Engineering biology最新文献_第2页

Designing of an extract production protocol for industrial application of cell-free protein synthesis technology: Building from a current best practice to a quality by design approach 为无细胞蛋白质合成技术的工业应用设计提取物生产方案：从当前最佳实践到设计质量方法

Engineering biology Pub Date : 2023-12-06 DOI: 10.1049/enb2.12029

Beatrice Judith Melinek, Jade Tuck, Philip Probert, Harvey Branton, Daniel G. Bracewell

{"title":"Designing of an extract production protocol for industrial application of cell-free protein synthesis technology: Building from a current best practice to a quality by design approach","authors":"Beatrice Judith Melinek, Jade Tuck, Philip Probert, Harvey Branton, Daniel G. Bracewell","doi":"10.1049/enb2.12029","DOIUrl":"https://doi.org/10.1049/enb2.12029","url":null,"abstract":"<p>Cell-Free Protein Synthesis (CFPS) has, over the past decade, seen a substantial increase in interest from both academia and industry. Applications range from fundamental research, through high-throughput screening to niche manufacture of therapeutic products. This review/perspective focuses on Quality Control in CFPS. The importance and difficulty of measuring the Raw Material Attributes (RMAs) of whole cell extract, such as constituent protein and metabolite concentrations, and of understanding and controlling these complicated enzymatic reactions is explored, for both centralised and distributed industrial production of biotherapeutics. It is suggested that a robust cell-free extract production process should produce cell extract of consistent quality; however, demonstrating this is challenging without a full understanding of the RMAs and their interaction with reaction conditions and product. Lack of technology transfer and knowledge sharing is identified as a key limiting factor in the development of CFPS. The article draws upon the experiences of industrial process specialists, discussions within the Future Targeted Healthcare Manufacturing Hub Specialist Working Groups and evidence drawn from various sources to identify sources of process variation and to propose an initial guide towards systematisation of CFPS process development and reporting. These proposals include the development of small scale screening tools, consistent reporting of selected process parameters and analytics and application of industrial thinking and manufacturability to protocol development.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"7 1-4","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/enb2.12029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138578183","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

Israel and the global synthetic biology ecosystem 以色列与全球合成生物学生态系统

Engineering biology Pub Date : 2023-10-14 DOI: 10.1049/enb2.12027

Yuval Dorfan, Aviv Zeevi, Gita Reinitz, Magi Mualem, Yosi Shacham-Diamand

引用次数: 0

The roadmap of bioeconomy in China 中国生物经济发展路线图

Engineering biology Pub Date : 2022-11-30 DOI: 10.1049/enb2.12026

Xu Zhang, Cuihuan Zhao, Ming-Wei Shao, Yi-Ling Chen, Puyuan Liu, Guo-Qiang Chen

引用次数: 3

Prediction of strain engineerings that amplify recombinant protein secretion through the machine learning approach MaLPHAS 预测通过机器学习方法MaLPHAS扩增重组蛋白分泌的菌株工程。

Engineering biology Pub Date : 2022-09-16 DOI: 10.1049/enb2.12025

Evgenia A. Markova, Rachel E. Shaw, Christopher R. Reynolds

{"title":"Prediction of strain engineerings that amplify recombinant protein secretion through the machine learning approach MaLPHAS","authors":"Evgenia A. Markova, Rachel E. Shaw, Christopher R. Reynolds","doi":"10.1049/enb2.12025","DOIUrl":"10.1049/enb2.12025","url":null,"abstract":"Abstract This article presents a discussion of the process of precision fermentation (PF), describing the history of the space, the expected 70% growth over the next 5 years, various applications of precision fermented products, and the markets available to be disrupted by the technology. A range of prokaryotic and eukaryotic host organisms used for PF are described, with the advantages, disadvantages and applications of each. The process of setting up PF and strain engineering is described, as well as various ways that computational analysis and design techniques can be employed to assist PF engineering. The article then describes the design and implementation of a machine learning method, machine learning predictions having amplified secretion (MaLPHAS) to predict strain engineerings, which optimise the secretion of a recombinant protein. This approach showed an in silico cross‐validated R 2 accuracy on the training data of up to 46.6% and in an in vitro test on a Komagataella phaffii strain, identified one gene engineering out of five predicted, which was shown to double the secretion of a heterologous protein and outperform three of the best‐known edits from the literature for improving secretion in K. phaffii.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"6 4","pages":"82-90"},"PeriodicalIF":0.0,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a4/85/ENB2-6-82.PMC9995161.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9197264","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

Corrigendum: Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions 勘误:用于电子废物生物修复的生物工程微生物:路标、挑战和未来方向

Engineering biology Pub Date : 2022-08-23 DOI: 10.1049/enb2.12023

引用次数: 0

A curcumin direct protein biosensor for cell-free prototyping 用于无细胞原型的姜黄素直接蛋白生物传感器

Engineering biology Pub Date : 2022-08-18 DOI: 10.1049/enb2.12024

Agata Kennedy, Guy Griffin, Paul S. Freemont, Karen M. Polizzi, Simon J. Moore

引用次数: 0

Engineering of optogenetic devices for biomedical applications in mammalian synthetic biology 用于哺乳动物合成生物学生物医学应用的光遗传学设备工程。

Engineering biology Pub Date : 2022-07-07 DOI: 10.1049/enb2.12022

Ningzi Guan, Xianyun Gao, Haifeng Ye

引用次数: 1

Reducing metabolic burden in the PACEmid evolver system by remastering high-copy phagemid vectors 通过重新控制高拷贝噬菌体载体来减轻PACEmid进化系统的代谢负担

Engineering biology Pub Date : 2022-05-20 DOI: 10.1049/enb2.12021

Beth India Davenport, Jure Tica, Mark Isalan

{"title":"Reducing metabolic burden in the PACEmid evolver system by remastering high-copy phagemid vectors","authors":"Beth India Davenport, Jure Tica, Mark Isalan","doi":"10.1049/enb2.12021","DOIUrl":"10.1049/enb2.12021","url":null,"abstract":"Abstract Orthogonal or non‐cross‐reacting transcription factors are used in synthetic biology as components of genetic circuits. Brödel et al. (2016) engineered 12 such cIλ transcription factor variants using a directed evolution ‘PACEmid’ system. The variants operate as dual activator/repressors and expand gene circuit construction possibilities. However, the high‐copy phagemid vectors carrying the cIλ variants imposed high metabolic burden upon cells. Here, the authors ‘remaster’ the phagemid backbones to relieve their burden substantially, exhibited by a recovery in Escherichia coli growth. The remastered phagemids' ability to function within the PACEmid evolver system is maintained, as is the cIλ transcription factors' activity within these vectors. The low‐burden phagemid versions are more suitable for use in PACEmid experiments and synthetic gene circuits; the authors have, therefore, replaced the original high‐burden phagemids on the Addgene repository. The authors’ work emphasises the importance of understanding metabolic burden and incorporating it into design steps in future synthetic biology ventures.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"6 2-3","pages":"50-61"},"PeriodicalIF":0.0,"publicationDate":"2022-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9996709/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9183898","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

The influences of substrates' physical properties on enzymatic PET hydrolysis: Implications for PET hydrolase engineering 底物性质对酶促PET水解的影响:对PET水解酶工程的启示

Engineering biology Pub Date : 2022-03-24 DOI: 10.1049/enb2.12018

Rupali Reddy Pasula, Sierin Lim, Farid J. Ghadessy, Barindra Sana

引用次数: 7

Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions 电子废物生物修复的生物工程微生物:路标、挑战和未来方向

Engineering biology Pub Date : 2022-02-26 DOI: 10.1049/enb2.12020

Ping Han, Wei Zhe Teo, Wen Shan Yew

{"title":"Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions","authors":"Ping Han, Wei Zhe Teo, Wen Shan Yew","doi":"10.1049/enb2.12020","DOIUrl":"10.1049/enb2.12020","url":null,"abstract":"<p>In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.</p>","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"6 1","pages":"23-34"},"PeriodicalIF":0.0,"publicationDate":"2022-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9995160/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10331050","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