1
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Imbriano A, Tricase A, Macchia E, Torsi L, Bollella P. Self-powered logically operated fluorescent detection of hepatitis B virus (HBV). Anal Chim Acta 2023; 1252:341037. [PMID: 36935148 DOI: 10.1016/j.aca.2023.341037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
In this study, a novel sensing strategy based on double sensing/actuating pathway is demonstrated, being capable to trigger the DNA-based AND gate for the sensitive and selective detection of hepatitis B virus DNA (HBV-DNA). Such an approach encompasses an enzymatic machinery logically operated using the variation of physiologically relevant biomarkers for liver dysfunctions. Alanine aminotransferase (ALT) and lactate dehydrogenase (LDH) are used as inputs of an AND gate generating an output signal, namely lactate. In particular, lactate is oxidized back to pyruvate at the anodic electrode by lactate oxidase connected in mediated electron transfer through ferrocene moieties (creating an amplifying recycling mechanism). The anodic electrode is further connected with a Myrothecium verrucaria bilirubin oxidase (MvBOx) based biocathode modified with SiO2 nanoparticles (SiO2NPs) functionalized with phenyl boronic acid and trigonelline, triggering the release of quenching DNA (qDNA) upon local pH change at the electrode surface (notably, modified SiONPs gets negatively recharged upon local pH gradient releasing negatively charged DNA). Next, the released qDNA labeled with BHQ2 and detecting DNA (dDNA, labeled with FAM) are detecting HBV-DNA. The proposed biosensor can discriminate between the absence and presence of HBV-DNA setting the threshold at 0.05 fM in model buffer solutions and 1 fM in human serum. This enzymatic/DNA logic network can be of particular interest for future biomedical applications (e.g., early detection of liver cancer disease etc.). In the future development this technology could be easily integrated with a smartphone camera, allowing more user-friendly applications.
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Affiliation(s)
- Anna Imbriano
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy
| | - Angelo Tricase
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy
| | - Eleonora Macchia
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Faculty of Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Luisa Torsi
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Faculty of Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Paolo Bollella
- Dipartimento di Chimica, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy; Centre for Colloid and Surface Science, Università degli Studi di Bari Aldo Moro, 70125, Bari, Italy.
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2
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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3
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Kim SK, Kim H, Woo SG, Kim TH, Rha E, Kwon KK, Lee H, Lee SG, Lee DH. CRISPRi-based programmable logic inverter cascade for antibiotic-free selection and maintenance of multiple plasmids. Nucleic Acids Res 2022; 50:13155-13171. [PMID: 36511859 PMCID: PMC9825151 DOI: 10.1093/nar/gkac1104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 12/14/2022] Open
Abstract
Antibiotics have been widely used for plasmid-mediated cell engineering. However, continued use of antibiotics increases the metabolic burden, horizontal gene transfer risks, and biomanufacturing costs. There are limited approaches to maintaining multiple plasmids without antibiotics. Herein, we developed an inverter cascade using CRISPRi by building a plasmid containing a single guide RNA (sgRNA) landing pad (pSLiP); this inhibited host cell growth by repressing an essential cellular gene. Anti-sgRNAs on separate plasmids restored cell growth by blocking the expression of growth-inhibitory sgRNAs in pSLiP. We maintained three plasmids in Escherichia coli with a single antibiotic selective marker. To completely avoid antibiotic use and maintain the CRISPRi-based logic inverter cascade, we created a novel d-glutamate auxotrophic E. coli. This enabled the stable maintenance of the plasmid without antibiotics, enhanced the production of the terpenoid, (-)-α-bisabolol, and generation of an antibiotic-resistance gene-free plasmid. CRISPRi is therefore widely applicable in genetic circuits and may allow for antibiotic-free biomanufacturing.
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Affiliation(s)
| | | | - Seung Gyun Woo
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Tae Hyun Kim
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea,Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34143, Republic of Korea
| | - Eugene Rha
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Kil Koang Kwon
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Hyewon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Seung-Goo Lee
- To whom correspondence should be addressed. Tel: +82 42 860 4373; Fax: +82 42 860 4489;
| | - Dae-Hee Lee
- Correspondence may also be addressed to Dae-Hee Lee. Tel: +82 42 879 8225; Fax: +82 42 860 4489;
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4
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Hu Y, Han X, Shi L, Cao B. Electrochemically active biofilm-enabled biosensors: Current status and opportunities for biofilm engineering. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.140917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Dong H, Girmatsion M, Wang R, Lu G, Xie Y, Guo Y, Qian H, Yao W. Construction of fluorescent logic gates for the detection of mercury(II) and ciprofloxacin based on phycocyanin. Methods Appl Fluoresc 2022; 10. [PMID: 35584692 DOI: 10.1088/2050-6120/ac7123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/18/2022] [Indexed: 11/12/2022]
Abstract
Chemical pollutants such as heavy metals and antibiotics in the environment pose a huge threat to humans and animals. Our studies have demonstrated that the fluorescence of phycocyanin showed quenching responses towards both mercury (Hg2+) and ciprofloxacin (CIP), which acted in accordance with the "OR" molecular logic gate. In order to discriminate Hg2+ and CIP in application scenarios, cysteine (Cys) was utilized to design another "INHIBIT" logic gate, in which Hg2+ and Cys were the two inputs. Thus, an intelligent biosensor with dual-target identification capacity was successfully developed by using a fluorescent natural protein in an ingenious logic gate system.
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Affiliation(s)
- Han Dong
- State Key Laboratory of Food Science and Technology, Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
| | - Mogos Girmatsion
- Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
| | - Ruoyu Wang
- Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
| | - Gang Lu
- Safety & Quality Management Department, Inner Mongolia Mengniu Dairy (group) CO., LTD., Inner Mongolia Mengniu Dairy (group) CO., LTD., Hohhot, Inner Mongolia, 011500, CHINA
| | - Yunfei Xie
- State Key Laboratory of Food Science and Technology, Jiangnan University School of Food Science and Technology, Wuxi, Wuxi, Jiangsu, 214122, CHINA
| | - Yahui Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
| | - He Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
| | - Weirong Yao
- State Key Laboratory of Food Science and Technology, Jiangnan University School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, CHINA
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6
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Ryzhkov NV, Nikolaev KG, Ivanov AS, Skorb EV. Infochemistry and the Future of Chemical Information Processing. Annu Rev Chem Biomol Eng 2021; 12:63-95. [PMID: 33909470 DOI: 10.1146/annurev-chembioeng-122120-023514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nowadays, information processing is based on semiconductor (e.g., silicon) devices. Unfortunately, the performance of such devices has natural limitations owing to the physics of semiconductors. Therefore, the problem of finding new strategies for storing and processing an ever-increasing amount of diverse data is very urgent. To solve this problem, scientists have found inspiration in nature, because living organisms have developed uniquely productive and efficient mechanisms for processing and storing information. We address several biological aspects of information and artificial models mimicking corresponding bioprocesses. For instance, we review the formation of synchronization patterns and the emergence of order out of chaos in model chemical systems. We also consider molecular logic and ion fluxes as information carriers. Finally, we consider recent progress in infochemistry, a new direction at the interface of chemistry, biology, and computer science, considering unconventional methods of information processing.
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Affiliation(s)
- Nikolay V Ryzhkov
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Konstantin G Nikolaev
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Artemii S Ivanov
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
| | - Ekaterina V Skorb
- Infochemistry Scientific Center of ITMO University, 191002 Saint Petersburg, Russia; , , ,
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7
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Krige A, Haluška J, Rova U, Christakopoulos P. Design and implementation of a low cost bio-printer modification, allowing for switching between plastic and gel extrusion. HARDWAREX 2021; 9:e00186. [PMID: 35492054 PMCID: PMC9041258 DOI: 10.1016/j.ohx.2021.e00186] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/15/2020] [Accepted: 02/21/2021] [Indexed: 05/09/2023]
Abstract
Due to the high cost of bioprinters they are not feasible for proof of concept experiments or educational purposes. Furthermore, the more affordable DIY methods all disable the plastic printing capability of the original printer. Here we present an affordable bio-printing modification that is easy to install and maintains the original capabilities of the printer. The modification used mostly 3D printed parts and is based on the popular, open-source Prusa i3 3D printer. The modifications are kept as simple as possible and uses standard slicing software, allowing for installation by less experienced builders. By using disposable syringes and easily sterilizable parts, an aseptic bioprinting setup can be achieved, depending on the environment. It also allows for 2 component printing as well as UV curing. The bio-printing and curing capabilities were shown by printing and curing an artificial biofilm of an electro-active bacteria, Geobacter sulfurreducens, onto a carbon-cloth electrode which was used in a microbial fuel cell.
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8
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Starwalt-Lee R, El-Naggar MY, Bond DR, Gralnick JA. Electrolocation? The evidence for redox-mediated taxis in Shewanella oneidensis. Mol Microbiol 2020; 115:1069-1079. [PMID: 33200455 DOI: 10.1111/mmi.14647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/11/2020] [Indexed: 11/27/2022]
Abstract
Shewanella oneidensis is a dissimilatory metal reducing bacterium and model for extracellular electron transfer (EET), a respiratory mechanism in which electrons are transferred out of the cell. In the last 10 years, migration to insoluble electron acceptors for EET has been shown to be nonrandom and tactic, seemingly in the absence of molecular or energy gradients that typically allow for taxis. As the ability to sense, locate, and respire electrodes has applications in bioelectrochemical technology, a better understanding of taxis in S. oneidensis is needed. While the EET conduits of S. oneidensis have been studied extensively, its taxis pathways and their interplay with EET are not yet understood, making investigation into taxis phenomena nontrivial. Since S. oneidensis is a member of an EET-encoding clade, the genetic circuitry of taxis to insoluble acceptors may be conserved. We performed a bioinformatic analysis of Shewanella genomes to identify S. oneidensis chemotaxis orthologs conserved in the genus. In addition to the previously reported core chemotaxis gene cluster, we identify several other conserved proteins in the taxis signaling pathway. We present the current evidence for the two proposed models of EET taxis, "electrokinesis" and flavin-mediated taxis, and highlight key areas in need of further investigation.
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Affiliation(s)
- Ruth Starwalt-Lee
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Daniel R Bond
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
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9
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Lenyk B, Figueroa‐Miranda G, Pavlushko I, Lo Y, Tanner JA, Offenhäusser A, Mayer D. Dual‐Transducer Malaria Aptasensor Combining Electrochemical Impedance and Surface Plasmon Polariton Detection on Gold Nanohole Arrays. ChemElectroChem 2020. [DOI: 10.1002/celc.202001212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Bohdan Lenyk
- Institute of Biological Information Processing (IBI-3) Forschungszentrum Jülich 52428 Jülich Germany
- Department of Physics University of Konstanz 78464 Konstanz Germany
| | - Gabriela Figueroa‐Miranda
- Institute of Biological Information Processing (IBI-3) Forschungszentrum Jülich 52428 Jülich Germany
- RWTH Aachen University Aachen 52062 Germany
| | - Ivan Pavlushko
- Institute of Biological Information Processing (IBI-3) Forschungszentrum Jülich 52428 Jülich Germany
- Faculty of Radio Physics Electronics and Computer Systems Taras Shevchenko National University of Kyiv Kyiv 03680 Ukraine
| | - Young Lo
- School of Biomedical Sciences Li Ka Shing Faculty of Medicine The University of Hong Kong Pokfulam, Hong Kong Special Administrative Region China
| | - Julian A. Tanner
- School of Biomedical Sciences Li Ka Shing Faculty of Medicine The University of Hong Kong Pokfulam, Hong Kong Special Administrative Region China
| | - Andreas Offenhäusser
- Institute of Biological Information Processing (IBI-3) Forschungszentrum Jülich 52428 Jülich Germany
- RWTH Aachen University Aachen 52062 Germany
| | - Dirk Mayer
- Institute of Biological Information Processing (IBI-3) Forschungszentrum Jülich 52428 Jülich Germany
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10
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VanArsdale E, Pitzer J, Payne GF, Bentley WE. Redox Electrochemistry to Interrogate and Control Biomolecular Communication. iScience 2020; 23:101545. [PMID: 33083771 PMCID: PMC7516135 DOI: 10.1016/j.isci.2020.101545] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
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11
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Integration of logic gates to CRISPR/Cas12a system for rapid and sensitive detection of pathogenic bacterial genes. Anal Chim Acta 2020; 1125:162-168. [DOI: 10.1016/j.aca.2020.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022]
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12
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Wu S, Liu J, Liu C, Yang A, Qiao J. Quorum sensing for population-level control of bacteria and potential therapeutic applications. Cell Mol Life Sci 2020; 77:1319-1343. [PMID: 31612240 PMCID: PMC11104945 DOI: 10.1007/s00018-019-03326-8] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 09/13/2019] [Accepted: 09/30/2019] [Indexed: 02/07/2023]
Abstract
Quorum sensing (QS), a microbial cell-to-cell communication process, dynamically regulates a variety of metabolism and physiological activities. In this review, we provide an update on QS applications based on autoinducer molecules including acyl-homoserine lactones (AHLs), auto-inducing peptides (AIPs), autoinducer 2 (AI-2) and indole in population-level control of bacteria, and highlight the potential in developing novel clinical therapies. We summarize the development in the combination of various genetic circuits such as genetic oscillators, toggle switches and logic gates with AHL-based QS devices in Gram-negative bacteria. An overview is then offered to the state-of-the-art of much less researched applications of AIP-based QS devices with Gram-positive bacteria, followed by a review of the applications of AI-2 and indole based QS for interspecies communication among microbial communities. Building on these general-purpose QS applications, we highlight the disruptions and manipulations of QS devices as potential clinical therapies for diseases caused by biofilm formation, antibiotic resistance and the phage invasion. The last part of reviewed literature is dedicated to mathematical modelling for QS applications. Finally, the key challenges and future perspectives of QS applications in monoclonal synthetic biology and synthetic ecology are discussed.
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Affiliation(s)
- Shengbo Wu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Jiaheng Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China
| | - Chunjiang Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China
| | - Aidong Yang
- Department of Engineering Science, University of Oxford, Oxford, OX1 3PJ, UK.
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin, 300072, China.
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13
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Martins DP, Barros MT, Balasubramaniam S. Quality and Capacity Analysis of Molecular Communications in Bacterial Synthetic Logic Circuits. IEEE Trans Nanobioscience 2019; 18:628-639. [PMID: 31352349 DOI: 10.1109/tnb.2019.2930960] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Synthetic logic circuits have been proposed as potential solutions for theranostics of biotechnological problems. One proposed model is the engineering of bacteria cells to create logic gates, and the communication between the bacteria populations will enable the circuit operation. In this paper, we analyze the quality of bacteria-based synthetic logic circuit through molecular communications that represent communication along a bus between three gates. In the bacteria-based synthetic logic circuit, the system receives environmental signals as molecular inputs and will process this information through a cascade of synthetic logic gates and free diffusion channels. We analyze the performance of this circuit by evaluating its quality and its relationship to the channel capacity of the molecular communications links that interconnect the bacteria populations. Our results show the effect of the molecular environmental delay and molecular amplitude differences over both the channel capacity and circuit quality. Furthermore, based on these metrics, we also obtain an optimum region for the circuit operation resulting in an accuracy of 80% for specific conditions. These results show that the performance of synthetic biology circuits can be evaluated through molecular communications, and lays the groundwork for combined systems that can contribute to future biomedical and biotechnology applications.
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14
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Arabahmadi R. A reversible fluorescence “ON–OFF–ON” sensor for sequential detection of F− and Cu2+ ions and its application as a molecular-scale logic device and security keypad lock. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1595604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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15
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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Zou L, Huang YH, Long ZE, Qiao Y. On-going applications of Shewanella species in microbial electrochemical system for bioenergy, bioremediation and biosensing. World J Microbiol Biotechnol 2018; 35:9. [PMID: 30569420 DOI: 10.1007/s11274-018-2576-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/07/2018] [Indexed: 11/24/2022]
Abstract
Microbial electrochemical system (MES) has attracted ever-growing interest as a promising platform for renewable energy conversion and bioelectrochemical remediation. Shewanella species, the dissimilatory metal reduction model bacteria with versatile extracellular electron transfer (EET) strategies, are the well-received microorganisms in diverse MES devices for various practical applications as well as microbial EET mechanism investigation. Meanwhile, the available genomic information and the unceasing established gene-editing toolbox offer an unprecedented opportunity to boost the applications of Shewanella species in MES. This review thoroughly summarizes the status quo of the applications of Shewanella species in microbial fuel cells for bioelectricity generation, microbial electrosynthesis for biotransformation of valuable chemicals and bioremediation of environment-hazardous pollutants with synoptical discussion on their EET mechanism. Recent advances in rational design and genetic engineering of Shewanella strains for either promoting the MES performance or broadening their applications are surveyed. Moreover, some emerging applications beyond electricity generation, such as biosensing and biocomputing, are also documented. The challenges and perspectives for Shewanella-based MES are also discussed elaborately for the sake of not only discovering new scientific lights on microbial extracellular respiratory but also propelling practical applications.
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Affiliation(s)
- Long Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Yun-Hong Huang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhong-Er Long
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
| | - Yan Qiao
- Institute for Clean Energy and Advanced Materials, Faculty of Materials and Energy, Southwest University, Chongqing, 400715, China.
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17
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Lienemann M, TerAvest MA, Pitkänen J, Stuns I, Penttilä M, Ajo‐Franklin CM, Jäntti J. Towards patterned bioelectronics: facilitated immobilization of exoelectrogenic Escherichia coli with heterologous pili. Microb Biotechnol 2018; 11:1184-1194. [PMID: 30296001 PMCID: PMC6196383 DOI: 10.1111/1751-7915.13309] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 07/02/2018] [Accepted: 08/07/2018] [Indexed: 12/01/2022] Open
Abstract
Biosensors detect signals using biological sensing components such as redox enzymes and biological cells. Although cellular versatility can be beneficial for different applications, limited stability and efficiency in signal transduction at electrode surfaces represent a challenge. Recent studies have shown that the Mtr electron conduit from Shewanella oneidensis MR-1 can be produced in Escherichia coli to generate an exoelectrogenic model system with well-characterized genetic tools. However, means to specifically immobilize this organism at solid substrates as electroactive biofilms have not been tested previously. Here, we show that mannose-binding Fim pili can be produced in exoelectrogenic E. coli and can be used to selectively attach cells to a mannose-coated material. Importantly, cells expressing fim genes retained current production by the heterologous Mtr electron conduit. Our results demonstrate the versatility of the exoelectrogenic E. coli system and motivate future work that aims to produce patterned biofilms for bioelectronic devices that can respond to various biochemical signals.
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Affiliation(s)
| | - Michaela A. TerAvest
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMIUSA
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Juha‐Pekka Pitkänen
- VTT Technical Research Centre of Finland LtdEspooFinland
- Current affiliation: Solar Foods LtdHelsinkiFinland
| | - Ingmar Stuns
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland LtdEspooFinland
| | - Caroline M. Ajo‐Franklin
- The Molecular FoundryLawrence Berkeley National LaboratoryMolecular Biophysics and Integrated Bioimaging DivisionSynthetic Biology InstituteBerkeleyCAUSA
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland LtdEspooFinland
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18
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Bhuyan T, Bhattacharjee M, Singh AK, Ghosh SS, Bandyopadhyay D. Boolean-chemotaxis of logibots deciphering the motions of self-propelling microorganisms. SOFT MATTER 2018; 14:3182-3191. [PMID: 29645047 DOI: 10.1039/c8sm00132d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We demonstrate the feasibility of a self-propelling mushroom motor, namely a 'logibot', as a functional unit for the construction of a host of optimized binary logic gates. Emulating the chemokinesis of unicellular prokaryotes or eukaryotes, the logibots made stimuli responsive conditional movements at varied speeds towards a pair of acid-alkali triggers. A series of integrative logic operations and cascaded logic circuits, namely, AND, NAND, NOT, OR, NOR, and NIMPLY, have been constructed employing the decisive chemotactic migrations of the logibot in the presence of the pH gradient established by the sole or coupled effects of acid (HCl-catalase) and alkali (NaOH) drips inside a peroxide bath. The imposed acid and/or alkali triggers across the logibots were realized as inputs while the logic gates were functionally reconfigured to several operational modes by varying the pH of the acid-alkali inputs. The self-propelling logibot could rapidly sense the external stimuli, decide, and act on the basis of intensities of the pH triggers. The impulsive responses of the logibots towards and away from the external acid-alkali stimuli were interpreted as the potential outputs of the logic gates. The external stimuli responsive self-propulsion of the logibots following different logic gates and circuits can not only be an eco-friendly alternative to the silicon-based computing operations but also be a promising strategy for the development of intelligent pH-responsive drug delivery devices.
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Affiliation(s)
- Tamanna Bhuyan
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Assam-781039, India.
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19
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Hu Y, Wu Y, Mukherjee M, Cao B. A near-infrared light responsive c-di-GMP module-based AND logic gate in Shewanella oneidensis. Chem Commun (Camb) 2018; 53:1646-1648. [PMID: 28098272 DOI: 10.1039/c6cc08584a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A novel, biofilm-based AND logic gate was constructed in Shewanella oneidensis through a near-infrared (NIR) light responsive c-di-GMP module. The logic gate was demonstrated in microbial fuel cells with isopropyl β-d-thiogalactoside (IPTG) and NIR light as the inputs and electrical signals as the output.
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Affiliation(s)
- Yidan Hu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yichao Wu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.
| | - Manisha Mukherjee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.
| | - Bin Cao
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551 and School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798.
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Abstract
Self-powered electrochemical biosensors utilize biofuel cells as a simultaneous power source and biosensor, which simplifies the biosensor system, because it no longer requires a potentiostat, power for the potentiostat, and/or power for the signaling device. This review article is focused on detailing the advances in the field of self-powered biosensors and discussing their advantages and limitations compared to other types of electrochemical biosensors. The review will discuss self-powered biosensors formed from enzymatic biofuel cells, organelle-based biofuel cells, and microbial fuel cells. It also discusses the different mechanisms of sensing, including utilizing the analyte being the substrate/fuel for the biocatalyst, the analyte binding the biocatalyst to the electrode surface, the analyte being an inhibitor of the biocatalyst, the analyte resulting in the blocking of the bioelectrocatalytic response, the analyte reactivating the biocatalyst, Boolean logic gates, and combining affinity-based biorecognition elements with bioelectrocatalytic power generation. The final section of this review details areas of future investigation that are needed in the field, as well as problems that still need to be addressed by the field.
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Affiliation(s)
- Matteo Grattieri
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Departments of Chemistry and Materials Science & Engineering, University of Utah, 315 S 1400 E Rm 2020, Salt Lake City, Utah 84112, United States
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21
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Pasternak G, Greenman J, Ieropoulos I. Self-powered, autonomous Biological Oxygen Demand biosensor for online water quality monitoring. SENSORS AND ACTUATORS. B, CHEMICAL 2017; 244:815-822. [PMID: 28579695 PMCID: PMC5362149 DOI: 10.1016/j.snb.2017.01.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Standard Biological Oxygen Demand (BOD) analysis requires 5 days to complete. To date, microbial fuel cell biosensors used as an alternative method for BOD assessment requires external apparatus, which limits their use for on-line monitoring in remote, off-grid locations. In this study, a self-powered, floating biosensor was developed for online water quality monitoring. This approach eliminated the need for external apparatus and maintenance that would otherwise be required by other techniques. The biosensor was able to detect urine in freshwater and turn ON a visual and sound cues (85 dB). The energy needed to operate the biosensor was produced by the system itself with the use of electroactive microorganisms, inside microbial fuel cells. The Chemical Oxygen Demand (COD) was used as a fast method of biosensor validation. When urine concentration exceeded the lower threshold, corresponding to a COD concentration of 57.7 ± 4.8 mgO2 L-1, the biosensor turned the alarm ON. The shortest observed actuation time, required to switch ON the alarm was 61 min, when the urine concentration was 149.7 ± 1.7 mgO2 L-1. Once the sensor was switched ON, the signal was emitted until the urine organic load decreased to 15.3 ± 1.9 mgO2 L-1. When ON, the microbial fuel cell sensor produced a maximum power of 4.3 mW. When switched OFF, the biosensor produced 25.4 μW. The frequency of the signal was proportional to the concentration of urine. The observed frequencies varied between 0.01 and 0.59 Hz. This approach allowed to correlate and quantitatively detect the presence of water contamination, based on signal frequency. The sensor was operating autonomously for 5 months. This is the first report of a self-powered, autonomous device, developed for online water quality monitoring.
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Affiliation(s)
- Grzegorz Pasternak
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY Bristol, UK
- Wroclaw University of Technology, 50-370 Wroclaw, Poland
- Corresponding author at: Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY Bristol, UK.
| | - John Greenman
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY Bristol, UK
| | - Ioannis Ieropoulos
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of England, BS16 1QY Bristol, UK
- Corresponding author.
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22
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Wood ML, Domanskyi S, Privman V. Design of High Quality Chemical XOR Gates with Noise Reduction. Chemphyschem 2017; 18:1773-1781. [DOI: 10.1002/cphc.201700018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Mackenna L. Wood
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
| | - Sergii Domanskyi
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
| | - Vladimir Privman
- Department of Physics; Clarkson University; Potsdam NY 13676 USA
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23
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Can UI, Nagarajan N, Vural DC, Zorlutuna P. Muscle-Cell-Based "Living Diodes". ACTA ACUST UNITED AC 2017; 1:e1600035. [PMID: 32646185 DOI: 10.1002/adbi.201600035] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Indexed: 12/14/2022]
Abstract
A new type of diode that is made entirely of electrically excitable muscle cells and nonexcitable fibroblast cells is designed, fabricated, and characterized. These two cell types in a rectangular pattern allow the signal initiated on the excitable side to pass to the nonexcitable side, and not in the opposite direction.
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Affiliation(s)
- Uryan Isik Can
- Aerospace and Mechanical Engineering Department, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Neerajha Nagarajan
- Aerospace and Mechanical Engineering Department, Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dervis Can Vural
- Department of Physics, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Pinar Zorlutuna
- Aerospace and Mechanical Engineering Department, University of Notre Dame, Notre Dame, IN, 46556, USA.,Aerospace and Mechanical Engineering Department, Bioengineering Graduate Program, University of Notre Dame, Notre Dame, IN, 46556, USA
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24
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Enzyme Logic Systems: Biomedical and Forensic Biosensor Applications. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2017. [DOI: 10.1007/5346_2017_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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25
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Li F, Li Y, Sun L, Li X, Yin C, An X, Chen X, Tian Y, Song H. Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:196. [PMID: 28804512 PMCID: PMC5549365 DOI: 10.1186/s13068-017-0881-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications. RESULTS Herein, to enable S. oneidensis to directly utilize xylose as the sole carbon source for bioelectricity production in MFCs, we used synthetic biology strategies to successfully construct four genetically engineered S. oneidensis (namely XE, GE, XS, and GS) by assembling one of the xylose transporters (from Candida intermedia and Clostridium acetobutylicum) with one of intracellular xylose metabolic pathways (the isomerase pathway from Escherichia coli and the oxidoreductase pathway from Scheffersomyces stipites), respectively. We found that among these engineered S. oneidensis strains, the strain GS (i.e. harbouring Gxf1 gene encoding the xylose facilitator from C. intermedi, and XYL1, XYL2, and XKS1 genes encoding the xylose oxidoreductase pathway from S. stipites) was able to generate the highest power density, enabling a maximum electricity power density of 2.1 ± 0.1 mW/m2. CONCLUSION To the best of our knowledge, this was the first report on the rationally designed Shewanella that could use xylose as the sole carbon source and electron donor to produce electricity. The synthetic biology strategies developed in this study could be further extended to rationally engineer other exoelectrogens for lignocellulosic biomass utilization to generate electricity power.
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Affiliation(s)
- Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yuanxiu Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Liming Sun
- Petrochemical Research Institute, PetroChina Company Limited, Beijing, 102206 People’s Republic of China
| | - Xiaofei Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Changji Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xingjuan An
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xiaoli Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yao Tian
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
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26
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Kim BJ, Chu I, Jusuf S, Kuo T, TerAvest MA, Angenent LT, Wu M. Oxygen Tension and Riboflavin Gradients Cooperatively Regulate the Migration of Shewanella oneidensis MR-1 Revealed by a Hydrogel-Based Microfluidic Device. Front Microbiol 2016; 7:1438. [PMID: 27703448 PMCID: PMC5028412 DOI: 10.3389/fmicb.2016.01438] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 08/30/2016] [Indexed: 11/13/2022] Open
Abstract
Shewanella oneidensis is a model bacterial strain for studies of bioelectrochemical systems (BESs). It has two extracellular electron transfer pathways: (1) shuttling electrons via an excreted mediator riboflavin; and (2) direct contact between the c-type cytochromes at the cell membrane and the electrode. Despite the extensive use of S. oneidensis in BESs such as microbial fuel cells and biosensors, many basic microbiology questions about S. oneidensis in the context of BES remain unanswered. Here, we present studies of motility and chemotaxis of S. oneidensis under well controlled concentration gradients of two electron acceptors, oxygen and oxidized form of riboflavin (flavin+), using a newly developed microfluidic platform. Experimental results demonstrate that either oxygen or flavin+ is a chemoattractant to S. oneidensis. The chemotactic tendency of S. oneidensis in a flavin+ concentration gradient is significantly enhanced in an anaerobic in contrast to an aerobic condition. Furthermore, either a low oxygen tension or a high flavin+ concentration considerably enhances the speed of S. oneidensis. This work presents a robust microfluidic platform for generating oxygen and/or flavin+ gradients in an aqueous environment, and demonstrates that two important electron acceptors, oxygen and oxidized riboflavin, cooperatively regulate S. oneidensis migration patterns. The microfluidic tools presented as well as the knowledge gained in this work can be used to guide the future design of BESs for efficient electron production.
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Affiliation(s)
- Beum Jun Kim
- Department of Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Injun Chu
- School of Chemical and Biomolecular Engineering, Cornell University Ithaca, NY, USA
| | - Sebastian Jusuf
- Department of Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Tiffany Kuo
- Department of Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Michaela A TerAvest
- Department of Biological and Environmental Engineering, Cornell University Ithaca, NY, USA
| | - Largus T Angenent
- Department of Biological and Environmental Engineering, Cornell UniversityIthaca, NY, USA; Atkinson Center for a Sustainable Future, Cornell UniversityIthaca, NY, USA
| | - Mingming Wu
- Department of Biological and Environmental Engineering, Cornell UniversityIthaca, NY, USA; Atkinson Center for a Sustainable Future, Cornell UniversityIthaca, NY, USA
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27
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Zhou AY, Zajdel TJ, TerAvest MA, Maharbiz MM. A miniaturized monitoring system for electrochemical biosensing using Shewanella oneidensis in environmental applications. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2016; 2015:7518-21. [PMID: 26738031 DOI: 10.1109/embc.2015.7320131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present a miniaturized, free-floating monitoring system which makes use of electron transfer in Shewanella oneidensis sequestered behind a permeable membrane while maintaining diffusive contact with the environment, allowing for sensing environmental conditions. The system makes use of a commercial off-the-shelf (COTS) integrated circuit (IC) which sets a potential between a working electrode and a Ag/AgCl reference electrode while recording the resulting current from the electroactive cells. We successfully sensed both pyruvate and the environmental presence of E. coli via changes in the currents sensed. This work will enable the development of mobile aquatic sensing systems which make use of bacterial electron transfer as a transduction method. Further miniaturization of the recording mote, electrodes, packaging, and system is discussed.
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28
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Wang T, Milton RD, Abdellaoui S, Hickey DP, Minteer SD. Laccase Inhibition by Arsenite/Arsenate: Determination of Inhibition Mechanism and Preliminary Application to a Self-Powered Biosensor. Anal Chem 2016; 88:3243-8. [DOI: 10.1021/acs.analchem.5b04651] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Tao Wang
- Departments of Chemistry
and Materials Science and Engineering, University of Utah, 315 South 1400
East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Ross D. Milton
- Departments of Chemistry
and Materials Science and Engineering, University of Utah, 315 South 1400
East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Sofiene Abdellaoui
- Departments of Chemistry
and Materials Science and Engineering, University of Utah, 315 South 1400
East, Room 2020, Salt Lake City, Utah 84112, United States
| | - David P. Hickey
- Departments of Chemistry
and Materials Science and Engineering, University of Utah, 315 South 1400
East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Shelley D. Minteer
- Departments of Chemistry
and Materials Science and Engineering, University of Utah, 315 South 1400
East, Room 2020, Salt Lake City, Utah 84112, United States
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29
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Bao H, Zheng Z, Yang B, Liu D, Li F, Zhang X, Li Z, Lei L. In situ monitoring of Shewanella oneidensis MR-1 biofilm growth on gold electrodes by using a Pt microelectrode. Bioelectrochemistry 2016; 109:95-100. [PMID: 26850925 DOI: 10.1016/j.bioelechem.2016.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/10/2016] [Accepted: 01/26/2016] [Indexed: 10/22/2022]
Abstract
Much attention has been focused on electrochemically active bacteria (EAB) in the application of bioelectrochemical systems (BESs). Studying the EAB biofilm growth mechanism as well as electron transfer mechanism provides a route to upgrade BES performance. But an effective bacterial growth monitoring method on the biofilm scale is still absent in this field. In this work, electrode-attached bacterial biofilms formed by Shewanella oneidensis MR-1 were dynamically monitored through a microelectrode method. For S. oneidensis MR-1, a respiratory electron transport chain is associated with the secretion of riboflavin, severing as the cofactor to the outer membrane c-type cytochromes. The biofilm growth was monitored through adopting riboflavin as an electrochemical probe during the approach of the microelectrode to the biofilm external surface. This method allows in vivo and in situ biofilm monitoring at different growth stages without destructive manipulation. Furthermore, the biofilm growth monitoring results have been proved to be relatively accurate through observation under confocal laser scanning microscopy. We further applied this method to investigate the effects of four environmental factors (the concentrations of dissolved oxygen, sodium lactate, riboflavin as well as the electrode potential) on S. oneidensis MR-1 biofilm development.
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Affiliation(s)
- Han Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhanwang Zheng
- School of Environmental and Resource Science, Zhejiang A & F University, Hangzhou, China
| | - Bin Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Ding Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Feifang Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Xingwang Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
| | - Lecheng Lei
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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30
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Friedman ES, McPhillips LE, Werner JJ, Poole AC, Ley RE, Walter MT, Angenent LT. Methane Emission in a Specific Riparian-Zone Sediment Decreased with Bioelectrochemical Manipulation and Corresponded to the Microbial Community Dynamics. Front Microbiol 2016; 6:1523. [PMID: 26793170 PMCID: PMC4707442 DOI: 10.3389/fmicb.2015.01523] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 12/18/2015] [Indexed: 11/13/2022] Open
Abstract
Dissimilatory metal-reducing bacteria are widespread in terrestrial ecosystems, especially in anaerobic soils and sediments. Thermodynamically, dissimilatory metal reduction is more favorable than sulfate reduction and methanogenesis but less favorable than denitrification and aerobic respiration. It is critical to understand the complex relationships, including the absence or presence of terminal electron acceptors, that govern microbial competition and coexistence in anaerobic soils and sediments, because subsurface microbial processes can effect greenhouse gas emissions from soils, possibly resulting in impacts at the global scale. Here, we elucidated the effect of an inexhaustible, ferrous-iron and humic-substance mimicking terminal electron acceptor by deploying potentiostatically poised electrodes in the sediment of a very specific stream riparian zone in Upstate New York state. At two sites within the same stream riparian zone during the course of 6 weeks in the spring of 2013, we measured CH4 and N2/N2O emissions from soil chambers containing either poised or unpoised electrodes, and we harvested biofilms from the electrodes to quantify microbial community dynamics. At the upstream site, which had a lower vegetation cover and highest soil temperatures, the poised electrodes inhibited CH4 emissions by ∼45% (when normalized to remove temporal effects). CH4 emissions were not significantly impacted at the downstream site. N2/N2O emissions were generally low at both sites and were not impacted by poised electrodes. We did not find a direct link between bioelectrochemical treatment and microbial community membership; however, we did find a correspondence between environment/function and microbial community dynamics.
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Affiliation(s)
- Elliot S Friedman
- Department of Biological and Environmental Engineering, Cornell University, Ithaca NY, USA
| | - Lauren E McPhillips
- Department of Biological and Environmental Engineering, Cornell University, Ithaca NY, USA
| | - Jeffrey J Werner
- Department of Biological and Environmental Engineering, Cornell University, IthacaNY, USA; Department of Chemistry, State University of New York College at CortlandCortland, NY, USA
| | - Angela C Poole
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY, USA
| | - Ruth E Ley
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY, USA
| | - M Todd Walter
- Department of Biological and Environmental Engineering, Cornell University, Ithaca NY, USA
| | - Largus T Angenent
- Department of Biological and Environmental Engineering, Cornell University, Ithaca NY, USA
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31
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Yong YC, Wu XY, Sun JZ, Cao YX, Song H. Engineering quorum sensing signaling of Pseudomonas for enhanced wastewater treatment and electricity harvest: A review. CHEMOSPHERE 2015; 140:18-25. [PMID: 25455678 DOI: 10.1016/j.chemosphere.2014.10.020] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 07/13/2014] [Accepted: 10/05/2014] [Indexed: 06/04/2023]
Abstract
Cell-cell communication that enables synchronized population behaviors in microbial communities dictates various biological processes. It is of great interest to unveil the underlying mechanisms of fine-tuning cell-cell communication to achieve environmental and energy applications. Pseudomonas is a ubiquitous microbe in environments that had wide applications in bioremediation and bioenergy generation. The quorum sensing (QS, a generic cell-cell communication mechanism) systems of Pseudomonas underlie the aromatics biodegradation, denitrification and electricity harvest. Here, we reviewed the recent progresses of the genetic strategies in engineering QS circuits to improve efficiency of wastewater treatment and the performance of microbial fuel cells.
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Affiliation(s)
- Yang-Chun Yong
- Biofuels Institute, School of the Environment, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China.
| | - Xiang-Yang Wu
- Biofuels Institute, School of the Environment, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Jian-Zhong Sun
- Biofuels Institute, School of the Environment, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, Jiangsu Province, China
| | - Ying-Xiu Cao
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; School of Chemical & Biomedical Engineering, and Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637457, Singapore
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; School of Chemical & Biomedical Engineering, and Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore 637457, Singapore.
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32
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Katz E, Minko S. Enzyme-based logic systems interfaced with signal-responsive materials and electrodes. Chem Commun (Camb) 2015; 51:3493-500. [PMID: 25578785 DOI: 10.1039/c4cc09851j] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Enzyme-based biocomputing systems were interfaced with signal-responsive membranes and electrodes resulting in bioelectronic devices switchable by logically processed biomolecular signals. "Smart" membranes, electrodes, biofuel cells, memristors and substance-releasing systems were activated by various combinations of biomolecular signals in the pre-programmed way implemented in biocatalytic cascades mimicking logic networks.
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Affiliation(s)
- Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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33
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Jayabharathi J, Thanikachalam V, Ramanathan P. Phenanthrimidazole as a fluorescent sensor with logic gate operations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:886-891. [PMID: 26116998 DOI: 10.1016/j.saa.2015.06.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 06/10/2015] [Accepted: 06/16/2015] [Indexed: 06/04/2023]
Abstract
A novel sensor namely, 1-(1-(p-tolyl)-1H-phenanthro[9,10-d]imidazol-2-yl)naphthalen-2-ol was synthesised for the detection of anion as well as cation through intramolecular charge transfer mechanism. This compound was used for the selective detection of Zn(2+) ion as compared to other metal ions and the binding was evidenced from the new absorption band at 356 nm and switch on fluorescence at 453 nm. The switch on fluorescence can be explained on the basis of photoinduced electron transfer (PET) mechanism and it was demonstrated by logic gate functions.
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Affiliation(s)
- J Jayabharathi
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India.
| | - V Thanikachalam
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
| | - P Ramanathan
- Department of Chemistry, Annamalai University, Annamalainagar 608 002, Tamil Nadu, India
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34
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Pearce DJG, Turner MS. Emergent behavioural phenotypes of swarming models revealed by mimicking a frustrated anti-ferromagnet. J R Soc Interface 2015; 12:20150520. [PMID: 26423438 PMCID: PMC4614490 DOI: 10.1098/rsif.2015.0520] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/09/2015] [Indexed: 12/01/2022] Open
Abstract
Self-propelled particle (SPP) models are often compared with animal swarms. However, the collective animal behaviour observed in experiments often leaves considerable unconstrained freedom in the structure of a proposed model. Essentially, multiple models can describe the observed behaviour of animal swarms in simple environments. To tackle this degeneracy, we study swarms of SPPs in non-trivial environments as a new approach to distinguish between candidate models. We restrict swarms of SPPs to circular (periodic) channels where they polarize in one of two directions (like spins) and permit information to pass through windows between neighbouring channels. Co-alignment between particles then couples the channels (anti-ferromagnetically) so that they tend to counter-rotate. We study channels arranged to mimic a geometrically frustrated anti-ferromagnet and show how the effects of this frustration allow us to better distinguish between SPP models. Similar experiments could therefore improve our understanding of collective motion in animals. Finally, we discuss how the spin analogy can be exploited to construct universal logic gates, and therefore swarming systems that can function as Turing machines.
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Affiliation(s)
- D J G Pearce
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK MOAC Doctoral Training Centre, University of Warwick, Coventry CV4 7AL, UK
| | - M S Turner
- Department of Physics, University of Warwick, Coventry CV4 7AL, UK Centre for Complexity Science, University of Warwick, Coventry CV4 7AL, UK
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35
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TerAvest MA, Ajo‐Franklin CM. Transforming exoelectrogens for biotechnology using synthetic biology. Biotechnol Bioeng 2015; 113:687-97. [DOI: 10.1002/bit.25723] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 08/09/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Michaela A. TerAvest
- California Institute for Quantitative BiosciencesUniversity of CaliforniaBerkeleyCalifornia94720
| | - Caroline M. Ajo‐Franklin
- Physical Biosciences DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
- Materials Science DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
- Synthetic Biology InstituteLawrence Berkeley National LaboratoryBerkeleyCalifornia94720
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36
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Zhou M. Recent Progress on the Development of Biofuel Cells for Self-Powered Electrochemical Biosensing and Logic Biosensing: A Review. ELECTROANAL 2015. [DOI: 10.1002/elan.201500173] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Fratto BE, Roby LJ, Guz N, Katz E. Enzyme-based logic gates switchable between OR, NXOR and NAND Boolean operations realized in a flow system. Chem Commun (Camb) 2015; 50:12043-6. [PMID: 25174490 DOI: 10.1039/c4cc05769d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The enzyme-based system performing a biocatalytic cascade reaction was realized in a flow device and was used to mimic Boolean logic operations. Chemical inputs applied to the system resulted in the activation of additional reaction steps, allowing the reversible switch of the logic operations between OR, NXOR and NAND gates for processing of two other biomolecular inputs.
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Affiliation(s)
- Brian E Fratto
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.
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38
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Wang B, Buck M. Rapid engineering of versatile molecular logic gates using heterologous genetic transcriptional modules. Chem Commun (Camb) 2015; 50:11642-4. [PMID: 25062273 PMCID: PMC4185417 DOI: 10.1039/c4cc05264a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Versatile modular molecular logic gates are engineered in Escherichia coli bacteria that can sense and integrate multiple chemical molecules in customised digital logic manner.
We designed and constructed versatile modular genetic logic gates in bacterial cells. These function as digital logic 1-input Buffer gate, 2-input and 3-input AND gates with one inverted input and integrate multiple chemical input signals in customised logic manners. Such rapidly engineered devices serve to achieve increased sensing signal selectivity.
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Affiliation(s)
- Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, UK.
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39
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Fratto BE, Katz E. Reversible Logic Gates Based on Enzyme-Biocatalyzed Reactions and Realized in Flow Cells: A Modular Approach. Chemphyschem 2015; 16:1405-15. [DOI: 10.1002/cphc.201500042] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 01/06/2023]
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40
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Hu Y, Yang Y, Katz E, Song H. Programming the quorum sensing-based AND gate in Shewanella oneidensis for logic gated-microbial fuel cells. Chem Commun (Camb) 2015; 51:4184-7. [DOI: 10.1039/c5cc00026b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A modularly structured, flexible, and reprogrammable AND logic gate gene circuit-controlled microbial fuel cell.
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Affiliation(s)
- Yidan Hu
- Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)
- School of Chemical Engineering and Technology
- Tianjin University
| | - Yun Yang
- School of Chemical and Biomedical Engineering
- Nanyang Technological University
- 637457 Singapore
- Singapore
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science
- Clarkson University
- Potsdam
- USA
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education)
- SynBio Research Platform
- Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin)
- School of Chemical Engineering and Technology
- Tianjin University
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41
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Ma L, Diao A. Design of enzyme-interfaced DNA logic operations (AND, OR and INHIBIT) with an assaying application for single-base mismatch. Chem Commun (Camb) 2015; 51:10233-5. [DOI: 10.1039/c5cc02835c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We devised AND, OR and INHIBIT logic gates.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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42
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Bereza-Malcolm LT, Franks AE. Coupling anaerobic bacteria and microbial fuel cells as whole-cell environmental biosensors. MICROBIOLOGY AUSTRALIA 2015. [DOI: 10.1071/ma15045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Microorganisms have evolved to respond to environmental factors allowing adaption to changing conditions and minimisation of potential harm. Microbes have the ability to sense a wide range of biotic and abiotic factors including nutrient levels, analytes, temperature, contaminants, community quorum, and metabolic activity. Due to this ability, the use of whole-cell microbes as biosensors is attractive as it can provide real-time in situ information on biologically relevant factors through qualitative and quantitative outputs. Interestingly, many of the environments where these biosensors will be of most of use lack oxygen; and as such the use of anaerobic microorganisms to sense environmental factors with easy to use outputs is essential. Furthermore, sensing of contaminants can be linked with bioremediation of known contaminated environments, allowing a flexible, multiplexed device.
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43
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TerAvest MA, Rosenbaum MA, Kotloski NJ, Gralnick JA, Angenent LT. Oxygen allows Shewanella oneidensis MR-1 to overcome mediator washout in a continuously fed bioelectrochemical system. Biotechnol Bioeng 2014; 111:692-9. [PMID: 24122485 DOI: 10.1002/bit.25128] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/30/2013] [Accepted: 10/01/2013] [Indexed: 11/07/2022]
Abstract
Many bioelectrochemical systems (BESs) harness the ability of electrode-active microbes to catalyze reactions between electrodes and chemicals, often to perform useful functions such as wastewater treatment, fuel production, and biosensing. A microbial fuel cell (MFC) is one type of BES, which generates electric power through microbial respiration with an anode as the electron acceptor, and typically with oxygen reduction at the cathode to provide the terminal electron acceptor. Oxygen intrusion into MFCs is typically viewed as detrimental because it competes with anodes for electrons and lowers the coulombic efficiency. However, recent evidence suggests that it does not necessarily lead to lower performances—particularly for the model organism Shewanella oneidensis MR-1. Because flavin-mediated electron transfer is important for Shewanella species, which can produce this electron shuttle endogenuously, we investigated the role of flavins in the performance of pure-culture BESs with S. oneidensis MR-1 with and without oxygen. We found that oxygen increases current production more than twofold under continuously fed conditions, but only modestly increases current production under batch-fed conditions.We hypothesized that oxygen is more beneficial under continuously fed conditions because it allows S. oneidensis to grow and produce flavins at a faster rate, and thus lowers flavin washout. Our conclusions were supported by experiments with a flavin-secretion deficient mutant of S. oneidensis.
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44
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Gerdt JP, McInnis CE, Schell TL, Rossi FM, Blackwell HE. Mutational analysis of the quorum-sensing receptor LasR reveals interactions that govern activation and inhibition by nonlactone ligands. ACTA ACUST UNITED AC 2014; 21:1361-1369. [PMID: 25242287 DOI: 10.1016/j.chembiol.2014.08.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 08/05/2014] [Accepted: 08/18/2014] [Indexed: 01/03/2023]
Abstract
Gram-negative bacteria use N-acyl L-homoserine lactone (AHL) quorum-sensing (QS) signals to regulate the expression of myriad phenotypes. Non-native AHL analogs can strongly attenuate QS receptor activity and thereby QS signaling; however, we currently lack a molecular understanding of the mechanisms by which most of these compounds elicit their agonistic or antagonistic profiles. In this study, we investigated the origins of striking activity profile switches (i.e., receptor activator to inhibitor, and vice versa) observed upon alteration of the lactone head group in certain AHL analogs. Reporter gene assays of mutant versions of the Pseudomonas aeruginosa QS receptor LasR revealed that interactions between the ligands and Trp60, Tyr56, and Ser129 govern whether these ligands behave as LasR activators or inhibitors. Using this knowledge, we propose a model for the modulation of LasR by AHL analogs-encompassing a subtly different interaction with the binding pocket to a global change in LasR conformation.
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Affiliation(s)
- Joseph P Gerdt
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Christine E McInnis
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Trevor L Schell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Francis M Rossi
- Department of Chemistry, SUNY Cortland, Cortland, NY 13045, USA
| | - Helen E Blackwell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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45
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de Campos Rodrigues T, Rosenbaum MA. Microbial Electroreduction: Screening for New Cathodic Biocatalysts. ChemElectroChem 2014. [DOI: 10.1002/celc.201402239] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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46
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Privman V, Domanskyi S, Mailloux S, Holade Y, Katz E. Kinetic Model for a Threshold Filter in an Enzymatic System for Bioanalytical and Biocomputing Applications. J Phys Chem B 2014; 118:12435-43. [DOI: 10.1021/jp508224y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | | | | | - Yaovi Holade
- Université de Poitiers, IC2MP, UMR-CNRS 7285, 4 rue Michel Brunet, B27 TSA 51106, 86073 Poitiers Cedex 9, France
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47
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TerAvest MA, Zajdel TJ, Ajo‐Franklin CM. The Mtr Pathway of
Shewanella oneidensis
MR‐1 Couples Substrate Utilization to Current Production in
Escherichia coli. ChemElectroChem 2014. [DOI: 10.1002/celc.201402194] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Michaela A. TerAvest
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720 (USA)
| | - Tom J. Zajdel
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, CA 94720 (USA)
| | - Caroline M. Ajo‐Franklin
- Physical Biosciences Division, Materials Science Division and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720 (USA)
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48
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A biocatalytic cascade with several output signals--towards biosensors with different levels of confidence. Anal Bioanal Chem 2014; 406:3365-70. [PMID: 24748446 DOI: 10.1007/s00216-014-7789-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 03/24/2014] [Indexed: 10/25/2022]
Abstract
The biocatalytic cascade based on enzyme-catalyzed reactions activated by several biomolecular input signals and producing output signal after each reaction step was developed as an example of a logically reversible information processing system. The model system was designed to mimic the operation of concatenated AND logic gates with optically readable output signals generated at each step of the logic operation. Implications include concurrent bioanalyses and data interpretation for medical diagnostics.
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49
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Effective control of bioelectricity generation from a microbial fuel cell by logical combinations of pH and temperature. ScientificWorldJournal 2014; 2014:186016. [PMID: 24741343 PMCID: PMC3972852 DOI: 10.1155/2014/186016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 01/27/2014] [Indexed: 11/17/2022] Open
Abstract
In this study, a microbial fuel cell (MFC) with switchable power release is designed, which can be logically controlled by combinations of the most physiologically important parameters such as "temperature" and "pH." Changes in voltage output in response to temperature and pH changes were significant in which voltage output decreased sharply when temperature was lowered from 30°C to 10°C or pH was decreased from 7.0 to 5.0. The switchability of the MFC comes from the microbial anode whose activity is affected by the combined medium temperature and pH. Changes in temperature and pH cause reversible activation-inactivation of the bioanode, thus affecting the activity of the entire MFC. With temperature and pH as input signals, an AND logic operation is constructed for the MFC whose power density is controlled. The developed system has the potential to meet the requirement of power supplies producing electrical power on-demand for self-powered biosensors or biomedical devices.
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50
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Abstract
AbstractThe focus of this review paper is on the design and implementation of smart ‘Sense-and-Treat’ systems using enzyme-biocatalytic systems. These systems were used to perform biomolecular computing and they were functionally integrated with signal responsive materials aiming towards their biomedical use. Electrode interfaces, functionalized with signal-responsive materials, find applications in biocomputing, biosensing, and, specifically, triggered release of bioactive substances. ‘Sense-and-Treat’ systems require multiple components working together, including biosensors, actuators, and filters, in order to achieve closed-loop and autonomous operation. In general, biochemical logic networks were developed to process single biochemical or chemical inputs as well as multiple inputs, responding to nonphysiological (for concept demonstration purposes) and physiological signals (for injury detection or diagnosis). Actuation of drug-mimicking release was performed using the responsive material iron-cross-linked alginate with entrapped biomolecular species, responding to physical, chemical or biochemical signals.
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