1
|
Ma Y, Zhang Z, Jia B, Yuan Y. Automated high-throughput DNA synthesis and assembly. Heliyon 2024; 10:e26967. [PMID: 38500977 PMCID: PMC10945133 DOI: 10.1016/j.heliyon.2024.e26967] [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: 04/23/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of lengthy oligonucleotides and the seamless assembly of numerous DNA fragments. With the advent of automated pipetting workstations and integrated experimental equipment, a substantial portion of repetitive tasks in the field of synthetic biology can now be efficiently accomplished through integrated liquid handling workstations. This not only reduces the need for manual labor but also enhances overall efficiency. This review explores the ongoing advancements in the oligonucleotide synthesis platform, automated DNA assembly techniques, and biofoundries. The development of accurate and high-throughput DNA synthesis and assembly technologies presents both challenges and opportunities.
Collapse
Affiliation(s)
- Yuxin Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhaoyang Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| |
Collapse
|
2
|
Jones CH, Androsavich JR, So N, Jenkins MP, MacCormack D, Prigodich A, Welch V, True JM, Dolsten M. Breaking the mold with RNA-a "RNAissance" of life science. NPJ Genom Med 2024; 9:2. [PMID: 38195675 PMCID: PMC10776758 DOI: 10.1038/s41525-023-00387-4] [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: 07/06/2023] [Accepted: 12/07/2023] [Indexed: 01/11/2024] Open
Abstract
In the past decade, RNA therapeutics have gone from being a promising concept to one of the most exciting frontiers in healthcare and pharmaceuticals. The field is now entering what many call a renaissance or "RNAissance" which is being fueled by advances in genetic engineering and delivery systems to take on more ambitious development efforts. However, this renaissance is occurring at an unprecedented pace, which will require a different way of thinking if the field is to live up to its full potential. Recognizing this need, this article will provide a forward-looking perspective on the field of RNA medical products and the potential long-term innovations and policy shifts enabled by this revolutionary and game-changing technological platform.
Collapse
Affiliation(s)
| | | | - Nina So
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | | | | | | | - Verna Welch
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA
| | - Jane M True
- Pfizer, 66 Hudson Boulevard, New York, NY, 10018, USA.
| | | |
Collapse
|
3
|
Bai S, Luo H, Tong H, Wu Y. Application and Technical Challenges in Design, Cloning, and Transfer of Large DNA. Bioengineering (Basel) 2023; 10:1425. [PMID: 38136016 PMCID: PMC10740618 DOI: 10.3390/bioengineering10121425] [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: 11/18/2023] [Revised: 11/23/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
In the field of synthetic biology, rapid advancements in DNA assembly and editing have made it possible to manipulate large DNA, even entire genomes. These advancements have facilitated the introduction of long metabolic pathways, the creation of large-scale disease models, and the design and assembly of synthetic mega-chromosomes. Generally, the introduction of large DNA in host cells encompasses three critical steps: design-cloning-transfer. This review provides a comprehensive overview of the three key steps involved in large DNA transfer to advance the field of synthetic genomics and large DNA engineering.
Collapse
Affiliation(s)
- Song Bai
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Han Luo
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Hanze Tong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| | - Yi Wu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Frontiers Research Institute for Synthetic Biology, Tianjin University, Tianjin 300072, China
| |
Collapse
|
4
|
Wei H, Rong Z, Liu L, Sang Y, Yang J, Wang S. Streamlined and on-demand preparation of mRNA products on a universal integrated platform. MICROSYSTEMS & NANOENGINEERING 2023; 9:97. [PMID: 37492616 PMCID: PMC10363538 DOI: 10.1038/s41378-023-00538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/28/2023] [Accepted: 04/07/2023] [Indexed: 07/27/2023]
Abstract
Vaccines are used to protect human beings from various diseases. mRNA vaccines simplify the development process and reduce the production cost of conventional vaccines, making it possible to respond rapidly to acute and severe diseases, such as coronavirus disease 2019. In this study, a universal integrated platform for the streamlined and on-demand preparation of mRNA products directly from DNA templates was established. Target DNA templates were amplified in vitro by a polymerase chain reaction module and transcribed into mRNA sequences, which were magnetically purified and encapsulated in lipid nanoparticles. As an initial example, enhanced green fluorescent protein (eGFP) was used to test the platform. The expression capacity and efficiency of the products were evaluated by transfecting them into HEK-293T cells. The batch production rate was estimated to be 200-300 μg of eGFP mRNA in 8 h. Furthermore, an mRNA vaccine encoding the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein was produced by this platform. The proposed integrated platform shows advantages for the universal and on-demand preparation of mRNA products, offering the potential to facilitate broad access to mRNA technology and enable the development of mRNA products, including the rapid supply of new mRNA-based vaccines in pandemic situations and personalized mRNA-based therapies for oncology and chronic infectious diseases, such as viral hepatitis and acquired immune deficiency syndrome.
Collapse
Affiliation(s)
- Hongjuan Wei
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| | - Zhen Rong
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| | - Liyan Liu
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| | - Ye Sang
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| | - Jing Yang
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing, 100850 P. R. China
| |
Collapse
|
5
|
Automated high-throughput genome editing platform with an AI learning in situ prediction model. Nat Commun 2022; 13:7386. [PMID: 36450740 PMCID: PMC9712529 DOI: 10.1038/s41467-022-35056-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
A great number of cell disease models with pathogenic SNVs are needed for the development of genome editing based therapeutics or broadly basic scientific research. However, the generation of traditional cell disease models is heavily dependent on large-scale manual operations, which is not only time-consuming, but also costly and error-prone. In this study, we devise an automated high-throughput platform, through which thousands of samples are automatically edited within a week, providing edited cells with high efficiency. Based on the large in situ genome editing data obtained by the automatic high-throughput platform, we develop a Chromatin Accessibility Enabled Learning Model (CAELM) to predict the performance of cytosine base editors (CBEs), both chromatin accessibility and the context-sequence are utilized to build the model, which accurately predicts the result of in situ base editing. This work is expected to accelerate the development of BE-based genetic therapies.
Collapse
|
6
|
Venter JC, Glass JI, Hutchison CA, Vashee S. Synthetic chromosomes, genomes, viruses, and cells. Cell 2022; 185:2708-2724. [DOI: 10.1016/j.cell.2022.06.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 10/17/2022]
|
7
|
A framework to efficiently describe and share reproducible DNA materials and construction protocols. Nat Commun 2022; 13:2894. [PMID: 35610233 PMCID: PMC9130275 DOI: 10.1038/s41467-022-30588-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/10/2022] [Indexed: 12/02/2022] Open
Abstract
DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Such resources have also been utilized in designing and building new DNA materials. However, as commonly seen in the life sciences, no framework exists to describe reproducible DNA construction processes. Furthermore, the use of previously developed DNA materials and building protocols is usually not appropriately credited. Here, we report a framework QUEEN (framework to generate quinable and efficiently editable nucleotide sequence resources) to resolve these issues and accelerate the building of DNA. QUEEN enables the flexible design of new DNA by using existing DNA material resource files and recording its construction process in an output file (GenBank file format). A GenBank file generated by QUEEN can regenerate the process code such that it perfectly clones itself and bequeaths the same process code to its successive GenBank files, recycling its partial DNA resources. QUEEN-generated GenBank files are compatible with existing DNA repository services and software. We propose QUEEN as a solution to start significantly advancing the material and protocol sharing of DNA resources. DNA constructs and their annotated sequence maps have been rapidly accumulating with the advancement of DNA cloning, synthesis, and assembly methods. Here the authors introduce QUEEN, a framework to describe and share DNA materials and construction protocols.
Collapse
|
8
|
Brookwell A, Oza JP, Caschera F. Biotechnology Applications of Cell-Free Expression Systems. Life (Basel) 2021; 11:life11121367. [PMID: 34947898 PMCID: PMC8705439 DOI: 10.3390/life11121367] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free systems are a rapidly expanding platform technology with an important role in the engineering of biological systems. The key advantages that drive their broad adoption are increased efficiency, versatility, and low cost compared to in vivo systems. Traditionally, in vivo platforms have been used to synthesize novel and industrially relevant proteins and serve as a testbed for prototyping numerous biotechnologies such as genetic circuits and biosensors. Although in vivo platforms currently have many applications within biotechnology, they are hindered by time-constraining growth cycles, homeostatic considerations, and limited adaptability in production. Conversely, cell-free platforms are not hindered by constraints for supporting life and are therefore highly adaptable to a broad range of production and testing schemes. The advantages of cell-free platforms are being leveraged more commonly by the biotechnology community, and cell-free applications are expected to grow exponentially in the next decade. In this study, new and emerging applications of cell-free platforms, with a specific focus on cell-free protein synthesis (CFPS), will be examined. The current and near-future role of CFPS within metabolic engineering, prototyping, and biomanufacturing will be investigated as well as how the integration of machine learning is beneficial to these applications.
Collapse
Affiliation(s)
- August Brookwell
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
| | - Javin P. Oza
- Department of Chemistry & Biochemistry, College of Science & Mathematics, California Polytechnic State University, San Luis Obispo, CA 93407, USA;
- Correspondence: (J.P.O.); (F.C.)
| | - Filippo Caschera
- Nuclera Nucleics Ltd., Cambridge CB4 0GD, UK
- Correspondence: (J.P.O.); (F.C.)
| |
Collapse
|
9
|
Song LF, Deng ZH, Gong ZY, Li LL, Li BZ. Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities. Front Bioeng Biotechnol 2021; 9:689797. [PMID: 34239862 PMCID: PMC8258115 DOI: 10.3389/fbioe.2021.689797] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications. Among them, de novo genome synthesis and DNA data storage are striking. However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements, which is a challenge to be met by the phosphoramidite chemistry. Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge. In this review, we first summarize the status of large-scale oligonucleotide synthesis technologies including the basic methodology and large-scale synthesis approaches, with special focus on the emerging enzymatic methods. Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.
Collapse
Affiliation(s)
- Li-Fu Song
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zheng-Hua Deng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zi-Yi Gong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lu-Lu Li
- LC-BIO Technologies Co., Ltd., Hangzhou, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| |
Collapse
|
10
|
Swank Z, Maerkl SJ. CFPU: A Cell-Free Processing Unit for High-Throughput, Automated In Vitro Circuit Characterization in Steady-State Conditions. BIODESIGN RESEARCH 2021; 2021:2968181. [PMID: 37849954 PMCID: PMC10521719 DOI: 10.34133/2021/2968181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/24/2021] [Indexed: 10/19/2023] Open
Abstract
Forward engineering synthetic circuits are at the core of synthetic biology. Automated solutions will be required to facilitate circuit design and implementation. Circuit design is increasingly being automated with design software, but innovations in experimental automation are lagging behind. Microfluidic technologies made it possible to perform in vitro transcription-translation (tx-tl) reactions with increasing throughput and sophistication, enabling screening and characterization of individual circuit elements and complete circuit designs. Here, we developed an automated microfluidic cell-free processing unit (CFPU) that extends high-throughput screening capabilities to a steady-state reaction environment, which is essential for the implementation and analysis of more complex and dynamic circuits. The CFPU contains 280 chemostats that can be individually programmed with DNA circuits. Each chemostat is periodically supplied with tx-tl reagents, giving rise to sustained, long-term steady-state conditions. Using microfluidic pulse width modulation (PWM), the device is able to generate tx-tl reagent compositions in real time. The device has higher throughput, lower reagent consumption, and overall higher functionality than current chemostat devices. We applied this technology to map transcription factor-based repression under equilibrium conditions and implemented dynamic gene circuits switchable by small molecules. We expect the CFPU to help bridge the gap between circuit design and experimental automation for in vitro development of synthetic gene circuits.
Collapse
Affiliation(s)
- Zoe Swank
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Switzerland
| |
Collapse
|
11
|
Stark JC, Jaroentomeechai T, Moeller TD, Hershewe JM, Warfel KF, Moricz BS, Martini AM, Dubner RS, Hsu KJ, Stevenson TC, Jones BD, DeLisa MP, Jewett MC. On-demand biomanufacturing of protective conjugate vaccines. SCIENCE ADVANCES 2021; 7:eabe9444. [PMID: 33536221 PMCID: PMC7857678 DOI: 10.1126/sciadv.abe9444] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/18/2020] [Indexed: 05/19/2023]
Abstract
Conjugate vaccines are among the most effective methods for preventing bacterial infections. However, existing manufacturing approaches limit access to conjugate vaccines due to centralized production and cold chain distribution requirements. To address these limitations, we developed a modular technology for in vitro conjugate vaccine expression (iVAX) in portable, freeze-dried lysates from detoxified, nonpathogenic Escherichia coli. Upon rehydration, iVAX reactions synthesize clinically relevant doses of conjugate vaccines against diverse bacterial pathogens in 1 hour. We show that iVAX-synthesized vaccines against Francisella tularensis subsp. tularensis (type A) strain Schu S4 protected mice from lethal intranasal F. tularensis challenge. The iVAX platform promises to accelerate development of new conjugate vaccines with increased access through refrigeration-independent distribution and portable production.
Collapse
Affiliation(s)
- Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA
| | - Tyler D Moeller
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA
| | - Jasmine M Hershewe
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Katherine F Warfel
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208-3120, USA
| | - Bridget S Moricz
- Department of Microbiology and Immunology, University of Iowa, 51 Newton Rd 3-403 Bowen Science Building, Iowa City, IA 52242, USA
| | - Anthony M Martini
- Department of Microbiology and Immunology, University of Iowa, 51 Newton Rd 3-403 Bowen Science Building, Iowa City, IA 52242, USA
| | - Rachel S Dubner
- Department of Biological Sciences, Northwestern University, 2205 Tech Drive Hogan Hall 2144, Evanston, IL 60208-3500, USA
| | - Karen J Hsu
- Department of Mechanical Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute B224, Evanston, IL 60208-3120, USA
| | - Taylor C Stevenson
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, NY 14853, USA
| | - Bradley D Jones
- Department of Microbiology and Immunology, University of Iowa, 51 Newton Rd 3-403 Bowen Science Building, Iowa City, IA 52242, USA
- Graduate Program in Genetics, 431 Newton Rd, University of Iowa, Iowa City, IA 52242, USA
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY 14853, USA.
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA.
- Center for Synthetic Biology, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL 60208-3120, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208-3120, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, 676 N. St Clair St, Suite 1200, Chicago, IL 60611-3068, USA
- Simpson-Querrey Institute, Northwestern University, 303 E. Superior St, Suite 11-131 Chicago, IL 60611-2875, USA
| |
Collapse
|
12
|
Dasgupta A, Chowdhury N, De RK. Metabolic pathway engineering: Perspectives and applications. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 192:105436. [PMID: 32199314 DOI: 10.1016/j.cmpb.2020.105436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering. CONCLUSION In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.
Collapse
Affiliation(s)
- Abhijit Dasgupta
- Department of Data Science, School of Interdisciplinary Studies, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India
| | - Nirmalya Chowdhury
- Department of Computer Science & Engineering, Jadavpur University, Kolkata 700032, India
| | - Rajat K De
- Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
| |
Collapse
|
13
|
Machine learning applications in systems metabolic engineering. Curr Opin Biotechnol 2020; 64:1-9. [DOI: 10.1016/j.copbio.2019.08.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/23/2019] [Accepted: 08/25/2019] [Indexed: 12/11/2022]
|
14
|
Chiocchini C, Vattem K, Liss M, Ludewig L, Reusch T, Rastogi I, Webb B, Trefzer A. From Electronic Sequence to Purified Protein Using Automated Gene Synthesis and In Vitro Transcription/Translation. ACS Synth Biol 2020; 9:1714-1724. [PMID: 32502345 DOI: 10.1021/acssynbio.0c00060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
De novo gene synthesis is the state-of-the-art method used to obtain genetic material adapted to the requirements of the host organism and a cornerstone for modern synthetic biology. Yet, little progress has been made regarding downstream processes of protein production from synthetic genetic material. The production of recombinant proteins traditionally requires extensive preparatory work including gene amplification, cloning, sequencing, transformation or transfection of the expression host, cultivation of living cells, and purification of the overexpressed protein. In this work we describe a fast and automated workflow for cell-free production of proteins starting from an electronic protein sequence or accession number. PRESTO (protein expression starting from oligonucleotides) seamlessly combines a tailored in silico sequence optimization with the assembly of short oligonucleotides into synthetic linear DNA expression cassettes, mammalian in vitro transcription/translation, and protein purification thereof. Integrated on a small liquid handling system it provides a hands-free high throughput source for functional synthetic proteins within 1 day.
Collapse
Affiliation(s)
- Claudia Chiocchini
- Thermo Fisher Scientific, GENEART GmbH, Im Gewerbepark B35, 93059 Regensburg, Germany
| | - Krishna Vattem
- Thermo Fisher Scientific, 3747 N Meridian Road, Rockford, Illinois 61101, United States
| | - Michael Liss
- Thermo Fisher Scientific, GENEART GmbH, Im Gewerbepark B35, 93059 Regensburg, Germany
| | - Lisa Ludewig
- Thermo Fisher Scientific, GENEART GmbH, Im Gewerbepark B35, 93059 Regensburg, Germany
| | - Tobias Reusch
- Thermo Fisher Scientific, GENEART GmbH, Im Gewerbepark B35, 93059 Regensburg, Germany
| | - Ischwaku Rastogi
- Thermo Fisher Scientific, 3747 N Meridian Road, Rockford, Illinois 61101, United States
| | - Brian Webb
- Thermo Fisher Scientific, 3747 N Meridian Road, Rockford, Illinois 61101, United States
| | - Axel Trefzer
- Thermo Fisher Scientific, GENEART GmbH, Im Gewerbepark B35, 93059 Regensburg, Germany
| |
Collapse
|
15
|
Goh CS, Ahl A, Woo WT. Sustainable Transformation of Land-Based Economic Development in the Era of Digital Revolution. Trends Biotechnol 2020; 39:1-4. [PMID: 32546309 DOI: 10.1016/j.tibtech.2020.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
Biotechnology will play a key role in transforming current land-use systems alongside the digital revolution by using five strategies: enhancing productivity at the farm or plantation level, replenishing degraded land, enabling landscape management for resilience, upgrading and diversifying downstream activities, and creating new value propositions.
Collapse
Affiliation(s)
- Chun Sheng Goh
- Harvard University Asia Center, Cambridge, MA, USA; Jeffrey Sachs Center on Sustainable Development, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Amanda Ahl
- Department of Innovation Science, School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan
| | - Wing Thye Woo
- Jeffrey Sachs Center on Sustainable Development, Sunway University, Bandar Sunway, Selangor Darul Ehsan, Malaysia; Department of Economics, University of California, Davis, CA, USA
| |
Collapse
|
16
|
Zhong J, Riordon J, Wu TC, Edwards H, Wheeler AR, Pardee K, Aspuru-Guzik A, Sinton D. When robotics met fluidics. LAB ON A CHIP 2020; 20:709-716. [PMID: 31895394 DOI: 10.1039/c9lc01042d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput fluidic technologies have increased the speed and accuracy of fluid processing to the extent that unlocking further gains will require replacing the human operator with a robotic counterpart. Recent advances in chemistry and biology, such as gene editing, have further exacerbated the need for smart, high-throughput experimentation. A growing number of innovations at the intersection of robotics and fluidics illustrate the tremendous opportunity in achieving fully self-driving fluid systems. We envision that the fields of synthetic chemistry and synthetic biology will be the first beneficiaries of AI-directed robotic and fluidic systems, and largely fall within two modalities: complex integrated centralized facilities that produce data, and distributed systems that synthesize products and conduct disease surveillance.
Collapse
Affiliation(s)
- Junjie Zhong
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S3G8, Canada.
| | - Jason Riordon
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S3G8, Canada.
| | - Tony C Wu
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada and Department of Computer Science, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Harrison Edwards
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Keith Pardee
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S3G8, Canada. and Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON M5S 3M2, Canada
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada and Department of Computer Science, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - David Sinton
- Department of Mechanical and Industrial Engineering, University of Toronto, Toronto, Ontario M5S3G8, Canada.
| |
Collapse
|
17
|
Silverman AD, Karim AS, Jewett MC. Cell-free gene expression: an expanded repertoire of applications. Nat Rev Genet 2019; 21:151-170. [DOI: 10.1038/s41576-019-0186-3] [Citation(s) in RCA: 246] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2019] [Indexed: 12/24/2022]
|
18
|
Wilding KM, Zhao EL, Earl CC, Bundy BC. Thermostable lyoprotectant-enhanced cell-free protein synthesis for on-demand endotoxin-free therapeutic production. N Biotechnol 2019; 53:73-80. [DOI: 10.1016/j.nbt.2019.07.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/16/2019] [Accepted: 07/21/2019] [Indexed: 12/15/2022]
|
19
|
Snyder JE, Walsh D, Carr PA, Rothschild LJ. A Makerspace for Life Support Systems in Space. Trends Biotechnol 2019; 37:1164-1174. [DOI: 10.1016/j.tibtech.2019.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
|
20
|
Henderson CJ, Pumford E, Seevaratnam DJ, Daly R, Hall EAH. Gene to diagnostic: Self immobilizing protein for silica microparticle biosensor, modelled with sarcosine oxidase. Biomaterials 2019; 193:58-70. [PMID: 30562636 DOI: 10.1016/j.biomaterials.2018.12.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/07/2018] [Accepted: 12/07/2018] [Indexed: 02/08/2023]
Abstract
A rational design approach is proposed for a multifunctional enzyme reagent for point-of-care diagnostics. The biomaterial reduces downstream isolation steps and eliminates immobilization coupling chemicals for integration in a diagnostic platform. Fusion constructs combined the central functional assay protein (e.g. monomeric sarcosine oxidase, mSOx, horseradish peroxidase, HRP), a visualizing protein (e.g. mCherry) and an in-built immobilization peptide (e.g. R5). Monitoring protein expression in E.coli was facilitated by following the increase in mCherry fluorescence, which could be matched to a color card, indicating when good protein expression has occurred. The R5 peptide (SSKKSGSYSGSKGSKRRIL) provided inbuilt affinity for silica and an immobilization capability for a silica based diagnostic, without requiring additional chemical coupling reagents. Silica particles extracted from beach sand were used to collect protein from crude protein extract with 85-95% selective uptake. The silica immobilized R5 proteins were stable for more than 2 months at room temperature. The Km for the silica-R52-mCh-mSOx-R5-6H was 16.5 ± 0.9 mM (compared with 16.5 ± 0.4 mM, 16.3 ± 0.3 mM, and 16.1 ± 0.4 mM for R52-mCh-mSOx-R5-6H, mSOx-R5-6H and mSOx-6H respectively in solution). The use of the "silica-enzymes" in sarcosine and peroxide assays was shown, and a design using particle sedimentation through the sample was examined. Using shadowgraphy and particle image velocimetry the particle trajectory through the sample was mapped and an hourglass design with a narrow waist shown to give good control of particle position. The hourglass biosensor was demonstrated for sarcosine assay in the clinically useful range of 2.5-10 μM in both a dynamic and end point measurement regime.
Collapse
Affiliation(s)
- Cassi J Henderson
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK; Department of Engineering, University of Cambridge, Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Elizabeth Pumford
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Dushanth J Seevaratnam
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Ronan Daly
- Department of Engineering, University of Cambridge, Charles Babbage Road, Cambridge, CB3 0FS, UK
| | - Elizabeth A H Hall
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| |
Collapse
|
21
|
Bundy BC, Hunt JP, Jewett MC, Swartz JR, Wood DW, Frey DD, Rao G. Cell-free biomanufacturing. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
22
|
Guschin VA, Manuilov VA, Makarov VV, Tkachuk AP. The proper structure of a biosafety system as a way of reducing the vulnerability of a society, economy or state in the face of a biogenic threat. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2018. [DOI: 10.24075/brsmu.2018.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To understand how vulnerable are a society, an economy and a state in the face of a biohazard, one should attempt to identify any potential holes in the national biosafety system, such as the lack of important components or technologies for biological monitoring and the inadequacy of existing analytical methods used to prevent or counteract biogenic threats. In Russia, biological monitoring is quite advanced. However, the agencies that ensure proper functioning of its components lack collaboration and do not form a well-coordinated network. Each of such agencies alone cannot provide comprehensive information on the subject. In the Russian Federation, there are at least 4 state-funded programs that collect epidemiological data and are quite efficient in performing the narrow task of monitoring infections. But because there is no central database where epidemiological data can be channeled and subsequently shared, these agencies do not complete each other. This leaves the Russian society, economy and state vulnerable to biogenic threats. We need an adequately organized, modern, fully functional and effective system for monitoring biohazards that will serve as a basis for the national biosafety system and also a tool for the identification and elimination of its weaknesses.
Collapse
Affiliation(s)
- V. A. Guschin
- Laboratory of Population Variability Mechanisms in Pathogenic Microorganisms, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow; Department of Virology, Faculty of Biology, Lomonosov Moscow State University, Moscow
| | - V. A. Manuilov
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
| | - V. V. Makarov
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, Moscow
| | - A. P. Tkachuk
- Laboratory of Translational Medicine, Gamaleya Research Institute of Epidemiology and Microbiology, Moscow
| |
Collapse
|
23
|
Crowell LE, Lu AE, Love KR, Stockdale A, Timmick SM, Wu D, Wang Y(A, Doherty W, Bonnyman A, Vecchiarello N, Goodwine C, Bradbury L, Brady JR, Clark JJ, Colant NA, Cvetkovic A, Dalvie NC, Liu D, Liu Y, Mascarenhas CA, Matthews CB, Mozdzierz NJ, Shah KA, Wu SL, Hancock WS, Braatz RD, Cramer SM, Love JC. On-demand manufacturing of clinical-quality biopharmaceuticals. Nat Biotechnol 2018; 36:nbt.4262. [PMID: 30272677 PMCID: PMC6443493 DOI: 10.1038/nbt.4262] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 08/27/2018] [Indexed: 12/18/2022]
Abstract
Conventional manufacturing of protein biopharmaceuticals in centralized, large-scale, single-product facilities is not well-suited to the agile production of drugs for small patient populations or individuals. Previous solutions for small-scale manufacturing are limited in both process reproducibility and product quality, owing to their complicated means of protein expression and purification. We describe an automated, benchtop, multiproduct manufacturing system, called Integrated Scalable Cyto-Technology (InSCyT), for the end-to-end production of hundreds to thousands of doses of clinical-quality protein biologics in about 3 d. Unlike previous systems, InSCyT includes fully integrated modules for sustained production, efficient purification without the use of affinity tags, and formulation to a final dosage form of recombinant biopharmaceuticals. We demonstrate that InSCyT can accelerate process development from sequence to purified drug in 12 weeks. We used integrated design to produce human growth hormone, interferon α-2b and granulocyte colony-stimulating factor with highly similar processes on this system and show that their purity and potency are comparable to those of marketed reference products.
Collapse
Affiliation(s)
- Laura E. Crowell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Amos E. Lu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Kerry R. Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | - Alan Stockdale
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | - Steven M. Timmick
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York,
USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York,
USA
- GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Di Wu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston,
Massachusetts, USA
| | - Yu (Annie) Wang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston,
Massachusetts, USA
| | - William Doherty
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | - Alexandra Bonnyman
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | - Nicholas Vecchiarello
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York,
USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York,
USA
| | - Chaz Goodwine
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York,
USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York,
USA
| | | | - Joseph R. Brady
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - John J. Clark
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Biogen, Cambridge, Massachusetts, USA
| | - Noelle A. Colant
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
- Department of Biochemical Engineering, University College London, London, England
| | - Aleksandar Cvetkovic
- Pall Life Sciences, Westborough, Massachusetts, USA
- Sanofi, Framingham, Massachusetts, USA
| | - Neil C. Dalvie
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Diana Liu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | - Yanjun Liu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston,
Massachusetts, USA
| | - Craig A. Mascarenhas
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Catherine B. Matthews
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Nicholas J. Mozdzierz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Kartik A. Shah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
| | | | - William S. Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston,
Massachusetts, USA
| | - Richard D. Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| | - Steven M. Cramer
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York,
USA
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York,
USA
| | - J. Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge,
Massachusetts, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts,
USA
| |
Collapse
|
24
|
Editorial overview: New technologies: multidisciplinary evolutions for drug discovery. Curr Opin Pharmacol 2018; 42:vii-ix. [PMID: 30241695 DOI: 10.1016/j.coph.2018.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
25
|
Wilding KM, Hunt JP, Wilkerson JW, Funk PJ, Swensen RL, Carver WC, Christian ML, Bundy BC. Endotoxin-Free E. coli-
Based Cell-Free Protein Synthesis: Pre-Expression Endotoxin Removal Approaches for on-Demand Cancer Therapeutic Production. Biotechnol J 2018; 14:e1800271. [DOI: 10.1002/biot.201800271] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/12/2018] [Indexed: 01/26/2023]
Affiliation(s)
- Kristen M. Wilding
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | - John P. Hunt
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | - Joshua W. Wilkerson
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | - Parker J. Funk
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | - Rebecca L. Swensen
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | - William C. Carver
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| | | | - Bradley C. Bundy
- Chemical Engineering; Brigham Young University; 350 Clyde Provo UT 84602 USA
| |
Collapse
|
26
|
Sapci AH, Sapci HA. Digital continuous healthcare and disruptive medical technologies: m-Health and telemedicine skills training for data-driven healthcare. J Telemed Telecare 2018; 25:623-635. [PMID: 30134779 DOI: 10.1177/1357633x18793293] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Disruptive medical technologies, wearable devices and new diagnostic solutions have been shaping the future of healthcare, and the health informatics skills gap has become a major problem for technology-centric healthcare applications. This study evaluated the relationships between a specific practical skills training method and students' confidence in using wireless monitoring devices along with the attitude towards technology adoption. METHODS Six practical exercises were developed to provide health informatics technical skills to transfer medical information and display multi-channel biological signals. Two hundred and six undergraduate nursing students received a telemedicine and homecare training course. Their familiarity with various data formats and likelihood to recommend telemedicine and remote monitoring applications were measured. RESULTS The skills training session changed students' attitudes towards remote patient monitoring, and the majority of students provided positive feedback about their confidence in using wireless monitoring devices after the training session. Students stated their plans to use the technology when they start practising and to educate their patients to promote the use of telemedicine. CONCLUSION We propose a skills training framework that covers (a) telemedicine, (b) m-Health and connected health, (c) health informatics application development, (d) health informatics device innovation, and (e) data science.
Collapse
|
27
|
de Lorenzo V. Evolutionary tinkering vs. rational engineering in the times of synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:18. [PMID: 30099657 PMCID: PMC6087506 DOI: 10.1186/s40504-018-0086-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology is not only a contemporary reformulation of the recombinant DNA technologies of the last 30 years, combined with descriptive language imported from electrical and industrial engineering. It is also a new way to interpret living systems and a statement of intent for the use and reprogramming of biological objects for human benefit. In this context, the notion of designer biology is often presented as opposed to natural selection following the powerful rationale formulated by François Jacob on evolution-as-tinkering. The onset of synthetic biology opens a different perspective by leaving aside the question about the evolutionary origin of biological phenomena and focusing instead on the relational logic and the material properties of the corresponding components that make biological system work as they do. Once a functional challenge arises, the solution space for the problem is not homogeneous but it has attractors that can be accessed either through random exploration (as evolution does) or rational design (as engineers do). Although these two paths (i.e. evolution and engineering) are essentially different, they can lead to solutions to specific mechanistic bottlenecks that frequently coincide or converge-and one can easily help to understand and improve the other. Alas, productive discussions on these matters are often contaminated by ideological preconceptions that prevent adoption of the engineering metaphor to understand and ultimately reshape living systems-as ambitioned by synthetic biology. Yet, some possible ways to overcome the impasse are feasible. In parallel to Monod's evolutionary paradox of teleo-logy (finality/purpose) vs. teleo-nomy (appearance of finality/purpose), a mechanistic paradox could be entertained between techno-logy (rational engineering) vs techno-nomy (appearance of rational engineering), all for the sake of understanding the relational logic that enables live systems to function as physico-chemical entities in time and space. This article thus proposes a radical vision of synthetic biology through the lens of the engineering metaphor.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
28
|
Kalmykova SD, Arapidi GP, Urban AS, Osetrova MS, Gordeeva VD, Ivanov VT, Govorun VM. In Silico Analysis of Peptide Potential Biological Functions. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2018. [DOI: 10.1134/s106816201804009x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
29
|
Point-of-care production of therapeutic proteins of good-manufacturing-practice quality. Nat Biomed Eng 2018; 2:675-686. [DOI: 10.1038/s41551-018-0259-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 06/06/2018] [Indexed: 12/19/2022]
|
30
|
Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
Collapse
Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
| |
Collapse
|
31
|
Turchin A, Denkenberger D. Classification of global catastrophic risks connected with artificial intelligence. AI & SOCIETY 2018. [DOI: 10.1007/s00146-018-0845-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
32
|
Wang Y, Liu Y, Liu J, Guo Y, Fan L, Ni X, Zheng X, Wang M, Zheng P, Sun J, Ma Y. MACBETH: Multiplex automated Corynebacterium glutamicum base editing method. Metab Eng 2018; 47:200-210. [PMID: 29580925 DOI: 10.1016/j.ymben.2018.02.016] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 01/27/2018] [Accepted: 02/28/2018] [Indexed: 11/27/2022]
Abstract
CRISPR/Cas9 or Cpf1-introduced double strand break dramatically decreases bacterial cell survival rate, which hampers multiplex genome editing in bacteria. In addition, the requirement of a foreign DNA template for each target locus is labor demanding and may encounter more GMO related regulatory hurdle in industrial applications. Herein, we developed a multiplex automated Corynebacterium glutamicum base editing method (MACBETH) using CRISPR/Cas9 and activation-induced cytidine deaminase (AID), without foreign DNA templates, achieving single-, double-, and triple-locus editing with efficiencies up to 100%, 87.2% and 23.3%, respectively. In addition, MACBETH was applied to generate a combinatorial gene inactivation library for improving glutamate production, and pyk&ldhA double inactivation strain was found to improve glutamate production by 3-fold. Finally, MACBETH was automated with an integrated robotic system, which would enable us to generate thousands of rationally engineered strains per month for metabolic engineering of C. glutamicum. As a proof of concept demonstration, the automation platform was used to construct an arrayed genome-scale gene inactivation library of 94 transcription factors with 100% success rate. Therefore, MACBETH would be a powerful tool for multiplex and automated bacterial genome editing in future studies and industrial applications.
Collapse
Affiliation(s)
- Yu Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ye Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiao Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanmei Guo
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Science, University of Science and Technology of China, Hefei 230026, China
| | - Xiaomeng Ni
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaomei Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Meng Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; School of Life Science, University of Science and Technology of China, Hefei 230026, China.
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| | - Yanhe Ma
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
33
|
Wang L, Dash S, Ng CY, Maranas CD. A review of computational tools for design and reconstruction of metabolic pathways. Synth Syst Biotechnol 2017; 2:243-252. [PMID: 29552648 PMCID: PMC5851934 DOI: 10.1016/j.synbio.2017.11.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 11/28/2022] Open
Abstract
Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.
Collapse
Affiliation(s)
- Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Satyakam Dash
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Chiam Yu Ng
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| |
Collapse
|
34
|
Gach PC, Iwai K, Kim PW, Hillson NJ, Singh AK. Droplet microfluidics for synthetic biology. LAB ON A CHIP 2017; 17:3388-3400. [PMID: 28820204 DOI: 10.1039/c7lc00576h] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Synthetic biology is an interdisciplinary field that aims to engineer biological systems for useful purposes. Organism engineering often requires the optimization of individual genes and/or entire biological pathways (consisting of multiple genes). Advances in DNA sequencing and synthesis have recently begun to enable the possibility of evaluating thousands of gene variants and hundreds of thousands of gene combinations. However, such large-scale optimization experiments remain cost-prohibitive to researchers following traditional molecular biology practices, which are frequently labor-intensive and suffer from poor reproducibility. Liquid handling robotics may reduce labor and improve reproducibility, but are themselves expensive and thus inaccessible to most researchers. Microfluidic platforms offer a lower entry price point alternative to robotics, and maintain high throughput and reproducibility while further reducing operating costs through diminished reagent volume requirements. Droplet microfluidics have shown exceptional promise for synthetic biology experiments, including DNA assembly, transformation/transfection, culturing, cell sorting, phenotypic assays, artificial cells and genetic circuits.
Collapse
Affiliation(s)
- Philip C Gach
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, California 94608, USA
| | | | | | | | | |
Collapse
|
35
|
Koblentz GD. The De Novo Synthesis of Horsepox Virus: Implications for Biosecurity and Recommendations for Preventing the Reemergence of Smallpox. Health Secur 2017; 15:620-628. [PMID: 28836863 DOI: 10.1089/hs.2017.0061] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In March 2017, the American biotech company Tonix announced that a Canadian scientist had synthesized horsepox virus as part of a project to develop a safer vaccine against smallpox. The first de novo synthesis of an orthopoxvirus, a closely related group of viruses that includes horsepox and the variola virus that causes smallpox, crosses an important Rubicon in the field of biosecurity. The synthesis of horsepox virus takes the world one step closer to the reemergence of smallpox as a threat to global health security. That threat has been held at bay for the past 40 years by the extreme difficulty of obtaining variola virus and the availability of effective medical countermeasures. The techniques demonstrated by the synthesis of horsepox have the potential to erase both of these barriers. The primary risk posed by this research is that it will open the door to the routine and widespread synthesis of other orthopoxviruses, such as vaccinia, for use in research, public health, and medicine. The normalization and globalization of orthopoxvirus synthesis for these beneficial applications will create a cadre of laboratories and scientists that will also have the capability and expertise to create infectious variola virus from synthetic DNA. Unless the safeguards against the synthesis of variola virus are strengthened, the capability to reintroduce smallpox into the human population will be globally distributed and either loosely or completely unregulated, providing the foundation for a disgruntled or radicalized scientist, sophisticated terrorist group, unscrupulous company, or rogue state to recreate one of humanity's most feared microbial enemies. The reemergence of smallpox-because of a laboratory accident or an intentional release-would be a global health disaster. International organizations, national governments, the DNA synthesis industry, and the synthetic biology community all have a role to play in devising new approaches to preventing the reemergence of smallpox.
Collapse
|
36
|
Caschera F. Bacterial cell-free expression technology to in vitro systems engineering and optimization. Synth Syst Biotechnol 2017; 2:97-104. [PMID: 29062966 PMCID: PMC5637228 DOI: 10.1016/j.synbio.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Cell-free expression system is a technology for the synthesis of proteins in vitro. The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.
Collapse
|