Engineering biology最新文献

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Building capacity for the engineering of biology in Australia 澳大利亚生物工程的能力建设
Engineering biology Pub Date : 2021-06-13 DOI: 10.1049/enb2.12009
Natalie Curach
{"title":"Building capacity for the engineering of biology in Australia","authors":"Natalie Curach","doi":"10.1049/enb2.12009","DOIUrl":"10.1049/enb2.12009","url":null,"abstract":"<p>In Australia, synthetic biology has taken a gradual and rational passage of growth from a collective of discrete practitioners and projects to capacity building initiatives. These initiatives fall under the National Innovation and Science Agenda [2] and have culminated into the formation of hubs of scientific expertise and education supported by the leveraging and enhancement of existing infrastructure networks across the country. The spotlight on science has also motivated more of a whole-of-government response to strengthening the nation's entire innovation ecosystem. Policy changes to tax incentives and gene technology regulation have created a momentum which is seeing increasingly more financial backing from Australian and international investors in synthetic biology. With these structures in place, the opportunities afforded by engineering biology have opened for uplifting innovation and the formation of new industries.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"5 2","pages":"43-47"},"PeriodicalIF":0.0,"publicationDate":"2021-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/28/8c/ENB2-5-43.PMC9996691.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Defense Advanced Research Projects Agency: Comment on ‘Engineering biology and the grand challenges: Do we need a new R&D&I model?’ 美国国防部高级研究计划局:评论《工程生物学和重大挑战:我们是否需要一个新的研发与创新模式?》”
Engineering biology Pub Date : 2021-03-31 DOI: 10.1049/enb2.12007
Ilya Klabukov, Olga Krasilnikova
{"title":"Defense Advanced Research Projects Agency: Comment on ‘Engineering biology and the grand challenges: Do we need a new R&D&I model?’","authors":"Ilya Klabukov,&nbsp;Olga Krasilnikova","doi":"10.1049/enb2.12007","DOIUrl":"10.1049/enb2.12007","url":null,"abstract":"<p>This comment paper refers to the article published by Gauvreau et al. in <i>Engineering Biology</i> in 2018. Gauvreau et al. discussed various civilian models in the private and public sectors that could boost R&amp;D plus Innovation (R&amp;D&amp;I) progress in the environmental sphere. The authors concluded that there is no tried-and-tested R&amp;D&amp;I model for engineering biology that is suited to help solve the problems of many grand and interacting challenges, and further, that the required model will not work without the private sector, so governments must collaborate to develop such a model. However, the authors have not mentioned one of the most famous classic Research &amp; Development (R&amp;D) models used in the creation of disruptive technologies—a unique model of the Defense Advanced Research Projects Agency (DARPA) of the US Department of Defense. The present commentary poses questions about the models currently used in innovative research, known as DARPA-like R&amp;D agencies, and the innovative ecosystems around them.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"5 2","pages":"48-49"},"PeriodicalIF":0.0,"publicationDate":"2021-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/30/7b/ENB2-5-48.PMC9996693.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9560627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Responsible innovation: Its role in an era of technological and regulatory transformation 负责任的创新:它在技术和监管变革时代的作用
Engineering biology Pub Date : 2021-03-29 DOI: 10.1049/enb2.12005
Joyce Tait, Alex Brown, Isabela Cabrera Lalinde, Daniel Barlow, Matthew Chiles, Paul Mason
{"title":"Responsible innovation: Its role in an era of technological and regulatory transformation","authors":"Joyce Tait,&nbsp;Alex Brown,&nbsp;Isabela Cabrera Lalinde,&nbsp;Daniel Barlow,&nbsp;Matthew Chiles,&nbsp;Paul Mason","doi":"10.1049/enb2.12005","DOIUrl":"10.1049/enb2.12005","url":null,"abstract":"<p>In the development of innovative technology products, companies of all sizes are being encouraged to innovate responsibly and regulators are encouraged to adapt their regulatory systems to be smarter, more proportionate and adaptive to the needs of innovative technologies. The British Standards Institution Responsible Innovation (RI) Guide (Publicly Available Specification [PAS] 440) is an industry-wide standard relevant to both these policy trends. It supports companies by providing a framework to demonstrate the balance between the potential benefits and harms and, if necessary, to take action to maximise the benefits and/or minimise the harms. It includes guidance on engagement with stakeholders and will codify what stakeholders can expect from companies undertaking responsible innovation, paving the way to more harmonious relationships among stakeholders with differing interests and values. A cross-sectoral survey of innovative companies showed that 90% favoured the development of such a standard. PAS 440 was also trialled in two early-stage biotechnology companies and its expected benefits included contributing to coordinated responsible behaviour along a supply chain; better company and stakeholder understanding of the product properties; supporting decision-making on whether or not to start a company; considering the risks of not developing the product and avoiding reputational risks. Benefits were expected to be increasingly significant as the RI standard becomes widely adopted.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"5 1","pages":"2-9"},"PeriodicalIF":0.0,"publicationDate":"2021-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996694/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183398","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Optimising protein synthesis in cell-free systems, a review 在无细胞系统中优化蛋白质合成,综述
Engineering biology Pub Date : 2021-02-21 DOI: 10.1049/enb2.12004
Angelo C. Batista, Paul Soudier, Manish Kushwaha, Jean-Loup Faulon
{"title":"Optimising protein synthesis in cell-free systems, a review","authors":"Angelo C. Batista,&nbsp;Paul Soudier,&nbsp;Manish Kushwaha,&nbsp;Jean-Loup Faulon","doi":"10.1049/enb2.12004","DOIUrl":"10.1049/enb2.12004","url":null,"abstract":"<p>Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"5 1","pages":"10-19"},"PeriodicalIF":0.0,"publicationDate":"2021-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/fe/7a/ENB2-5-10.PMC9996726.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9191213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
Gene modification strategies using AO-mediated exon skipping and CRISPR/Cas9 as potential therapies for Duchenne muscular dystrophy patients 利用ao介导的外显子跳变和CRISPR/Cas9基因修饰策略作为治疗杜氏肌营养不良症的潜在疗法
Engineering biology Pub Date : 2020-12-09 DOI: 10.1049/enb.2020.0017
Marthe Helene Solberg, Maryam Shariatzadeh, Samantha L Wilson
{"title":"Gene modification strategies using AO-mediated exon skipping and CRISPR/Cas9 as potential therapies for Duchenne muscular dystrophy patients","authors":"Marthe Helene Solberg,&nbsp;Maryam Shariatzadeh,&nbsp;Samantha L Wilson","doi":"10.1049/enb.2020.0017","DOIUrl":"10.1049/enb.2020.0017","url":null,"abstract":"<div>\u0000 <p>Duchenne muscular dystrophy (DMD) is an X-linked genetic disease affecting 1 in 5000 young males worldwide annually. Patients experience muscle weakness and loss of ambulation at an early age, with ∼75% reduced life expectancy. Recently developed genetic editing strategies aim to convert severe DMD phenotypes to a milder disease course. Among these, the antisense oligonucleotide (AO)-mediated exon skipping and the adeno-associated viral-delivered clustered regularly interspaced short palindromic repeat (CRISPR) associated protein 9 (adeno-associated viral (AAV)-delivered CRISPR/Cas9) gene editing have shown promising results in restoring dystrophin protein expression and functionality in skeletal and heart muscle in both animals and human cells in vivo and in vitro. However, therapeutic benefits currently remain unclear. The aim of this review is to compare the potential therapeutic benefits, efficacy, safety, and clinical progress of AO-mediated exon skipping and CRISPR/Cas9 gene-editing strategies. Both techniques have demonstrated therapeutic benefit and long-term efficacy in clinical trials. AAV-delivery of CRISPR/Cas9 may potentially correct disease-causing mutations following a single treatment compared to the required continuous AO/PMO-delivery of exon skipping drugs. The latter has the potential to increase the dystrophin expression in skeletal/heart muscle with sustained effects. However, therapeutic challenges including the need for optimised delivery must be overcome in to advance current clinical data.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 3","pages":"37-42"},"PeriodicalIF":0.0,"publicationDate":"2020-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9187301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthetic biology, engineering biology, market expectation 合成生物学、工程生物学、市场预期
Engineering biology Pub Date : 2020-12-02 DOI: 10.1049/enb.2020.0021
Lionel Clarke
{"title":"Synthetic biology, engineering biology, market expectation","authors":"Lionel Clarke","doi":"10.1049/enb.2020.0021","DOIUrl":"10.1049/enb.2020.0021","url":null,"abstract":"<div>\u0000 <p>‘Engineering biology’ is being increasingly adopted as a term by organisations that seek to deliver benefits from ‘synthetic biology’. However, are ‘engineering biology’ and ‘synthetic biology’ different words with the same meaning or do they signal important differences? By observing how these two terms are currently being described and applied in practice, it is possible to differentiate the two whilst also acknowledging significant overlaps and complementarity. Increasing adoption of the term ‘engineering biology’ reflects the maturing of synthetic biology since the early years of this century from a research concept to a technological platform that is facilitating the delivery of commercial products and services. The term ‘synthetic biology’ retains a strong association with its original goal to help make biology engineerable, a challenge that will inevitably continue to stimulate research for decades to come as ever more complex and demanding systems are tackled. In comparison, the term ‘engineering biology’ relates more commonly to the utilisation of the synthetic biology platform alongside other related technologies to deliver effective solutions in response to increasing market challenges and expectations.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 3","pages":"33-36"},"PeriodicalIF":0.0,"publicationDate":"2020-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996698/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Data-driven enzyme immobilisation: a case study using DNA to immobilise galactose oxidase 数据驱动的酶固定化:使用DNA固定化半乳糖氧化酶的案例研究
Engineering biology Pub Date : 2020-11-27 DOI: 10.1049/enb.2020.0014
Wolfgang Ott, Alessandro Ceccarelli, Jack Manning, Nicholas J. Turner, Robert Oppenheimer
{"title":"Data-driven enzyme immobilisation: a case study using DNA to immobilise galactose oxidase","authors":"Wolfgang Ott,&nbsp;Alessandro Ceccarelli,&nbsp;Jack Manning,&nbsp;Nicholas J. Turner,&nbsp;Robert Oppenheimer","doi":"10.1049/enb.2020.0014","DOIUrl":"10.1049/enb.2020.0014","url":null,"abstract":"<div>\u0000 <p>Biocatalysis has the potential to enable green chemistry. New methods of enzyme immobilisation will be required to improve enzyme stability, product purification, and compatibility of different enzymes in the same reaction conditions. Deoxyribonucleic acid (DNA) stands out among supramolecular scaffolds, as simple Watson–Crick base-pairing rules can be used to rationally design a unique nanoscale environment around each individual enzyme in a cascade. Enhancements of enzyme activity and stability on DNA nanostructures have previously been reported, but never in the context of industrially relevant chemical syntheses or reaction conditions. Here, the authors show DNA can enhance the activity and stability of a galactose oxidase mutant, which could be used in a cascade to produce bioplastics from lignin. The enzyme was enhanced in the cell-free extract, which to their knowledge has not been shown before for any enzymes on DNA. This is significant because crude biocatalytic reactions are vastly more cost-effective. This opens the door to further work on multienzyme cascades by tuning the properties of individual enzymes.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 3","pages":"43-46"},"PeriodicalIF":0.0,"publicationDate":"2020-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/75/e2/ENB2-4-43.PMC9996703.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hydrogen oxidising bacteria for production of single-cell protein and other food and feed ingredients 用于生产单细胞蛋白质及其它食品和饲料原料的氧化氢细菌
Engineering biology Pub Date : 2020-06-25 DOI: 10.1049/enb.2020.0005
Bart Pander, Zahara Mortimer, Craig Woods, Callum McGregor, Andrew Dempster, Lisa Thomas, Joshua Maliepaard, Robert Mansfield, Peter Rowe, Preben Krabben
{"title":"Hydrogen oxidising bacteria for production of single-cell protein and other food and feed ingredients","authors":"Bart Pander,&nbsp;Zahara Mortimer,&nbsp;Craig Woods,&nbsp;Callum McGregor,&nbsp;Andrew Dempster,&nbsp;Lisa Thomas,&nbsp;Joshua Maliepaard,&nbsp;Robert Mansfield,&nbsp;Peter Rowe,&nbsp;Preben Krabben","doi":"10.1049/enb.2020.0005","DOIUrl":"10.1049/enb.2020.0005","url":null,"abstract":"<div>\u0000 <p>Using hydrogen oxidising bacteria to produce protein and other food and feed ingredients is a form of industrial biotechnology that is gaining traction. The technology fixes carbon dioxide into products without the light requirements of agriculture and biotech that rely on primary producers such as plants and algae while promising higher growth rates, drastically less land, fresh water, and mineral requirements. The significant body of scientific knowledge on hydrogen oxidising bacteria continues to grow and genetic engineering tools are well developed for specific species. The scale-up success of other types of gas- fermentation using carbon monoxide or methane has paved the way for scale-up of a process that uses a mix of hydrogen, oxygen, and carbon dioxide to produce bacteria as a food and feed ingredients in a highly sustainable fashion.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 2","pages":"21-24"},"PeriodicalIF":0.0,"publicationDate":"2020-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2020.0005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9192480","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 26
Dynamical model fitting to a synthetic positive feedback circuit in E. coli 拟合大肠杆菌合成正反馈电路的动力学模型
Engineering biology Pub Date : 2020-06-23 DOI: 10.1049/enb.2020.0009
Jure Tica, Tong Zhu, Mark Isalan
{"title":"Dynamical model fitting to a synthetic positive feedback circuit in E. coli","authors":"Jure Tica,&nbsp;Tong Zhu,&nbsp;Mark Isalan","doi":"10.1049/enb.2020.0009","DOIUrl":"10.1049/enb.2020.0009","url":null,"abstract":"<div>\u0000 <p>Applying the principles of engineering to Synthetic Biology relies on the development of robust and modular genetic components, as well as underlying quantitative dynamical models that closely predict their behaviour. This study looks at a simple positive feedback circuit built by placing filamentous phage secretin pIV under a phage shock promoter. A single-equation ordinary differential equation model is developed to closely replicate the behaviour of the circuit, and its response to inhibition by TetR. A stepwise approach is employed to fit the model's parameters to time-series data for the circuit. This approach allows the dissection of the role of different parameters and leads to the identification of dependencies and redundancies between parameters. The developed genetic circuit and associated model may be used as a building block for larger circuits with more complex dynamics, which require tight quantitative control or tuning.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 2","pages":"25-31"},"PeriodicalIF":0.0,"publicationDate":"2020-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1049/enb.2020.0009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9561601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Mechanistic modelling of tyrosine recombination reveals key parameters determining the performance of a CAR T cell switching circuit 酪氨酸重组的机制建模揭示了决定CAR - T细胞开关电路性能的关键参数
Engineering biology Pub Date : 2020-03-24 DOI: 10.1049/enb.2019.0020
Jack E. Bowyer, Deboki Chakravarti, Wilson W. Wong, Declan G. Bates
{"title":"Mechanistic modelling of tyrosine recombination reveals key parameters determining the performance of a CAR T cell switching circuit","authors":"Jack E. Bowyer,&nbsp;Deboki Chakravarti,&nbsp;Wilson W. Wong,&nbsp;Declan G. Bates","doi":"10.1049/enb.2019.0020","DOIUrl":"10.1049/enb.2019.0020","url":null,"abstract":"<div>\u0000 <p>Inducible genetic switches based on tyrosine recombinase-based DNA excision are a promising platform for the regulation and control of chimeric antigen receptor (CAR) T cell activity in cancer immunotherapy. These switches exploit the increased stability of DNA excision in tyrosine recombinases through an inversion–excision circuit design. Here, the authors develop the first mechanistic mathematical model of switching dynamics in tyrosine recombinases and validate it against experimental data through both global optimisation and statistical approximation approaches. Analysis of this model provides guidelines regarding which system parameters are best suited to experimental tuning in order to establish optimal switch performance in vivo. In particular, they find that the switching response can be made significantly faster by increasing the concentration of the inducer drug 4-OHT and/or by using promoters generating higher expression levels of the FlpO recombinase.</p>\u0000 </div>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"4 1","pages":"10-19"},"PeriodicalIF":0.0,"publicationDate":"2020-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996713/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9561130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
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