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Full-Text Articles in Engineering
Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan
Crowd Control: Regulating The Spatial Organization Of Biopolymers And Gene Expression By Macromolecular Crowding, Gaurav Chauhan
Doctoral Dissertations
The intracellular environment is crowded with macromolecules that can occupy a significant fraction of the cellular volume. This can give rise to attractive depletion interactions that impact the conformations and interactions of biopolymers, as well as their interactions with confining surfaces. We used computer simulations to study the effects of crowding on biologically-inspired models of polymers. We showed that crowding can lead to attractive interactions between two flexible ring polymers, and we further characterized the adsorption of both flexible and semiflexible polymers onto confining surfaces. These results indicate that crowding-induced depletion interactions could play a role in the spatial organization …
Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo
Engineering Modularity Of Ester Biosynthesis Across Biological Scales, Hyeongmin Seo
Doctoral Dissertations
Metabolic engineering and synthetic biology enable controlled manipulation of whole-cell biocatalysts to produce valuable chemicals from renewable feedstocks in a rapid and efficient manner, helping reduce our reliance on the conventional petroleum-based chemical synthesis. However, strain engineering process is costly and time-consuming that developing economically competitive bioprocess at industrial scale is still challenging. To accelerate the strain engineering process, modular cell engineering has been proposed as an innovative approach that harnesses modularity of metabolism for designing microbial cell factories. It is important to understand biological modularity and to develop design principles for effective implementation of modular cell engineering. In this …
A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus
A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus
The Summer Undergraduate Research Fellowship (SURF) Symposium
Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …
Refactoring The Silent Spectinabilin Gene Cluster Using A Plug-And-Play Scaffold, Zengyi Shao, Guodong Rao, Chun Li, Zhanar Abil, Yunzi Luo, Huimin Zhao
Refactoring The Silent Spectinabilin Gene Cluster Using A Plug-And-Play Scaffold, Zengyi Shao, Guodong Rao, Chun Li, Zhanar Abil, Yunzi Luo, Huimin Zhao
Zengyi Shao
Natural products (secondary metabolites) are a rich source of compounds with important biological activities. Eliciting pathway expression is always challenging but extremely important in natural product discovery because an individual pathway is tightly controlled through a unique regulation mechanism and hence often remains silent under the routine culturing conditions. To overcome the drawbacks of the traditional approaches that lack general applicability, we developed a simple synthetic biology approach that decouples pathway expression from complex native regulations. Briefly, the entire silent biosynthetic pathway is refactored using a plug-and-play scaffold and a set of heterologous promoters that are functional in a heterologous …
Rapid Characterization And Engineering Of Natural Product Biosynthetic Pathways Via Dna Assembler, Zengyi Shao, Yunzi Luo, Huimin Zhao
Rapid Characterization And Engineering Of Natural Product Biosynthetic Pathways Via Dna Assembler, Zengyi Shao, Yunzi Luo, Huimin Zhao
Zengyi Shao
We report a synthetic biology strategy for rapid genetic manipulation of natural product biosynthetic pathways. Based on DNA assembler, this method synthesizes the entire expression vector containing the target biosynthetic pathway and the genetic elements required for DNA maintenance and replication in various hosts in a single-step manner through yeast homologous recombination, offering unprecedented flexibility and versatility in pathway manipulations.