1
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Agiza A, Marriott S, Rosenstein JK, Kim E, Reda S. pH-Controlled enzymatic computing for digital circuits and neural networks. Phys Chem Chem Phys 2024; 26:20898-20907. [PMID: 39045608 DOI: 10.1039/d4cp02039a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Unconventional computing paradigms explore new methods for processing information beyond the capabilities of traditional electronic architectures. In this work, we present our approach to digital computation through enzymatic reactions in chemically buffered environments. A key aspect of this approach is its reliance on pH-sensitive enzymatic reactions, with the direction of the reaction controlled by maintaining pH levels within a specific range. When the pH crosses a defined threshold, the reaction moves forward and vice versa, akin to the switching action of electronic switches in digital circuits. The binary signals (0 and 1) are encoded as different concentrations of strong acids or bases, offering a bio-inspired method for computation. The final readout is done using UV-vis spectroscopy after applying detection reactions to indicate whether the output is 1 (indicated by the presence of the enzymatic reaction's product) or 0 (indicated by the absence of the enzymatic reaction's product). We build and evaluate a set of digital circuits in the lab using our proposed methodology to model the circuits using chemical reactions. In addition, we demonstrate the implementation of a neural network classifier using our framework.
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Affiliation(s)
- Ahmed Agiza
- Computer Science Department, Brown University, Providence, RI, USA.
| | | | | | - Eunsuk Kim
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Sherief Reda
- School of Engineering, Brown University, Providence, RI, USA
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2
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Wang H, Li M, Zhang H, Yang L. A Tunable Threshold Colorimetric DNA Logic Gate for Intuitive Assessment of Chemical Contaminant Exceedance. Anal Chem 2024; 96:11862-11868. [PMID: 38989925 DOI: 10.1021/acs.analchem.4c01529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Current molecular logic gates are predominantly focused on the qualitative assessment of target presence, which has certain limitations in scenarios requiring quantitative assessment, such as chemical contaminant monitoring. To bridge this gap, we have developed a novel DNA logic gate featuring a tunable threshold, specifically tailored to the limits of contaminants. At the core of this logic gate is a DNA-gold nanoparticle (AuNP) hybrid film that incorporates aptamer sequences to selectively bind to acetamiprid (ACE) and atrazine (ATR). Upon interaction with these contaminants, the film degrades, releasing AuNPs that, in the presence of Hg2+, catalyze the oxidation of TMB, resulting in a visible blue coloration on test paper. This aptamer-enabled process effectively establishes an OR logic gate, with ACE and ATR as inputs and the appearance of blue color as the output. A key innovation of our system is its tunable input threshold. By adjusting the concentration of Hg2+, we can fine-tune the color mutation points to match the input threshold to predefined limits, such as Maximum Residue Limits (MRLs). This alignment allows semiquantitative assessment of contaminant levels, providing intuitive visual feedback of contaminant exceedance. Validation experiments with spiked samples confirm its accuracy and reliability by closely matching HPLC results. Therefore, our colorimetric DNA logic gate is emerging as a promising tool for easy and semiquantitative monitoring of chemical contaminants across diverse applications.
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Affiliation(s)
- Hao Wang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Mingming Li
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Hanyang Zhang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
| | - Limin Yang
- Center for Bioengineering and Biotechnology, College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, P.R. China
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3
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Gunji YP, Adamatzky A. Computation Implemented by the Interaction of Chemical Reaction, Clustering, and De-Clustering of Molecules. Biomimetics (Basel) 2024; 9:432. [PMID: 39056873 PMCID: PMC11274543 DOI: 10.3390/biomimetics9070432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
A chemical reaction and its reaction environment are intrinsically linked, especially within the confines of narrow cellular spaces. Traditional models of chemical reactions often use differential equations with concentration as the primary variable, neglecting the density heterogeneity in the solution and the interaction between the reaction and its environment. We model the interaction between a chemical reaction and its environment within a geometrically confined space, such as inside a cell, by representing the environment through the size of molecular clusters. In the absence of fluctuations, the interplay between cluster size changes and the activation and inactivation of molecules induces oscillations. However, in unstable environments, the system reaches a fluctuating steady state. When an enzyme is introduced to this steady state, oscillations akin to action potential spike trains emerge. We examine the behavior of these spike trains and demonstrate that they can be used to implement logic gates. We discuss the oscillations and computations that arise from the interaction between a chemical reaction and its environment, exploring their potential for contributing to chemical intelligence.
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Affiliation(s)
- Yukio Pegio Gunji
- Department of Intermedia Art and Science, School of Fundamental Science and Technology, Waseda University, Ohkubo 3-4-1, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Andrew Adamatzky
- Unconventional Computing Laboratory, University of the West of England, Bristol BS16 1QY, UK;
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4
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Fu R, Hou J, Wang Z, Xianyu Y. DNA Molecular Computation Using the CRISPR-Mediated Reaction and Surface Growth of Gold Nanoparticles. ACS NANO 2024; 18:14754-14763. [PMID: 38781600 DOI: 10.1021/acsnano.4c04265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
DNA has emerged as a promising tool to build logic gates for biocomputing. However, prevailing methodologies predominantly rely on hybridization reactions or structural alterations to construct DNA logic gates, which are limited in simplicity and diversity. Herein, we developed simple and smart DNA-based logic gates for biocomputing through the DNA-mediated growth of gold nanomaterials without precise structure design and probe modification. Capitalizing on their excellent plasmonic properties, the surface growth of gold nanomaterials enables distinct wavelength shifts and unique shapes, which are modulated by the composition, length, and concentration of the DNA sequences. Combined with a CRISPR-mediated reaction, we constructed DNA circuits to achieve complicated biocomputing to modulate the surface growth of gold nanomaterials. By implementing logic functions controlled by input-mediated growth of gold nanomaterials, we established YES/NOT, AND/NAND, OR/NOR, XOR, and INHIBIT gates and further constructed cascade logic circuits, parity checker for natural numbers, and gray code encoder, which are promising for DNA biocomputing.
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Affiliation(s)
- Ruijie Fu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Jinjie Hou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Zexiang Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, People's Republic of China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Hangzhou 310016, People's Republic of China
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5
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Choudhery MS, Arif T, Mahmood R, Harris DT. CAR-T-Cell-Based Cancer Immunotherapies: Potentials, Limitations, and Future Prospects. J Clin Med 2024; 13:3202. [PMID: 38892913 PMCID: PMC11172642 DOI: 10.3390/jcm13113202] [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: 03/14/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Cancer encompasses various elements occurring at the cellular and genetic levels, necessitating an immunotherapy capable of efficiently addressing both aspects. T cells can combat cancer cells by specifically recognizing antigens on them. This innate capability of T cells has been used to develop cellular immunotherapies, but most of them can only target antigens through major histocompatibility complexes (MHCs). New gene-editing techniques such as clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (CRISPR-cas9) can precisely edit the DNA sequences. CRISPR-cas9 has made it possible to generate genetically engineered chimeric antigen receptors (CARs) that can overcome the problems associated with old immunotherapies. In chimeric antigen receptor T (CAR-T) cell therapy, the patient's T cells are isolated and genetically modified to exhibit synthetic CAR(s). CAR-T cell treatment has shown remarkably positive clinical outcomes in cancers of various types. Nevertheless, there are various challenges that reduce CAR-T effectiveness in solid tumors. It is required to address these challenges in order to make CAR-T cell therapy a better and safer option. Combining CAR-T treatment with other immunotherapies that target multiple antigens has shown positive outcomes. Moreover, recently generated Boolean logic-gated advanced CARs along with artificial intelligence has expanded its potential to treat solid tumors in addition to blood cancers. This review aims to describe the structure, types, and various methods used to develop CAR-T cells. The clinical applications of CAR-T cells in hematological malignancies and solid tumours have been described in detail. In addition, this discussion has addressed the limitations associated with CAR-T cells, explored potential strategies to mitigate CAR-T-related toxicities, and delved into future perspectives.
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Affiliation(s)
- Mahmood S. Choudhery
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
| | - Taqdees Arif
- Department of Human Genetics & Molecular Biology, University of Health Sciences, Lahore 54600, Pakistan;
| | - Ruhma Mahmood
- Jinnah Hospital, Allama Iqbal Medical College, Lahore 54700, Pakistan;
| | - David T. Harris
- Department of Immunobiology, College of Medicine, University of Arizona Health Sciences Biorepository, The University of Arizona, Tucson, AZ 85724-5221, USA;
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6
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Chen J, Hu J, Kapral R. Chemical Logic Gates on Active Colloids. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305695. [PMID: 38450886 PMCID: PMC11095161 DOI: 10.1002/advs.202305695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/28/2023] [Indexed: 03/08/2024]
Abstract
Recent studies have shown that active colloidal motors using enzymatic reactions for propulsion hold special promise for applications in fields ranging from biology to material science. It will be desirable to have active colloids with capability of computation so that they can act autonomously to sense their surroundings and alter their own dynamics. It is shown how small chemical networks that make use of enzymatic chemical reactions on the colloid surface can be used to construct motor-based chemical logic gates. The basic features of coupled enzymatic reactions that are responsible for propulsion and underlie the construction and function of chemical gates are described using continuum theory and molecular simulation. Examples are given that show how colloids with specific chemical logic gates, can perform simple sensing tasks. Due to the diverse functions of different enzyme gates, operating alone or in circuits, the work presented here supports the suggestion that synthetic motors using such gates could be designed to operate in an autonomous way in order to complete complicated tasks.
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Affiliation(s)
- Jiang‐Xing Chen
- Department of PhysicsHangzhou Normal UniversityHangzhou311121China
| | - Jia‐Qi Hu
- Department of PhysicsHangzhou Normal UniversityHangzhou311121China
| | - Raymond Kapral
- Chemical Physics Theory GroupDepartment of ChemistryUniversity of TorontoTorontoOntarioM5S 3H6Canada
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7
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Daly ML, Nishi K, Klawa SJ, Hinton KY, Gao Y, Freeman R. Designer peptide-DNA cytoskeletons regulate the function of synthetic cells. Nat Chem 2024:10.1038/s41557-024-01509-w. [PMID: 38654104 DOI: 10.1038/s41557-024-01509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 03/15/2024] [Indexed: 04/25/2024]
Abstract
The bottom-up engineering of artificial cells requires a reconfigurable cytoskeleton that can organize at distinct locations and dynamically modulate its structural and mechanical properties. Here, inspired by the vast array of actin-binding proteins and their ability to reversibly crosslink or bundle filaments, we have designed a library of peptide-DNA crosslinkers varying in length, valency and geometry. Peptide filaments conjoint through DNA hybridization give rise to tactoid-shaped bundles with tunable aspect ratios and mechanics. When confined in cell-sized water-in-oil droplets, the DNA crosslinker design guides the localization of cytoskeletal structures at the cortex or within the lumen of the synthetic cells. The tunable spatial arrangement regulates the passive diffusion of payloads within the droplets and complementary DNA handles allow for the reversible recruitment and release of payloads on and off the cytoskeleton. Heat-induced reconfiguration of peptide-DNA architectures triggers shape deformations of droplets, regulated by DNA melting temperatures. Altogether, the modular design of peptide-DNA architectures is a powerful strategy towards the bottom-up assembly of synthetic cells.
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Affiliation(s)
- Margaret L Daly
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kengo Nishi
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Stephen J Klawa
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kameryn Y Hinton
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Yuan Gao
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Ronit Freeman
- Department of Applied Physical Sciences, University of North Carolina, Chapel Hill, NC, USA.
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8
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Paul R, Paul R, Dutta D, Dash J. pH-dependent complex formation with TAR RNA and DNA: application towards logic gates. Analyst 2024; 149:1976-1980. [PMID: 38465447 DOI: 10.1039/d4an00074a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Nucleic acid-based logic gates have shown great potential in biotechnology, medicine as well as diagnostics. Herein, we have constructed pH-responsive logic devices by utilizing HIV-1 TAR hairpins in combination with a thiazole peptide that exhibits turn-on fluorescence upon interacting with TAR RNA or DNA. Based on this, INHIBIT-AND and YES-INHIBIT-AND logic gates were constructed in parallel. The pH alteration leads to conformational changes of the hairpin structure, enabling the construction of a multi-reset reusable logic system which could be developed for in vitro sensing of the HIV-1 viral RNA.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, West Bengal, India.
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9
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Matzko RO, Konur S. BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering. BIOINFORMATICS ADVANCES 2024; 4:vbae046. [PMID: 38571784 PMCID: PMC10990683 DOI: 10.1093/bioadv/vbae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/22/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
Summary Motivated by the need to parameterize ongoing multicellular simulation research, this paper documents the culmination of a ChatGPT augmented software engineering cycle resulting in an integrated visual platform for efficient cytohistological RNA-seq and bioregulatory network exploration. As contrasted to other systems and synthetic biology tools, BioNexusSentinel was developed de novo to uniquely combine these features. Reactome served as the primary source of remotely accessible biological models, accessible using BioNexusSentinel's novel search engine and REST API requests. The innovative, feature-rich gene expression profiler component was developed to enhance the exploratory experience for the researcher, culminating in the cytohistological RNA-seq explorer based on Human Protein Atlas data. A novel cytohistological classifier would be integrated via pre-processed analysis of the RNA-seq data via R statistical language, providing for useful analytical functionality and good performance for the end-user. Implications of the work span prospects for model orthogonality evaluations, gap identification in network modelling, prototyped automatic kinetics parameterization, and downstream simulation and cellular biological state analysis. This unique computational biology software engineering collaboration with generative natural language processing artificial intelligence was shown to enhance worker productivity, with evident benefits in terms of accelerating coding and machine-human intelligence transfer. Availability and implementation BioNexusSentinel project releases, with corresponding data and installation instructions, are available at https://github.com/RichardMatzko/BioNexusSentinel.
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Affiliation(s)
- Richard Oliver Matzko
- School of Computer Science, AI and Electronics, University of Bradford, Bradford BD7 1HR, United Kingdom
| | - Savas Konur
- School of Computer Science, AI and Electronics, University of Bradford, Bradford BD7 1HR, United Kingdom
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10
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Hou X, Ga L, Zhang X, Ai J. Advances in the application of logic gates in nanozymes. Anal Bioanal Chem 2024:10.1007/s00216-024-05240-w. [PMID: 38488951 DOI: 10.1007/s00216-024-05240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/17/2024]
Abstract
Nanozymes are a class of nanomaterials with biocatalytic function and enzyme-like activity, whose advantages include high stability, low cost, and mass production. They can catalyze the substrates of natural enzymes based on specific nanostructures and serve as substitutes for natural enzymes. Their applied research involves a wide range of fields such as biomedicine, environmental governance, agriculture, and food. Molecular logic gates are a new cross-disciplinary discipline, which can simulate the function of silicon circuits on a molecular scale, perform single or multiple input logic operations, and generate logic outputs. A molecular logic gate is a binary operation that converts an input signal into an output signal according to the rules of Boolean logic, generating two signals, a high level, and a low level. The high and low levels represent the "true" and "false" values of the logic gates, and their outputs correspond to "l" and "0" of the molecular logic gates, respectively. The combination of nanozymes and logic gates is a novel and attractive research direction, and the cross-application of the two brings new opportunities and ideas for various fields, such as the construction of efficient biocomputers, intelligent drug delivery systems, and the precise diagnosis of diseases. This review describes the application of logic gates based on nanozymes, which is expected to provide a certain theoretical foundation for researchers' subsequent studies.
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Affiliation(s)
- Xiangru Hou
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China
| | - Lu Ga
- College of Pharmacy, Inner Mongolia Medical University, Jinchuankaifaqu, Hohhot, 010110, China
| | - Xin Zhang
- College of Chemical Engineering, Inner Mongolia University of Technology, 49 Aimin Road, Hohhot, 010051, China.
| | - Jun Ai
- College of Chemistry and Enviromental Science, Inner Mongolia Key Laboratory of Environmental Chemistry, Inner Mongolia Normal University, 81 zhaowudalu, Hohhot, 010022, China.
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11
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Kaplan M, Yavuz O, Ozdemir E, Alcay Y, Kaya K, Yilmaz I. Architecture of Easy-to-Synthesize and Superior Probe Based on Aminoquinoline Appended Naphthoquinone: Instant and On-Site Cu 2+ Ion Quantification in Real Samples and Unusual Crystal Structure and Logic Gate Operations. Inorg Chem 2024; 63:2257-2267. [PMID: 38221778 DOI: 10.1021/acs.inorgchem.3c04229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Easy-to-synthesize aminoquinoline (AQ) appended naphthoquinone (NQ)-based colorimetric and ratiometric probe (AQNQ) was successfully synthesized in one step with high yield and low cost, and was utilized to supply an effective solution to critical shortcomings encountered in Cu2+ analysis. The structure of AQNQ and its interaction with Cu2+ forming an unusual AQNQ-Cu complex were enlightened with single-crystal X-ray diffraction analysis and different spectroscopic methods. AQNQ-Cu complex is the first Cu2+ containing dinuclear crystal where the octahedral coordination sphere is fulfilled through the coordination of a NQ oxygen atom. AQNQ exhibited long-term stability (more than 1 month), superior probe ability toward Cu2+ with quite fast response (30 s), high selectivity among many ions, and limit of detection of 12.13 ppb that is significantly below the highest amount of Cu2+ allowed in drinking water established by both WHO and EPA. Ratiometric determination of Cu2+ using AQNQ was performed with high recovery and low RSD values for drinking water, tap water, lake water, cherry, and watermelon samples. Colorimetric on-site determination including smartphone and paper strip applications, IMPLICATION, and INHIBIT logic gate applications were successfully carried out. The reversibility and reusability of the response to Cu2+ ions with the paper strip application were examined for the first time.
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Affiliation(s)
- Mehmet Kaplan
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
| | - Ozgur Yavuz
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
| | - Emre Ozdemir
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
| | - Yusuf Alcay
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
| | - Kerem Kaya
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
| | - Ismail Yilmaz
- Department of Chemistry, Istanbul Technical University, Istanbul 34469, Maslak, Turkey
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12
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Santos FP, Tryggvason G, Ferreira GGS. Droplet-based logic gates simulation of viscoelastic fluids under electric field. Sci Rep 2024; 14:1771. [PMID: 38245567 PMCID: PMC10799872 DOI: 10.1038/s41598-024-52139-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/14/2024] [Indexed: 01/22/2024] Open
Abstract
Nano and microfluidic technologies have shown great promise in the development of controlled drug delivery systems and the creation of microfluidic devices with logic-like functionalities. Here, we focused on investigating a droplet-based logic gate that can be used for automating medical diagnostic assays. This logic gate uses viscoelastic fluids, which are particularly relevant since bio-fluids exhibit viscoelastic properties. The operation of the logic gate is determined by evaluating various parameters, including the Weissenberg number, the Capillary number, and geometric factors. To effectively classify the logic gates operational conditions, we employed a deep learning classification to develop a reduced-order model. This approach accelerates the prediction of operating conditions, eliminating the need for complex simulations. Moreover, the deep learning model allows for the combination of different AND/OR branches, further enhancing the versatility of the logic gate. We also found that non-operating regions, where the logic gate does not function properly, can be transformed into operational regions by applying an external force. By utilizing an electrical induction technique, we demonstrated that the application of an electric field can repel or attract droplets, thereby improving the performance of the logic gate. Overall, our research shows the potential of the droplet-based logic gates in the field of medical diagnostics. The integration of deep learning classification algorithms enables rapid evaluation of operational conditions and facilitates the design of complex logic circuits. Additionally, the introduction of external forces and electrical induction techniques opens up new possibilities for enhancing the functionality and reliability of these logic gates.
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Affiliation(s)
- F P Santos
- Systems Engineering and Computer Science Program, Federal University of Rio de Janeiro, 21941-909, Rio de Janeiro, Brazil.
| | - G Tryggvason
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MA, 21218, USA
| | - G G S Ferreira
- Chemical Engineering Program, Federal University of Rio de Janeiro, 21941-972, Rio de Janeiro, Brazil
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13
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Shu JJ, Tan ZH, Wang QW, Yong KY. Programmable Biomolecule-Mediated Processors. J Am Chem Soc 2023; 145:25033-25042. [PMID: 37864571 PMCID: PMC10682996 DOI: 10.1021/jacs.3c04142] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Programmable biomolecule-mediated computing is a new computing paradigm as compared to contemporary electronic computing. It employs nucleic acids and analogous biomolecular structures as information-storing and -processing substrates to tackle computational problems. It is of great significance to investigate the various issues of programmable biomolecule-mediated processors that are capable of automatically processing, storing, and displaying information. This Perspective provides several conceptual designs of programmable biomolecule-mediated processors and provides some insights into potential future research directions for programmable biomolecule-mediated processors.
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Affiliation(s)
- Jian-Jun Shu
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Zi Hian Tan
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Qi-Wen Wang
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
| | - Kian-Yan Yong
- School of Mechanical &
Aerospace Engineering, Nanyang Technological
University, 50 Nanyang Avenue, Singapore 639798
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14
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Kumar S, Reddy G. Mechanism of Fluoride Ion Encapsulation by Magnesium Ions in a Bacterial Riboswitch. J Phys Chem B 2023; 127:9267-9281. [PMID: 37851949 DOI: 10.1021/acs.jpcb.3c03941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
Riboswitches sense various ions in bacteria and activate gene expression to synthesize proteins that help maintain ion homeostasis. The crystal structure of the aptamer domain (AD) of the fluoride riboswitch shows that the F- ion is encapsulated by three Mg2+ ions bound to the ligand-binding domain (LBD) located at the core of the AD. The assembly mechanism of this intricate structure is unknown. To this end, we performed computer simulations using coarse-grained and all-atom RNA models to bridge multiple time scales involved in riboswitch folding and ion binding. We show that F- encapsulation by the Mg2+ ions bound to the riboswitch involves multiple sequential steps. Broadly, two Mg2+ ions initially interact with the phosphate groups of the LBD using water-mediated outer-shell coordination and transition to a direct inner-shell interaction through dehydration to strengthen their interaction with the LBD. We propose that the efficient binding mode of the third Mg2+ and F- is that they form a water-mediated ion pair and bind to the LBD simultaneously to minimize the electrostatic repulsion between three Mg2+ bound to the LBD. The tertiary stacking interactions among the LBD nucleobases alone are insufficient to stabilize the alignment of the phosphate groups to facilitate Mg2+ binding. We show that the stability of the whole assembly is an intricate balance of the interactions among the five phosphate groups, three Mg2+, and the encapsulated F- ion aided by the Mg2+ solvated water. These insights are helpful in the rational design of RNA-based ion sensors and fast-switching logic gates.
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Affiliation(s)
- Sunil Kumar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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15
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Zeng J, Zeng XX. Systems Medicine for Precise Targeting of Glioblastoma. Mol Biotechnol 2023; 65:1565-1584. [PMID: 36859639 PMCID: PMC9977103 DOI: 10.1007/s12033-023-00699-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/14/2023] [Indexed: 03/03/2023]
Abstract
Glioblastoma (GBM) is a malignant cancer that is fatal even after standard therapy and the effects of current available therapeutics are not promising due its complex and evolving epigenetic and genetic profile. The mysteries that lead to GBM intratumoral heterogeneity and subtype transitions are not entirely clear. Systems medicine is an approach to view the patient in a whole picture integrating systems biology and synthetic biology along with computational techniques. Since the GBM oncogenesis involves genetic mutations, various therapies including gene therapeutics based on CRISPR-Cas technique, MicroRNAs, and implanted synthetic cells endowed with synthetic circuits against GBM with neural stem cells and mesenchymal stem cells acting as potential vehicles carrying therapeutics via the intranasal route, avoiding the risks of invasive methods in order to reach the GBM cells in the brain are discussed and proposed in this review. Systems medicine approach is a rather novel strategy, and since the GBM of a patient is complex and unique, thus to devise an individualized treatment strategy to tailor personalized multimodal treatments for the individual patient taking into account the phenotype of the GBM, the unique body health profile of the patient and individual responses according to the systems medicine concept might show potential to achieve optimum effects.
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Affiliation(s)
- Jie Zeng
- Benjoe Institute of Systems Bio-Engineering, High Technology Park, Xinbei District, Changzhou, 213022 Jiangsu People’s Republic of China
| | - Xiao Xue Zeng
- Department of Health Management, Centre of General Practice, The Seventh Affiliated Hospital, Southern Medical University, No. 28, Desheng Road Section, Liguan Road, Lishui Town, Nanhai District, Foshan, 528000 Guangdong People’s Republic of China
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16
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Zhou Z, Zhang Y, Xia S, Chen X. Red-Light-Activatable AND-Gated Antitumor Immunosuppressant. Cells 2023; 12:2351. [PMID: 37830565 PMCID: PMC10571834 DOI: 10.3390/cells12192351] [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: 07/12/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023] Open
Abstract
Immunosuppressants are emerging as promising candidates for cancer therapy with lower cytotoxicity compared to traditional chemotherapy drugs; yet, the intrinsic side effects such as immunosuppression remain a critical concern. Herein, we introduce a photoactivatable antitumor immunosuppressant called dmBODIPY-FTY720 (BF) that shows no cytotoxicity but can be temporally and locally activated by deep-red light illumination to induce tumor cell apoptosis. To further reduce potential side effects, we integrate BF with another classic photosensitizer called methylene blue (MB) that is activated under the same wavelength of deep-red light (>650 nm) and successfully establish a red-light-activatable AND Boolean logic gate through a mechanism that we found to be synergetic apoptotic induction. At further decreased dosages, deep-red light illumination does not induce cell death in the presence of either BF or MB, but significant cancer cell death is triggered in the presence of both drugs. Therefore, the dosage of BF is further reduced, which will be highly beneficial to minimize any potential side effects of BF. This AND-gated strategy has been successfully applied in vivo for effective suppression of hepatocarcinoma tumors in living mice.
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Affiliation(s)
- Ziqi Zhou
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
| | - Yan Zhang
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
| | - Simin Xia
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
| | - Xi Chen
- Laboratory of Chemical Biology and Frontier Biotechnologies, The HIT Center for Life Sciences (HCLS), Harbin Institute of Technology (HIT), Harbin 150001, China; (Z.Z.); (Y.Z.)
- School of Life Science and Technology, Harbin Institute of Technology (HIT), Harbin 150001, China
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17
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Shi L, Tang Q, Yang B, Liu W, Li B, Yang C, Jin Y. Logic-Gates of Gas Pressure for Portable, Intelligent and Multiple Analysis of Metal Ions. Anal Chem 2023; 95:5702-5709. [PMID: 36939344 DOI: 10.1021/acs.analchem.2c05677] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
DNA logic gates have shown outstanding magic in intelligent biology applications, but it remains challenging to construct a portable, affordable and convenient DNA logic gate. Herein, logic gates of gas pressure were innovatively developed for multiplex analysis of metal ions. Hg2+ and Ag+ were input to interact specifically with the respective mismatched base pairs, which activated DNA extension reaction by polymerase and led to the enrichment of platinum nanoparticles for catalyzing the decomposition of peroxide hydrogen. Thus, the gas pressure obtained from a sealed well was used as output for detecting or identifying metal ions. Hg2+ and Ag+ were sensitively and selectively detected, and the assay of the real samples was also satisfactory. Based on this, DNA logic gates, including YES, NOT, AND, OR, NAND, NOR, INHIBIT, and XOR were successfully established using a portable and hand-held gas pressure meter as detector. So, the interactions between DNA and metal ions were intelligently transferred into the output of gas pressure, which made metal ions to be detected portably and identified intelligently. Given the remarkable merits of simplicity, logic operation, and portable output, the metal ion-driven DNA logic gate of gas pressure provides a promising way for intelligent and portable biosensing.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Qiaorong Tang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bing Yang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Wei Liu
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Baoxin Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chaoyong Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, Key Laboratory for Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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18
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Kieffer C, Genot AJ, Rondelez Y, Gines G. Molecular Computation for Molecular Classification. Adv Biol (Weinh) 2023; 7:e2200203. [PMID: 36709492 DOI: 10.1002/adbi.202200203] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/28/2022] [Indexed: 01/30/2023]
Abstract
DNA as an informational polymer has, for the past 30 years, progressively become an essential molecule to rationally build chemical reaction networks endowed with powerful signal-processing capabilities. Whether influenced by the silicon world or inspired by natural computation, molecular programming has gained attention for diagnosis applications. Of particular interest for this review, molecular classifiers have shown promising results for disease pattern recognition and sample classification. Because both input integration and computation are performed in a single tube, at the molecular level, this low-cost approach may come as a complementary tool to molecular profiling strategies, where all biomarkers are quantified independently using high-tech instrumentation. After introducing the elementary components of molecular classifiers, some of their experimental implementations are discussed either using digital Boolean logic or analog neural network architectures.
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Affiliation(s)
- Coline Kieffer
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Anthony J Genot
- LIMMS, CNRS-Institute of Industrial Science, IRL 2820, University of Tokyo, Tokyo, 153-8505, Japan
| | - Yannick Rondelez
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
| | - Guillaume Gines
- Laboratoire Gulliver, UMR 7083, CNRS, ESPCI Paris, PSL Research University, 10 rue Vauquelin, Paris, 75005, France
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19
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Dang Z, Gao M, Wang L, Wu J, Guo Y, Zhu Z, Huang H, Kang G. Synthetic bacterial therapies for intestinal diseases based on quorum- sensing circuits. Biotechnol Adv 2023; 65:108142. [PMID: 36977440 DOI: 10.1016/j.biotechadv.2023.108142] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/28/2023]
Abstract
Bacterial therapy has become a key strategy against intestinal infectious diseases in recent years. Moreover, regulating the gut microbiota through traditional fecal microbiota transplantation and supplementation of probiotics faces controllability, efficacy, and safety challenges. The infiltration and emergence of synthetic biology and microbiome provide an operational and safe treatment platform for live bacterial biotherapies. Synthetic bacterial therapy can artificially manipulate bacteria to produce and deliver therapeutic drug molecules. This method has the advantages of solid controllability, low toxicity, strong therapeutic effects, and easy operation. As an essential tool for dynamic regulation in synthetic biology, quorum sensing (QS) has been widely used for designing complex genetic circuits to control the behavior of bacterial populations and achieve predefined goals. Therefore, QS-based synthetic bacterial therapy might become a new direction for the treatment of diseases. The pre-programmed QS genetic circuit can achieve a controllable production of therapeutic drugs on particular ecological niches by sensing specific signals released from the digestive system in pathological conditions, thereby realizing the integration of diagnosis and treatment. Based on this as well as the modular idea of synthetic biology, QS-based synthetic bacterial therapies are divided into an environmental signal sensing module (senses gut disease physiological signals), a therapeutic molecule producing module (plays a therapeutic role against diseases), and a population behavior regulating module (QS system). This review article summarized the structure and function of these three modules and discussed the rational design of QS gene circuits as a novel intervention strategy for intestinal diseases. Moreover, the application prospects of QS-based synthetic bacterial therapy were summarized. Finally, the challenges faced by these methods were analyzed to make the targeted recommendations for developing a successful therapeutic strategy for intestinal diseases.
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20
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Gomide MDS, Leitão MDC, Coelho CM. Biocircuits in plants and eukaryotic algae. FRONTIERS IN PLANT SCIENCE 2022; 13:982959. [PMID: 36212277 PMCID: PMC9545776 DOI: 10.3389/fpls.2022.982959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
As one of synthetic biology's foundations, biocircuits are a strategy of genetic parts assembling to recognize a signal and to produce a desirable output to interfere with a biological function. In this review, we revisited the progress in the biocircuits technology basis and its mandatory elements, such as the characterization and assembly of functional parts. Furthermore, for a successful implementation, the transcriptional control systems are a relevant point, and the computational tools help to predict the best combinations among the biological parts planned to be used to achieve the desirable phenotype. However, many challenges are involved in delivering and stabilizing the synthetic structures. Some research experiences, such as the golden crops, biosensors, and artificial photosynthetic structures, can indicate the positive and limiting aspects of the practice. Finally, we envision that the modulatory structural feature and the possibility of finer gene regulation through biocircuits can contribute to the complex design of synthetic chromosomes aiming to develop plants and algae with new or improved functions.
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Affiliation(s)
- Mayna da Silveira Gomide
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
- School of Medicine, Federal University of Juiz de Fora (UFJF), Juiz de Fora, Minas Gerais, Brazil
| | - Matheus de Castro Leitão
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
| | - Cíntia Marques Coelho
- Laboratory of Synthetic Biology, Department of Genetics and Morphology, Institute of Biological Science, University of Brasília (UnB), Brasília, Distrito Federal, Brazil
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21
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Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. BIODESIGN RESEARCH 2022; 2022:9794510. [PMID: 37850136 PMCID: PMC10521664 DOI: 10.34133/2022/9794510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/10/2022] [Indexed: 10/19/2023] Open
Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.
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Affiliation(s)
- Samuel M. D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
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22
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Affiliation(s)
- Theodorus W J Gadella
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy (LCAM), Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
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23
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Davies JA. Synthetic Morphogenesis: introducing IEEE journal readers to programming living mammalian cells to make structures. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2022; 110:688-707. [PMID: 36590991 PMCID: PMC7614003 DOI: 10.1109/jproc.2021.3137077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Synthetic morphogenesis is a new engineering discipline, in which cells are genetically engineered to make designed shapes and structures. At least in this early phase of the field, devices tend to make use of natural shape-generating processes that operate in embryonic development, but invoke them artificially at times and in orders of a technologist's choosing. This requires construction of genetic control, sequencing and feedback systems that have close parallels to electronic design, which is one reason the field may be of interest to readers of IEEE journals. The other reason is that synthetic morphogenesis allows the construction of two-way interfaces, especially opto-genetic and opto-electronic, between the living and the electronic, allowing unprecedented information flow and control between the two types of 'machine'. This review introduces synthetic morphogenesis, illustrates what has been achieved, drawing parallels wherever possible between biology and electronics, and looks forward to likely next steps and challenges to be overcome.
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Affiliation(s)
- Jamie A Davies
- Professor of Experimental Anatomy at the University of Edinburgh, UK, and a member of the Centre for Mammalian Synthetic Biology at that University
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24
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Ziegler MJ, Yserentant K, Dunsing V, Middel V, Gralak AJ, Pakari K, Bargstedt J, Kern C, Petrich A, Chiantia S, Strähle U, Herten DP, Wombacher R. Mandipropamid as a chemical inducer of proximity for in vivo applications. Nat Chem Biol 2022; 18:64-69. [PMID: 34934192 PMCID: PMC8709788 DOI: 10.1038/s41589-021-00922-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/13/2021] [Indexed: 11/26/2022]
Abstract
Direct control of protein interactions by chemically induced protein proximity holds great potential for both cell and synthetic biology as well as therapeutic applications. Low toxicity, orthogonality and excellent cell permeability are important criteria for chemical inducers of proximity (CIPs), in particular for in vivo applications. Here, we present the use of the agrochemical mandipropamid (Mandi) as a highly efficient CIP in cell culture systems and living organisms. Mandi specifically induces complex formation between a sixfold mutant of the plant hormone receptor pyrabactin resistance 1 (PYR1) and abscisic acid insensitive (ABI). It is orthogonal to other plant hormone-based CIPs and rapamycin-based CIP systems. We demonstrate the applicability of the Mandi system for rapid and efficient protein translocation in mammalian cells and zebrafish embryos, protein network shuttling and manipulation of endogenous proteins.
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Affiliation(s)
- Michael J Ziegler
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Klaus Yserentant
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Valentin Dunsing
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Volker Middel
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Antoni J Gralak
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Kaisa Pakari
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Jörn Bargstedt
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Christoph Kern
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
| | - Annett Petrich
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Salvatore Chiantia
- Institute of Biology and Biochemistry, University of Potsdam, Potsdam, Germany
| | - Uwe Strähle
- Institute of Biological and Chemical Systems (IBCS)-Biological Information Processing (BIP), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Dirk-Peter Herten
- Institute of Physical Chemistry, Heidelberg University, Heidelberg, Germany
- Institute of Cardiovascular Sciences & School of Chemistry, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), Universities of Birmingham and Nottingham, Midlands, UK
| | - Richard Wombacher
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany.
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany.
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25
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Chen T, Ali Al-Radhawi M, Voigt CA, Sontag ED. A synthetic distributed genetic multi-bit counter. iScience 2021; 24:103526. [PMID: 34917900 PMCID: PMC8666654 DOI: 10.1016/j.isci.2021.103526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/30/2021] [Accepted: 11/23/2021] [Indexed: 11/12/2022] Open
Abstract
A design for genetically encoded counters is proposed via repressor-based circuits. An N-bit counter reads sequences of input pulses and displays the total number of pulses, modulo 2N. The design is based on distributed computation with specialized cell types allocated to specific tasks. This allows scalability and bypasses constraints on the maximal number of circuit genes per cell due to toxicity or failures due to resource limitations. The design starts with a single-bit counter. The N-bit counter is then obtained by interconnecting (using diffusible chemicals) a set of N single-bit counters and connector modules. An optimization framework is used to determine appropriate gate parameters and to compute bounds on admissible pulse widths and relaxation (inter-pulse) times, as well as to guide the construction of novel gates. This work can be viewed as a step toward obtaining circuits that are capable of finite automaton computation in analogy to digital central processing units. A single-bit counter is designed for a repressor-based genetic circuit A scalable multi-bit counter is enabled by distributing the design across cells A computational optimization framework is proposed to guide the design
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Affiliation(s)
- Tianchi Chen
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - M Ali Al-Radhawi
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eduardo D Sontag
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA.,Department of Electrical and Computer Engineering, Northeastern University, Boston, MA 02115, USA.,Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, MA 02115, USA
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26
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Massana Roquero D, McCorduck B, Bollella P, Smutok O, Melman A, Katz E. Biomolecule Release from Alginate Composite Hydrogels Triggered by Logically Processed Signals. Chemphyschem 2021; 22:1967-1975. [PMID: 34309163 DOI: 10.1002/cphc.202100458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Indexed: 12/31/2022]
Abstract
Alginate composite hydrogels that exhibit highly sensitive stimuli-responsive behavior were used for signal-stimulated release of pre-loaded insulin. The alginate pores, particularly located at the periphery, were blocked by interpenetration of polyvinyl alcohol (PVA) cross-linked with 1,3-benzenediboronic acid (IPN), thus, significantly reducing uncontrolled leakage of the entrapped biomolecules. The beads were loaded with insulin and various enzymes mimicking different Boolean logic gates (AND, OR, NOR, IMP, INHIB). The enzymes were activated with biologically relevant input signals applied in four logic combinations: 0,0; 1,0; 0,1; 1,1, having the production of H2 O2 as the result of the biocatalytic reactions. The "successful" combination of the input signals leading to the H2 O2 production was different for different logic gates, following the corresponding truth tables of the logic gates. When H2 O2 was produced, boronate ester bonds were oxidized and the IPN was irreversibly degraded, thus re-opening the original pores of the hydrogel. This process allowed release of insulin from the alginate beads. The smart soft material that we have developed tackled well-known limitations of these systems and it may prove valuable in future medical diagnostics or treatments.
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Affiliation(s)
- Daniel Massana Roquero
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Brandon McCorduck
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA.,Department of Chemistry, University of Bari A. Moro, Via E. Orabona 4, 70125, Bari, Italy
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699, USA
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27
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Miyamoto T, Uosaki H, Mizunoe Y, Han SI, Goto S, Yamanaka D, Masuda M, Yoneyama Y, Nakamura H, Hattori N, Takeuchi Y, Ohno H, Sekiya M, Matsuzaka T, Hakuno F, Takahashi SI, Yahagi N, Ito K, Shimano H. Rapid manipulation of mitochondrial morphology in a living cell with iCMM. CELL REPORTS METHODS 2021; 1:100052. [PMID: 35475143 PMCID: PMC9017203 DOI: 10.1016/j.crmeth.2021.100052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/12/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Engineered synthetic biomolecular devices that integrate elaborate information processing and precisely regulate living cell behavior have potential in various applications. Although devices that directly regulate key biomolecules constituting inherent biological systems exist, no devices have been developed to control intracellular membrane architecture, contributing to the spatiotemporal functions of these biomolecules. This study developed a synthetic biomolecular device, termed inducible counter mitochondrial morphology (iCMM), to manipulate mitochondrial morphology, an emerging informative property for understanding physiopathological cellular behaviors, on a minute timescale by using a chemically inducible dimerization system. Using iCMM, we determined cellular changes by altering mitochondrial morphology in an unprecedented manner. This approach serves as a platform for developing more sophisticated synthetic biomolecular devices to regulate biological systems by extending manipulation targets from conventional biomolecules to mitochondria. Furthermore, iCMM might serve as a tool for uncovering the biological significance of mitochondrial morphology in various physiopathological cellular processes.
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Affiliation(s)
- Takafumi Miyamoto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Hideki Uosaki
- Division of Regenerative Medicine, Center for Molecular Medicine, Jichi Medical University, Shimotsuke, Tochigi 329-0498, Japan
| | - Yuhei Mizunoe
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Song-Iee Han
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Satoi Goto
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Daisuke Yamanaka
- Department of Veterinary Medical Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kasama, Ibaraki 319-0206, Japan
| | - Masato Masuda
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yosuke Yoneyama
- Institute of Research, Division of Advanced Research, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hideki Nakamura
- Johns Hopkins University School of Medicine, Department of Cell Biology and Center for Cell Dynamics, MD 21205, USA
- Kyoto University Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, Kyoto 606-8501, Japan
| | - Naoko Hattori
- Division of Epigenomics, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Yoshinori Takeuchi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Hiroshi Ohno
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Motohiro Sekiya
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Takashi Matsuzaka
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiko Hakuno
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shin-Ichiro Takahashi
- Departments of Animal Sciences and Applied Biological Chemistry, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Naoya Yahagi
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
| | - Koichi Ito
- Department of Veterinary Medical Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Kasama, Ibaraki 319-0206, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Endocrinology and Metabolism), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki 305-8575, Japan
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Yu Y, Guo Q, Jiang W, Zhang H, Cai C. Dual-Aptamer-Assisted AND Logic Gate for Cyclic Enzymatic Signal Amplification Electrochemical Detection of Tumor-Derived Small Extracellular Vesicles. Anal Chem 2021; 93:11298-11304. [PMID: 34369142 DOI: 10.1021/acs.analchem.1c02489] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small extracellular vesicles (sEVs), often referred to as exosomes, are potential biomarkers for noninvasive cancer diagnosis. However, because of their phenotype heterogeneity, precise detection of tumor-derived sEVs is a great challenge. Herein, a dual-aptamer-assisted AND logic gate was fabricated for sensitive electrochemical detection of tumor-derived sEVs based on a cyclic enzymatic signal amplification strategy. Four different tumor-derived sEVs were used to verify the feasibility of the AND logic gate, and CCRF-CEM sEVs were successfully detected by this assay. The electrochemical assay shows a good linear response from 4 × 103 to 8 × 107 particles/μL, with a detection limit of 920 particles/μL, for CCRF-CEM sEVs, indicating potential application in accurate cancer diagnostics.
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Affiliation(s)
- Yongqi Yu
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Qunqun Guo
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Wenli Jiang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Hui Zhang
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
| | - Chenxin Cai
- Jiangsu Key Laboratory of New Power Batteries, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210097, P. R. China
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29
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Wurtz T. Nested information processing in the living world. Ann N Y Acad Sci 2021; 1500:5-16. [PMID: 34042190 PMCID: PMC8518751 DOI: 10.1111/nyas.14612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/26/2021] [Accepted: 04/26/2021] [Indexed: 12/25/2022]
Abstract
Living organisms create, copy, and make use of information, the content depending on the level of organization. In cells, a network of signal chain proteins regulates gene expression and other cell functions. Incoming information is encoded through signal reception, processed by the network, and decoded by the synthesis of new gene products and other biological functions. Signaling proteins represent nodes, and signal transmission proceeds via allosteric binding, chemical and structural modifications, synthesis, sequestering, and degradation. The induction of the gene caudal type homeobox 2 (CDX2) in the mammalian preimplantation embryo is outlined as a demonstration of this concept. CDX2 is involved in the decision of cells to enter the trophoblast lineage. Two signal chains are coordinated into an information processing model with the help of logic gates. The model introduces a formal structure that incorporates experimental and morphological data. Above the cell level, information flow relates to tissue formation and functioning, and whole cells play the role of network nodes. This is described for the anatomical patterning of bone with implications for bone formation and homeostasis. The information usage in cells and tissues is set into a context of the nervous system and the interaction of human individuals in societies, both established scenes of information processing.
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Bollella P, Kadambar VK, Melman A, Katz E. Reconfigurable Implication and Inhibition Boolean logic gates based on NAD
+
‐dependent enzymes: Application to signal‐controlled biofuel cells and molecule release. ELECTROCHEMICAL SCIENCE ADVANCES 2021. [DOI: 10.1002/elsa.202100008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam New York USA
- Dipartimento di Chimica Università degli Studi di Bari “Aldo Moro” 70125 Bari Italy
| | | | - Artem Melman
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam New York USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam New York USA
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31
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Madec M, Rosati E, Lallement C. Feasibility and reliability of sequential logic with gene regulatory networks. PLoS One 2021; 16:e0249234. [PMID: 33784367 PMCID: PMC8009411 DOI: 10.1371/journal.pone.0249234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 03/14/2021] [Indexed: 11/19/2022] Open
Abstract
Gene regulatory networks exhibiting Boolean behaviour, e.g. AND, OR or XOR, have been routinely designed for years. However, achieving more sophisticated functions, such as control or computation, usually requires sequential circuits or so-called state machines. For such a circuit, outputs depend both on inputs and the current state of the system. Although it is still possible to design such circuits by analogy with digital electronics, some particularities of biology make the task trickier. The impact of two of them, namely the stochasticity of biological processes and the inhomogeneity in the response of regulation mechanisms, are assessed in this paper. Numerical simulations performed in two use cases point out high risks of malfunctions even for designed GRNs functional from a theoretical point of view. Several solutions to improve reliability of such systems are also discussed.
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Affiliation(s)
- Morgan Madec
- Laboratory of Engineering Sciences, Computer Sciences and Imaging, UMR 7357 (University of Strasbourg / CNRS), Illkirch, France
| | - Elise Rosati
- Laboratory of Engineering Sciences, Computer Sciences and Imaging, UMR 7357 (University of Strasbourg / CNRS), Illkirch, France
| | - Christophe Lallement
- Laboratory of Engineering Sciences, Computer Sciences and Imaging, UMR 7357 (University of Strasbourg / CNRS), Illkirch, France
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Chen W, Cheng CA, Xiang D, Zink JI. Expanding nanoparticle multifunctionality: size-selected cargo release and multiple logic operations. NANOSCALE 2021; 13:5497-5506. [PMID: 33687426 DOI: 10.1039/d1nr00642h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Physically stimulated nanoparticles that deliver size-selected cargo and function as logic gates are reported. To achieve this goal the particle requires multiple components, and we recognized early on that the components, not just the released cargo, could be used to demonstrate logic operations (OR and AND logic). For stimuli, we chose two non-invasive types, red light and alternating magnetic fields (AMF), because they both have potential biological relevance. To realize cargo delivery with size selection and logic operations, we mechanized the surface of core@shell nanoparticles with a superparamagnetic core that generates localized heating when exposed to an AMF, and a mesoporous silica shell into which cargo molecules with different sizes were loaded. We demonstrate the core@shell nanoparticles can load the dual cargos with different sizes and subsequently release the smaller (∼0.5 nm) and bigger (∼2 nm) cargos in succession when stimulated by a red light followed by an AMF. Finally, we demonstrate that the multi-component nanoparticles could function as nanoparticle-based Boolean logic gates where AMF and red light served as the two inputs and the release of small cargo, and free cyclodextrin served as the outputs. The construction of two Boolean logic gates (OR, and AND) was realized.
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Affiliation(s)
- Wei Chen
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Chi-An Cheng
- California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA and Department of Bioengineering, University of California Los Angeles, Los Angeles, California, 90095, USA
| | - Danlei Xiang
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA.
| | - Jeffrey I Zink
- Department of Chemistry & Biochemistry, University of California Los Angeles, Los Angeles, California, 90095, USA. and California NanoSystems Institute, University of California Los Angeles, Los Angeles, California, 90095, USA
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33
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Tas H, Goñi-Moreno Á, Lorenzo VD. A Standardized Inverter Package Borne by Broad Host Range Plasmids for Genetic Circuit Design in Gram-Negative Bacteria. ACS Synth Biol 2021; 10:213-217. [PMID: 33336567 DOI: 10.1021/acssynbio.0c00529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genetically encoded logic gates, especially inverters-NOT gates-are the building blocks for designing circuits, engineering biosensors, or decision-making devices in synthetic biology. However, the repertoire of inverters readily available for different species is rather limited. In this work, a large whole of NOT gates that was shown to function previously in a specific strain of Escherichia coli, was recreated as broad host range (BHR) collection of constructs assembled in low, medium, and high copy number plasmid backbones of the SEVA (Standard European Vector Architecture) collection. The input/output function of each of the gates was characterized and parametrized in the environmental bacterium and metabolic engineering chassis Pseudomonas putida. Comparisons of the resulting fluorescence cytometry data with those published for the same gates in Escherichia coli provided useful hints on the portability of the corresponding gates. The hereby described inverter package (20 different versions of 12 distinct gates) borne by BHR plasmids thus becomes a toolbox of choice for designing genetic circuitries in a variety of Gram-negative species other than E. coli.
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Affiliation(s)
- Huseyin Tas
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
| | - Ángel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle Upon Tyne, NE4 5TG, U.K
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Campus de Montegancedo-UPM, Pozuelo de Alarcón, Madrid, 28223, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid, 28049, Spain
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Bollella P, Guo Z, Edwardraja S, Krishna Kadambar V, Alexandrov K, Melman A, Katz E. Self-powered molecule release systems activated with chemical signals processed through reconfigurable Implication or Inhibition Boolean logic gates. Bioelectrochemistry 2020; 138:107735. [PMID: 33482577 DOI: 10.1016/j.bioelechem.2020.107735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023]
Abstract
The Implication (IMPLY) and Inhibition (INHIB) Boolean logic gates were realized using switchable chimeric pyrroloquinoline quinone-dependent glucose dehydrogenase (PQQ-GDH-Clamp) containing a fused affinity clamp unit recognizing a signal-peptide. The second component of the logic gate was the wild-type PQQ-glucose dehydrogenase working cooperatively with the PQQ-GDH-Clamp enzyme. The IMPLY and INHIB gates were realized using the same enzyme composition activated with differently defined input signals, thus representing reconfigurable logic systems. The logic gates were first tested while operating in a solution with optical analysis of the output signals. Then, the enzymes were immobilized on a buckypaper electrode for electrochemical transduction of the output signals. The switchable modified electrodes mimicking the IMPLY or INHIB logic gates were integrated with an oxygen-reducing electrode modified with bilirubin oxidase to operate as a biofuel cell activated/inhibited by various input signal combinations processed either by IMPLY or INHIB logic gates. The switchable biofuel cell was used as a self-powered device triggering molecule release function controlled by the logically processed molecule signals.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane 4072, QLD, Australia
| | - Vasantha Krishna Kadambar
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane 4001, QLD, Australia.
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Ave., Potsdam, NY 13699, USA.
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36
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Kaniewska K, Bollella P, Katz E. Implication and Inhibition Boolean Logic Gates Mimicked with Enzyme Reactions. Chemphyschem 2020; 21:2150-2154. [DOI: 10.1002/cphc.202000653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/14/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Klaudia Kaniewska
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
- Faculty of Chemistry Biological and Chemical Research Center University of Warsaw 101 Żwirki i Wigury Av. 02-089 Warsaw Poland
| | - Paolo Bollella
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science Clarkson University Potsdam NY 13699 USA
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37
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Krishnaswamy B, McClean MN. Shining light on molecular communication. PROCEEDINGS OF THE 7TH ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION : VIRTUAL CONFERENCE, SEPTEMBER 23-25, 2020 : NANOCOM 2020. ACM INTERNATIONAL CONFERENCE ON NANOSCALE COMPUTING AND COMMUNICATION (7TH : 2020 :... 2020; 2020:11. [PMID: 35425948 PMCID: PMC9006593 DOI: 10.1145/3411295.3411307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Molecules and combinations of molecules are the natural communication currency of microbes; microbes have evolved and been engineered to sense a variety of compounds, often with exquisite sensitivity. The availability of microbial biosensors, combined with the ability to genetically engineer biological circuits to process information, make microbes attractive bionanomachines for propagating information through molecular communication (MC) networks. However, MC networks built entirely of biological components suffer a number of limitations. They are extremely slow due to processing and propagation delays and must employ simple algorithms due to the still limited computational capabilities of biological circuits. In this work, we propose a hybrid bio-electronic framework which utilizes biological components for sensing but offloads processing and computation to traditional electronic systems and communication infrastructure. This is achieved by using tools from the burgeoning field of optogenetics to trigger biosensing through an optoelectronic interface, alleviating the need for computation and communication in the biological domain.
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38
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Barnoy EA, Popovtzer R, Fixler D. Fluorescence for biological logic gates. JOURNAL OF BIOPHOTONICS 2020; 13:e202000158. [PMID: 32537894 DOI: 10.1002/jbio.202000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 05/03/2023]
Abstract
Biological logic gates are smart probes able to respond to biological conditions in behaviors similar to computer logic gates, and they pose a promising challenge for modern medicine. Researchers are creating many kinds of smart nanostructures that can respond to various biological parameters such as pH, ion presence, and enzyme activity. Each of these conditions alone might be interesting in a biological sense, but their interactions are what define specific disease conditions. Researchers over the past few decades have developed a plethora of stimuli-responsive nanodevices, from activatable fluorescent probes to DNA origami nanomachines, many explicitly defining logic operations. Whereas many smart configurations have been explored, in this review we focus on logic operations actuated through fluorescent signals. We discuss the applicability of fluorescence as a means of logic gate implementation, and consider the use of both fluorescence intensity as well as fluorescence lifetime.
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Affiliation(s)
- Eran A Barnoy
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Rachela Popovtzer
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Dror Fixler
- Faculty of Engineering and the Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
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39
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Kojima R, Aubel D, Fussenegger M. Building sophisticated sensors of extracellular cues that enable mammalian cells to work as "doctors" in the body. Cell Mol Life Sci 2020; 77:3567-3581. [PMID: 32185403 PMCID: PMC7452942 DOI: 10.1007/s00018-020-03486-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/27/2020] [Accepted: 02/17/2020] [Indexed: 12/24/2022]
Abstract
Mammalian cells are inherently capable of sensing extracellular environmental signals and activating complex biological functions on demand. Advances in synthetic biology have made it possible to install additional capabilities, which can allow cells to sense the presence of custom biological molecules and provide defined outputs on demand. When implanted/infused in patients, such engineered cells can work as intrabody "doctors" that diagnose disease states and produce and deliver therapeutic molecules when and where necessary. The key to construction of such theranostic cells is the development of a range of sensor systems for detecting various extracellular environmental cues that can be rewired to custom outputs. In this review, we introduce the state-of-art engineering principles utilized in the design of sensor systems to detect soluble factors and also to detect specific cell contact, and we discuss their potential role in treating intractable diseases by delivering appropriate therapeutic functions on demand. We also discuss the challenges facing these emerging technologies.
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Affiliation(s)
- Ryosuke Kojima
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
| | - Dominque Aubel
- IUTA Département Génie Biologique, Université Claude Bernard Lyon 1, Boulevard du 11 Novembre 1918, 69622, Villeurbanne Cedex, France
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.
- Faculty of Science, University of Basel, Mattenstrasse 26, 4058, Basel, Switzerland.
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40
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Wang J, Zhang Q, Hu D, Zhan T, Guo Z, Wang S, Hu Y. Reprogrammable fluorescence logic sensing for biomolecules via RNA-like coenzyme A-based coordination polymer. Biosens Bioelectron 2020; 165:112405. [PMID: 32729525 DOI: 10.1016/j.bios.2020.112405] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/13/2020] [Accepted: 06/21/2020] [Indexed: 01/28/2023]
Abstract
In this study, coenzyme A (CoA)-based coordination polymers (CPs) have been generated in situ by exploiting the reaction of thiols with metal ion (Au(III) or Ag(I)), which are dependent on both thiol-metal and aurophilic metal∙metal interaction. It is interesting to note that CPs-related biosensing capabilities toward some biomolecules including ascorbic acid (AA), cysteine (Cys) and glutathione (GSH) are also investigated via SYBR Green II (SGII)-derived fluorescence switchable mechanisms. The synthesized CPs display especial RNA-like structure and are capable of initiating the fluorescence of SGII. Conversely, AA, Cys or GSH can give rise to the structural destruction of RNA-like CPs, thus inhibiting the fluorescence signal, and quantitative detection of these biomolecules are achieved favorably with a detection limit of 7.2, 0.55 and 0.48 nM, respectively. Meanwhile, the fascinating fluorescence on-off property and simple synthetic process are employed to build a series of basic logic gates (YES, NOT, OR, AND, INHIBIT and NOR) and multiple configurable logic gates (OR-AND and OR-OR-INHIBIT) along with different logic inputs. In view of these, developing CoA-based CPs as a new material to execute logic operations provides a valuable platform to establish the next generation of advanced molecular devices for clinic diagnostic and biomedical research.
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Affiliation(s)
- Jiao Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Qingqing Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China
| | - Dandan Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Tianyu Zhan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Zhiyong Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Sui Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China
| | - Yufang Hu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang, 315211, PR China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, PR China.
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G A, Vibija J M, K S. Azide functionalized porphyrin based dendritic polymers for in vivo monitoring of Hg 2+ ions in living cells. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2995-3003. [PMID: 32930159 DOI: 10.1039/d0ay00769b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A porphyrin cored azide functionalised dendritic polymer was developed as a selective sensor for in vivo monitoring of mercuric ions in living (normal and cancer) cells and in an aqueous medium. The developed sensor could sense mercuric ions even at a nanomolar concentration with a limit of detection value of 0.9 nM. This probe can be used to monitor mercuric ions in living cells due to its low cytotoxicity and high cell permeability. The hydrophilic nature of the polymer makes it a promising candidate for sensing mercuric ions in real water samples. Moreover, the reversibility of this sensing strategy helps in constructing a logic gate, which is particularly useful in smart sensor design.
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Affiliation(s)
- Avudaiappan G
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi-682022, Kerala, India.
| | - Mariya Vibija J
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi-682022, Kerala, India.
| | - Sreekumar K
- Department of Applied Chemistry, Cochin University of Science and Technology, Kochi-682022, Kerala, India.
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Kawasaki S, Ono H, Hirosawa M, Saito H. RNA and protein-based nanodevices for mammalian post-transcriptional circuits. Curr Opin Biotechnol 2020; 63:99-110. [DOI: 10.1016/j.copbio.2019.11.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022]
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Ullrich T, Weirich S, Jeltsch A. Development of an epigenetic tetracycline sensor system based on DNA methylation. PLoS One 2020; 15:e0232701. [PMID: 32379807 PMCID: PMC7205209 DOI: 10.1371/journal.pone.0232701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/19/2020] [Indexed: 12/17/2022] Open
Abstract
Bacterial live cell sensors are potentially powerful tools for the detection of environmental toxins. In this work, we have established and validated a flow cytometry readout for an existing bacterial arabinose sensor system with DNA methylation based memory function (Maier et al., 2017, Nat. Comm., 8:15336). Flow cytometry readout is convenient and enables a multiparameter analysis providing information about single-cell variability, which is beneficial for further development of sensor systems of this type in the future. We then designed a tetracycline sensor system, because of the importance of antibiotics pollution in the light of multi-resistant pathogens. To this end, a tetracycline trigger plasmid was constructed by replacing the araC repressor gene and the ara operator of the arabinose trigger plasmid with the tetR gene coding for the tetracycline repressor and the tet operon. After combination with the memory plasmid, the tetracycline sensor system was shown to be functional in E. coli allowing to detect and memorize the presence of tetracycline. Due to a positive feedback between the trigger and memory systems, the combined whole-cell biosensor showed a very high sensitivity for tetracycline with a detection threshold at 0.1 ng/ml tetracycline, which may be a general property of sensors of this type. Moreover, acute presence of tetracycline and past exposure can be detected by this sensor using the dual readout of two reporter fluorophores.
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Affiliation(s)
- Timo Ullrich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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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: 84] [Impact Index Per Article: 21.0] [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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L Adonias G, Yastrebova A, Barros MT, Koucheryavy Y, Cleary F, Balasubramaniam S. Utilizing Neurons for Digital Logic Circuits: A Molecular Communications Analysis. IEEE Trans Nanobioscience 2020; 19:224-236. [PMID: 32092011 DOI: 10.1109/tnb.2020.2975942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
With the advancement of synthetic biology, several new tools have been conceptualized over the years as alternative treatments for current medical procedures. As part of this work, we investigate how synthetically engineered neurons can operate as digital logic gates that can be used towards bio-computing inside the brain and its impact on epileptic seizure-like behaviour. We quantify the accuracy of logic gates under high firing rates amid a network of neurons and by how much it can smooth out uncontrolled neuronal firings. To test the efficacy of our method, simulations composed of computational models of neurons connected in a structure that represents a logic gate are performed. Our simulations demonstrate the accuracy of performing the correct logic operation, and how specific properties such as the firing rate can play an important role in the accuracy. As part of the analysis, the mean squared error is used to quantify the quality of our proposed model and predict the accurate operation of a gate based on different sampling frequencies. As an application, the logic gates were used to smooth out epileptic seizure-like activity in a biological neuronal network, where the results demonstrated the effectiveness of reducing its mean firing rate. Our proposed system has the potential to be used in future approaches to treating neurological conditions in the brain.
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46
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Agrawal DK, Dolan EM, Hernandez NE, Blacklock KM, Khare SD, Sontag ED. Mathematical Models of Protease-Based Enzymatic Biosensors. ACS Synth Biol 2020; 9:198-208. [PMID: 32017536 DOI: 10.1021/acssynbio.9b00279] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.
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Affiliation(s)
- Deepak K. Agrawal
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Elliott M. Dolan
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Nancy E. Hernandez
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Kristin M. Blacklock
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Eduardo D. Sontag
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02120, United States
- Department of Electrical and Computer Engineering, Northeastern University, Boston, Massachusetts 02115, United States
- Laboratory of Systems Pharmacology, Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts 02115, United States
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Omersa N, Aden S, Kisovec M, Podobnik M, Anderluh G. Design of Protein Logic Gate System Operating on Lipid Membranes. ACS Synth Biol 2020; 9:316-328. [PMID: 31995709 PMCID: PMC7308068 DOI: 10.1021/acssynbio.9b00340] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 12/16/2022]
Abstract
Lipid membranes are becoming increasingly popular in synthetic biology due to their biophysical properties and crucial role in communication between different compartments. Several alluring protein-membrane sensors have already been developed, whereas protein logic gates designs on membrane-embedded proteins are very limited. Here we demonstrate the construction of a two-level protein-membrane logic gate with an OR-AND logic. The system consists of an engineered pH-dependent pore-forming protein listeriolysin O and its DARPin-based inhibitor, conjugated to a lipid vesicle membrane. The gate responds to low pH and removal of the inhibitor from the membrane either by switching to a reducing environment, protease cleavage, or any other signal depending on the conjugation chemistry used for inhibitor attachment to the membrane. This unique protein logic gate vesicle system advances generic sensing and actuator platforms used in synthetic biology and could be utilized in drug delivery.
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Affiliation(s)
- Neža Omersa
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Saša Aden
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
- Biomedicine
Doctoral Program, University of Ljubljana, Vrazov trg 2, 1000 Ljubljana, Slovenia
| | - Matic Kisovec
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Marjetka Podobnik
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
| | - Gregor Anderluh
- Department
of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova ulica 19, 1001 Ljubljana, Slovenia
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Lin Q, Wang A, Liu S, Li J, Wang J, Quan K, Yang X, Huang J, Wang K. A DNA tetrahedron-based molecular computation device for the logic sensing of dual microRNAs in living cells. Chem Commun (Camb) 2020; 56:5303-5306. [DOI: 10.1039/d0cc01231a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Endogenous miRNA expression patterns are specific to cell type and thus offer high prediction accuracy with regard to different cell identities compared to single miRNA analysis.
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Affiliation(s)
- Qing Lin
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Anmin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Shiyuan Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jiaoli Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Ke Quan
- School of Chemistry and Food Engineering
- Changsha University of Science and Technology
- Changsha
- China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University
- Changsha
- China
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49
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Synthetic biology for improving cell fate decisions and tissue engineering outcomes. Emerg Top Life Sci 2019; 3:631-643. [PMID: 33523179 DOI: 10.1042/etls20190091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/02/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
Abstract
Synthetic biology is a relatively new field of science that combines aspects of biology and engineering to create novel tools for the construction of biological systems. Using tools within synthetic biology, stem cells can then be reprogrammed and differentiated into a specified cell type. Stem cells have already proven to be largely beneficial in many different therapies and have paved the way for tissue engineering and regenerative medicine. Although scientists have made great strides in tissue engineering, there still remain many questions to be answered in regard to regeneration. Presented here is an overview of synthetic biology, common tools built within synthetic biology, and the way these tools are being used in stem cells. Specifically, this review focuses on how synthetic biologists engineer genetic circuits to dynamically control gene expression while also introducing emerging topics such as genome engineering and synthetic transcription factors. The findings mentioned in this review show the diverse use of stem cells within synthetic biology and provide a foundation for future research in tissue engineering with the use of synthetic biology tools. Overall, the work done using synthetic biology in stem cells is in its early stages, however, this early work is leading to new approaches for repairing diseased and damaged tissues and organs, and further expanding the field of tissue engineering.
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50
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Gorman SD, Boehr DD. Energy and Enzyme Activity Landscapes of Yeast Chorismate Mutase at Cellular Concentrations of Allosteric Effectors. Biochemistry 2019; 58:4058-4069. [DOI: 10.1021/acs.biochem.9b00721] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Scott D. Gorman
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - David D. Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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