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Title: Controlling biofilms using synthetic biology approaches
Creator: Fang, Kuili, Park, Oh-Jin, Hong, Seok Hoon
Date: 2020
Description: Bacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene...
Show moreBacterial biofilms are formed by the complex but ordered regulation of intra- or inter-cellular communication, environmentally responsive gene expression, and secretion of extracellular polymeric substances. Given the robust nature of bio?lms due to the non-growing nature of bio?lm bacteria and the physical barrier provided by the extracellular matrix, eradicating bio?lms is a very di?cult task to accomplish with conventional antibiotic or disinfectant treatments. Synthetic biology holds substantial promise for controlling bio?lms by improving and expanding existing biological tools, introducing novel functions to the system, and re-conceptualizing gene regulation. This review summarizes synthetic biology approaches used to eradicate bio?lms via protein engineering of bio?lm-related enzymes, utilization of synthetic genetic circuits, and the development of functional living agents. Synthetic biology also enables bene?cial applications of bio?lms through the production of biomaterials and patterning bio?lms with speci?c temporal and spatial structures. Advances in synthetic biology will add novel bio?lm functionalities for future therapeutic, biomanufacturing, and environmental applications.
Sponsorship: NIH-R15AI130988, NSF CBET-1917130
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Title: Engineering Escherichia coli to produce and secrete colicins for rapid and selective biofilm cell killing
Creator: Jin, Xing, An, Sungjun, Kightlinger, Weston, Zhou, Jiacheng, Hong, Seok Hoon
Date: 2021
Description: Bacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial...
Show moreBacterial biofilms are associated with chronic infectious diseases and are highly resistant to conventional antibiotics. Antimicrobial bacteriocins are alternatives to conventional antibiotics and are characterized by unique cell-killing mechanisms, including pore formation on cell membranes, nuclease activity, and cell wall synthesis inhibition. Here, we used cell-free protein synthesis to rapidly evaluate the antibiofilm activities of colicins E1, E2, and E3. We found that E2 (with DNase activity) most effectively killed target biofilm cells (i.e., the K361 strain) while leaving nontargeted biofilms intact. We then engineered probiotic Escherichia coli microorganisms with genetic circuits to controllably synthesize and secrete colicin E2, which successfully inhibited biofilms and killed preformed indicator biofilms. Our findings suggest that colicins rapidly and selectively kill target biofilm cells in multispecies biofilms and demonstrate the potential of using microorganisms engineered to produce antimicrobial colicin proteins as live therapeutic strategies to treat biofilm-associated infections.
Sponsorship: NIH-R15AI130988
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Title: Editorial, "Cell-Free Synthetic Biology": Synthetic Biology Meets Cell-Free Protein Synthesis
Creator: Hong, Seok Hoon
Date: 2019
Publisher: MDPI
Description: Sponsorship: NIH R15AI130988

Title: Incorporation of non-standard amino acids into proteins: challenges, recent achievements, and emerging applications
Creator: Jin, Xing, Park Oh-Jin, Hong, Seok Hoon
Date: 2019
Description: The natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the...
Show moreThe natural genetic code only allows for 20 standard amino acids in protein translation, but genetic code reprogramming enables the incorporation of non-standard amino acids (NSAAs). Proteins containing NSAAs provide enhanced or novel properties and open diverse applications. With increased attention to the recent advancements in synthetic biology, various improved and novel methods have been developed to incorporate single and multiple distinct NSAAs into proteins. However, various challenges remain in regard to NSAA incorporation, such as low yield and misincorporation. In this review, we summarize the recent efforts to improve NSAA incorporation by utilizing orthogonal translational system optimization, cell-free protein synthesis, genomically recoded organisms, artificial codon boxes, quadruplet codons, and orthogonal ribosomes, before closing with a discussion of the emerging applications of NSAA incorporation.
Sponsorship: NIH R15AI130988
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Title: Undecanoic Acid, Lauric Acid, and N-Tridecanoic Acid Inhibit Escherichia coli Persistence and Biofilm Formation
Creator: Jin, Xing, Zhou, Jiacheng, Richey, Gabriella, Wang, Mengya, Hong, Sung Min Choi, Hong, Seok Hoon
Date: 2021
Description: Persister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating...
Show morePersister cell formation and biofilms of pathogens are extensively involved in the development of chronic infectious diseases. Eradicating persister cells is challenging, owing to their tolerance to conventional antibiotics, which cannot kill cells in a metabolically dormant state. A high frequency of persisters in biofilms makes inactivating biofilm cells more difficult, because the biofilm matrix inhibits antibiotic penetration. Fatty acids may be promising candidates as antipersister or antibiofilm agents, because some fatty acids exhibit antimicrobial effects. We previously reported that fatty acid ethyl esters effectively inhibit Escherichia coli persister formation by regulating an antitoxin. In this study, we screened a fatty acid library consisting of 65 different fatty acid molecules for altered persister formation. We found that undecanoic acid, lauric acid, and N-tridecanoic acid inhibited E. coli BW25113 persister cell formation by 25-, 58-, and 44-fold, respectively. Similarly, these fatty acids repressed persisters of enterohemorrhagic E. coli EDL933. These fatty acids were all medium-chain saturated forms. Furthermore, the fatty acids repressed Enterohemorrhagic E. coli (EHEC) biofilm formation (for example, by 8-fold for lauric acid) without having antimicrobial activity. This study demonstrates that medium-chain saturated fatty acids can serve as antipersister and antibiofilm agents that may be applied to treat bacterial infections.
Sponsorship: NIH-R15AI130988; NSF REU-1757989
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Title: Research in Architectural Education: Theory and Practice of Visual Training
Creator: Jones, Kristin
Date: 2016, 12/12/2016
Collection: Enquiry

Title: The City in the Landscape: Alfred Caldwell's Broader Perspective on Urban Design
Creator: Jones, Kristin, Garcia-Requejo, Zaida
Date: 2020, 2020
Publisher: Editorial Universitat Politècnica de València
Description: Alfred Caldwell was among the first full- time American professors Mies van der Rohe hired at the Illinois Institute of Technology (IIT). Many...
Show moreAlfred Caldwell was among the first full- time American professors Mies van der Rohe hired at the Illinois Institute of Technology (IIT). Many have admired Mies’s architecture since the 1920s, and know that his ideas were also transmitted as a professor, first at the Bauhaus in Europe and then as Director of the Department of Architecture at IIT. Caldwell, a practicing landscape architect and protégé of Jens Jensen, is perhaps less widely known, but was a major influence on IIT’s program especially in the areas of construction, landscape, and architectural history. Caldwell completed a Master of Science in City Planning with a thesis entitled The City in the Landscape: A Preface for Planning, which can be considered a manifesto of both his professional ideas and IIT’s planning pedagogy. In addition to his own works, Caldwell collaborated with Mies and architect Ludwig Hilberseimer, Director of City and Regional Planning at IIT and former Head of Building Theory at the Bauhaus, on the design of built works which left behind artifacts representing the ideal of “the city in the landscape.” This communication examines the broader perspective on urban design influenced by the symbiotic disciplines of architecture, city-regional planning and landscape as manifested in the individual and collaborative built work and pedagogy of Caldwell, Hilberseimer, and Mies.
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Collection: EAAE-ARCC International Conference & 2nd Valencia International Biennial

Title: Stephen Fienberg's influence on algebraic statistics, Special Volume in honor of memory of S.E.Fienberg
Creator: Petrović, Sonja, Slavkovic, Aleksandra, Yoshida, Ruriko
Date: 2019, 2019-04-12
Description: Stephen (Steve) E. Fienberg (1942-2016) was an eminent statistician, whose impact on research, education and the practice of statistics, and...
Show moreStephen (Steve) E. Fienberg (1942-2016) was an eminent statistician, whose impact on research, education and the practice of statistics, and many other fields is astonishing in its breadth. He was a visionary when it came to linking many different areas to address real scientific issues. He professed the importance of statistics in many disciplines, but recognized that true interdisciplinary work requires joining of the expertise across different areas, and it is in this spirit that he helped steer algebraic statistics toward becoming a thriving subject. Many of his favorite topics in the area are covered in this special issue. We are grateful to all authors for contributing to this volume to honor him and his influence on the field. During the preparation of this issue, we learned about the tragic killing of his widow, Joyce Fienberg, during the Tree of Life Synagogue massacre in Pittsburgh, PA on October 27, 2018. This issue is dedicated to their memory.
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Collection: Journal of Algebraic Statistics

Title: From Critical to Transformative Pedagogy in Architectural Education
Creator: Jones, Kristin
Date: 2019, 2019
Publisher: Association of Collegiate Schools of Architecture, Washington, DC
Collection: 2019 ACSA/EAAE Teachers Conference Proceeding

Title: Informed Consent in Digital Data Management
Creator: Hildt, Elisabeth, Laas, Kelly
Date: 2022, 2022-01-03
Publisher: Springer, Cham
Description: This article discusses the role of informed consent, a well-known concept and standard established in the field of medicine, in ethics codes...
Show moreThis article discusses the role of informed consent, a well-known concept and standard established in the field of medicine, in ethics codes relating to digital data management. It analyzes the significance allotted to informed consent and informed consent-related principles in ethics codes, policies, and guidelines by presenting the results of a study focused on 31 ethics codes, policies, and guidelines held as part of the Ethics Codes Collection. The analysis reveals that up to now, there is a limited number of codes of ethics, policies, and guidelines on digital data management. Informed consent often is a central component in these codes and guidelines. While there undoubtedly are significant similarities between informed consent in medicine and digital data management, in ethics codes and guidelines, informed consent-related standards in some fields such as marketing are weaker and less strict. The article concludes that informed consent is an essential standard in digital data management that can help effectively shape future practices in the field. However, a more detailed reflection on the specific content and role of informed consent and informed consent-related standards in the various areas of digital data management is needed to avoid the weakening and dilution of standards in contexts where there are no clear legal regulations.
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Collection: Codes of Ethics and Ethical Guidelines: Emerging Technologies and Changing Fields

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