Progress in molecular biology and translational science最新文献

Preface. 前言。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 DOI: 10.1016/S1877-1173(26)00077-3

Vijai Singh

引用次数: 0

Artificial intelligence for cell-free systems. 无细胞系统的人工智能。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-09-20 DOI: 10.1016/bs.pmbts.2025.08.009

Ingita Dey Munshi, Indra Mani

{"title":"Artificial intelligence for cell-free systems.","authors":"Ingita Dey Munshi, Indra Mani","doi":"10.1016/bs.pmbts.2025.08.009","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.08.009","url":null,"abstract":"Cell-free systems let researchers carry out biological processes like protein synthesis and metabolism without using living cells. This approach has become increasingly important in synthetic biology because it allows for quick testing of ideas, running many experiments simultaneously, and maintaining tight control over reaction conditions. The main challenge has been figuring out how to optimize these systems, since there are so many variables that interact in unpredictable ways. Artificial intelligence (AI), including machine learning, deep learning, and generative models, has begun to tackle this problem by helping predict experimental outcomes, design new proteins, and find better reaction conditions. The discovery of antimicrobial peptides through deep learning and cell-free protein synthesis, along with a 34-fold increase in protein yield through buffer optimization guided by active learning, are some of the major advancements made possible. The use of Bayesian optimization and neural networks has helped to streamline metabolic pathway designing, enzyme engineering as well as yield prediction, which in turn has diversified the use of AI-driven approaches in biomanufacturing, pharmaceuticals, and diagnostics. In spite of hurdles like data requirements, model transferability, and scalability, the compatibility of AI and cell-free systems gives adequate probabilities of innovations like digital twins and self-driven biomanufacturing units. This chapter explores the integration of AI with cell-free systems, focusing on recent advances, industrial applications, and ending with future directions for synthetic biology.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"87-108"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047255","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Challenges and opportunities in cell-free systems. 无细胞系统的挑战和机遇。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-09-06 DOI: 10.1016/bs.pmbts.2025.08.006

Hue Vu Thi, Yen-Vy Nguyen Thi, Minh Chau Nguyen, Huong Ly Nguyen, Phuong Anh Nguyen, Dinh-Toi Chu

{"title":"Challenges and opportunities in cell-free systems.","authors":"Hue Vu Thi, Yen-Vy Nguyen Thi, Minh Chau Nguyen, Huong Ly Nguyen, Phuong Anh Nguyen, Dinh-Toi Chu","doi":"10.1016/bs.pmbts.2025.08.006","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.08.006","url":null,"abstract":"Cell-free systems (CFS) are in vitro technologies (outside living cells) that use cellular components to reproduce cellular processes outside living organisms, such as protein synthesis, gene expression, and metabolic reactions. Nowadays, CFS has been improved over time and is considered one of the most useful tools for exploring and illustrating the fundamental principles of biological systems. In the medical field, CFS is being widely applied in vaccine production, gene expression research and point-of-care diagnostics. However, despite its significant benefits, CFS still faces many technological challenges and scientific limitations. In addition, sustainable development goes hand in hand with the balance between innovation and ethical, environmental and social issues. However, in the context of promoting biological solutions, CFS also opens many new opportunities. Therefore, challenges and some issues related to CFS technologies have been comprehensively evaluated in this chapter. The opportunities of CFS technologies have also been discussed in this chapter to highlight the huge potential of this technology in the near future. The evidence presented can serve as a foundational reference for research, teaching, and strategic policy-making in the field of next-generation synthetic biology.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"219 ","pages":"237-254"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146195673","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Preface. 前言。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 DOI: 10.1016/S1877-1173(26)00029-3

Vijai Singh

引用次数: 0

Development of cell-free transcription translation. 无细胞转录翻译的研究进展。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-09-09 DOI: 10.1016/bs.pmbts.2025.08.003

Ajay Kumar, Juveriya Israr, Shabroz Alam

{"title":"Development of cell-free transcription translation.","authors":"Ajay Kumar, Juveriya Israr, Shabroz Alam","doi":"10.1016/bs.pmbts.2025.08.003","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.08.003","url":null,"abstract":"Cell-free transcription-translation (TXTL) systems provide a robust platform for in vitro protein synthesis, transforming molecular biology, synthetic biology, and biotechnology by replicating natural protein synthesis outside of living cells with exceptional control and flexibility. Initially developed by Nirenberg and Matthaei in the 1960s using E. coli extracts, these systems have undergone substantial evolution, and now incorporate extracts from bacteria, yeast, and eukaryotes to construct comprehensive TXTL platforms. A cell-free extract comprises essential components, such as ribosomes, RNA polymerase, and tRNAs, enabling protein synthesis directed by DNA templates through transcription and translation. TXTL systems, offer distinct advantages, including rapid, efficient, and accurate synthesis of natural and non-natural proteins, enhanced chemical resistance, and streamlined labeling-often surpassing cell-based techniques. Their extensive application span synthetic biology and biopharmaceutical production. Despite this promise, challanges remain, including high cost, limited protein yield, lack of complex post-translational modifications, and extract instability. Future efforts will focus on overcoming these challenges by reducing costs, improving yields, expanding post-translational modification capabilities, enhancing stability, and developing continuous-flow systems. Ultimately, cell-free systems are poised to deepen our understanding of biological processes and drive the development of innovative biotechnological tools.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"49-64"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell-free systems for biotransformation. 生物转化的无细胞系统。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-10-11 DOI: 10.1016/bs.pmbts.2025.09.005

Huzaifa Ibrahim, Nimra Arshad, Hunaiza Fatima, Alvina Gul, Jayakumar Rajadas, Mustafeez Mujtaba Babar

{"title":"Cell-free systems for biotransformation.","authors":"Huzaifa Ibrahim, Nimra Arshad, Hunaiza Fatima, Alvina Gul, Jayakumar Rajadas, Mustafeez Mujtaba Babar","doi":"10.1016/bs.pmbts.2025.09.005","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.09.005","url":null,"abstract":"The cell-free systems based biotransformation has significantly transformed the field of biotechnology by facilitating the synthesis of therapeutic agents, biofuels and other commercially valuable chemicals. The current chapter initially focuses on presenting how the biotransformation process has conveniently transformed form the conventional cell-free based systems to modern cell-free protein synthesis (CFPS). This transformation has enabled the biomedical engineers and researchers to optimize the processes effectively. The chapter also looks into the three main biotransformation reactions i.e., enzymatic catalysis, redox transformation and hydrolytic processes while focusing on the optimization of pathways and processes that effectively enhance the modular design. The chapter also presents the practical benefits through various case studies in biofuel generation, synthesis of therapeutic proteins and eco-friendly manufacturing which ensures better yield, adaptability and reduction of unwanted substances in the industries. The chapter further illustrates the discussion on how cell-free systems have been designed and how the synthetic biology platforms outline the integration of machine learning and high throughput screening for the development of effective and efficient pathways. Furthermore, breakthroughs in eco-friendly chemistry, creation of artificial cells and synthetic biologicals ensure that the development of cell-free system is effective in biotransformation and is the fundamental basis for future production and advancements.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"219 ","pages":"147-170"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146195546","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell free systems for production of chemicals. 用于生产化学品的无电池系统。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-11-27 DOI: 10.1016/bs.pmbts.2025.10.003

Sandeep Kaur, Gholamreza Abdi, Vaseem Raja, Mukul Machhindra Barwant, Ruchita Shrivastava

{"title":"Cell free systems for production of chemicals.","authors":"Sandeep Kaur, Gholamreza Abdi, Vaseem Raja, Mukul Machhindra Barwant, Ruchita Shrivastava","doi":"10.1016/bs.pmbts.2025.10.003","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.10.003","url":null,"abstract":"Modern technologies have also prompted biotechnologists to change their focus towards in vitro methods whereby biochemicals and biomaterials are prepared using cell-free conditions. Nevertheless, with many obstacles, the evolution of cell-free systems (CFSs) is thought to create additional opportunities in the creation of biologically-relevant molecules and materials. Cell-free biosynthesis serves to address significant discrepancies in traditional whole cell-based metabolic processes, and has a number of benefits, including the reduced structural and functional complexity, and the possibility to bypass cell viability problems and employ a controlled environment. These in vitro systems permit reconstitution of metabolic pathways with purified enzymes or crude lysates with rapid prototyping, precise control of reaction conditions and increased production of target compounds. The chapter presents a general overview of the design, optimization, and utilization of cell-free systems to prepare industrial chemicals, biofuels, pharmaceutical precursors, and specialty compounds. In this chapter, we explain the different categories of cell-free systems, like enzyme-based (PURE systems), lysate-based (TX-TL), and hybrid systems, that will be used to emphasize the functions of these systems in modular pathway construction, cofactor balancing, and energy regeneration. In addition, the synthesis of chemicals like isoprenoids, polyketides, organic acids, and aromatic compounds will also be a part of it. There is also an emphasis on synthetic biology tools, system engineering strategies, and scale-up techniques, which contribute to productivity and reduce production costs. The chapter is also intended to be read by the researchers, synthetic biologists, and industrial biotechnologists interested in sustainable biomanufacturing and synthetic biochemistry.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"219 ","pages":"107-146"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146195579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Non-canonical amino acid incorporation via genetic code reprogramming in a cell-free translation system. 在无细胞翻译系统中通过遗传密码重编程的非规范氨基酸整合。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-10-22 DOI: 10.1016/bs.pmbts.2025.09.004

Harinarayana Ankamareddy, Hemasundar Alavilli, Vini Madathil, Sahil Kanjilal, Sushma Chauhan, Sudheer Dv N Pamidimarri

引用次数: 0

Computational biology for cell-free systems. 无细胞系统的计算生物学。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-09-17 DOI: 10.1016/bs.pmbts.2025.08.007

Mansi Acharya, Indra Mani

{"title":"Computational biology for cell-free systems.","authors":"Mansi Acharya, Indra Mani","doi":"10.1016/bs.pmbts.2025.08.007","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.08.007","url":null,"abstract":"Cell-free systems (CFS) decouple gene expression and metabolic pathways from living cells, offering a rapid, modular platform for biosensing, pathway prototyping, and protein production. This review surveys mechanistic and data-driven computational approaches tailored to CFS design and optimization. We compare deterministic ordinary differential equation (ODE) and stochastic simulation frameworks for modeling transcription-translation dynamics, describe adaptations of genome-scale metabolic models (GEMs) and flux balance analysis (FBA) for extract-based systems, and evaluate machine-learning strategies that learn sequence-to-function mappings from high-throughput cell-free assays. We summarize key software and discuss applications in paper-based diagnostics, reconstructed metabolic pathways, and high-yield cell-free protein synthesis. Recent advances in CRISPR based regulation using pre expressed dCas9 or RNA processing enzymes enable construction of multi-layer genetic circuits in extracts. Finally, we identify current gaps limited standardization of kinetic assays, sparse public datasets, and few hybrids kinetic-constraint modeling studies and propose a roadmap for community resources and hybrid modeling efforts that combine mechanistic clarity with machine learning (ML)-driven speed.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"65-85"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047277","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cell-free systems for low-cost diagnostics. 低成本诊断的无细胞系统。

3区生物学

Progress in molecular biology and translational science Pub Date : 2026-01-01 Epub Date: 2025-09-20 DOI: 10.1016/bs.pmbts.2025.08.005

Rupal Dhariwal, Mukul Jain

{"title":"Cell-free systems for low-cost diagnostics.","authors":"Rupal Dhariwal, Mukul Jain","doi":"10.1016/bs.pmbts.2025.08.005","DOIUrl":"https://doi.org/10.1016/bs.pmbts.2025.08.005","url":null,"abstract":"Cell-free systems have also become a revolutionary platform for low-cost diagnostics, providing fast, flexible, and scalable solutions to the conventional cell-based assays. Such systems, which utilize the fundamental biochemical machinery of cells without the intricacies of living organisms, have been of great use in point-of-care (POC) diagnostics, particularly in resource-poor environments. This chapter offers a broad overview of the basic principles, design approaches, and technological breakthroughs behind cell-free diagnostic development. It discusses the biochemical underpinnings of cell-free expression, such as ribosomal function, transcriptional control, and energy regeneration, with emphases on the leading platforms including E. coli lysates, wheat germ extracts, and PURE systems. The application of synthetic biology in the form of gene circuits, CRISPR-Cas tools, and RNA aptamers is presented here in the framework of improving the sensitivity and specificity of diagnostics. The chapter further discusses recent innovations in paper-based assays, microfluidic biosensors, and wearable biosensors, which are capable of offering real-time and field-deployable diagnostics. Major challenges in the form of reagent stability, scalability, and regulatory implications are analyzed carefully along with recent trends such as AI-based system design and personalization of diagnostics. In extensive case studies, the chapter highlights the promise of cell-free systems in filling diagnostic gaps, enhancing access to healthcare, and revolutionizing global health. This book strives to offer an encyclopedic sourcebook for researchers, clinicians, and innovators interested in bringing cell-free diagnostics forward.","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"157-185"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0