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Lee B, Sunden F, Miller M, Pak B, Krebber A, Lutz S, Fordyce PM. Hydrophilic/Omniphobic Droplet Arrays for High-throughput and Quantitative Enzymology. Anal Chem 2025; 97:8957-8967. [PMID: 40238746 PMCID: PMC12044592 DOI: 10.1021/acs.analchem.5c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/21/2025] [Accepted: 03/24/2025] [Indexed: 04/18/2025]
Abstract
Engineered enzymes with enhanced or novel functions are specific catalysts with wide-ranging applications in industry and medicine. Here, we introduce droplet array microfluidic enzyme kinetics (DA-MEK), a high-throughput enzyme screening platform that combines water-in-air droplet microarrays formed on patterned superhydrophilic/omniphobic surfaces with cell-free protein synthesis to enable cost-effective expression and quantitative kinetic characterization of enzyme variants. By printing DNA templates encoding enzyme variants onto hydrophilic spots, stamping slides to add cell-free expression mix, and imaging the resulting arrays, we demonstrate reproducible expression of enzyme variants across hundreds of microwells per slide, with line of sight toward replicating this across larger libraries. By specifically patterning slides with antibodies, we further demonstrate parallel immobilization, purification, and iterative characterization of the expressed variants. Subsequent stamping of fluorogenic substrates and time-lapse imaging allows determination of Michaelis-Menten parameters for each variant, with measured catalytic efficiencies spanning 5 orders of magnitude and agreeing well with values obtained via traditional microtiter plate assays. DA-MEK consumes orders of magnitude less reagents than plate-based assays, while providing accurate and detailed kinetic information for both beneficial and deleterious mutations. In future work, we anticipate that DA-MEK will provide a powerful and versatile platform to accelerate enzyme engineering and enable screening of large variant libraries under diverse conditions.
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Affiliation(s)
- Byungjin Lee
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
| | - Fanny Sunden
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
| | - Michael Miller
- Codexis,
Inc., Redwood
City, California 94063, United States
| | - Bumshik Pak
- Codexis,
Inc., Redwood
City, California 94063, United States
| | - Anke Krebber
- Codexis,
Inc., Redwood
City, California 94063, United States
| | - Stefan Lutz
- Codexis,
Inc., Redwood
City, California 94063, United States
| | - Polly Morrell Fordyce
- Department
of Genetics, Stanford University, Stanford, California 94305, United States
- Department
of Biochemistry, Stanford University, Stanford, California 94305, United States
- Sarafan
ChEM-H, Stanford, California 94305, United States
- Chan
Zuckerberg Biohub San Francisco, San Francisco, California 94110, United States
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2
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Zhang Z, Zhou X, Fang Y, Xiong Z, Zhang T. AI-driven 3D bioprinting for regenerative medicine: From bench to bedside. Bioact Mater 2025; 45:201-230. [PMID: 39651398 PMCID: PMC11625302 DOI: 10.1016/j.bioactmat.2024.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 11/01/2024] [Accepted: 11/16/2024] [Indexed: 12/11/2024] Open
Abstract
In recent decades, 3D bioprinting has garnered significant research attention due to its ability to manipulate biomaterials and cells to create complex structures precisely. However, due to technological and cost constraints, the clinical translation of 3D bioprinted products (BPPs) from bench to bedside has been hindered by challenges in terms of personalization of design and scaling up of production. Recently, the emerging applications of artificial intelligence (AI) technologies have significantly improved the performance of 3D bioprinting. However, the existing literature remains deficient in a methodological exploration of AI technologies' potential to overcome these challenges in advancing 3D bioprinting toward clinical application. This paper aims to present a systematic methodology for AI-driven 3D bioprinting, structured within the theoretical framework of Quality by Design (QbD). This paper commences by introducing the QbD theory into 3D bioprinting, followed by summarizing the technology roadmap of AI integration in 3D bioprinting, including multi-scale and multi-modal sensing, data-driven design, and in-line process control. This paper further describes specific AI applications in 3D bioprinting's key elements, including bioink formulation, model structure, printing process, and function regulation. Finally, the paper discusses current prospects and challenges associated with AI technologies to further advance the clinical translation of 3D bioprinting.
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Affiliation(s)
- Zhenrui Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, PR China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, PR China
- “Biomanufacturing and Engineering Living Systems” Innovation International Talents Base (111 Base), Beijing, 100084, PR China
| | - Xianhao Zhou
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, PR China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, PR China
- “Biomanufacturing and Engineering Living Systems” Innovation International Talents Base (111 Base), Beijing, 100084, PR China
| | - Yongcong Fang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, PR China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, PR China
- “Biomanufacturing and Engineering Living Systems” Innovation International Talents Base (111 Base), Beijing, 100084, PR China
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, 100084, PR China
| | - Zhuo Xiong
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, PR China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, PR China
- “Biomanufacturing and Engineering Living Systems” Innovation International Talents Base (111 Base), Beijing, 100084, PR China
| | - Ting Zhang
- Biomanufacturing Center, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, PR China
- Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Beijing, 100084, PR China
- “Biomanufacturing and Engineering Living Systems” Innovation International Talents Base (111 Base), Beijing, 100084, PR China
- State Key Laboratory of Tribology in Advanced Equipment, Tsinghua University, Beijing, 100084, PR China
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3
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Wu J, Torresi L, Hu M, Reiser P, Zhang J, Rocha-Ortiz JS, Wang L, Xie Z, Zhang K, Park BW, Barabash A, Zhao Y, Luo J, Wang Y, Lüer L, Deng LL, Hauch JA, Guldi DM, Pérez-Ojeda ME, Seok SI, Friederich P, Brabec CJ. Inverse design workflow discovers hole-transport materials tailored for perovskite solar cells. Science 2024; 386:1256-1264. [PMID: 39666797 DOI: 10.1126/science.ads0901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 11/05/2024] [Indexed: 12/14/2024]
Abstract
The inverse design of tailored organic molecules for specific optoelectronic devices of high complexity holds an enormous potential but has not yet been realized. Current models rely on large data sets that generally do not exist for specialized research fields. We demonstrate a closed-loop workflow that combines high-throughput synthesis of organic semiconductors to create large datasets and Bayesian optimization to discover new hole-transporting materials with tailored properties for solar cell applications. The predictive models were based on molecular descriptors that allowed us to link the structure of these materials to their performance. A series of high-performance molecules were identified from minimal suggestions and achieved up to 26.2% (certified 25.9%) power conversion efficiency in perovskite solar cells.
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Affiliation(s)
- Jianchang Wu
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Luca Torresi
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - ManMan Hu
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Patrick Reiser
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Jiyun Zhang
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Juan S Rocha-Ortiz
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Luyao Wang
- State Key Lab for Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Zhiqiang Xie
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Kaicheng Zhang
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Byung-Wook Park
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Anastasia Barabash
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yicheng Zhao
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- National Key Laboratory of Electronic Films and Integrated Devices, School of Integrated Circuit Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Junsheng Luo
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- National Key Laboratory of Electronic Films and Integrated Devices, School of Integrated Circuit Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Yunuo Wang
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Larry Lüer
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Lin-Long Deng
- State Key Lab for Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Pen-Tung Sah Institute of Micro-Nano Science and Technology, Xiamen University, Xiamen, China
| | - Jens A Hauch
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Dirk M Guldi
- Department of Chemistry and Pharmacy & Interdisciplinary Center of Molecular Materials (ICMM), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - M Eugenia Pérez-Ojeda
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sang Il Seok
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
| | - Pascal Friederich
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Christoph J Brabec
- Forschungszentrum Jülich GmbH, Helmholtz-Institute Erlangen-Nürnberg (HI-ERN), Erlangen, Germany
- Faculty of Engineering, Department of Material Science, Materials for Electronics and Energy Technology (i-MEET), Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
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4
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Asl ZR, Rezaee K, Ansari M, Zare F, Roknabadi MHA. A review of biopolymer-based hydrogels and IoT integration for enhanced diabetes diagnosis, management, and treatment. Int J Biol Macromol 2024; 280:135988. [PMID: 39322132 DOI: 10.1016/j.ijbiomac.2024.135988] [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: 02/29/2024] [Revised: 08/10/2024] [Accepted: 09/22/2024] [Indexed: 09/27/2024]
Abstract
The prevalence of diabetes has been increasing globally, necessitating innovative approaches beyond conventional blood sugar monitoring and insulin control. Diabetes is associated with complex health complications, including cardiovascular diseases. Continuous Glucose Monitoring (CGM) devices, though automated, have limitations such as irreversibility and interference with bodily fluids. Hydrogel technologies provide non-invasive alternatives to traditional methods, addressing the limitations of current approaches. This review explores hydrogels as macromolecular biopolymeric materials capable of absorbing and retaining a substantial amount of water within their structure. Due to their high-water absorption properties, these macromolecules are utilized as coating materials for wound care and diabetes management. The study emphasizes the need for early diagnosis and monitoring, especially during the COVID-19 pandemic, where heightened attention to diabetic patients is crucial. Additionally, the article examines the role of the Internet of Things (IoT) and machine learning-based systems in enhancing diabetes management effectiveness. By leveraging these technologies, there is potential to revolutionize diabetes care, providing more personalized and proactive solutions. This review explores cutting-edge hydrogel-based systems as a promising avenue for diabetes diagnosis, management, and treatment, highlighting key biopolymers and technological integrations.
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Affiliation(s)
- Zahra Rahmani Asl
- Department of Biomedical Engineering, Meybod University, Meybod, Iran
| | - Khosro Rezaee
- Department of Biomedical Engineering, Meybod University, Meybod, Iran.
| | - Mojtaba Ansari
- Department of Biomedical Engineering, Meybod University, Meybod, Iran
| | - Fatemeh Zare
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA
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5
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Xu C, Alameri A, Leong W, Johnson E, Chen Z, Xu B, Leong KW. Multiscale engineering of brain organoids for disease modeling. Adv Drug Deliv Rev 2024; 210:115344. [PMID: 38810702 PMCID: PMC11265575 DOI: 10.1016/j.addr.2024.115344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/23/2024] [Accepted: 05/25/2024] [Indexed: 05/31/2024]
Abstract
Brain organoids hold great potential for modeling human brain development and pathogenesis. They recapitulate certain aspects of the transcriptional trajectory, cellular diversity, tissue architecture and functions of the developing brain. In this review, we explore the engineering strategies to control the molecular-, cellular- and tissue-level inputs to achieve high-fidelity brain organoids. We review the application of brain organoids in neural disorder modeling and emerging bioengineering methods to improve data collection and feature extraction at multiscale. The integration of multiscale engineering strategies and analytical methods has significant potential to advance insight into neurological disorders and accelerate drug development.
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Affiliation(s)
- Cong Xu
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Alia Alameri
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Wei Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Emily Johnson
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Zaozao Chen
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Bin Xu
- Department of Psychiatry, Columbia University, New York, NY 10032, USA.
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA.
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6
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Li Z, Song P, Li G, Han Y, Ren X, Bai L, Su J. AI energized hydrogel design, optimization and application in biomedicine. Mater Today Bio 2024; 25:101014. [PMID: 38464497 PMCID: PMC10924066 DOI: 10.1016/j.mtbio.2024.101014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024] Open
Abstract
Traditional hydrogel design and optimization methods usually rely on repeated experiments, which is time-consuming and expensive, resulting in a slow-moving of advanced hydrogel development. With the rapid development of artificial intelligence (AI) technology and increasing material data, AI-energized design and optimization of hydrogels for biomedical applications has emerged as a revolutionary breakthrough in materials science. This review begins by outlining the history of AI and the potential advantages of using AI in the design and optimization of hydrogels, such as prediction and optimization of properties, multi-attribute optimization, high-throughput screening, automated material discovery, optimizing experimental design, and etc. Then, we focus on the various applications of hydrogels supported by AI technology in biomedicine, including drug delivery, bio-inks for advanced manufacturing, tissue repair, and biosensors, so as to provide a clear and comprehensive understanding of researchers in this field. Finally, we discuss the future directions and prospects, and provide a new perspective for the research and development of novel hydrogel materials for biomedical applications.
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Affiliation(s)
- Zuhao Li
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Peiran Song
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Guangfeng Li
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Yafei Han
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Xiaoxiang Ren
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Long Bai
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
| | - Jiacan Su
- Department of Orthopedics, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Organoid Research Center, Institute of Translational Medicine, Shanghai University, Shanghai, 200444, China
- National Center for Translational Medicine (Shanghai) SHU Branch, Shanghai University, Shanghai, 200444, China
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