151
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Davies JA. Real-World Synthetic Biology: Is It Founded on an Engineering Approach, and Should It Be? Life (Basel) 2019; 9:life9010006. [PMID: 30621107 PMCID: PMC6463249 DOI: 10.3390/life9010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 12/20/2018] [Accepted: 12/29/2018] [Indexed: 12/22/2022] Open
Abstract
Authors often assert that a key feature of 21st-century synthetic biology is its use of an 'engineering approach'; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. What is more, consideration of the special features of living systems suggest that a conventional engineering approach will often not be helpful. The article concludes that the engineering approach may be useful in some projects, but it should not be used to define or constrain synthetic biological endeavour, and that in fact the conventional engineering has more to gain by expanding and embracing more biological ways of working.
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Affiliation(s)
- Jamie A Davies
- UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK.
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152
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Calero P, Nikel PI. Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms. Microb Biotechnol 2019; 12:98-124. [PMID: 29926529 PMCID: PMC6302729 DOI: 10.1111/1751-7915.13292] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 12/27/2022] Open
Abstract
The last few years have witnessed an unprecedented increase in the number of novel bacterial species that hold potential to be used for metabolic engineering. Historically, however, only a handful of bacteria have attained the acceptance and widespread use that are needed to fulfil the needs of industrial bioproduction - and only for the synthesis of very few, structurally simple compounds. One of the reasons for this unfortunate circumstance has been the dearth of tools for targeted genome engineering of bacterial chassis, and, nowadays, synthetic biology is significantly helping to bridge such knowledge gap. Against this background, in this review, we discuss the state of the art in the rational design and construction of robust bacterial chassis for metabolic engineering, presenting key examples of bacterial species that have secured a place in industrial bioproduction. The emergence of novel bacterial chassis is also considered at the light of the unique properties of their physiology and metabolism, and the practical applications in which they are expected to outperform other microbial platforms. Emerging opportunities, essential strategies to enable successful development of industrial phenotypes, and major challenges in the field of bacterial chassis development are also discussed, outlining the solutions that contemporary synthetic biology-guided metabolic engineering offers to tackle these issues.
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Affiliation(s)
- Patricia Calero
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark2800Kongens LyngbyDenmark
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153
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Huang WE, Nikel PI. The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back. Microb Biotechnol 2019; 12:5-7. [PMID: 30461208 PMCID: PMC6302714 DOI: 10.1111/1751-7915.13337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
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154
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Nora LC, Westmann CA, Martins‐Santana L, Alves LDF, Monteiro LMO, Guazzaroni M, Silva‐Rocha R. The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 2019; 12:125-147. [PMID: 30259693 PMCID: PMC6302727 DOI: 10.1111/1751-7915.13318] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022] Open
Abstract
When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities, including those whose genomes can only be revealed through metagenomics. We remark how synthetic biology became a turning point in designing these genetic tools to create meaningful innovations. We have placed special focus on the tools for engineering bacteria and fungi (both yeast and filamentous fungi) and those available to construct metagenomic libraries. Based on this overview, future goals would include the development of modular vectors bearing standardized parts and orthogonally designed circuits, a task not fully addressed thus far. Finally, we present some challenges that should be overcome to enable the next generation of vector design and ways to address it.
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Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - Luana de Fátima Alves
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - María‐Eugenia Guazzaroni
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Rafael Silva‐Rocha
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
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155
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Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation. Genes (Basel) 2018; 10:genes10010017. [PMID: 30597824 PMCID: PMC6356944 DOI: 10.3390/genes10010017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 12/21/2018] [Accepted: 12/21/2018] [Indexed: 02/08/2023] Open
Abstract
The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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156
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Hecht A, Filliben J, Munro SA, Salit M. A minimum information standard for reproducing bench-scale bacterial cell growth and productivity. Commun Biol 2018; 1:219. [PMID: 30534611 PMCID: PMC6283831 DOI: 10.1038/s42003-018-0220-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/29/2018] [Indexed: 11/09/2022] Open
Abstract
Reproducing, exchanging, comparing, and building on each other's work is foundational to technological advances. Advancing biotechnology calls for reliable reuse of engineered organisms. Reliable reuse of engineered organisms requires reproducible growth and productivity. Here, we identify the experimental factors that have the greatest effect on the growth and productivity of our engineered organisms in order to demonstrate reproducibility for biotechnology. We present a draft of a Minimum Information Standard for Engineered Organism Experiments (MIEO) based on this method. We evaluate the effect of 22 factors on Escherichia coli engineered to produce the small molecule lycopene, and 18 factors on E. coli engineered to produce red fluorescent protein. Container geometry and shaking have the greatest effect on product titer and yield. We reproduce our results under two different conditions of reproducibility: conditions of use (different fractional factorial experiments), and time (48 biological replicates performed on 12 different days over 4 months).
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Affiliation(s)
- Ariel Hecht
- Joint Initiative for Metrology in Biology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Room 325, Stanford, CA 94035 USA
| | - James Filliben
- Statistical Engineering Division, 100 Bureau Drive, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Sarah A. Munro
- Joint Initiative for Metrology in Biology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Room 325, Stanford, CA 94035 USA
- Present Address: Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota, 55455 USA
| | - Marc Salit
- Joint Initiative for Metrology in Biology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Genome-scale Measurements Group, National Institute of Standards and Technology, 443 Via Ortega, Room 325, Stanford, CA 94305 USA
- Department of Bioengineering, Stanford University, 443 Via Ortega, Room 325, Stanford, CA 94035 USA
- SLAC National Accelerator Laboratory, Menlo Park, CA 94025 USA
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157
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Autologous fibrin scaffolds: When platelet- and plasma-derived biomolecules meet fibrin. Biomaterials 2018; 192:440-460. [PMID: 30500725 DOI: 10.1016/j.biomaterials.2018.11.029] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/08/2018] [Accepted: 11/20/2018] [Indexed: 02/06/2023]
Abstract
The healing of vascularized mammalian tissue injuries initiate with hemostasis and clotting as part of biological defense system leading to the formation of a fibrin clot in which activated platelets are trapped to quickly stop bleeding and destroy microbials. In order to harness the therapeutic potential of biomolecules secreted by platelets and stemmed from plasma, blood deconstruction has allowed to yield autologous platelet-and plasma-derived protein fibrin scaffold. The autologous growth factors and microparticles stemmed from platelets and plasma, interact with fibrin, extracellular matrix, and tissue cells in a combinatorial, synergistic, and multidirectional way on mechanisms governing tissue repair. This interplay will induce a wide range of cell specifications during inflammation and repair process including but not limited to fibrogenesis, angiogenesis, and immunomodulation. As biology-as-a-drug approach, autologous platelet-and plasma-derived protein fibrin scaffold is emerging as a safe and efficacious natural human-engineered growth factor delivery system to repair musculoskeletal tissues, and skin and corneal ulcers and burns. In doing so, it acts as therapeutic agent not perfect but close to biological precision. However, this autologous, biocompatible, biodegradable, and long in vivo lasting strategy faces several challenges, including its non-conventional single dose-response effect, the lack of standardization in its preparation and application, and the patient's biological features. In this review, we give an account of the main events of tissue repair. Then, we describe the procedure to prepare autologous platelet-and plasma-derived protein fibrin scaffolds, and the rationale behind these biomaterials, and finally, we highlight the significance of strategic accuracy in their application.
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158
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Bharanikumar R, Premkumar KAR, Palaniappan A. PromoterPredict: sequence-based modelling of Escherichia coli σ 70 promoter strength yields logarithmic dependence between promoter strength and sequence. PeerJ 2018; 6:e5862. [PMID: 30425888 PMCID: PMC6228582 DOI: 10.7717/peerj.5862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the -35 and -10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the -35 and -10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the -10 and -35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts -10 and -35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
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Affiliation(s)
- Ramit Bharanikumar
- Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Keshav Aditya R Premkumar
- Computer Science and Engineering, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Ashok Palaniappan
- Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
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159
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Farny NG. A Vision for Teaching the Values of Synthetic Biology. Trends Biotechnol 2018; 36:1097-1100. [DOI: 10.1016/j.tibtech.2018.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 01/01/2023]
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160
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161
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Kearnes M, Kuch D, Johnston A. How to do things with metaphors: engineering life as hodgepodge. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:22. [PMID: 30221313 PMCID: PMC6389216 DOI: 10.1186/s40504-018-0084-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
This paper presents a collaboration between social scientists and a chemist exploring the promises for new therapy development at the intersection between synthetic biology and nanotechnology. Drawing from ethnographic studies of laboratories and a recorded discussion between the three authors, we interrogate the metaphors that underpin what Mackenzie (Futures 48:5-12 2013) has identified as a recursive relationship in the iconography of the life sciences and its infrastructure. Focusing specifically on the use of gene editing techniques in synthetic biology and bio-nanotechnology, we focus our analysis on the key metaphors of 'evolutionary life as hodge-podge' within which 'cutting' of DNA and the 'sticking' and 'binding' of engineered particles to proteins can be performed by researchers in laboratory settings. Taken together, we argue that these metaphors are consequential for understanding metaphors of life-as-machine and the prevalence of notions of 'engineering life'. Exploring the ways in which notions of cutting, targeting and life as an evolutionary hodgepodge prefigure a more contingent notion of engineering and synthesis we close by considering the interpretive implications for ethnomethodological approaches to contemporary life science research.
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Affiliation(s)
- Matthew Kearnes
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), School of Humanities and Languages, University of New South Wales, Sydney, Australia
| | - Declan Kuch
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), School of Humanities and Languages, University of New South Wales, Sydney, Australia
| | - Angus Johnston
- ARC Centre of Excellence in Convergent Bio-Nano Science & Technology (CBNS), Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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162
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Boeing P, Leon M, Nesbeth DN, Finkelstein A, Barnes CP. Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology. Processes (Basel) 2018; 6:167. [PMID: 30568914 PMCID: PMC6296438 DOI: 10.3390/pr6090167] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Work on synthetic biology has largely used a component-based metaphor for system construction. While this paradigm has been successful for the construction of numerous systems, the incorporation of contextual design issues-either compositional, host or environmental-will be key to realising more complex applications. Here, we present a design framework that radically steps away from a purely parts-based paradigm by using aspect-oriented software engineering concepts. We believe that the notion of concerns is a powerful and biologically credible way of thinking about system synthesis. By adopting this approach, we can separate core concerns, which represent modular aims of the design, from cross-cutting concerns, which represent system-wide attributes. The explicit handling of cross-cutting concerns allows for contextual information to enter the design process in a modular way. As a proof-of-principle, we implemented the aspect-oriented approach in the Python tool, SynBioWeaver, which enables the combination, or weaving, of core and cross-cutting concerns. The power and flexibility of this framework is demonstrated through a number of examples covering the inclusion of part context, combining circuit designs in a context dependent manner, and the generation of rule, logic and reaction models from synthetic circuit designs.
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Affiliation(s)
- Philipp Boeing
- Department of Computer Science, UCL, London WC1E 6BT, UK
| | - Miriam Leon
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
| | | | | | - Chris P. Barnes
- Department of Cell and Developmental Biology, UCL, London WC1E 6BT, UK
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163
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Beal J, Haddock-Angelli T, Farny N, Rettberg R. Time to Get Serious about Measurement in Synthetic Biology. Trends Biotechnol 2018; 36:869-871. [DOI: 10.1016/j.tibtech.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/11/2018] [Accepted: 05/14/2018] [Indexed: 10/14/2022]
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164
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Porcar M, Peretó J. Creating life and the media: translations and echoes. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:19. [PMID: 30123943 PMCID: PMC6098992 DOI: 10.1186/s40504-018-0087-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology is the engineering view on biotechnology that ultimately aims at fulfilling the quest of building an artificial cell. From the very first attempts of synthesizing life, this subject has made an impact on the media through, very often, misleading headlines and news. We review here the historical journalistic approach on synthetic biology and related disciplines, from the early twentieth century to the lastest achievements on designing protocells or genome reduction. However, it would be very naive to consider the research community and the media to be unidirectionally linked, with the latter being mere displayers (and disrupters) of the research "reality". On the contrary, the research community has also received a strong influence from the media, as evidenced by statements from researchers, common metaphors and, even, a trend to unconsciously develop shared techno-social paradigms. We conclude that, beyond overstatements from researchers and journalists' misunderstandings, both communities provide strong feedback to each other and, together, contribute to define the dream that synthetic biologists are aiming for.
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Affiliation(s)
- Manuel Porcar
- Institute for Integrative Systems Biology I2SysBio (UV-CSIC), Parc Científic de la Universitat de València, C. Catedràtic José Beltrán 2, 46980, Paterna, Spain.
- Darwin Bioprospecting Excellence SL, Paterna, Spain.
| | - Juli Peretó
- Institute for Integrative Systems Biology I2SysBio (UV-CSIC), Parc Científic de la Universitat de València, C. Catedràtic José Beltrán 2, 46980, Paterna, Spain.
- Darwin Bioprospecting Excellence SL, Paterna, Spain.
- Department of Biochemistry and Molecular Biology, Universitat de València, Burjassot, Spain.
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165
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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.
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Affiliation(s)
- Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, 28049, Madrid, Spain.
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166
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Designing with living systems in the synthetic yeast project. Nat Commun 2018; 9:2950. [PMID: 30054478 PMCID: PMC6063962 DOI: 10.1038/s41467-018-05332-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/28/2018] [Indexed: 11/08/2022] Open
Abstract
Synthetic biology is challenged by the complexity and the unpredictability of living systems. While one response to this complexity involves simplifying cells to create more fully specified systems, another approach utilizes directed evolution, releasing some control and using unpredictable change to achieve design goals. Here we discuss SCRaMbLE, employed in the synthetic yeast project, as an example of synthetic biology design through working with living systems. SCRaMbLE is a designed tool without being a design tool, harnessing the activities of the yeast rather than relying entirely on scientists’ deliberate choices. We suggest that directed evolution at the level of the whole organism allows scientists and microorganisms to “collaborate” to achieve design goals, suggesting new directions for synthetic biology. Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.
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167
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Plesa T, Zygalakis KC, Anderson DF, Erban R. Noise control for molecular computing. J R Soc Interface 2018; 15:20180199. [PMID: 29997258 PMCID: PMC6073653 DOI: 10.1098/rsif.2018.0199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement in nucleic-acid-based technology in general, and strand-displacement DNA computing in particular, a large class of abstract biochemical networks may be physically realized using nucleic acids. Methods for systematic design of the abstract systems with prescribed behaviours have been predominantly developed at the (less-detailed) deterministic level. However, stochastic effects, neglected at the deterministic level, are increasingly found to play an important role in biochemistry. In such circumstances, methods for controlling the intrinsic noise in the system are necessary for a successful network design at the (more-detailed) stochastic level. To bridge the gap, the noise-control algorithm for designing biochemical networks is developed in this paper. The algorithm structurally modifies any given reaction network under mass-action kinetics, in such a way that (i) controllable state-dependent noise is introduced into the stochastic dynamics, while (ii) the deterministic dynamics are preserved. The capabilities of the algorithm are demonstrated on a production-decay reaction system, and on an exotic system displaying bistability. For the production-decay system, it is shown that the algorithm may be used to redesign the network to achieve noise-induced multistability. For the exotic system, the algorithm is used to redesign the network to control the stochastic switching, and achieve noise-induced oscillations.
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Affiliation(s)
- Tomislav Plesa
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, UK
| | - Konstantinos C Zygalakis
- School of Mathematics, University of Edinburgh, Maxwell Building, Peter Guthrie Tait Road, Edinburgh, UK
| | - David F Anderson
- Department of Mathematics, University of Wisconsin-Madison, Lincoln Drive, Madison, WI, USA
| | - Radek Erban
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Radcliffe Observatory Quarter, Woodstock Road, Oxford, UK
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168
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Kong W, Meldgin DR, Collins JJ, Lu T. Designing microbial consortia with defined social interactions. Nat Chem Biol 2018; 14:821-829. [DOI: 10.1038/s41589-018-0091-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 05/10/2018] [Indexed: 11/09/2022]
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169
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Döring M. Synthetic biology in the German press: how implications of metaphors shape representations of morality and responsibility. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:14. [PMID: 29936670 PMCID: PMC6015587 DOI: 10.1186/s40504-018-0079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/22/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology (SynBio) represents a relatively young field of research which has developed into an important scientific endeavour. Characterised by a high degree of interdisciplinary work crossing disciplinary boundaries, such as biology, mathematics and engineering, SynBio has been, since its beginning, devoted to creating new biological functions, metabolic pathways or even minimal organisms. Although its often-articulated aim of developing new forms of life has so far not been archived, SynBio nowadays represents a well-established biotechnological approach and it has also attracted public concern, especially since Craig Venter's work on Mycoplasma Mycoides JCVI-syn1.0. Taking these developments as a starting point, the paper empirically investigates the metaphorical representations of SynBio in two leading German media publications, the daily newspaper Die Frankfurter Allgemeine Zeitung and the weekly magazine Der Spiegel between 2000 and 2010. Using a novel combination of metaphor and co-occurrence analysis, the paper engages in a systematic examination of implicit moral implications inherent in linguistic images permeating this news coverage. It demonstrates a method of how media-metaphorical representations and their moral implications of SynBio could analytically be revealed and analysed. In doing so, it aims at contributing to empirical ethical analyses of the news coverage on SynBio in particular and offers an approach that methodologically adds to literature on responsible language use, which is emerging in science and technology studies and ethical analyses of new technologies.
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Affiliation(s)
- Martin Döring
- Institute of Geography, University of Hamburg, Bundesstraße 55, 20146, Hamburg, Germany.
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170
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Jiang N, Ying GL, Yetisen AK, Montelongo Y, Shen L, Xiao YX, Busscher HJ, Yang XY, Su BL. A bilayered nanoshell for durable protection of single yeast cells against multiple, simultaneous hostile stimuli. Chem Sci 2018; 9:4730-4735. [PMID: 29910923 PMCID: PMC5982223 DOI: 10.1039/c8sc01130c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 12/19/2022] Open
Abstract
Single cell surface engineering provides the most efficient, non-genetic strategy to enhance cell stability. However, it remains a huge challenge to improve cell stability in complex artificial environments. Here, a soft biohybrid interfacial layer is fabricated on individual living-cell surfaces by their exposure to a suspension of gold nanoparticles and l-cysteine to form a protecting functional layer to which porous silica layers were bound yielding pores with a diameter of 3.9 nm. The living cells within the bilayered nanoshells maintained high viability (96 ± 2%) as demonstrated by agar plating, even after five cycles of simultaneous exposure to high temperature (40 °C), lyticase and UV light. Moreover, yeast cells encapsulated in bilayered nanoshells were more recyclable than native cells due to nutrient storage in the shell.
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Affiliation(s)
- Nan Jiang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing , Wuhan University of Technology , 122 Luoshi Road , Wuhan , 430070 , China .
- School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - Guo-Liang Ying
- School of Materials Science and Engineering , Wuhan Institute of Technology , Wuhan , 430205 , China
- Division of Engineering in Medicine , Brigham and Women's Hospital , Harvard Medical School , Cambridge , Massachusetts 02139 , USA
| | - Ali K Yetisen
- School of Chemical Engineering , University of Birmingham , Birmingham B15 2TT , UK
| | | | - Ling Shen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing , Wuhan University of Technology , 122 Luoshi Road , Wuhan , 430070 , China .
| | - Yu-Xuan Xiao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing , Wuhan University of Technology , 122 Luoshi Road , Wuhan , 430070 , China .
| | - Henk J Busscher
- University of Groningen , University Medical Center Groningen , Department of Biomedical Engineering , Antonius Deusinglaan 1 , 9713 AV , Groningen , The Netherlands
| | - Xiao-Yu Yang
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing , Wuhan University of Technology , 122 Luoshi Road , Wuhan , 430070 , China .
- School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , USA .
| | - Bao-Lian Su
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing , Wuhan University of Technology , 122 Luoshi Road , Wuhan , 430070 , China .
- Laboratory of Inorganic Materials Chemistry , University of Namur , 61, rue de Bruxelles , 5000 Namur , Belgium .
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171
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Abstract
Neurobiological engineering is the process of making models of brain function and psychoanalytic psychology as these interact in a social environment to hide complexity while remaining true to science. One-fourth of Americans are killed by drugs. The engineering model described is applied to psychodynamic therapy of addicted patients. It helps us understand why addiction is ubiquitous, hostile, malicious, and intractable. Drugs take over the will by changing the ventral tegmental dopaminergic SEEKING system.
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172
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Majumdar S, Pal S. Information transmission in microbial and fungal communication: from classical to quantum. J Cell Commun Signal 2018; 12:491-502. [PMID: 29476316 PMCID: PMC5910326 DOI: 10.1007/s12079-018-0462-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 02/08/2018] [Indexed: 01/05/2023] Open
Abstract
Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.
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Affiliation(s)
- Sarangam Majumdar
- Dipartimento di Ingegneria Scienze Informatiche e Matematica, Università degli Studi di L’ Aquila, Via Vetoio – Loc. Coppito, 67010 L’ Aquila, Italy
| | - Sukla Pal
- Theoretical Physics Division, Physical Research Laboratory, Navrangpura, Ahmedabad, Gujarat 380009 India
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173
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Azam MR, Fazal S, Ullah M, Bhatti AI. System-based strategies for p53 recovery. IET Syst Biol 2018; 12:101-107. [PMID: 29745903 PMCID: PMC8687347 DOI: 10.1049/iet-syb.2017.0025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/25/2017] [Accepted: 11/19/2017] [Indexed: 11/19/2022] Open
Abstract
The authors have proposed a systems theory-based novel drug design approach for the p53 pathway. The pathway is taken as a dynamic system represented by ordinary differential equations-based mathematical model. Using control engineering practices, the system analysis and subsequent controller design is performed for the re-activation of wild-type p53. p53 revival is discussed for both modes of operation, i.e. the sustained and oscillatory. To define the problem in control system paradigm, modification in the existing mathematical model is performed to incorporate the effect of Nutlin. Attractor point analysis is carried out to select the suitable domain of attraction. A two-loop negative feedback control strategy is devised to drag the system trajectories to the attractor point and to regulate cellular concentration of Nutlin, respectively. An integrated framework is constituted to incorporate the pharmacokinetic effects of Nutlin in the cancerous cells. Bifurcation analysis is also performed on the p53 model to see the conditions for p53 oscillation.
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Affiliation(s)
- Muhammad Rizwan Azam
- CASPR, Department of Electronics Engineering, Capital University of Science and Technology, Islamabad, Pakistan
| | - Sahar Fazal
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad, Pakistan
| | - Mukhtar Ullah
- Department of Electrical Engineering, National University of Computer and Emerging Sciences, Islamabad, Pakistan
| | - Aamer I Bhatti
- CASPR, Department of Electronics Engineering, Capital University of Science and Technology, Islamabad, Pakistan.
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174
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Salehi SA, Liu X, Riedel MD, Parhi KK. Computing Mathematical Functions using DNA via Fractional Coding. Sci Rep 2018; 8:8312. [PMID: 29844537 PMCID: PMC5974329 DOI: 10.1038/s41598-018-26709-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 05/18/2018] [Indexed: 12/22/2022] Open
Abstract
This paper discusses the implementation of mathematical functions such as exponentials, trigonometric functions, the sigmoid function and the perceptron function with molecular reactions in general, and DNA strand displacement reactions in particular. The molecular constructs for these functions are predicated on a novel representation for input and output values: a fractional encoding, in which values are represented by the relative concentrations of two molecular types, denoted as type-1 and type-0. This representation is inspired by a technique from digital electronic design, termed stochastic logic, in which values are represented by the probability of 1's in a stream of randomly generated 0's and 1's. Research in the electronic realm has shown that a variety of complex functions can be computed with remarkably simple circuitry with this stochastic approach. This paper demonstrates how stochastic electronic designs can be translated to molecular circuits. It presents molecular implementations of mathematical functions that are considerably more complex than any shown to date. All designs are validated using mass-action simulations of the chemical kinetics of DNA strand displacement reactions.
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Affiliation(s)
- Sayed Ahmad Salehi
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Xingyi Liu
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Marc D Riedel
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA
| | - Keshab K Parhi
- Department of Electrical and Computer Engineering, University of Minnesota, 200 Union St. S.E., Minneapolis, MN, 55455, USA.
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175
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Abstract
Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry—biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.
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Affiliation(s)
- Caleb J. Bashor
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
| | - James J. Collins
- Institute for Medical Engineering and Science, Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;,
- Harvard–MIT Program in Health Sciences and Technology, Cambridge, Massachusetts 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA
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176
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Wagner SG, Ziegler M, Löwe H, Kremling A, Pflüger-Grau K. pTRA - A reporter system for monitoring the intracellular dynamics of gene expression. PLoS One 2018; 13:e0197420. [PMID: 29772009 PMCID: PMC5957375 DOI: 10.1371/journal.pone.0197420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 05/02/2018] [Indexed: 11/19/2022] Open
Abstract
The presence of standardised tools and methods to measure and represent accurately biological parts and functions is a prerequisite for successful metabolic engineering and crucial to understand and predict the behaviour of synthetic genetic circuits. Many synthetic gene networks are based on transcriptional circuits, thus information on transcriptional and translational activity is important for understanding and fine-tuning the synthetic function. To this end, we have developed a toolkit to analyse systematically the transcriptional and translational activity of a specific synthetic part in vivo. It is based on the plasmid pTRA and allows the assignment of specific transcriptional and translational outputs to the gene(s) of interest (GOI) and to compare different genetic setups. By this, the optimal combination of transcriptional strength and translational activity can be identified. The design is tested in a case study using the gene encoding the fluorescent mCherry protein as GOI. We show the intracellular dynamics of mRNA and protein formation and discuss the potential and shortcomings of the pTRA plasmid.
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Affiliation(s)
- Sabine G. Wagner
- Systems Biotechnology, Faculty of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Martin Ziegler
- Systems Biotechnology, Faculty of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Hannes Löwe
- Systems Biotechnology, Faculty of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Andreas Kremling
- Systems Biotechnology, Faculty of Mechanical Engineering, Technical University of Munich, Garching, Germany
| | - Katharina Pflüger-Grau
- Systems Biotechnology, Faculty of Mechanical Engineering, Technical University of Munich, Garching, Germany
- * E-mail:
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177
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Guiziou S, Ulliana F, Moreau V, Leclere M, Bonnet J. An Automated Design Framework for Multicellular Recombinase Logic. ACS Synth Biol 2018; 7:1406-1412. [PMID: 29641183 PMCID: PMC5962929 DOI: 10.1021/acssynbio.8b00016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Tools
to systematically reprogram cellular behavior are crucial
to address pressing challenges in manufacturing, environment, or healthcare.
Recombinases can very efficiently encode Boolean and history-dependent
logic in many species, yet current designs are performed on a case-by-case
basis, limiting their scalability and requiring time-consuming optimization.
Here we present an automated workflow for designing recombinase logic
devices executing Boolean functions. Our theoretical framework uses
a reduced library of computational devices distributed into different
cellular subpopulations, which are then composed in various manners
to implement all desired logic functions at the multicellular level.
Our design platform called CALIN (Composable Asynchronous Logic using
Integrase Networks) is broadly accessible via a web
server, taking truth tables as inputs and providing corresponding
DNA designs and sequences as outputs (available at http://synbio.cbs.cnrs.fr/calin). We anticipate that this automated design workflow will streamline
the implementation of Boolean functions in many organisms and for
various applications.
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Affiliation(s)
- Sarah Guiziou
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Federico Ulliana
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Violaine Moreau
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
| | - Michel Leclere
- Laboratoire d’Informatique, de Robotique et de Microelectronique de Montpellier (LIRMM), CNRS UMR 5506, University of Montpellier, 34090 Montpellier, France
| | - Jerome Bonnet
- Centre de Biochimie Structurale (CBS), INSERM U1054, CNRS UMR5048, University of Montpellier, 34090 Montpellier, France
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178
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Sengupta A, Pakrasi HB, Wangikar PP. Recent advances in synthetic biology of cyanobacteria. Appl Microbiol Biotechnol 2018; 102:5457-5471. [PMID: 29744631 DOI: 10.1007/s00253-018-9046-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/11/2022]
Abstract
Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO2. Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO2, diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.
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Affiliation(s)
- Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, USA.,Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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179
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Tang Q, Lu T, Liu SJ. Engineering the bacterium Comamonas testosteroni CNB-1: Plasmid curing and genetic manipulation. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.01.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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180
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Brooks DS, Eronen MI. The significance of levels of organization for scientific research: A heuristic approach. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018; 68-69:34-41. [PMID: 29653763 DOI: 10.1016/j.shpsc.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/18/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of 'levels' is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research.
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Affiliation(s)
- Daniel S Brooks
- Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, A-3400 Klosterneuburg, Austria.
| | - Markus I Eronen
- Centre for Logic and Analytic Philosophy, KU Leuven, Andreas Vesaliusstraat 2-Box 3220, 3000 Leuven, Belgium.
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181
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In situ biomolecule production by bacteria; a synthetic biology approach to medicine. J Control Release 2018; 275:217-228. [DOI: 10.1016/j.jconrel.2018.02.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/14/2018] [Accepted: 02/15/2018] [Indexed: 02/06/2023]
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182
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Danchin A, Sekowska A, Noria S. Functional Requirements in the Program and the Cell Chassis for Next-Generation Synthetic Biology. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Agnieszka Sekowska
- Institute of Cardiometabolism and Nutrition; 47 boulevard de l'Hôpital Paris 75013 France
| | - Stanislas Noria
- Fondation Fourmentin-Guilbert; 2 avenue du Pavé Neuf Noisy le Grand 93160 France
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183
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Ottoz DSM, Rudolf F. Constitutive and Regulated Promoters in Yeast: How to Design and Make Use of Promoters in S. cerevisiae. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Diana S. M. Ottoz
- ETH Zurich; Department of Biosystems Science and Engineering; Mattenstrasse 26 4058 Basel Switzerland
- Yale University; Department of Molecular Biophysics and Biochemistry; 333 Cedar street SHM C-111 New Haven CT 06520 USA
| | - Fabian Rudolf
- ETH Zurich; Department of Biosystems Science and Engineering; Mattenstrasse 26 4058 Basel Switzerland
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184
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Pothoulakis G, Ellis T. Construction of hybrid regulated mother-specific yeast promoters for inducible differential gene expression. PLoS One 2018; 13:e0194588. [PMID: 29566038 PMCID: PMC5864024 DOI: 10.1371/journal.pone.0194588] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 03/06/2018] [Indexed: 11/18/2022] Open
Abstract
Engineered promoters with predefined regulation are a key tool for synthetic biology that enable expression on demand and provide the logic for genetic circuits. To expand the availability of synthetic biology tools for S. cerevisiae yeast, we here used hybrid promoter engineering to construct tightly-controlled, externally-inducible promoters that only express in haploid mother cells that have contributed a daughter cell to the population. This is achieved by combining elements from the native HO promoter and from a TetR-repressible synthetic promoter, with the performance of these promoters characterized by both flow cytometry and microfluidics-based fluorescence microscopy. These new engineered promoters are provided as an enabling tool for future synthetic biology applications that seek to exploit differentiation within a yeast population.
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Affiliation(s)
- Georgios Pothoulakis
- Centre for Synthetic Biology and Innovation, Imperial College London, London, United Kingdom.,Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Tom Ellis
- Centre for Synthetic Biology and Innovation, Imperial College London, London, United Kingdom.,Department of Bioengineering, Imperial College London, London, United Kingdom
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185
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Bioethanol a Microbial Biofuel Metabolite; New Insights of Yeasts Metabolic Engineering. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4010016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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186
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Modular assembling process of an in-silico protocell. Biosystems 2018; 165:8-21. [DOI: 10.1016/j.biosystems.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/15/2017] [Accepted: 12/07/2017] [Indexed: 11/17/2022]
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187
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Couto JM, McGarrity A, Russell J, Sloan WT. The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain. Microb Cell Fact 2018; 17:8. [PMID: 29357936 PMCID: PMC5776760 DOI: 10.1186/s12934-018-0858-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/15/2018] [Indexed: 12/14/2022] Open
Abstract
Background Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability. Results Here we employed a chemostat design which enabled us to maintained two strains of E. coli K12 under sustained starvation stress: first the reduced genome synthetic biology chassis MDS42 and then, the control parent strain MG1655. We estimated mutation rates and utilised them as indicators of an increase in genome instability. We show that within 24 h the spontaneous mutation rate had increased similarly in both strains, destabilizing the genomes. High rates were maintained for the duration of the experiment. Growth rates of a cohort of randomly sampled mutants from both strains were utilized as a proxy for emerging phenotypic, and by association genetic variation. Mutant growth rates were consistently less than rates in non-mutants, an indicator of reduced fitness and the presence of mildly deleterious mutations in both the strains. In addition, the effect of these mutations on the populations as a whole varied by strain. Conclusions Overall, this study shows that genome reductions in the MDS42 did not stabilize the chassis under metabolic stress. Over time, this could compromise the effectiveness of synthetic organisms built on chassis in environmental applications. Electronic supplementary material The online version of this article (10.1186/s12934-018-0858-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jillian M Couto
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK.
| | - Anne McGarrity
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
| | - Julie Russell
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
| | - William T Sloan
- Division of Infrastructure and Environment, School of Engineering, University of Glasgow, Rankine Building, Level 5, Glasgow, G12 8QQ, UK
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188
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Affiliation(s)
- Jason E. McDermott
- Computational Biology and Bioinformatics, Pacific Northwest National Laboratory, Richland, Washington, United States of America
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, United States of America
- * E-mail:
| | - Matthew Partridge
- Engineering Photonics, Cranfield University, Cranfield, Bedfordshire, United Kingdom
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
- Institute for Advanced Study, Technische Universität München, Garching, Germany
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189
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Song X, Wang Y, Diao J, Li S, Chen L, Zhang W. Direct Photosynthetic Production of Plastic Building Block Chemicals from CO 2. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:215-238. [PMID: 30091097 DOI: 10.1007/978-981-13-0854-3_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydroxy acids have attracted attention as building block chemicals due to their roles as precursors for the production of various pharmaceuticals, vitamins, antibiotics, and flavor compounds as well as monomers for biodegradable plastic polyesters. The current approach to hydroxy acid production relies on nonrenewable fossil resources such as petroleum for raw materials, raising issues such as the rising costs of starting materials and environmental incompatibility. Recently, synthetic biology approaches based on the rational design and reconstruction of new biological systems were implemented to produce chemicals from a variety of renewable substrates. In addition to research using heterotrophic organic carbon-dependent Escherichia coli or yeasts, photosynthetic microorganisms such as cyanobacteria possessing the ability to absorb solar radiation and fix carbon dioxide (CO2) as a sole carbon source have been engineered into a new type of microbial cell factory to directly produce hydroxy acids from CO2. In this chapter, recent progress regarding the direct photosynthetic production of three important hydroxy acids-3-hydroxypropionate (3-HP), 3-hydroxybutyrate (3-HB), and 3-hydroxyvalerate (3-HV)-from CO2 in cyanobacteria is summarized and discussed.
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Affiliation(s)
- Xinyu Song
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China.,Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.,School of Environmental Science and Engineering, Tianjin University, Tianjin, China
| | - Yunpeng Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Jinjin Diao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China
| | - Weiwen Zhang
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, China. .,Laboratory of Synthetic Microbiology, School of Chemical Engineering & Technology, Tianjin University, Tianjin, China. .,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin, China.
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190
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Marchisio MA. Introduction. INTRODUCTION IN SYNTHETIC BIOLOGY 2018:1-5. [DOI: 10.1007/978-981-10-8752-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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191
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de Lorenzo V, Schmidt M. Biological standards for the Knowledge-Based BioEconomy: What is at stake. N Biotechnol 2018; 40:170-180. [DOI: 10.1016/j.nbt.2017.05.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 05/03/2017] [Indexed: 02/07/2023]
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192
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Ramzi AB. Metabolic Engineering and Synthetic Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1102:81-95. [DOI: 10.1007/978-3-319-98758-3_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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193
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Affiliation(s)
- Lionel J. Clarke
- 3.16 RSM Department of Bioengineering Imperial College, UK Synthetic Biology Leadership Council Exhibition Road London SW7 2BX UK
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194
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Bhatia SP, Smanski MJ, Voigt CA, Densmore DM. Genetic Design via Combinatorial Constraint Specification. ACS Synth Biol 2017; 6:2130-2135. [PMID: 28874044 DOI: 10.1021/acssynbio.7b00154] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We present a formal language for specifying via constraints a "design space" of DNA constructs composed of genetic parts, and an algorithm for automatically and correctly creating a novel representation of the space of satisfying designs. The language is simple, captures a large class of design spaces, and possesses algorithms for common operations on design spaces. The flexibility of this approach is demonstrated using a 16-gene nitrogen fixation pathway and genetic logic circuits.
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Affiliation(s)
- Swapnil P. Bhatia
- Biological
Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Michael J. Smanski
- Department
of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, St Paul, Minnesota 55108, United States
| | - Christopher A. Voigt
- Synthetic
Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas M. Densmore
- Biological
Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
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195
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Shepherd TR, Du L, Liljeruhm J, Samudyata, Wang J, Sjödin MOD, Wetterhall M, Yomo T, Forster AC. De novo design and synthesis of a 30-cistron translation-factor module. Nucleic Acids Res 2017; 45:10895-10905. [PMID: 28977654 PMCID: PMC5737471 DOI: 10.1093/nar/gkx753] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 08/17/2017] [Indexed: 11/17/2022] Open
Abstract
Two of the many goals of synthetic biology are synthesizing large biochemical systems and simplifying their assembly. While several genes have been assembled together by modular idempotent cloning, it is unclear if such simplified strategies scale to very large constructs for expression and purification of whole pathways. Here we synthesize from oligodeoxyribonucleotides a completely de-novo-designed, 58-kb multigene DNA. This BioBrick plasmid insert encodes 30 of the 31 translation factors of the PURE translation system, each His-tagged and in separate transcription cistrons. Dividing the insert between three high-copy expression plasmids enables the bulk purification of the aminoacyl-tRNA synthetases and translation factors necessary for affordable, scalable reconstitution of an in vitro transcription and translation system, PURE 3.0.
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Affiliation(s)
- Tyson R Shepherd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Liping Du
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Josefine Liljeruhm
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Samudyata
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Jinfan Wang
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden
| | - Marcus O D Sjödin
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Magnus Wetterhall
- Department of Physical and Analytical Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Tetsuya Yomo
- Institute of Biology and Information Science, School of Computer Science and Software Engineering, School of Life Sciences, East China Normal University, Shanghai 200062, PR China
| | - Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Uppsala 751 36, Sweden.,Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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196
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Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 2017; 22:1-12. [PMID: 29110088 DOI: 10.1007/s00792-017-0974-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
Abstract
Lignocellulosic biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a 'toolbox' of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.
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197
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Stano P, Altamura E, Mavelli F. Novel directions in molecular systems design: The case of light-transducing synthetic cells. Commun Integr Biol 2017; 10:e1365993. [PMID: 29260799 PMCID: PMC5731512 DOI: 10.1080/19420889.2017.1365993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022] Open
Abstract
Important progresses have been achieved in the past years in the field of bottom-up synthetic biology, especially aiming at constructing cell-like systems based on lipid vesicles (liposomes) entrapping both biomolecules or synthetic compounds. These "synthetic cells" mimic the behaviour of biological cells but are constituted by a minimal number of components. One key aspect related to this research is the energetic needs of synthetic cells. Up to now, high-energy compounds have been given in order to drive biochemical reactions inside the vesicle lumen. In order to be autonomous, synthetic cells must produce their own biochemical energy from available energy sources. At this aim we started a long-term research program focused on the construction of photoautotrophic synthetic cells, starting with the reconstitution, in active and highly oriented form, of the photosynthetic reaction centre in giant lipid vesicles (Altamura et al., PNAS 2017, 114, 3837-3842). Here we comment this first milestone by showing the synthetic biology context wherein it is developed, the future steps, and the experimental approach that might allow such an achievement.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, Lecce, Italy
| | | | - Fabio Mavelli
- Chemistry Department, University “Aldo Moro,” Bari, Italy
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198
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Li A, Cai L, Chen Z, Wang M, Wang N, Nakanishi H, Gao XD, Li Z. Recent advances in the synthesis of rare sugars using DHAP-dependent aldolases. Carbohydr Res 2017; 452:108-115. [PMID: 29096183 DOI: 10.1016/j.carres.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 01/02/2023]
Abstract
The occurrence rates of non-communicable diseases like obesity, diabetes and hyperlipidemia have increased remarkably due to excessive consumption of a high-energy diet. Rare sugars therefore have become increasingly attractive owing to their unique nutritional properties. In the past two decades, various rare sugars have been successfully prepared guided by the "Izumoring strategy". As a valuable complement to the Izumoring approach, the controllable dihydroxyacetone phosphate (DHAP)-dependent aldolases have generally predictable regio- and stereoselectivity, which makes them powerful tools in C-C bond construction and rare sugar production. However, the main disadvantage for this group of aldolases is their strict substrate specificity toward the donor molecule DHAP, a very expensive and relatively unstable compound. Among the current methods involving DHAP, the one that couples DHAP production from inexpensive starting materials (for instance, glycerol, DL-glycerol 3-phosphate, dihydroxyacetone, and glucose) with aldol condensation appears to be the most promising. This review thus focuses on recent advances in the application of L-rhamnulose-1-phosphate aldolase (RhaD), L-fuculose-1-phosphate aldolase (FucA), and D-fructose-1,6-bisphosphate aldolase (FruA) for rare sugar synthesis in vitro and in vivo, while illustrating strategies for supplying DHAP in efficient and economical ways.
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Affiliation(s)
- Aimin Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Li Cai
- Department of Chemistry, University of South Carolina Lancaster, 476 Hubbard Drive, Lancaster, SC, 29720, USA
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Mayan Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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199
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Martínez-García E, de Lorenzo V. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas. Curr Opin Biotechnol 2017; 47:120-132. [DOI: 10.1016/j.copbio.2017.06.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 06/19/2017] [Indexed: 11/26/2022]
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200
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West J. Open Source Platforms Beyond Software: From ICT to Biotechnology. ADVANCES IN STRATEGIC MANAGEMENT-A RESEARCH ANNUAL 2017. [DOI: 10.1108/s0742-332220170000037011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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