1
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Then SN, Lipworth W, Stewart C, Kerridge I. A framework for ethics review of applications to store, reuse and share tissue samples. Monash Bioeth Rev 2021; 39:115-124. [PMID: 33635509 DOI: 10.1007/s40592-021-00126-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/31/2021] [Indexed: 11/25/2022]
Abstract
The practice of biobank networking-where biobanks are linked together, and researchers share human tissue samples-is an increasingly common practice both domestically and internationally. The benefits from networking in this way are well established. However, there is a need for ethical oversight in the sharing of human tissue. Ethics committees will increasingly be called upon to approve the sharing of tissue and data with other researchers, often via biobanks, and little guidance currently exists for such committees. In this paper, we provide a structured approach to the ethical review of on-sharing of data and tissue for research purposes.
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Affiliation(s)
- Shih-Ning Then
- Australian Centre for Health Law Research, Law School, Queensland University of Technology, 2 George Street, Brisbane, Australia.
| | - Wendy Lipworth
- Sydney Health Ethics, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Cameron Stewart
- Faculty of Law, The University of Sydney, Camperdown, Australia
| | - Ian Kerridge
- Sydney Health Ethics, Faculty of Medicine and Health, The University of Sydney, Camperdown, Australia
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2
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Young R, Haines M, Storch M, Freemont PS. Combinatorial metabolic pathway assembly approaches and toolkits for modular assembly. Metab Eng 2020; 63:81-101. [PMID: 33301873 DOI: 10.1016/j.ymben.2020.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 11/16/2020] [Accepted: 12/03/2020] [Indexed: 12/18/2022]
Abstract
Synthetic Biology is a rapidly growing interdisciplinary field that is primarily built upon foundational advances in molecular biology combined with engineering design principles such as modularity and interoperability. The field considers living systems as programmable at the genetic level and has been defined by the development of new platform technologies and methodological advances. A key concept driving the field is the Design-Build-Test-Learn cycle which provides a systematic framework for building new biological systems. One major application area for synthetic biology is biosynthetic pathway engineering that requires the modular assembly of different genetic regulatory elements and biosynthetic enzymes. In this review we provide an overview of modular DNA assembly and describe and compare the plethora of in vitro and in vivo assembly methods for combinatorial pathway engineering. Considerations for part design and methods for enzyme balancing are also presented, and we briefly discuss alternatives to intracellular pathway assembly including microbial consortia and cell-free systems for biosynthesis. Finally, we describe computational tools and automation for pathway design and assembly and argue that a deeper understanding of the many different variables of genetic design, pathway regulation and cellular metabolism will allow more predictive pathway design and engineering.
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Affiliation(s)
- Rosanna Young
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Matthew Haines
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK
| | - Marko Storch
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK
| | - Paul S Freemont
- Department of Infectious Disease, Sir Alexander Fleming Building, South Kensington Campus, Imperial College London, SW7 2AZ, UK; London Biofoundry, Imperial College Translation & Innovation Hub, London, W12 0BZ, UK; UK DRI Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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3
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Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F. Universal loop assembly: open, efficient and cross-kingdom DNA fabrication. Synth Biol (Oxf) 2020; 5:ysaa001. [PMID: 32161816 PMCID: PMC7052795 DOI: 10.1093/synbio/ysaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Tamara Matute
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Cerda
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Lopez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Vargas
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Vincent Bielinski
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía de Chile, Concepción, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chris L Dupont
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fernán Federici
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Santiago, Chile
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