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Elgabry M, Johnson S. Cyber-biological convergence: a systematic review and future outlook. Front Bioeng Biotechnol 2024; 12:1456354. [PMID: 39380896 PMCID: PMC11458441 DOI: 10.3389/fbioe.2024.1456354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/05/2024] [Indexed: 10/10/2024] Open
Abstract
The introduction of the capability to "program" a biological system is referred to as Engineered biology and can be compared to the introduction of the internet and the capability of programming a computer. Engineered biology is supported by a digital infrastructure that includes data, data storage, computer-dependent laboratory equipment, internet-connected communication networks, and supply chains. This connectivity is important. It can improve workflows and enhance productivity. At the same time and unlike computer programs, biological systems introduce unique threats as they can self-assemble, self-repair, and self-replicate. The aim of this paper is to systematically review the cyber implications of engineered biology. This includes cyber-bio opportunities and threats as engineered biology continues to integrate into cyberspace. We used a systematic search methodology to review the academic literature, and supplemented this with a review of opensource materials and "grey" literature that is not disseminated by academic publishers. A comprehensive search of articles published in or after 2017 until the 21st of October 2022 found 52 studies that focus on implications of engineered biology to cyberspace. The search was conducted using search engines that index over 60 databases-databases that specifically cover the information security, and biology literatures, as well as the wider set of academic disciplines. Across these 52 articles, we identified a total of 7 cyber opportunities including automated bio-foundries and 4 cyber threats such as Artificial Intelligence misuse and biological dataset targeting. We highlight the 4 main types of cyberbiosecurity solutions identified in the literature and we suggest a total of 9 policy recommendations that can be utilized by various entities, including governments, to ensure that cyberbiosecurity remains frontline in a growing bioeconomy.
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Affiliation(s)
- Mariam Elgabry
- DAWES Center for Future Crime at UCL, Jill Dando Institute for Security and Crime Science, London, United Kingdom
- Bronic, London, United Kingdom
| | - Shane Johnson
- DAWES Center for Future Crime at UCL, Jill Dando Institute for Security and Crime Science, London, United Kingdom
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2
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Ramos PD, Almeida MS, Olsson IAS. What do people think about genetic engineering? A systematic review of questionnaire surveys before and after the introduction of CRISPR. Front Genome Ed 2023; 5:1284547. [PMID: 38192431 PMCID: PMC10773783 DOI: 10.3389/fgeed.2023.1284547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/27/2023] [Indexed: 01/10/2024] Open
Abstract
The advent of CRISPR-Cas9 in 2012 started revolutionizing the field of genetics by broadening the access to a method for precise modification of the human genome. It also brought renewed attention to the ethical issues of genetic modification and the societal acceptance of technology for this purpose. So far, many surveys assessing public attitudes toward genetic modification have been conducted worldwide. Here, we present the results of a systematic review of primary publications of surveys addressing public attitudes toward genetic modification as well as the awareness and knowledge about the technology required for genetic modification. A total of 53 primary publications (1987-2020) focusing on applications in humans and non-human animals were identified, covering countries in four continents. Of the 53 studies, 30 studies from until and including 2012 (pre-CRISPR) address gene therapy in humans and genetic modification of animals for food production and biomedical research. The remaining 23 studies from after 2013 (CRISPR) address gene editing in humans and animals. Across countries, respondents see gene therapy for disease treatment or prevention in humans as desirable and highly acceptable, whereas enhancement is generally met with opposition. When the study distinguishes between somatic and germline applications, somatic gene editing is generally accepted, whereas germline applications are met with ambivalence. The purpose of the application is also important for assessing attitudes toward genetically modified animals: modification in food production is much less accepted than for biomedical application in pre-CRISPR studies. A relationship between knowledge/awareness and attitude toward genetic modification is often present. A critical appraisal of methodology quality in the primary publications with regards to sampling and questionnaire design, development, and administration shows that there is considerable scope for improvement in the reporting of methodological detail. Lack of information is more common in earlier studies, which probably reflects the changing practice in the field.
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Affiliation(s)
- Pedro Dias Ramos
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Maria Strecht Almeida
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Ingrid Anna Sofia Olsson
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
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3
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Hankamer B, Pregelj L, O'Kane S, Hussey K, Hine D. Delivering impactful solutions for the bioeconomy. TRENDS IN PLANT SCIENCE 2023; 28:583-596. [PMID: 36941134 DOI: 10.1016/j.tplants.2023.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 05/22/2023]
Abstract
We are increasingly challenged to operate within our planetary boundaries, while delivering on United Nations (UN) Sustainable Development Goal (SDG) 2030 targets, and net-zero emissions by 2050. Failure to solve these challenges risks economic, social, political, climate, food, water, and fuel security. Therefore, new, scalable, and adoptable circular economy solutions are urgently required. The ability of plants to use light, capture CO2, and drive complex biochemistry is pivotal to delivering these solutions. However, harnessing this capability efficiently also requires robust accompanying economic, financial, market, and strategic analytics. A framework for this is presented here in the Commercialization Tourbillon. It supports the delivery of emerging plant biotechnologies and bio-inspired light-driven industry solutions within the critical 2030-2050 timeframe, to achieve validated economic, social, and environmental benefits.
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Affiliation(s)
- Ben Hankamer
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lisette Pregelj
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Shane O'Kane
- Treble Cone Advisory Brisbane Qld, Suite 75, 12 Welsby Street, New Farm, QLD 4005, Australia
| | - Karen Hussey
- Centre for Policy Futures, Faculty of Humanities and Social Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Damian Hine
- Queensland Alliance for Agriculture and Food innovation, The University of Queensland, Brisbane, QLD 4072, Australia.
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4
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A global forum on synthetic biology: the need for international engagement. Nat Commun 2022; 13:3516. [PMID: 35717402 PMCID: PMC9206396 DOI: 10.1038/s41467-022-31265-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 06/13/2022] [Indexed: 12/03/2022] Open
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5
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Runkle BRK. Review: biological engineering for nature-based climate solutions. J Biol Eng 2022; 16:7. [PMID: 35351176 PMCID: PMC8966256 DOI: 10.1186/s13036-022-00287-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
Nature-based Climate Solutions are landscape stewardship techniques to reduce greenhouse gas emissions and increase soil or biomass carbon sequestration. These mitigation approaches to climate change present an opportunity to supplement energy sector decarbonization and provide co-benefits in terms of ecosystem services and landscape productivity. The biological engineering profession must be involved in the research and implementation of these solutions-developing new tools to aid in decision-making, methods to optimize across different objectives, and new messaging frameworks to assist in prioritizing among different options. Furthermore, the biological engineering curriculum should be redesigned to reflect the needs of carbon-based landscape management. While doing so, the biological engineering community has an opportunity to embed justice, equity, diversity, and inclusion within both the classroom and the profession. Together these transformations will enhance our capacity to use sustainable landscape management as an active tool to mitigate the risks of climate change.
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Affiliation(s)
- Benjamin R K Runkle
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, USA.
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Vennis IM, Schaap MM, Hogervorst PAM, de Bruin A, Schulpen S, Boot MA, van Passel MWJ, Rutjes SA, Bleijs DA. Dual-Use Quickscan: A Web-Based Tool to Assess the Dual-Use Potential of Life Science Research. Front Bioeng Biotechnol 2021; 9:797076. [PMID: 34957083 PMCID: PMC8696162 DOI: 10.3389/fbioe.2021.797076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/03/2021] [Indexed: 12/02/2022] Open
Abstract
Research on pathogenic organisms is crucial for medical, biological and agricultural developments. However, biological agents as well as associated knowledge and techniques, can also be misused, for example for the development of biological weapons. Potential malicious use of well-intended research, referred to as “dual-use research”, poses a threat to public health and the environment. There are various international resources providing frameworks to assess dual-use potential of the research concerned. However, concrete instructions for researchers on how to perform a dual-use risk assessment is largely lacking. The international need for practical dual-use monitoring and risk assessment instructions, in addition to the need to raise awareness among scientists about potential dual-use aspects of their research has been identified over the last years by the Netherlands Biosecurity Office, through consulting national and international biorisk stakeholders. We identified that Biorisk Management Advisors and researchers need a practical tool to facilitate a dual-use assessment on their specific research. Therefore, the Netherlands Biosecurity Office developed a web-based Dual-Use Quickscan (www.dualusequickscan.com), that can be used periodically by researchers working with microorganisms to assess potential dual-use risks of their research by answering a set of fifteen yes/no questions. The questions for the tool were extracted from existing international open resources, and categorized into three themes: characteristics of the biological agent, knowledge and technology about the biological agent, and consequences of misuse. The results of the Quickscan provide the researcher with an indication of the dual-use potential of the research and can be used as a basis for further discussions with a Biorisk Management Advisor. The Dual-Use Quickscan can be embedded in a broader system of biosafety and biosecurity that includes dual-use monitoring and awareness within organizations. Increased international attention to examine pathogens with pandemic potential has been enhanced by the current COVID-19 pandemic, hence monitoring of dual-use potential urgently needs to be encouraged.
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Affiliation(s)
- Iris M Vennis
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Mirjam M Schaap
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Petra A M Hogervorst
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Arnout de Bruin
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Sjors Schulpen
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Marijke A Boot
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Mark W J van Passel
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Saskia A Rutjes
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Diederik A Bleijs
- Biosecurity Office, National Institute for Public Health and the Environment, Bilthoven, Netherlands
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Moore SJ, Hleba YB, Bischoff S, Bell D, Polizzi KM, Freemont PS. Refactoring of a synthetic raspberry ketone pathway with EcoFlex. Microb Cell Fact 2021; 20:116. [PMID: 34112158 PMCID: PMC8193874 DOI: 10.1186/s12934-021-01604-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/31/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND A key focus of synthetic biology is to develop microbial or cell-free based biobased routes to value-added chemicals such as fragrances. Originally, we developed the EcoFlex system, a Golden Gate toolkit, to study genes/pathways flexibly using Escherichia coli heterologous expression. In this current work, we sought to use EcoFlex to optimise a synthetic raspberry ketone biosynthetic pathway. Raspberry ketone is a high-value (~ £20,000 kg-1) fine chemical farmed from raspberry (Rubeus rubrum) fruit. RESULTS By applying a synthetic biology led design-build-test-learn cycle approach, we refactor the raspberry ketone pathway from a low level of productivity (0.2 mg/L), to achieve a 65-fold (12.9 mg/L) improvement in production. We perform this optimisation at the prototype level (using microtiter plate cultures) with E. coli DH10β, as a routine cloning host. The use of E. coli DH10β facilitates the Golden Gate cloning process for the screening of combinatorial libraries. In addition, we also newly establish a novel colour-based phenotypic screen to identify productive clones quickly from solid/liquid culture. CONCLUSIONS Our findings provide a stable raspberry ketone pathway that relies upon a natural feedstock (L-tyrosine) and uses only constitutive promoters to control gene expression. In conclusion we demonstrate the capability of EcoFlex for fine-tuning a model fine chemical pathway and provide a range of newly characterised promoter tools gene expression in E. coli.
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Affiliation(s)
- Simon J Moore
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,School of Biosciences, University of Kent, CT2 7NJ, Canterbury, England
| | - Yonek B Hleba
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK
| | - Sarah Bischoff
- School of Biosciences, University of Kent, CT2 7NJ, Canterbury, England
| | - David Bell
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK
| | - Karen M Polizzi
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department of Life Sciences, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department of Chemical Engineering, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK.
| | - Paul S Freemont
- Centre for Synthetic Biology and Innovation, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,Department Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, South Kensington Campus, Exhibition Road, London, SW7 2AZ, UK. .,The London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ, UK. .,Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.
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8
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Autran D, Bassel GW, Chae E, Ezer D, Ferjani A, Fleck C, Hamant O, Hartmann FP, Jiao Y, Johnston IG, Kwiatkowska D, Lim BL, Mahönen AP, Morris RJ, Mulder BM, Nakayama N, Sozzani R, Strader LC, ten Tusscher K, Ueda M, Wolf S. What is quantitative plant biology? QUANTITATIVE PLANT BIOLOGY 2021; 2:e10. [PMID: 37077212 PMCID: PMC10095877 DOI: 10.1017/qpb.2021.8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 05/03/2023]
Abstract
Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.
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Affiliation(s)
- Daphné Autran
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - George W. Bassel
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Eunyoung Chae
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Daphne Ezer
- The Alan Turing Institute, London, United Kingdom
- Department of Statistics, University of Warwick, Coventry, United Kingdom
- Department of Biology, University of York, York, United Kingdom
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Tokyo, Japan
| | - Christian Fleck
- Freiburg Center for Data Analysis and Modeling (FDM), University of Freiburg, Breisgau, Germany
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, École normale supérieure (ENS) de Lyon, Université Claude Bernard Lyon (UCBL), Lyon, France
- Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE), CNRS, Université de Lyon, Lyon, France
| | | | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Dorota Kwiatkowska
- Institute of Biology, Biotechnology and Environment Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Boon L. Lim
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Ari Pekka Mahönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Richard J. Morris
- Computational and Systems Biology, John Innes Centre, Norwich, United Kingdom
| | - Bela M. Mulder
- Department of Living Matter, Institute AMOLF, Amsterdam, The Netherlands
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Ross Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North CarolinaUSA
| | - Lucia C. Strader
- Department of Biology, Duke University, Durham, North Carolina, USA
- NSF Science and Technology Center for Engineering Mechanobiology, Department of Biology, Washington University in St. Louis, St. Louis, MissouriUSA
| | - Kirsten ten Tusscher
- Theoretical Biology, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Minako Ueda
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Sebastian Wolf
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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Taylor NG, Grillas P, Al Hreisha H, Balkız Ö, Borie M, Boutron O, Catita A, Champagnon J, Cherif S, Çiçek K, Costa LT, Dakki M, Fois M, Galewski T, Galli A, Georgiadis NM, Green AJ, Hermoso V, Kapedani R, Lange MA, Mateljak Z, Osta M, Papastergiadou E, Papazoglou C, Sabater S, Samraoui B, Samraoui F, Bachir AS, Tankovic E, Thévenet M, Troya A, Sutherland WJ. The future for Mediterranean wetlands: 50 key issues and 50 important conservation research questions. REGIONAL ENVIRONMENTAL CHANGE 2021; 21:33. [PMID: 33776560 PMCID: PMC7982080 DOI: 10.1007/s10113-020-01743-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/28/2020] [Indexed: 06/01/2023]
Abstract
UNLABELLED Wetlands are critically important for biodiversity and human wellbeing, but face a range of challenges. This is especially true in the Mediterranean region, where wetlands support endemic and threatened species and remain integral to human societies, but have been severely degraded in recent decades. Here, in order to raise awareness of future challenges and opportunities for Mediterranean wetlands, and to inform proactive research and management, we identified (a) 50 key issues that might affect Mediterranean wetlands between 2020 and 2050, and (b) 50 important research questions that, if answered, would have the greatest impact on the conservation of Mediterranean wetlands between 2020 and 2050. We gathered ideas through an online survey and review of recent literature. A diverse assessment panel prioritised ideas through an iterative, anonymised, Delphi-like process of scoring, voting and discussion. The prioritised issues included some that are already well known but likely to have a large impact on Mediterranean wetlands in the next 30 years (e.g. the accumulation of dams and reservoirs, plastic pollution and weak governance), and some that are currently overlooked in the context of Mediterranean wetlands (e.g. increasing desalination capacity and development of antimicrobial resistance). Questions largely focused on how best to carry out conservation interventions, or understanding the impacts of threats to inform conservation decision-making. This analysis will support research, policy and practice related to environmental conservation and sustainable development in the Mediterranean, and provides a model for similar analyses elsewhere in the world. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10113-020-01743-1.
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Affiliation(s)
- Nigel G. Taylor
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
| | - Patrick Grillas
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
| | | | - Özge Balkız
- Doğa Koruma Merkezi (Nature Conservation Centre), Çiğdem Mah. 1594. Sok. No:3 06530, Çankaya, Ankara Turkey
| | - Maud Borie
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
- Department of Geography, King’s College London, London, WC2R 2LS UK
| | - Olivier Boutron
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
| | - Ana Catita
- Development and Innovation Network (RCDI), Centro Empresarial de Grândola, Fracção E - Incubadora de Empresas- Estrada da Aldeia do Futuro, 7570-272 Grândola, Portugal
- Associação Portuguesa de Geógrafos, Instituto de Ciências Sociais, Av. Professor Aníbal Bettencourt, n.° 9, 1600-189 Lisboa, Portugal
- Associação Portuguesa para o Desenvolvimento Regional, Universidade dos Açores, Rua Capitão João D’Ávila, 9700-042 Angra do Heroísmo, Portugal
| | - Jocelyn Champagnon
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
| | - Semia Cherif
- Laboratoire de Recherche des Matériaux et de l’Environnement pour le Développement Durable (LR18ES10), ISSBAT, Université de Tunis El Manar, 9 Avenue Zouheir Essefi, 1006 Tunis, Tunisia
| | - Kerim Çiçek
- Section of Zoology, Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
| | - Luís T. Costa
- MAVA Foundation, Rue Mauverney 28, 1196 Gland, Switzerland
| | - Mohamed Dakki
- Département de Zoologie et Écologie Animale, Institut Scientifique, Université Mohammed V de Rabat, Rabat, Morocco
- Centre d’Etude des Migrations d’Oiseaux (CEMO), Institut Scientifique, Université Mohammed V de Rabat, Rabat, Morocco
| | - Mauro Fois
- Centro Conservazione Biodiversità, Dipartimento di Scienze della Vita e dell’Ambiente, Università degli Studi di Cagliari, Viale S. Ignazio da Laconi, 13, 09123 Cagliari, Italy
| | - Thomas Galewski
- Tour du Valat, Research Institute for the Conservation of Mediterranean Wetlands, 13200 Arles, France
| | - Alessandro Galli
- Global Footprint Network, Avenue Louis-Casaï, 18, 1209 Geneva, Switzerland
| | | | - Andy J. Green
- Department of Wetland Ecology, Estación Biológica de Doñana, EBD-CSIC, Américo Vespucio 26, 41092 Sevilla, Spain
| | - Virgilio Hermoso
- Centre de Ciència i Tecnologia Forestal de Catalunya (CTFC), Solsona, Spain
- Australian Rivers Institute, Griffith University, Nathan, Queensland Australia
| | - Rezart Kapedani
- Regional Environmental Center Albania, Rr. Ismail Qemali, No. 27, Kati/Floor 3, 1000 Tirana, Albania
| | - Manfred A. Lange
- Energy, Environment and Water Research Center, The Cyprus Institute, Nicosia, Cyprus
- Future Earth MENA Regional Center at the Cyprus Institute, Nicosia, Cyprus
| | | | - Maher Osta
- Society for the Protection of Nature in Lebanon, Awad Bldg, 6th Floor, Abdel Aziz Street, P.O. Box 11-5665, Beirut, Lebanon
| | - Eva Papastergiadou
- Department of Biology, University of Patras, University Campus Rio, Patras, 26500 Greece
| | | | - Sergi Sabater
- Catalan Institute for Water Research (ICRA), Emili Grahit 101, 17003 Girona, Spain
- Institute of Aquatic Ecology, University of Girona, Girona, 17003 Spain
| | - Boudjéma Samraoui
- Department of Biology, University Badji Mokhtar Annaba, Annaba, Algeria
- Laboratoire de Conservation des Zones Humides, Université 8 Mai 1945 Guelma, Guelma, Algeria
| | - Farrah Samraoui
- Laboratoire de Conservation des Zones Humides, Université 8 Mai 1945 Guelma, Guelma, Algeria
- Department of Ecology, University 8 Mai 1945 Guelma, Guelma, Algeria
| | - Abdelkrim Si Bachir
- Department of Ecology and Environment, Faculty of Life and Nature Sciences, University of Batna 2, Batna, Algeria
| | - Eva Tankovic
- Mediterranean Small Islands Initiative (PIM), Lycée des Calanques, 89 Traverse Parangon, 13008 Marseille, France
| | - Mathieu Thévenet
- Mediterranean Small Islands Initiative (PIM), Lycée des Calanques, 89 Traverse Parangon, 13008 Marseille, France
| | - Antonio Troya
- IUCN Centre for Mediterranean Cooperation, C/ Marie Curie 22, Edif. Habitec, Parque Tecnológico de Andalucía, 29590 Campanillas, Málaga, Spain
| | - William J. Sutherland
- Department of Zoology, University of Cambridge, The David Attenborough Building, Pembroke Street, Cambridge, CB2 3QZ UK
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10
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Mao N, Aggarwal N, Poh CL, Cho BK, Kondo A, Liu C, Yew WS, Chang MW. Future trends in synthetic biology in Asia. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10038. [PMID: 36618442 PMCID: PMC9744534 DOI: 10.1002/ggn2.10038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/10/2021] [Accepted: 01/21/2021] [Indexed: 05/06/2023]
Abstract
Synthetic biology research and technology translation has garnered increasing interest from the governments and private investors in Asia, where the technology has great potential in driving a sustainable bio-based economy. This Perspective reviews the latest developments in the key enabling technologies of synthetic biology and its application in bio-manufacturing, medicine, food and agriculture in Asia. Asia-centric strengths in synthetic biology to grow the bio-based economy, such as advances in genome editing and the presence of biofoundries combined with the availability of natural resources and vast markets, are also highlighted. The potential barriers to the sustainable development of the field, including inadequate infrastructure and policies, with suggestions to overcome these by building public-private partnerships, more effective multi-lateral collaborations and well-developed governance framework, are presented. Finally, the roles of technology, education and regulation in mitigating potential biosecurity risks are examined. Through these discussions, stakeholders from different groups, including academia, industry and government, are expectantly better positioned to contribute towards the establishment of innovation and bio-economy hubs in Asia.
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Affiliation(s)
- Ning Mao
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
| | - Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringNational University of SingaporeSingaporeSingapore
| | - Byung Kwan Cho
- Department of Biological Sciences, and KI for the BioCenturyKorea Advanced Institute of Science and TechnologyDaejeonSouth Korea
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, and Engineering Biology Research CenterKobe UniversityKobeJapan
| | - Chenli Liu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina
| | - Wen Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research Program and Department of Biochemistry, Yong Loo Ling School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Biomedical EngineeringNational University of SingaporeSingaporeSingapore
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11
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Elgabry M, Nesbeth D, Johnson SD. A Systematic Review of the Criminogenic Potential of Synthetic Biology and Routes to Future Crime Prevention. Front Bioeng Biotechnol 2020; 8:571672. [PMID: 33123514 PMCID: PMC7573185 DOI: 10.3389/fbioe.2020.571672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/01/2020] [Indexed: 11/21/2022] Open
Abstract
Synthetic biology has the potential to positively transform society in many application areas, including medicine. In common with all revolutionary new technologies, synthetic biology can also enable crime. Like cybercrime, that emerged following the advent of the internet, biocrime can have a significant effect on society, but may also impact on peoples' health. For example, the scale of harm caused by the SARS-CoV-2 pandemic illustrates the potential impact of future biocrime and highlights the need for prevention strategies. Systematic evidence quantifying the crime opportunities posed by synthetic biology has to date been very limited. Here, we systematically reviewed forms of crime that could be facilitated by synthetic biology with a view to informing their prevention. A total of 794 articles from four databases were extracted and a three-step screening phase resulted in 15 studies that met our threshold criterion for thematic synthesis. Within those studies, 13 exploits were identified. Of these, 46% were dependent on technologies characteristic of synthetic biology. Eight potential crime types emerged from the studies: bio-discrimination, cyber-biocrime, bio-malware, biohacking, at-home drug manufacturing, illegal gene editing, genetic blackmail, and neuro-hacking. 14 offender types were identified. For the most commonly identified offenders (>3 mentions) 40% were outsider threats. These observations suggest that synthetic biology presents substantial new offending opportunities. Moreover, that more effective engagement, such as ethical hacking, is needed now to prevent a crime harvest from developing in the future. A framework to address the synthetic biology crime landscape is proposed.
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Affiliation(s)
- Mariam Elgabry
- Dawes Center for Future Crime, Jill Dando Institute, Department of Security and Crime Science, University College London, London, United Kingdom.,Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Darren Nesbeth
- Advanced Centre for Biochemical Engineering, University College London, London, United Kingdom
| | - Shane D Johnson
- Dawes Center for Future Crime, Jill Dando Institute, Department of Security and Crime Science, University College London, London, United Kingdom
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12
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Mueller S. Facing the 2020 pandemic: What does cyberbiosecurity want us to know to safeguard the future? BIOSAFETY AND HEALTH 2020; 3:11-21. [PMID: 33015604 PMCID: PMC7518802 DOI: 10.1016/j.bsheal.2020.09.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 01/26/2023] Open
Abstract
As the entire world is under the grip of the coronavirus disease 2019 (COVID-19), and as many are eagerly trying to explain the origins of the virus and cause of the pandemic, it is imperative to place more attention on related potential biosafety risks. Biology and biotechnology have changed dramatically during the last ten years or so. Their reliance on digitization, automation, and their cyber-overlaps have created new vulnerabilities for unintended consequences and potentials for intended exploitation that are mostly under-appreciated. This study summarizes and elaborates on these new cyberbiosecurity challenges, (1) in terms of comprehending the evolving threat landscape and determining new risk potentials, (2) in developing adequate safeguarding measures, their validation and implementation, and (3) specific critical risks and consequences, many of them unique to the life-sciences. Drawing other's expertise and my previous work, this article reviews and critically interprets our current bio-economy situation. The goal is not to attribute causative aspects of past biosafety or biosecurity events, but to highlight the fact that the bioeconomy harbors unique features that have to be more critically assessed for their potential to unintentionally cause harm to human health or environment, or to be re-tasked with an intention to cause harm. It is concluded with recommendations that will need to be considered to help ensure converging and emerging biorisk challenges, in order to minimize vulnerabilities to the life-science enterprise, public health, and national security.
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13
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Kemp L, Adam L, Boehm CR, Breitling R, Casagrande R, Dando M, Djikeng A, Evans NG, Hammond R, Hills K, Holt LA, Kuiken T, Markotić A, Millett P, Napier JA, Nelson C, ÓhÉigeartaigh SS, Osbourn A, Palmer MJ, Patron NJ, Perello E, Piyawattanametha W, Restrepo-Schild V, Rios-Rojas C, Rhodes C, Roessing A, Scott D, Shapira P, Simuntala C, Smith RDJ, Sundaram LS, Takano E, Uttmark G, Wintle BC, Zahra NB, Sutherland WJ. Bioengineering horizon scan 2020. eLife 2020; 9:e54489. [PMID: 32479263 PMCID: PMC7259952 DOI: 10.7554/elife.54489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 05/14/2020] [Indexed: 01/01/2023] Open
Abstract
Horizon scanning is intended to identify the opportunities and threats associated with technological, regulatory and social change. In 2017 some of the present authors conducted a horizon scan for bioengineering (Wintle et al., 2017). Here we report the results of a new horizon scan that is based on inputs from a larger and more international group of 38 participants. The final list of 20 issues includes topics spanning from the political (the regulation of genomic data, increased philanthropic funding and malicious uses of neurochemicals) to the environmental (crops for changing climates and agricultural gene drives). The early identification of such issues is relevant to researchers, policy-makers and the wider public.
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Affiliation(s)
- Luke Kemp
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | | | - Christian R Boehm
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Faculty of Science and Bioengineering, University of ManchesterManchesterUnited Kingdom
| | | | - Malcolm Dando
- Division of Peace Studies and International Development, University of BradfordBradfordUnited Kingdom
| | - Appolinaire Djikeng
- Centre for Tropical Livestock Genetics and Health, Royal (Dick) School of Veterinary StudiesEdinburghUnited Kingdom
| | - Nicholas G Evans
- Department of Philosophy, University of MassachusettsLowellUnited States
- Rogue BioethicsLowellUnited States
| | | | | | - Lauren A Holt
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Todd Kuiken
- Genetic Engineering and Society Center, North Carolina State UniversityRaleighUnited States
| | - Alemka Markotić
- University Hospital for Infectious DiseasesZagrebCroatia
- Medical School, University of RijekaRijekaCroatia
- Catholic University of CroatiaZagrebCroatia
| | - Piers Millett
- Future of Humanity Institute, University of OxfordOxfordUnited Kingdom
- iGem FoundationBostonUnited States
| | | | - Cassidy Nelson
- Future of Humanity Institute, University of OxfordOxfordUnited Kingdom
| | - Seán S ÓhÉigeartaigh
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | | | - Megan J Palmer
- Center for International Security and Cooperation (CSIAC), Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | | | | | - Wibool Piyawattanametha
- Biomedical Engineering Department, Faculty of Engineering, King Mongkut's Institute of Technology LadkrabangBangkokThailand
- Institute for Quantitative Health Sciences and Engineering, Michigan State UniversityEast LansingUnited States
| | | | - Clarissa Rios-Rojas
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Ekpa’Palek: Empowering Latin-American Young ProfessionalsLimaPeru
| | - Catherine Rhodes
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Anna Roessing
- Department of Politics, Languages and International Studies, University of BathBathUnited Kingdom
| | - Deborah Scott
- Science, Technology & Innovation Studies, School of Social and Political Science, University of EdinburghEdinburghUnited Kingdom
| | - Philip Shapira
- Manchester Institute of Innovation Research, Alliance Manchester Business School, University of ManchesterManchesterUnited Kingdom
- SYNBIOCHEM, University of ManchesterManchesterUnited Kingdom
- School of Public Policy, Georgia Institute of TechnologyAtlantaUnited States
| | | | - Robert DJ Smith
- Science, Technology & Innovation Studies, School of Social and Political Science, University of EdinburghEdinburghUnited Kingdom
| | - Lalitha S Sundaram
- Centre for the Study of Existential Risk (CSER), University of CambridgeCambridgeUnited Kingdom
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
| | - Eriko Takano
- Manchester Institute of Biotechnology, Faculty of Science and Bioengineering, University of ManchesterManchesterUnited Kingdom
| | - Gwyn Uttmark
- Department of Chemistry, Stanford UniversityStanfordUnited States
| | - Bonnie C Wintle
- School of BioSciences, University of MelbourneMelbourneAustralia
| | - Nadia B Zahra
- Department of Biotechnology, Qarshi UniversityLahorePakistan
| | - William J Sutherland
- Biosecurity Research Initiative at St Catharine’s College, University of CambridgeCambridgeUnited Kingdom
- Department of Zoology, University of CambridgeCambridgeUnited Kingdom
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14
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Esmail N, Wintle BC, t Sas‐Rolfes M, Athanas A, Beale CM, Bending Z, Dai R, Fabinyi M, Gluszek S, Haenlein C, Harrington LA, Hinsley A, Kariuki K, Lam J, Markus M, Paudel K, Shukhova S, Sutherland WJ, Verissimo D, Wang Y, Waugh J, Wetton JH, Workman C, Wright J, Milner‐Gulland EJ. Emerging illegal wildlife trade issues: A global horizon scan. Conserv Lett 2020. [DOI: 10.1111/conl.12715] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Affiliation(s)
- Nafeesa Esmail
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
| | | | - Michael t Sas‐Rolfes
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
| | | | - Colin M. Beale
- University of York York United Kingdom of Great Britain and Northern Ireland
| | - Zara Bending
- The Jane Goodall Institute Global Vienna Austria
- Macquarie University Sydney Australia
| | - Ran Dai
- King Mongkut's University of Technology Thonburi Bangkok Thailand
| | | | - Sarah Gluszek
- Fauna & Flora International Cambridge United Kingdom of Great Britain and Northern Ireland
| | - Cathy Haenlein
- Royal United Services Institute for Defence and Security Studies London London United Kingdom of Great Britain and Northern Ireland
| | - Lauren A. Harrington
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
| | - Amy Hinsley
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
| | | | - Jack Lam
- City University of Hong Kong Hong Kong China
| | | | | | - Sofiya Shukhova
- Animal Concerns Research and Education Society Singapore Singapore
| | - William J. Sutherland
- University of Cambridge Cambridge United Kingdom of Great Britain and Northern Ireland
| | - Diogo Verissimo
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
- Institute for Conservation ResearchSan Diego Zoo Global San Diego United States
| | - Yifu Wang
- University of Cambridge Cambridge United Kingdom of Great Britain and Northern Ireland
| | - John Waugh
- Integra Government Services International Washington United States
| | - Jon H. Wetton
- Department of Genetics and Genome BiologyUniversity of Leicester Leicester United Kingdom of Great Britain and Northern Ireland
| | | | - Joss Wright
- University of Oxford Oxford United Kingdom of Great Britain and Northern Ireland
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15
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Understanding and Harnessing Variability in Regenerative Engineering. REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE 2020. [DOI: 10.1007/s40883-020-00155-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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A Dixon T, C Curach N, Pretorius IS. Bio-informational futures: The convergence of artificial intelligence and synthetic biology. EMBO Rep 2020; 21:e50036. [PMID: 32043291 DOI: 10.15252/embr.202050036] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Synthetic biology and artificial intelligence naturally converge in the biofoundry. Navigating the ethical and societal issues of the biofoundry's potential remains a major challenge.
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Affiliation(s)
- Thom A Dixon
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Natalie C Curach
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia.,Bioplatforms Australia, Macquarie University, Sydney, NSW, Australia
| | - Isak S Pretorius
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
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17
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What is the resource footprint of a computer science department? Place, people, and Pedagogy. DATA & POLICY 2020. [DOI: 10.1017/dap.2020.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractInternet and Communication Technology/electrical and electronic equipment (ICT/EEE) form the bedrock of today’s knowledge economy. This increasingly interconnected web of products, processes, services, and infrastructure is often invisible to the user, as are the resource costs behind them. This ecosystem of machine-to-machine and cyber-physical-system technologies has a myriad of (in)direct impacts on the lithosphere, biosphere, atmosphere, and hydrosphere. As key determinants of tomorrow’s digital world, academic institutions are critical sites for exploring ways to mitigate and/or eliminate negative impacts. This Report is a self-deliberation provoked by the questionHow do we create more resilient and healthier computer science departments: living laboratories for teaching and learning about resource-constrained computing, computation, and communication?Our response for University College London (UCL) Computer Science is to reflect on how, when, and where resources—energy, (raw) materials including water, space, and time—are consumed by the building (place), its occupants (people), and their activities (pedagogy). This perspective and attendant first-of-its-kind assessment outlines a roadmap and proposes high-level principles to aid our efforts, describing challenges and difficulties hindering quantification of the Department’s resource footprint. Qualitatively, we find a need to rematerialise the ICT/EEE ecosystem: to reveal the full costs of the seemingly intangible information society by interrogating the entire life history of paraphernalia from smartphones through servers to underground/undersea cables; another approach is demonstrating the corporeality of commonplace phrases and Nature-inspired terms such as artificial intelligence, social media, Big Data, smart cities/farming, the Internet, the Cloud, and the Web. We sketch routes to realising three interlinked aims: cap annual power consumption and greenhouse gas emissions, become a zero waste institution, and rejuvenate and (re)integrate the natural and built environments.
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18
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Hraber P, O'Maille PE, Silberfarb A, Davis-Anderson K, Generous N, McMahon BH, Fair JM. Resources to Discover and Use Short Linear Motifs in Viral Proteins. Trends Biotechnol 2020; 38:113-127. [PMID: 31427097 PMCID: PMC7114124 DOI: 10.1016/j.tibtech.2019.07.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/11/2019] [Accepted: 07/15/2019] [Indexed: 12/23/2022]
Abstract
Viral proteins evade host immune function by molecular mimicry, often achieved by short linear motifs (SLiMs) of three to ten consecutive amino acids (AAs). Motif mimicry tolerates mutations, evolves quickly to modify interactions with the host, and enables modular interactions with protein complexes. Host cells cannot easily coordinate changes to conserved motif recognition and binding interfaces under selective pressure to maintain critical signaling pathways. SLiMs offer potential for use in synthetic biology, such as better immunogens and therapies, but may also present biosecurity challenges. We survey viral uses of SLiMs to mimic host proteins, and information resources available for motif discovery. As the number of examples continues to grow, knowledge management tools are essential to help organize and compare new findings.
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Affiliation(s)
- Peter Hraber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Paul E O'Maille
- Biosciences Division, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Andrew Silberfarb
- Artificial Intelligence Center, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025, USA
| | - Katie Davis-Anderson
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nicholas Generous
- Global Security Directorate, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Jeanne M Fair
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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19
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Coleman MA, Goold HD. Harnessing synthetic biology for kelp forest conservation 1. JOURNAL OF PHYCOLOGY 2019; 55:745-751. [PMID: 31152453 DOI: 10.1111/jpy.12888] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/17/2019] [Indexed: 06/09/2023]
Abstract
Environmental and climatic change is outpacing the ability of organisms to adapt, at an unprecedented level, resulting in range contractions and global ecosystem shifts to novel states. At the same time, scientific advances continue to accelerate, providing never-before imagined solutions to current and emerging environmental problems. Synthetic biology, the creation of novel and engineered genetic variation, is perhaps the fastest developing and transformative scientific field. Its application to solve extant and emerging environmental problems is vast, at times controversial, and technological advances have outpaced the social, ethical, and practical considerations of its use. Here, we discuss the potential direct and indirect applications of synthetic biology to kelp forest conservation. Rather than advocate or oppose its use, we identify where and when it may play a role in halting or reversing global kelp loss and discuss challenges and identify pathways of research needed to bridge the gap between technological advances and organismal biology and ecology. There is a pressing need for prompt collaboration and dialogue among synthetic biologists, ecologists, and conservationists to identify opportunities for use and ensure that extant research directions are set on trajectories to allow these currently disparate fields to converge toward practical environmental solutions.
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Affiliation(s)
- Melinda A Coleman
- Department of Primary Industries, NSW Fisheries, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, New South Wales, 2450, Australia
- Southern Cross University, National Marine Science Centre, 2 Bay Drive, Coffs Harbour, New South Wales, 2450, Australia
- University of Western Australia Oceans Institute and School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Hugh D Goold
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, New South Wales, 2568, Australia
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, 2109, Australia
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20
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Richardson LC, Connell ND, Lewis SM, Pauwels E, Murch RS. Cyberbiosecurity: A Call for Cooperation in a New Threat Landscape. Front Bioeng Biotechnol 2019; 7:99. [PMID: 31245363 PMCID: PMC6562220 DOI: 10.3389/fbioe.2019.00099] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The life sciences now interface broadly with information technology (IT) and cybersecurity. This convergence is a key driver in the explosion of biotechnology research and its industrial applications in health care, agriculture, manufacturing, automation, artificial intelligence, and synthetic biology. As the information and handling mechanisms for biological materials have become increasingly digitized, many market sectors are now vulnerable to threats at the digital interface. This growing landscape will be addressed by cyberbiosecurity, the emerging field at the convergence of both the life sciences and IT disciplines. This manuscript summarizes the current cyberbiosecurity landscape, identifies existing vulnerabilities, and calls for formalized collaboration across a swath of disciplines to develop frameworks for early response systems to anticipate, identify, and mitigate threats in this emerging domain.
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Affiliation(s)
| | - Nancy D Connell
- Johns Hopkins Center for Health Security, Bloomberg School of Public Health, Baltimore, MD, United States
| | | | - Eleonore Pauwels
- Wilson Center Science and Technology Innovation Program, The Wilson Center, Washington, DC, United States
| | - Randy S Murch
- Virginia Tech Research Center, School of Public and International Affairs, Virginia Polytechnic Institute and State University, Arlington, VA, United States
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21
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Rhee SY, Birnbaum KD, Ehrhardt DW. Towards Building a Plant Cell Atlas. TRENDS IN PLANT SCIENCE 2019; 24:303-310. [PMID: 30777643 PMCID: PMC7449582 DOI: 10.1016/j.tplants.2019.01.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 05/03/2023]
Abstract
Enormous societal challenges, such as feeding and providing energy for a growing population in a dramatically changing climate, necessitate technological advances in plant science. Plant cells are fundamental organizational units that mediate the production, transport, and storage of our primary food sources, and they sequester a significant proportion of the world's carbon. New technologies allow comprehensive descriptions of cells that could accelerate research across fields of plant science. Complementary to the efforts towards understanding the cellular diversity in human brain and immune systems, a Plant Cell Atlas (PCA) that maps molecular machineries to cellular and subcellular domains, follows their dynamic movements, and describes their interactions would accelerate discovery in plant science and help to solve imminent societal problems.
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Affiliation(s)
- Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
| | | | - David W Ehrhardt
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA 94305, USA.
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22
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Schabacker DS, Levy LA, Evans NJ, Fowler JM, Dickey EA. Assessing Cyberbiosecurity Vulnerabilities and Infrastructure Resilience. Front Bioeng Biotechnol 2019; 7:61. [PMID: 31001526 PMCID: PMC6455068 DOI: 10.3389/fbioe.2019.00061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/05/2019] [Indexed: 01/03/2023] Open
Abstract
The convergence of advances in biotechnology with laboratory automation, access to data, and computational biology has democratized biotechnology and accelerated the development of new therapeutics. However, increased access to biotechnology in the digital age has also introduced additional security concerns and ultimately, spawned the new discipline of cyberbiosecurity, which encompasses cybersecurity, cyber-physical security, and biosecurity considerations. With the emergence of this new discipline comes the need for a logical, repeatable, and shared approach for evaluating facility and system vulnerabilities to cyberbiosecurity threats. In this paper, we outline the foundation of an assessment framework for cyberbiosecurity, accounting for both security and resilience factors in the physical and cyber domains. This is a unique problem set, but despite the complexity of the cyberbiosecurity field in terms of operations and governance, previous experience developing and implementing physical and cyber assessments applicable to a wide spectrum of critical infrastructure sectors provides a validated point of departure for a cyberbiosecurity assessment framework. This approach proposes to integrate existing capabilities and proven methodologies from the infrastructure assessment realm (e.g., decision science, physical security, infrastructure resilience, cybersecurity) with new expertise and requirements in the cyberbiosecurity space (e.g., biotechnology, biomanufacturing, genomics) in order to forge a flexible and defensible approach to identifying and mitigating vulnerabilities. Determining where vulnerabilities reside within cyberbiosecurity business processes can help public and private sector partners create an assessment framework to identify mitigation options for consideration that are both economically and practically viable and ultimately, allow them to manage risk more effectively.
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Affiliation(s)
- Daniel S Schabacker
- Argonne National Laboratory (DOE), Strategic Security Sciences Division, Lemont, IL, United States
| | - Leslie-Anne Levy
- Argonne National Laboratory (DOE), Decision and Infrastructure Sciences Division, Lemont, IL, United States
| | - Nate J Evans
- Argonne National Laboratory (DOE), Strategic Security Sciences Division, Lemont, IL, United States
| | - Jennifer M Fowler
- Argonne National Laboratory (DOE), Strategic Security Sciences Division, Lemont, IL, United States
| | - Ellen A Dickey
- Argonne National Laboratory (DOE), Strategic Security Sciences Division, Lemont, IL, United States
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Duncan SE, Reinhard R, Williams RC, Ramsey F, Thomason W, Lee K, Dudek N, Mostaghimi S, Colbert E, Murch R. Cyberbiosecurity: A New Perspective on Protecting U.S. Food and Agricultural System. Front Bioeng Biotechnol 2019; 7:63. [PMID: 30984752 PMCID: PMC6450256 DOI: 10.3389/fbioe.2019.00063] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
Our national data and infrastructure security issues affecting the "bioeconomy" are evolving rapidly. Simultaneously, the conversation about cyber security of the U.S. food and agricultural system (cyber biosecurity) is incomplete and disjointed. The food and agricultural production sectors influence over 20% of the nation's economy ($6.7T) and 15% of U.S. employment (43.3M jobs). The food and agricultural sectors are immensely diverse and they require advanced technologies and efficiencies that rely on computer technologies, big data, cloud-based data storage, and internet accessibility. There is a critical need to safeguard the cyber biosecurity of our bio economy, but currently protections are minimal and do not broadly exist across the food and agricultural system. Using the food safety management Hazard Analysis Critical Control Point system concept as an introductory point of reference, we identify important features in broad food and agricultural production and food systems: dairy, food animals, row crops, fruits and vegetables, and environmental resources (water). This analysis explores the relevant concepts of cyber biosecurity from food production to the end product user (such as the consumer) and considers the integration of diverse transportation, supplier, and retailer networks. We describe common challenges and unique barriers across these systems and recommend solutions to advance the role of cyber biosecurity in the food and agricultural sectors.
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Affiliation(s)
- Susan E. Duncan
- Virginia Agricultural Experiment Station, Virginia Tech, Blacksburg, VA, United States
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Robert Reinhard
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
- Tyson Foods, Chicago, IL, United States
| | - Robert C. Williams
- Department of Food Science and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Ford Ramsey
- Department of Agricultural and Applied Economics, Virginia Tech, Blacksburg, VA, United States
| | - Wade Thomason
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Kiho Lee
- Department of Animal and Poultry Science, Virginia Tech, Blacksburg, VA, United States
| | - Nancy Dudek
- Virginia Agricultural Experiment Station, Virginia Tech, Blacksburg, VA, United States
| | - Saied Mostaghimi
- Virginia Agricultural Experiment Station, Virginia Tech, Blacksburg, VA, United States
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, United States
| | - Edward Colbert
- Hume Center for National Security and Technology, Virginia Tech, Blacksburg, VA, United States
| | - Randall Murch
- Department of Agricultural and Applied Economics, Virginia Tech, Blacksburg, VA, United States
- School of Public and International Affairs, Virginia Tech, Arlington, VA, United States
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24
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Goñi-Moreno A, de la Cruz F, Rodríguez-Patón A, Amos M. Dynamical Task Switching in Cellular Computers. Life (Basel) 2019; 9:E14. [PMID: 30691149 PMCID: PMC6463194 DOI: 10.3390/life9010014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/23/2018] [Accepted: 01/23/2019] [Indexed: 01/24/2023] Open
Abstract
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.
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Affiliation(s)
- Angel Goñi-Moreno
- School of Computing, Newcastle University, Newcastle Upon Tyne NE4 5TG, UK.
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria, 39011 Santander, Spain.
| | - Alfonso Rodríguez-Patón
- Departamento de Inteligencia Artificial, Universidad Politécnica de Madrid, 28660 Madrid, Spain.
| | - Martyn Amos
- Department of Computer and Information Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK.
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25
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Goold HD, Wright P, Hailstones D. Emerging Opportunities for Synthetic Biology in Agriculture. Genes (Basel) 2018; 9:E341. [PMID: 29986428 PMCID: PMC6071285 DOI: 10.3390/genes9070341] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/27/2018] [Accepted: 07/03/2018] [Indexed: 12/11/2022] Open
Abstract
Rapid expansion in the emerging field of synthetic biology has to date mainly focused on the microbial sciences and human health. However, the zeitgeist is that synthetic biology will also shortly deliver major outcomes for agriculture. The primary industries of agriculture, fisheries and forestry, face significant and global challenges; addressing them will be assisted by the sector’s strong history of early adoption of transformative innovation, such as the genetic technologies that underlie synthetic biology. The implementation of synthetic biology within agriculture may, however, be hampered given the industry is dominated by higher plants and mammals, where large and often polyploid genomes and the lack of adequate tools challenge the ability to deliver outcomes in the short term. However, synthetic biology is a rapidly growing field, new techniques in genome design and synthesis, and more efficient molecular tools such as CRISPR/Cas9 may harbor opportunities more broadly than the development of new cultivars and breeds. In particular, the ability to use synthetic biology to engineer biosensors, synthetic speciation, microbial metabolic engineering, mammalian multiplexed CRISPR, novel anti microbials, and projects such as Yeast 2.0 all have significant potential to deliver transformative changes to agriculture in the short, medium and longer term. Specifically, synthetic biology promises to deliver benefits that increase productivity and sustainability across primary industries, underpinning the industry’s prosperity in the face of global challenges.
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Affiliation(s)
- Hugh Douglas Goold
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
| | - Philip Wright
- New South Wales Department of Primary Industries, Locked Bag 21, 161 Kite St, Orange, NSW 2800, Australia.
| | - Deborah Hailstones
- New South Wales Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Road, Menangle, NSW 2568, Australia.
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26
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Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
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Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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27
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Starr S. How to talk about genome editing. Br Med Bull 2018; 126:5-12. [PMID: 29697749 PMCID: PMC5998984 DOI: 10.1093/bmb/ldy015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/15/2018] [Indexed: 11/13/2022]
Abstract
Background Human genome editing is an area of growing prominence, with many potential therapeutic applications. Sources of data A project by two UK charities, whose participants included fertility sector patients and practitioners and also people affected by genetic disease and rare disease. Scientific research into, and wider discussion of, genomics and genome editing. Areas of agreement There is a need for improved public and professional understanding of genome editing. Areas of controversy The way genome editing is discussed is often inconsistent and confusing. Simply defining and explaining the term 'genome' can present challenges. Growing points There are approaches that lend themselves to achieving greater clarity and coherence in discussion of genome editing. Areas timely for developing research People's understanding should ideally be able to withstand and evolve alongside current developments in genome editing, rather than being tied firmly to specific aspects of genome editing (which may in future be supplanted).
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Affiliation(s)
- Sandy Starr
- Progress Educational Trust, 140 Grays Inn Road, London, UK
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