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Title: Hilbert Polynomial of the Kimura 3-Parameter Model, AS2012 Special Volume, part 1: This issue includes a second series of papers from talks, posters and collaborations resulting from and inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July 2012.
Creator: Kubjas, Kaie, inspired by the Algebraic Statistics in the Alleghenies Conference at Penn State, which took place in July
Description: In [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on...
Show moreIn [2] Buczyn ́ska and Wi ́sniewski showed that the Hilbert polynomial of the algebraic variety associated to the Jukes-Cantor binary model on a trivalent tree depends only on the number of leaves of the tree and not on its shape. We ask if this can be generalized to other group-based models. The Jukes-Cantor binary model has Z2 as the underlying group. We consider the Kimura 3-parameter model with Z2 × Z2 as the underlying group. We show that the generalization of the statement about the Hilbert polynomials to the Kimura 3-parameter model is not possible as the Hilbert polynomial depends on the shape of a trivalent tree.
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Collection: Journal of Algebraic Statistics

Title: Optimizing Cell-Free Protein Synthesis for Increased Yield and Activity of Colicins
Creator: Jin, Xing, Kightlinger, Weston, Hong, Seok Hoon
Date: 2019
Publisher: MDPI
Description: Colicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics....
Show moreColicins are antimicrobial proteins produced by Escherichia coli that hold great promise as viable complements or alternatives to antibiotics. Cell-free protein synthesis (CFPS) is a useful production platform for toxic proteins because it eliminates the need to maintain cell viability, a common problem in cell-based production. Previously, we demonstrated that colicins produced by CFPS based on crude Escherichia coli lysates are e?ective in eradicating antibiotic-tolerant bacteria known as persisters. However, we also found that some colicins have poor solubility or low cell-killing activity. In this study, we improved the solubility of colicin M from 16% to nearly 100% by producing it in chaperone-enriched E. coli extracts, resulting in enhanced cell-killing activity. We also improved the cytotoxicity of colicin E3 by adding or co-expressing the E3 immunity protein during the CFPS reaction, suggesting that the E3 immunity protein enhances colicin E3 activity in addition to protecting the host strain. Finally, we con?rmed our previous ?nding that active colicins can be rapidly synthesized by observing colicin E1 production over time in CFPS. Within three hours of CFPS incubation, colicin E1 reached its maximum production yield and maintained high cytotoxicity during longer incubations up to 20 h. Taken together, our ?ndings indicate that colicin production can be easily optimized for improved solubility and activity using the CFPS platform.
Sponsorship: NIH R15AI130988
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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: Priming Movie Product Placements: New Insights from a Cross-National Case Study
Creator: Balasubramanian,Siva K, Gistri, Giacomo
Date: 44354, 44327
Publisher: Taylor & Francis
Description: The paucity of research on priming product placements and insights from practitioners (Study 1) motivated our investigation into how and when...
Show moreThe paucity of research on priming product placements and insights from practitioners (Study 1) motivated our investigation into how and when priming works in movie placements. Study 2 explores the impact of media priming (a media story announcing a movie placement before the movie’s release) and ad priming (a similar ad announcement) on recall through contrasts with no priming (control). US students watched a movie in a theatre after such priming for a subtle or a prominent placement. When compared to no priming, both media priming and ad priming enhanced recall for the subtle placement; no difference in recall performance emerged between no priming and either type of priming for the prominent placement. Contrast tests comparing media priming and ad priming indicated no differences in recall for either subtle or prominent placement. Study 3 replicated these recall findings with Italian moviegoers, and supported additional hypotheses and propositions for brand attitude. For the subtle (prominent) placement, attitude did not change (decreased) when comparing either media priming or ad priming with no priming. Contrast tests comparing media priming and ad priming indicated no differences in attitude outcomes, for either subtle or prominent placement. Using no priming as a baseline for comparison, the converging conclusion is that any type of priming improves (does not change) recall and does not change (worsens) attitude for subtle (prominent) placements. Overall, results do not support priming for prominent placements; selective use of any type of priming for subtle placements appears appropriate to improve recall outcomes.
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Collection: International Journal of Advertising

Title: From positivism to conventionalism: Comte, Renouvier, and Poincaré
Creator: Schmaus, Warren
Date: 2019, 2019
Publisher: Elsevier

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: 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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