Pub Date : 2026-03-01Epub Date: 2025-12-18DOI: 10.1016/j.biotechadv.2025.108782
Jiwoo Nam , Yuna Lee , Sion Lee , Hyungjun Choi , Sang Yup Lee , Dongsoo Yang
Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome—a complex community of microorganisms residing in the human body—has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.
{"title":"Synthetic biology strategies for engineering probiotics and commensal bacteria for diagnostics and therapeutics","authors":"Jiwoo Nam , Yuna Lee , Sion Lee , Hyungjun Choi , Sang Yup Lee , Dongsoo Yang","doi":"10.1016/j.biotechadv.2025.108782","DOIUrl":"10.1016/j.biotechadv.2025.108782","url":null,"abstract":"<div><div>Microorganisms inhabit diverse environments, including nearly every organ in the human body. The human microbiome—a complex community of microorganisms residing in the human body—has gained increasing attention as a key contributor to human health and disease, making it an important target for the development of diagnostic and therapeutic strategies. However, the inherent complexity of microbial communities and the challenges of engineering diverse non-model microorganisms present significant barriers. To address these challenges, synthetic biology has provided powerful tools and strategies to engineer microorganisms capable of sensing disease-specific environments and performing targeted therapeutic functions. In particular, the development of synthetic genetic circuits has significantly improved the precision and reliability of disease diagnosis and treatment, enabling real-time disease monitoring, therapeutic, and even preventive interventions. This review highlights state-of-the-art synthetic biology tools and strategies for engineering the probiotics and commensal bacteria aimed at the diagnosis and treatment of human diseases, with accompanying examples. Future challenges and prospects are also discussed.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108782"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-18DOI: 10.1016/j.biotechadv.2026.108805
Jiahao Wang , Guangjie Liang , Zixuan Wang , Cong Gao , Guipeng Hu , Liming Liu , Jing Wu
Methanol is a highly promising feedstock for biomanufacturing owing to its broad availability, low cost, and high energy density. Methylotrophic fermentations have been exploited to produce diverse fuels, chemicals, and materials. However, although such processes have been practiced for decades, their applications have been constrained by low methanol assimilation efficiency, insufficient cellular energy and reducing equivalents supply, the cytotoxicity of methanol and its intermediates, and inadequate robustness of chassis strains. In this review, progress is synthesized along four pillars for constructing high-performance methanol bio-converting cell factories: methanol assimilation pathways, energy-supply strategies, tolerance-enhancement approaches, and metabolic engineering for chemical synthesis, with the aim of informing the rational design and construction of efficient methanol bio-converting cell factories.
{"title":"Construction and applications of methanol bio-converting cell factories","authors":"Jiahao Wang , Guangjie Liang , Zixuan Wang , Cong Gao , Guipeng Hu , Liming Liu , Jing Wu","doi":"10.1016/j.biotechadv.2026.108805","DOIUrl":"10.1016/j.biotechadv.2026.108805","url":null,"abstract":"<div><div>Methanol is a highly promising feedstock for biomanufacturing owing to its broad availability, low cost, and high energy density. Methylotrophic fermentations have been exploited to produce diverse fuels, chemicals, and materials. However, although such processes have been practiced for decades, their applications have been constrained by low methanol assimilation efficiency, insufficient cellular energy and reducing equivalents supply, the cytotoxicity of methanol and its intermediates, and inadequate robustness of chassis strains. In this review, progress is synthesized along four pillars for constructing high-performance methanol bio-converting cell factories: methanol assimilation pathways, energy-supply strategies, tolerance-enhancement approaches, and metabolic engineering for chemical synthesis, with the aim of informing the rational design and construction of efficient methanol bio-converting cell factories.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108805"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145995160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-18DOI: 10.1016/j.biotechadv.2026.108802
Yan Xia , Yi-Xin Huo
Cis-regulatory elements (CREs) play a crucial role in regulating gene expression by controlling transcription, making the understanding and design of these elements essential for the advancement of biology. Traditional approaches often rely on empirical rules and iterative experimentation, which can be time-consuming and labor-intensive. Recent advances in deep learning have begun to influence this field by improving the accuracy of predictions for existing elements and offering preliminary strategies for designing synthetic CREs. Specialized design models can incorporate high-throughput experimental data, and DNA foundation models draw on pre-trained genomic representations to inform the design process. These approaches have shown encouraging progress in generating promoters, enhancers and more complex regulatory architectures. Nonetheless, substantial challenges remain, including limited data availability, gaps between computational predictions and experimental outcomes, and limited model interpretability. Moreover, although AI-driven methods hold considerable promise for CRE prediction and design, their generative capabilities are still constrained by data quality and by the tendency of current models to rely predominantly on sequence-level features without fully capturing broader regulatory context. In this review, we examine how emerging AI technologies may support more systematic and targeted design of synthetic CREs, and we discuss key challenges and future directions, including multimodal modeling, reinforcement learning (RL), and system-level regulatory network design.
{"title":"Controlling gene expression using AI designed Cis-regulatory elements","authors":"Yan Xia , Yi-Xin Huo","doi":"10.1016/j.biotechadv.2026.108802","DOIUrl":"10.1016/j.biotechadv.2026.108802","url":null,"abstract":"<div><div><em>Cis</em>-regulatory elements (CREs) play a crucial role in regulating gene expression by controlling transcription, making the understanding and design of these elements essential for the advancement of biology. Traditional approaches often rely on empirical rules and iterative experimentation, which can be time-consuming and labor-intensive. Recent advances in deep learning have begun to influence this field by improving the accuracy of predictions for existing elements and offering preliminary strategies for designing synthetic CREs. Specialized design models can incorporate high-throughput experimental data, and DNA foundation models draw on pre-trained genomic representations to inform the design process. These approaches have shown encouraging progress in generating promoters, enhancers and more complex regulatory architectures. Nonetheless, substantial challenges remain, including limited data availability, gaps between computational predictions and experimental outcomes, and limited model interpretability. Moreover, although AI-driven methods hold considerable promise for CRE prediction and design, their generative capabilities are still constrained by data quality and by the tendency of current models to rely predominantly on sequence-level features without fully capturing broader regulatory context. In this review, we examine how emerging AI technologies may support more systematic and targeted design of synthetic CREs, and we discuss key challenges and future directions, including multimodal modeling, reinforcement learning (RL), and system-level regulatory network design.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108802"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145995163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-29DOI: 10.1016/j.biotechadv.2025.108767
Jing Qiu , Amna Bibi , Alvaro R. Lara , Qinhong Wang , Zongjie Dai
Coenzyme A thioester derivatives, particularly acetyl-CoA, malonyl-CoA and fatty acyl-CoA, are essential central metabolites in microorganisms. These compounds play pivotal roles in numerous metabolic pathways and serve as key precursors in the biosynthesis of various high-value compounds, including fatty acids, polyketides, and flavonoids. The spatiotemporal distribution of CoA thioester derivatives is variable and tightly regulated, making real-time monitoring worthwhile. Biosensors have emerged as valuable tools for rapid and immediate detection because of their respond to changes of inducers. This has facilitated the development of efficient metabolic engineering strategies, including dynamic regulation and high-throughput screening. In this context, the review offers a comprehensive overview of the current progress, optimization, applications and limitations of biosensors for acetyl-CoA, malonyl-CoA, fatty acyl-CoA and other CoA thioester derivatives. Based on these limitations, it also outlines prospects for further development and discusses potential biosensor elements for CoA thioester derivatives.
{"title":"Biosensors for coenzyme A thioester derivatives: Development, optimization and applications","authors":"Jing Qiu , Amna Bibi , Alvaro R. Lara , Qinhong Wang , Zongjie Dai","doi":"10.1016/j.biotechadv.2025.108767","DOIUrl":"10.1016/j.biotechadv.2025.108767","url":null,"abstract":"<div><div>Coenzyme A thioester derivatives, particularly acetyl-CoA, malonyl-CoA and fatty acyl-CoA, are essential central metabolites in microorganisms. These compounds play pivotal roles in numerous metabolic pathways and serve as key precursors in the biosynthesis of various high-value compounds, including fatty acids, polyketides, and flavonoids. The spatiotemporal distribution of CoA thioester derivatives is variable and tightly regulated, making real-time monitoring worthwhile. Biosensors have emerged as valuable tools for rapid and immediate detection because of their respond to changes of inducers. This has facilitated the development of efficient metabolic engineering strategies, including dynamic regulation and high-throughput screening. In this context, the review offers a comprehensive overview of the current progress, optimization, applications and limitations of biosensors for acetyl-CoA, malonyl-CoA, fatty acyl-CoA and other CoA thioester derivatives. Based on these limitations, it also outlines prospects for further development and discusses potential biosensor elements for CoA thioester derivatives.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108767"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619678","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-28DOI: 10.1016/j.biotechadv.2025.108768
Zhaodong Li , Zihui Gao , Haonan Song , Jialiang He , Wei Xiong
Integrating biological systems with artificial optoelectronic materials for efficient solar energy conversion has emerged as a cutting-edge and promising research direction in the pursuit of sustainable energy solutions. Natural photosynthesis, through intricate biological mechanisms, converts solar energy into chemical energy, serving as an inspiration for human innovation; concurrently, photovoltaic technologies utilize semiconductor materials to directly transform solar radiation into electricity. Recent interdisciplinary research efforts have led to the development of bio-abiotic hybrid interfaces, combining the regenerative capabilities of biological systems with the tunable optoelectronic properties of artificial materials, aiming to enhance solar energy conversion efficiency. This review focuses on the latest advancements in artificial photosynthesis, bio-photoelectrochemical systems, and bio-photovoltaic systems, emphasizing their potential to improve solar energy conversion efficiency. We explore the design principles, operational mechanisms, and performance metrics of these hybrid devices, and conduct an in-depth analysis of technical challenges such as interface stability and electron transfer efficiency. Furthermore, we propose future research directions to optimize these systems for practical applications in sustainable energy production. By integrating knowledge from biology, materials science, and energy engineering, we aim to provide new perspectives and strategies for the development of solar energy conversion technologies, advancing toward more efficient and sustainable energy solutions.
{"title":"Bridging photosynthesis and photovoltaics: Biotechnological pathways for sustainable solar energy","authors":"Zhaodong Li , Zihui Gao , Haonan Song , Jialiang He , Wei Xiong","doi":"10.1016/j.biotechadv.2025.108768","DOIUrl":"10.1016/j.biotechadv.2025.108768","url":null,"abstract":"<div><div>Integrating biological systems with artificial optoelectronic materials for efficient solar energy conversion has emerged as a cutting-edge and promising research direction in the pursuit of sustainable energy solutions. Natural photosynthesis, through intricate biological mechanisms, converts solar energy into chemical energy, serving as an inspiration for human innovation; concurrently, photovoltaic technologies utilize semiconductor materials to directly transform solar radiation into electricity. Recent interdisciplinary research efforts have led to the development of bio-abiotic hybrid interfaces, combining the regenerative capabilities of biological systems with the tunable optoelectronic properties of artificial materials, aiming to enhance solar energy conversion efficiency. This review focuses on the latest advancements in artificial photosynthesis, bio-photoelectrochemical systems, and bio-photovoltaic systems, emphasizing their potential to improve solar energy conversion efficiency. We explore the design principles, operational mechanisms, and performance metrics of these hybrid devices, and conduct an in-depth analysis of technical challenges such as interface stability and electron transfer efficiency. Furthermore, we propose future research directions to optimize these systems for practical applications in sustainable energy production. By integrating knowledge from biology, materials science, and energy engineering, we aim to provide new perspectives and strategies for the development of solar energy conversion technologies, advancing toward more efficient and sustainable energy solutions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108768"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Flavin reductases (FRs) are essential redox enzymes that supply reduced flavin cofactors (FMNH−/FADH−) to various monooxygenase partners in two-component flavin-dependent monooxygenase (TC-FDMO) systems. These enzymes play critical roles in numerous biological processes and industrial biocatalytic reactions, including hydroxylation, halogenation, and epoxidation. In this review, we provide a comprehensive analysis of the structural features, oligomeric states, kinetic mechanisms, and newly proposed classification strategies of FRs. We highlight the limitations of existing classification systems that rely solely on physiological function and propose a more informative framework based on amino acid sequences and domain architectures. Detailed mechanistic insights from transient kinetics, charge-transfer complex formation, and flavin transfer pathways are discussed, with emphasis on enzyme-specific features such as half-site reactivity and substrate-enhanced catalysis. Advances in protein engineering and fusion protein design aimed at improving FR stability, catalytic performance, and cofactor regeneration are also critically evaluated. In addition, we explore alternative strategies for supplying reduced flavin to monooxygenase partners, including non-enzymatic regeneration methods and the use of nicotinamide analogs. Finally, we outline key challenges and future directions for developing next-generation FRs with enhanced industrial applicability. This knowledge provides a foundation for engineering TC-FDMO systems for scalable, sustainable, and industrially relevant biocatalysis.
{"title":"Flavin reductases in two-component systems: Mechanistic insights, structural classification, and biotechnological advances","authors":"Panu Pimviriyakul , Piyanuch Anuwan , Pimchai Chaiyen , Thanyaporn Wongnate","doi":"10.1016/j.biotechadv.2025.108779","DOIUrl":"10.1016/j.biotechadv.2025.108779","url":null,"abstract":"<div><div>Flavin reductases (FRs) are essential redox enzymes that supply reduced flavin cofactors (FMNH<sup>−</sup>/FADH<sup>−</sup>) to various monooxygenase partners in two-component flavin-dependent monooxygenase (TC-FDMO) systems. These enzymes play critical roles in numerous biological processes and industrial biocatalytic reactions, including hydroxylation, halogenation, and epoxidation. In this review, we provide a comprehensive analysis of the structural features, oligomeric states, kinetic mechanisms, and newly proposed classification strategies of FRs. We highlight the limitations of existing classification systems that rely solely on physiological function and propose a more informative framework based on amino acid sequences and domain architectures. Detailed mechanistic insights from transient kinetics, charge-transfer complex formation, and flavin transfer pathways are discussed, with emphasis on enzyme-specific features such as half-site reactivity and substrate-enhanced catalysis. Advances in protein engineering and fusion protein design aimed at improving FR stability, catalytic performance, and cofactor regeneration are also critically evaluated. In addition, we explore alternative strategies for supplying reduced flavin to monooxygenase partners, including non-enzymatic regeneration methods and the use of nicotinamide analogs. Finally, we outline key challenges and future directions for developing next-generation FRs with enhanced industrial applicability. This knowledge provides a foundation for engineering TC-FDMO systems for scalable, sustainable, and industrially relevant biocatalysis.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108779"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145780161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-19DOI: 10.1016/j.biotechadv.2025.108763
Yuki Uno , Yusuke Hayashi , Hirokazu Sugiyama , Jun Okuda , Tetsuji Nakamura , Masahiro Kino-oka
The projected expansion of the global market for cell manufacturing, which contributes to regenerative medicine and cell therapies, warrants the designing and development of scalable cryopreservation processes for cell-based products (CBPs) for use in both standard and personalized therapies. However, the change in scale causes variations in process parameters, which affects the stability of the CBP quality. Therefore, the cryopreservation process for CBPs needs to be designed based on the concept of cell manufacturability and consideration of both engineering and biological aspects. In this review, we discussed strategies to enhance the quality stability of CBPs during cryopreservation, focusing primarily on four key processes: dispensing, freezing, storage, and thawing. Additionally, we discussed the application of simulation technologies because they aid in constructing digital twins for the designing and development of the cryopreservation process and facilitate efficiency with limited time and resources.
{"title":"Strategies to Enhance Stability of Cryopreservation Processes for Cell-Based Products","authors":"Yuki Uno , Yusuke Hayashi , Hirokazu Sugiyama , Jun Okuda , Tetsuji Nakamura , Masahiro Kino-oka","doi":"10.1016/j.biotechadv.2025.108763","DOIUrl":"10.1016/j.biotechadv.2025.108763","url":null,"abstract":"<div><div>The projected expansion of the global market for cell manufacturing, which contributes to regenerative medicine and cell therapies, warrants the designing and development of scalable cryopreservation processes for cell-based products (CBPs) for use in both standard and personalized therapies. However, the change in scale causes variations in process parameters, which affects the stability of the CBP quality. Therefore, the cryopreservation process for CBPs needs to be designed based on the concept of cell manufacturability and consideration of both engineering and biological aspects. In this review, we discussed strategies to enhance the quality stability of CBPs during cryopreservation, focusing primarily on four key processes: dispensing, freezing, storage, and thawing. Additionally, we discussed the application of simulation technologies because they aid in constructing digital twins for the designing and development of the cryopreservation process and facilitate efficiency with limited time and resources.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108763"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145553879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-21DOI: 10.1016/j.biotechadv.2025.108764
Kumar Vishven Naveen , Akanksha Tyagi , Omnia Mohammed Hamid Ibrahium, Rainer E.A.W. Fischer, Raluca Ostafe
Cell viability assays (CVAs) are widely used in cell biology, biomedical research, drug development, and biotechnology to assess cell health, proliferation, cytotoxicity, and functional activity under various conditions. Key applications span from everyday cell culture monitoring to drug screening and toxicology studies, immunology, vaccine development, and stem cell and regenerative medicine. Despite the long history and widespread use of CVAs, selecting the right assay remains a challenge for researchers. The increasing number of available assay options has led to confusion and inefficiencies, as scientists struggle to navigate the differences, trade-offs, and technical limitations of each method. Many researchers continue using the assays they were trained with, rather than exploring newer, more sensitive, or more appropriate techniques. Lab protocols are often passed down without reassessment, and new projects frequently adopt assays based on convenience (e.g., reagent availability or existing equipment) rather than rational selection criteria. Some groups deliberately choose less sensitive assays under the assumption that they produce “better-distributed” data. However, this incorrect justification arises because assays with a high limit of detection (LOD) fail to capture small variations, creating the misleading perception of clean and well-distributed data. Ignoring small variations does not improve accuracy - it simply reduces sensitivity, potentially leading to incorrect conclusions. Hence, the purpose of this review is to provide a comprehensive overview of contemporary CVAs by categorizing detection methods and summarizing their concepts, applications, benefits, and limitations, while also highlighting the potential need for novel approaches in this field. To assist researchers in selecting the most appropriate assay for their experimental goals, we also present a visual decision tree that integrates mechanistic insights with practical considerations.
{"title":"From dye exclusion to high-throughput screening: A review of cell viability assays and their applications","authors":"Kumar Vishven Naveen , Akanksha Tyagi , Omnia Mohammed Hamid Ibrahium, Rainer E.A.W. Fischer, Raluca Ostafe","doi":"10.1016/j.biotechadv.2025.108764","DOIUrl":"10.1016/j.biotechadv.2025.108764","url":null,"abstract":"<div><div>Cell viability assays (CVAs) are widely used in cell biology, biomedical research, drug development, and biotechnology to assess cell health, proliferation, cytotoxicity, and functional activity under various conditions. Key applications span from everyday cell culture monitoring to drug screening and toxicology studies, immunology, vaccine development, and stem cell and regenerative medicine. Despite the long history and widespread use of CVAs, selecting the right assay remains a challenge for researchers. The increasing number of available assay options has led to confusion and inefficiencies, as scientists struggle to navigate the differences, trade-offs, and technical limitations of each method. Many researchers continue using the assays they were trained with, rather than exploring newer, more sensitive, or more appropriate techniques. Lab protocols are often passed down without reassessment, and new projects frequently adopt assays based on convenience (e.g., reagent availability or existing equipment) rather than rational selection criteria. Some groups deliberately choose less sensitive assays under the assumption that they produce “better-distributed” data. However, this incorrect justification arises because assays with a high limit of detection (LOD) fail to capture small variations, creating the misleading perception of clean and well-distributed data. Ignoring small variations does not improve accuracy - it simply reduces sensitivity, potentially leading to incorrect conclusions. Hence, the purpose of this review is to provide a comprehensive overview of contemporary CVAs by categorizing detection methods and summarizing their concepts, applications, benefits, and limitations, while also highlighting the potential need for novel approaches in this field. To assist researchers in selecting the most appropriate assay for their experimental goals, we also present a visual decision tree that integrates mechanistic insights with practical considerations.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108764"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145567418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2025-11-29DOI: 10.1016/j.biotechadv.2025.108772
Nisar Uddin , Muhammad Wajid Ullah , Daochen Zhu , Xiangyang Li , Sanwei Yang , Xin Xie
Lignin biosynthesis and plant cell wall engineering are central to plant structural integrity and biomass utility. Recent advances in molecular and synthetic biology have opened opportunities to tailor lignin contents, composition, and polymer structure for renewable bioenergy and sustainable biomaterial applications. This review provides an integrative perspective on biosynthesis, regulation, and engineering of lignin. It summarizes the current progress in understanding the genetic, transcriptional, epigenetic, and metabolic networks that control lignin formation, with a focus on emerging tools such as CRISPR/Cas genome editing, synthetic promoters, and metabolic rewiring. Beyond cataloguing current knowledge, it critically analyzes the trade-offs involved in lignin modification for biomaterials, addressing unresolved challenges such as monolignol transport, metabolic flux control, and species-specific regulatory divergence. Engineered lignin and modified plant cell walls hold significant potential for biorefineries, advanced polymers, pharmaceuticals, and carbon sequestration, yet their translation from the laboratory to the field remains limited. Engineered lignin offers real-world applications across diverse industries, including bioenergy, bioplastics, carbon fiber composites, pharmaceuticals, and sustainable construction materials, thereby reinforcing its pivotal role in advancing a circular bioeconomy. The review further proposes future research directions that integrate multi-omics, single-cell technologies, machine learning, and field-based validation to enable precision lignin engineering. Strategic advances in this field will support next-generation bioenergy systems, advanced biomaterials, and the transition to a circular bioeconomy.
{"title":"Engineering lignin pathway, plant cell wall modification, and genome editing for advanced renewable bioenergy and material applications","authors":"Nisar Uddin , Muhammad Wajid Ullah , Daochen Zhu , Xiangyang Li , Sanwei Yang , Xin Xie","doi":"10.1016/j.biotechadv.2025.108772","DOIUrl":"10.1016/j.biotechadv.2025.108772","url":null,"abstract":"<div><div>Lignin biosynthesis and plant cell wall engineering are central to plant structural integrity and biomass utility. Recent advances in molecular and synthetic biology have opened opportunities to tailor lignin contents, composition, and polymer structure for renewable bioenergy and sustainable biomaterial applications. This review provides an integrative perspective on biosynthesis, regulation, and engineering of lignin. It summarizes the current progress in understanding the genetic, transcriptional, epigenetic, and metabolic networks that control lignin formation, with a focus on emerging tools such as CRISPR/Cas genome editing, synthetic promoters, and metabolic rewiring. Beyond cataloguing current knowledge, it critically analyzes the trade-offs involved in lignin modification for biomaterials, addressing unresolved challenges such as monolignol transport, metabolic flux control, and species-specific regulatory divergence. Engineered lignin and modified plant cell walls hold significant potential for biorefineries, advanced polymers, pharmaceuticals, and carbon sequestration, yet their translation from the laboratory to the field remains limited. Engineered lignin offers real-world applications across diverse industries, including bioenergy, bioplastics, carbon fiber composites, pharmaceuticals, and sustainable construction materials, thereby reinforcing its pivotal role in advancing a circular bioeconomy. The review further proposes future research directions that integrate multi-omics, single-cell technologies, machine learning, and field-based validation to enable precision lignin engineering. Strategic advances in this field will support next-generation bioenergy systems, advanced biomaterials, and the transition to a circular bioeconomy.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108772"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145619679","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01Epub Date: 2026-01-14DOI: 10.1016/j.biotechadv.2026.108804
Bianca Costa Bernardo Port , Paula Rogovski , Gislaine Fongaro , Thiago Caon
Bacteriophage(phage)-based interventions have been considered for environmental and biomedical applications as well as during food processing, representing a promising alternative when multidrug-resistant bacteria are found. Although liquid and semi-solid formulations are easier to prepare as few unit operations are required, stability issues or short-term effects have led to the prioritization of solid formulations. Polymeric films have gained prominence as a strict control of phage release or improved phage stability can be achieved. During film preparation, phages are deposited onto a pre-ready solid support or incorporated in a film-forming solution. Advantages and disadvantages of each preparation method as well as the impact of different processing conditions (temperature, pH, ionic strength and agitation) on phage viability/stability are discussed in detail in this review. High viral titer broadens the spectrum of materials and film preparation methods that can be considered. The orientation of some phages during immobilization into solid supports, in turn, has proven to be a key aspect for phage infectivity, particularly for tailed phages. The points raised in this review are certainly an important direction for future technological developments in this field, contributing to the development of films with longer-lasting action.
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