KU ScholarWorks
KU ScholarWorks is the institutional repository of the University of Kansas, featuring scholarly work by KU faculty, staff and students. As of July 30, 2024, we've upgraded to a new version of the software, but you will still be able to search for items in the repository, download files, and work with us to deposit new content.
For more information about KU ScholarWorks, please see About KU ScholarWorks .
If you have any questions, please contact Marianne Reed, Digital Publishing and Repository Manager at mreed@ku.edu.
Recent Submissions
Publication Chloroplast Genome Provides Insights into Molecular Evolution and Species Relationship of Fleabanes (: Tribe Astereae, Asteraceae) in the Juan Fernández Islands, Chile(MDPI, 2024-02-23)Erigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola–E. luteoviridis and E. fernandezia–E. ingae–E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex.Publication Expanding the CRISPR Toolbox for Engineering Lycopene Biosynthesis in Corynebacterium Glutamicum(MDPI, 2024-04-16)Lycopene represents one of the central compounds in the carotenoid pathway and it exhibits a potent antioxidant ability with wide potential applications in medicine, food, and cosmetics. The microbial production of lycopene has received increasing concern in recent years. () is considered to be a safe and beneficial industrial production platform, naturally endowed with the ability to produce lycopene. However, the scarcity of efficient genetic tools and the challenge of identifying crucial metabolic genes impede further research on for achieving high-yield lycopene production. To address these challenges, a novel genetic editing toolkit, CRISPR/MAD7 system, was established and developed. By optimizing the promoter, ORI and PAM sequences, the CRISPR/MAD7 system facilitated highly efficient gene deletion and exhibited a broad spectrum of PAM sites. Notably, 25 kb of DNA from the genome was successfully deleted. In addition, the CRISPR/MAD7 system was effectively utilized in the metabolic engineering of , allowing for the simultaneous knockout of and genes in one step to enhance the accumulation of lycopene by blocking the branching pathway. Through screening crucial genes such as , , , , , and , an optimal carotenogenic gene combination was obtained. Particularly, , a membrane protein gene, was found to play a vital role in lycopene production. Therefore, the CBIEbR strain was obtained by overexpressing , , and while strategically blocking the by-products of the lycopene pathway. As a result, the final engineered strain produced lycopene at 405.02 mg/L (9.52 mg/g dry cell weight, DCW) in fed-batch fermentation, representing the highest reported lycopene yield in to date. In this study, a powerful and precise genetic tool was used to engineer for lycopene production. Through the modifications between the host cell and the carotenogenic pathway, the lycopene yield was stepwise improved by 102-fold as compared to the starting strain. This study highlights the usefulness of the CRISPR/MAD7 toolbox, demonstrating its practical applications in the metabolic engineering of industrially robust .Publication Integrative methods reveal multiple drivers of diversification in rice paddy snakes(Nature Research, 2024-03-12)Divergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.Publication Publication Gastrointestinal Delivery of an mRNA Vaccine Using Immunostimulatory Polymeric Nanoparticles.(US Department of Health and Human Services, 2023-08-17)mRNA vaccines can be translated into protein antigens, in vivo, to effectively induce humoral and cellular immunity against these proteins. While current mRNA vaccines have generated potent immune responses, the need for ultracold storage conditions (- 80 °C) and healthcare professionals to administer the vaccine through the parenteral route has somewhat limited their distribution in rural areas and developing countries. Overcoming these challenges stands to transform future deployment of mRNA vaccines. In this study, we developed an mRNA vaccine that can trigger a systemic immune response through administration via the gastrointestinal (GI) tract and is stable at 4 °C. A library of cationic branched poly(β-amino ester) (PBAE) polymers was synthesized and characterized, from which a polymer with high intracellular mRNA delivery efficiency and immune stimulation capacity was down-selected. mRNA vaccines made with the lead polymer-elicited cellular and humoral immunity in mice. Furthermore, lyophilization conditions of the formulation were optimized to enable storage under refrigeration. Our results suggest that PBAE nanoparticles are potent mRNA delivery platforms that can elicit B cell and T cell activation, including antigen-specific cellular and humoral responses. This system can serve as an easily administrable, potent oral mRNA vaccine.
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