Engineering biology最新文献

Software System Design to Support Scale in Mammalian Cell Line Engineering 支持哺乳动物细胞系工程规模的软件系统设计。

Engineering biology Pub Date : 2025-12-20 DOI: 10.1049/enb2.70005

David W. McClymont, Baird McIlwraith, Althea Green, Sam Coulson, Elizabeth Scott

{"title":"Software System Design to Support Scale in Mammalian Cell Line Engineering","authors":"David W. McClymont, Baird McIlwraith, Althea Green, Sam Coulson, Elizabeth Scott","doi":"10.1049/enb2.70005","DOIUrl":"10.1049/enb2.70005","url":null,"abstract":"Cell line engineering (CLE) is the process of gene editing cell lines for a variety of purposes including research and development or bioproduction processes. Traditionally, CLE workflows have been manual and low throughput. Here, we describe the development of several software-based processes, implemented alongside wet lab automation and robotics, built to improve the throughput of our CLE platform to three times its previous capacity. A markup language (GEML) was developed to enable e-commerce capabilities and connections to internal manufacturing systems. A laboratory information management system (LIMS), specifically designed to track CLE projects through all stages, was created to manufacture the cell line specified by the GEML. Cell line engineering required analysis of images in brightfield without fluorescent staining; therefore, a machine learning (ML)-based method for analysing engineered clones imaged captured on an automated imaging platform was created. Our work demonstrates that combining both wet lab automation and software approaches is essential to allow CLE workflows to reach their full potential, allowing the development of high-throughput robust platforms that meet the increasing demands of the field.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12717875/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145806614","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

Creating Enforceable Biosecurity Standards for Nucleic Acid Providers 为核酸供应商制定可执行的生物安全标准。

Engineering biology Pub Date : 2025-12-17 DOI: 10.1049/enb2.70003

Jacob Beal, Tessa Alexanian

引用次数: 0

Plant Cell Strain Improvement Through Engineering Biology for Industrial Plant Cell Culture 工业植物细胞培养用工程生物学技术改良植物细胞株

Engineering biology Pub Date : 2025-11-28 DOI: 10.1049/enb2.70002

Yuan Li, Andrew Mark Hall-Ponselè

{"title":"Plant Cell Strain Improvement Through Engineering Biology for Industrial Plant Cell Culture","authors":"Yuan Li, Andrew Mark Hall-Ponselè","doi":"10.1049/enb2.70002","DOIUrl":"10.1049/enb2.70002","url":null,"abstract":"Plant cell culture (PCC) presents a promising and sustainable alternative to traditional agricultural methods for producing specialty bioactive compounds. However, its widespread industrial application has been hindered by challenges such as low yields, cell line instability and inconsistent product quality. engineering biology (EB) offers a powerful toolkit to overcome these limitations by systematically improving plant cell lines. This review focuses on the application of EB principles to enhance PCC for the production of high-value bioactives from an industry-oriented perspective. We explore three core pillars of the EB toolkit: (1) Multiomics and in silico design, which leverage comprehensive data integration and predictive modelling for rational target identification; (2) gene manipulation and pathway bioengineering, encompassing precise genome editing (e.g., CRISPR/Cas), synthetic gene circuits and directed evolution for targeted metabolic reprogramming and (3) biosensors for high-throughput screening and real-time monitoring, enabling rapid testing and optimisation of engineered cell lines. The synergistic integration of these tools within the iterative design-build-test-learn (DBTL) cycle is highlighted as a key strategy for accelerating strain improvement. Ultimately, the convergence of these EB approaches is transforming PCC into a robust platform for producing pharmaceuticals, functional foods and green chemicals, contributing to a biobased economy with a minimal ecological footprint.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ietresearch.onlinelibrary.wiley.com/doi/epdf/10.1049/enb2.70002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619283","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

If You're Not Thinking About Intellectual Property, You’re Not Thinking About Impact 如果你不考虑知识产权，你就不会考虑影响

Engineering biology Pub Date : 2025-11-07 DOI: 10.1049/enb2.70001

Sara L. Holland

引用次数: 0

Synthetic and Engineering Biology in Australia: Advances in Infrastructure, Coordination and Impact 澳大利亚的合成和工程生物学：基础设施、协调和影响的进展。

Engineering biology Pub Date : 2025-11-05 DOI: 10.1049/enb2.70000

Robert E. Speight

{"title":"Synthetic and Engineering Biology in Australia: Advances in Infrastructure, Coordination and Impact","authors":"Robert E. Speight","doi":"10.1049/enb2.70000","DOIUrl":"10.1049/enb2.70000","url":null,"abstract":"Synthetic and engineering biology in Australia is a vibrant and expanding area, with the potential to contribute to Australian priorities, industry growth and international initiatives. This paper provides a progress update on the field in Australia since 2021. The initial section provides historical context and an overview of the importance and potential impact. The second section focuses on the building and expansion of a strong community and mechanisms for coordination, noting need for industry coordination beyond the research sector. Governments have an important role in enabling development, with the Australian Government and State Governments implementing strategies and initiatives linked to national and regional priorities. The regulatory landscape for genetic technologies is also described, highlighting recent approvals and the overall enabling environment in Australia. The penultimate section provides details on major research initiatives, showing the growth in funding and how synthetic and engineering biology technologies are being developed and applied in an increasing range of application areas. Finally, there has been a notable expansion in the number of start-up companies and industry partnerships in Australia since 2021, with details provided about the companies and the drivers for this growth, as well as the challenges in accessing scale-up and commercialisation infrastructure.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12588174/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145460727","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 in Mexico: Brief history, current landscape, and perspectives towards a bio-based economy 合成生物学在墨西哥：简史，当前的景观，并对生物经济的观点

Engineering biology Pub Date : 2025-01-07 DOI: 10.1049/enb2.12037

Uriel E. Barboza-Pérez, Ma de L. Pérez-Zavala, José E. Barboza-Corona

{"title":"Synthetic biology in Mexico: Brief history, current landscape, and perspectives towards a bio-based economy","authors":"Uriel E. Barboza-Pérez, Ma de L. Pérez-Zavala, José E. Barboza-Corona","doi":"10.1049/enb2.12037","DOIUrl":"10.1049/enb2.12037","url":null,"abstract":"Synthetic biology (SynBio) makes biology easier by leveraging engineering principles and other disciplines to design and construct biological systems with novel or enhanced functions. SynBio has led to the development of more sustainable biotechnological innovations that are in harmony with the environment, aiding the shift from a traditional to a bio-based economy. Mexico has made significant advancements in biotechnology in academia and industry, but progress in engineering biology has been different. Nevertheless, several initiatives, mainly supported by the participation of Mexican International Genetically Engineered Machine (iGEM) teams in the jamboree, have contributed to the interest of SynBio. This review provides a brief overview of the significant role of the iGEM competition and the current landscape of synthetic biology in Mexico, including educational and citizen science initiatives, as well as an overview of Synbio research and the industrial landscape. Additionally, a brief description of the current laws governing biotechnology in the country is provided. Finally, we highlight the challenges, opportunities and perspectives for the development of synthetic biology and the potential that Mexico has for a biologically based economy.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/enb2.12037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143112971","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

Supercharging engineering biology with automation 用自动化为工程生物学增添动力。

Engineering biology Pub Date : 2024-12-23 DOI: 10.1049/enb2.12036

Sébastien Lambertucci, Faye Deakin

{"title":"Supercharging engineering biology with automation","authors":"Sébastien Lambertucci, Faye Deakin","doi":"10.1049/enb2.12036","DOIUrl":"10.1049/enb2.12036","url":null,"abstract":"Breakthroughs in engineering biology will solve the challenges facing humanity, by harnessing life itself. Standing in the way of these breakthroughs are the technical challenges of collecting the requisite data. Data variability and reproducibility problems, mean the odds are stacked against emerging biotechs. Automation has long been known to solve both problems; Let a robot do the pipetting and get reproducible data with less hands-on time. Although transitioning to automation has clear benefits, it can introduce additional complexity if done incorrectly. Analytik Jena UK has focused on supporting this transition to automation. We have found the combining of industry expertise with the biology know-how at the bench is paramount. Great automation should empower the scientist. Scientists should be trained on how to harness their automation. Through industry-customer relationships, we have successfully automated platforms for building DNA to antibody development. Through this partnership, we can enable a smooth translation of engineering biology to scalable industrial solutions. In this communication we have highlighted some successful examples where translating engineering biology workflows onto automation has proven beneficial, paving the way to industry ready solutions.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"8 4","pages":"69-73"},"PeriodicalIF":0.0,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681250/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142904277","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

Routes to industrial scalability to maximise investment in engineering biology in the UK—A bioplastics small and medium-sized enterprise perspective 英国工程生物学投资最大化的工业可扩展性途径--生物塑料中小企业的视角

Engineering biology Pub Date : 2024-09-04 DOI: 10.1049/enb2.12033

Amy Switzer, Laima Šusta, Paul Mines

引用次数: 0

A decade of translational engineering biology: Measuring success 转化工程生物学十年：衡量成功

Engineering biology Pub Date : 2024-07-31 DOI: 10.1049/enb2.12034

David Bell

引用次数: 0

Engineering biology and automation–Replicability as a design principle 工程生物学与自动化--作为设计原则的可复制性

Engineering biology Pub Date : 2024-07-12 DOI: 10.1049/enb2.12035

Matthieu Bultelle, Alexis Casas, Richard Kitney

{"title":"Engineering biology and automation–Replicability as a design principle","authors":"Matthieu Bultelle, Alexis Casas, Richard Kitney","doi":"10.1049/enb2.12035","DOIUrl":"10.1049/enb2.12035","url":null,"abstract":"Applications in engineering biology increasingly share the need to run operations on very large numbers of biological samples. This is a direct consequence of the application of good engineering practices, the limited predictive power of current computational models and the desire to investigate very large design spaces in order to solve the hard, important problems the discipline promises to solve. Automation has been proposed as a key component for running large numbers of operations on biological samples. This is because it is strongly associated with higher throughput, and with higher replicability (thanks to the reduction of human input). The authors focus on replicability and make the point that, far from being an additional burden for automation efforts, replicability should be considered central to the design of the automated pipelines processing biological samples at scale—as trialled in biofoundries. There cannot be successful automation without effective error control. Design principles for an IT infrastructure that supports replicability are presented. Finally, the authors conclude with some perspectives regarding the evolution of automation in engineering biology. In particular, they speculate that the integration of hardware and software will show rapid progress, and offer users a degree of control and abstraction of the robotic infrastructure on a level significantly greater than experienced today.","PeriodicalId":72921,"journal":{"name":"Engineering biology","volume":"8 4","pages":"53-68"},"PeriodicalIF":0.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1049/enb2.12035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141653379","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