@article{vento_durmusoglu_li_patinios_sullivan_ttofali_schaik_yu_wang_barquist_et al._2024, title={A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria}, volume={84}, ISSN={["1097-4164"]}, DOI={10.1016/j.molcel.2024.06.003}, abstractNote={The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic biological chassis. However, genetically manipulating these strains has faced a long-standing bottleneck: how to efficiently transform DNA. Here, we report imitating methylation patterns rapidly in TXTL (IMPRINT), a generalized, rapid, and scalable approach based on cell-free transcription-translation (TXTL) to overcome DNA restriction, a prominent barrier to transformation. IMPRINT utilizes TXTL to express DNA methyltransferases from a bacterium's restriction-modification systems. The expressed methyltransferases then methylate DNA in vitro to match the bacterium's DNA methylation pattern, circumventing restriction and enhancing transformation. With IMPRINT, we efficiently multiplex methylation by diverse DNA methyltransferases and enhance plasmid transformation in gram-negative and gram-positive bacteria. We also develop a high-throughput pipeline that identifies the most consequential methyltransferases, and we apply IMPRINT to screen a ribosome-binding site library in a hard-to-transform Bifidobacterium. Overall, IMPRINT can enhance DNA transformation, enabling the use of sophisticated genetic manipulation tools across the bacterial world.}, number={14}, journal={MOLECULAR CELL}, author={Vento, Justin M. and Durmusoglu, Deniz and Li, Tianyu and Patinios, Constantinos and Sullivan, Sean and Ttofali, Fani and Schaik, John and Yu, Yanying and Wang, Yanyan and Barquist, Lars and et al.}, year={2024}, month={Jul} }
 @article{bang_bergman_li_mukherjee_alshehri_abbott_crook_velev_hall_you_2023, title={An integrated chemical engineering approach to understanding microplastics}, volume={1}, ISSN={["1547-5905"]}, DOI={10.1002/aic.18020}, abstractNote={AbstractEnvironmental and health risks posed by microplastics (MPs) have spurred numerous studies to better understand MPs' properties and behavior. Yet, we still lack a comprehensive understanding due to MP's heterogeneity in properties and complexity of plastic property evolution during aging processes. There is an urgent need to thoroughly understand the properties and behavior of MPs as there is increasing evidence of MPs' adverse health and environmental effects. In this perspective, we propose an integrated chemical engineering approach to improve our understanding of MPs. The approach merges artificial intelligence, theoretical methods, and experimental techniques to integrate existing data into models of MPs, investigate unknown features of MPs, and identify future areas of research. The breadth of chemical engineering, which spans biological, computational, and materials sciences, makes it well‐suited to comprehensively characterize MPs. Ultimately, this perspective charts a path for cross‐disciplinary collaborative research in chemical engineering to address the issue of MP pollution.}, journal={AICHE JOURNAL}, author={Bang, Rachel S. and Bergman, Michael and Li, Tianyu and Mukherjee, Fiona and Alshehri, Abdulelah S. and Abbott, Nicholas L. and Crook, Nathan C. and Velev, Orlin D. and Hall, Carol K. and You, Fengqi}, year={2023}, month={Jan} }
 @article{li_menegatti_crook_2023, title={Breakdown of polyethylene therepthalate microplastics under saltwater conditions using engineered Vibrio natriegens}, volume={9}, ISSN={["1547-5905"]}, url={https://doi.org/10.1002/aic.18228}, DOI={10.1002/aic.18228}, abstractNote={AbstractPoly(ethylene terephthalate) (PET) is a highly recyclable plastic that has been extensively used and manufactured. Like other plastics, PET resists natural degradation, thus accumulating in the environment. Several recycling strategies have been applied to PET, but these tend to result in downcycled products that eventually end up in landfills. This accumulation of landfilled PET waste contributes to the formation of microplastics, which pose a serious threat to marine life and ecosystems, and potentially to human health. To address this issue, our project leveraged synthetic biology to develop a whole‐cell biocatalyst capable of depolymerizing PET in seawater environments by using the fast‐growing, nonpathogenic, moderate halophile Vibrio natriegens. By leveraging a two‐enzyme system—comprising a chimera of IsPETase and IsMHETase from Ideonella sakaiensis—displayed on V. natriegens, we constructed whole‐cell catalysts that depolymerize PET and convert it into its monomers in salt‐containing media and at a temperature of 30°C.}, journal={AICHE JOURNAL}, author={Li, Tianyu and Menegatti, Stefano and Crook, Nathan}, year={2023}, month={Sep} }