inoculated with Salmonella at one day post-transplant, 13% (8/60) of the plants were shown to translocate the organism to the lower stem (ca. 4 cm) by 7 days post-inoculation (dpi). We observed Salmonella persistence in the soil up to 60 dpi with S. Newport being the predominant serovar at 10 and 20 dpi. These data demonstrate that contaminated soil and blossoms can lead to Salmonella internalization into the plant or fruit at a relatively high frequency. • Salmonella- contaminated soil and blossoms lead to plant or fruit internalization. • Blossom inoculations resulted in a high percentage of Salmonella internalization to fruit. • Serovar Panama was the most commonly isolated serovar from the surface of fruit. • S. Panama and S . Poona were the most prevalent serovars internalized to fruit. • Salmonella persisted in soils up to 60 days post inoculation.}, journal={FOOD MICROBIOLOGY}, author={Burris, Kellie P. and Simmons, Otto D., III and Webb, Hannah M. and Moore, Robin Grant and Jaykus, Lee-Ann and Zheng, Jie and Reed, Elizabeth and Ferreira, Christina M. and Brown, Eric and Bell, Rebecca L.}, year={2021}, month={Feb} }
 @article{burris_simmons_webb_deese_moore_jaykus_zheng_reed_ferreira_brown_et al._2020, title={Colonization and Internalization of Salmonella enterica and Its Prevalence in Cucumber Plants}, volume={11}, ISSN={1664-302X}, url={http://dx.doi.org/10.3389/fmicb.2020.01135}, DOI={10.3389/fmicb.2020.01135}, abstractNote={Consumption of cucumbers (Cucumis sativus var. sativus) has been linked to several foodborne outbreaks involving Salmonella enterica. The purpose of this work was to investigate the efficiency of colonization and internalization of S. enterica into cucumber plants by various routes of contamination. Produce-associated outbreak strains of Salmonella (a cocktail of serovars Javiana, Montevideo, Newport, Poona and Typhimurium) were introduced to three cultivars of cucumber plants (two slicing cultivars and one pickling) via blossoms (ca. 6.4 log10 CFU/blossom, 4.5 log10 CFU/blossom or 2.5 log10 CFU/blossom) or soil (ca. 8.3 log10 CFU/root zone) and were analyzed for prevalence of Salmonella contamination (internal and external) and serovar predominance in fruit and stems. Of the total slicing fruit harvested from Salmonella-inoculated blossoms (ca. 6.4, 4.5 or 2.5 log10 CFU/blossom), 83.9% (47/56), 81.4% (48/59) or 71.2% (84/118) were found colonized and 67.9% (38/56), 35.6% (21/59) or 22.0% (26/118) had Salmonella internalized into the fruit, respectively. S. Poona was the most prevalent serovar isolated on or in cucumber fruits at all inoculation levels. When soil was inoculated at 1 day post transplant (dpt), 8% (10/120) of the plants were shown to translocate Salmonella to the lower stem 7 days post inoculation (dpi). Results identified blossoms as an important route by which Salmonella internalized at a high percentage into cucumbers, and S. Poona, the same strain isolated from the 2015 outbreak of cucumbers imported from Mexico, was shown to be well adapted to the blossom niche.}, journal={Frontiers in Microbiology}, publisher={Frontiers Media SA}, author={Burris, Kellie P. and Simmons, Otto D. and Webb, Hannah M. and Deese, Lauren M. and Moore, Robin Grant and Jaykus, Lee-Ann and Zheng, Jie and Reed, Elizabeth and Ferreira, Christina M. and Brown, Eric W. and et al.}, year={2020}, month={May} }
 @article{leebens-mack_barker_carpenter_deyholos_gitzendanner_graham_grosse_li_melkonian_mirarab_et al._2019, title={One thousand plant transcriptomes and the phylogenomics of green plants}, volume={574}, ISSN={["1476-4687"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85074238403&partnerID=MN8TOARS}, DOI={10.1038/s41586-019-1693-2}, abstractNote={Green plants (Viridiplantae) include around 450,000-500,000 species1,2 of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.}, number={7780}, journal={NATURE}, author={Leebens-Mack, James H. and Barker, Michael S. and Carpenter, Eric J. and Deyholos, Michael K. and Gitzendanner, Matthew A. and Graham, Sean W. and Grosse, Ivo and Li, Zheng and Melkonian, Michael and Mirarab, Siavash and et al.}, year={2019}, month={Oct}, pages={679-+} }
 @article{rempe_burris_lenaghan_stewart_2017, title={The Potential of Systems Biology to Discover Antibacterial Mechanisms of Plant Phenolics}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.00422}, abstractNote={Drug resistance of bacterial pathogens is a growing problem that can be addressed through the discovery of compounds with novel mechanisms of antibacterial activity. Natural products, including plant phenolic compounds, are one source of diverse chemical structures that could inhibit bacteria through novel mechanisms. However, evaluating novel antibacterial mechanisms of action can be difficult and is uncommon in assessments of plant phenolic compounds. With systems biology approaches, though, antibacterial mechanisms can be assessed without the bias of target-directed bioassays to enable the discovery of novel mechanism(s) of action against drug resistant microorganisms. This review article summarizes the current knowledge of antibacterial mechanisms of action of plant phenolic compounds and discusses relevant methodology.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Rempe, Caroline S. and Burris, Kellie P. and Lenaghan, Scott C. and Stewart, C. Neal, Jr.}, year={2017}, month={Mar} }
 @inproceedings{isukapati_list_2016, title={Comparing actuated and bid-based control strategies}, DOI={10.1109/itsc.2016.7795758}, abstractNote={In this paper we explore some fundamental differences between control strategies modeled based on economic theory principles as opposed to more traditional control theory principles. More specifically, we explored differences between our bid-based control model and various actuated control models. The comparisons include situations where maximum greens are imposed in actuated control, and situations where they are not. To incorporate these ideas, two bid-based (b1, and b2)and four actuated (a1, a2, a3, and a4) control options are considered. Simulation experiments have been conducted to test these ideas for an intersection with two one-way, one-lane approaches, one eastbound and one northbound. Here are some of the inferences that can be drawn: 1) with actuated control, vehicles on the NB approach, with the larger volumes, always experience higher delays than the EB approach, while the differences between the NB and EB approaches are less significant for bid-based control; 2) Actuated control scenarios where maximum green are imposed (a2, a4) produced lower delay distributions than the scenarios where they are not imposed (a1, a3); 3) it is possible to find a combination of max-greens for a given flow condition that allow the actuated controller to match the performance (at least in terms of delays) of bid-based control; 4)bid-based control produced cycle length distributions that are smaller than those produced by various actuated control models; 5)Actuated control scenarios where maximum green are imposed (a2, a4) produced lower cycle length distributions than the scenarios where they are not imposed (a1, a3).}, booktitle={2016 IEEE 19th International Conference on Intelligent Transportation Systems (ITSC)}, author={Isukapati, I. K. and List, G. F.}, year={2016}, pages={1516–1521} }