Biotechnology advances最新文献

{"title":"From dye exclusion to high-throughput screening: A review of cell viability assays and their applications","authors":"Kumar Vishven Naveen ,&nbsp;Akanksha Tyagi ,&nbsp;Omnia Mohammed Hamid Ibrahium,&nbsp;Rainer E.A.W. Fischer,&nbsp;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}

{"title":"Engineering lignin pathway, plant cell wall modification, and genome editing for advanced renewable bioenergy and material applications","authors":"Nisar Uddin ,&nbsp;Muhammad Wajid Ullah ,&nbsp;Daochen Zhu ,&nbsp;Xiangyang Li ,&nbsp;Sanwei Yang ,&nbsp;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}

{"title":"Immobilization/incorporation methods of bacteriophages into polymeric films: Technological challenges & perspectives","authors":"Bianca Costa Bernardo Port ,&nbsp;Paula Rogovski ,&nbsp;Gislaine Fongaro ,&nbsp;Thiago Caon","doi":"10.1016/j.biotechadv.2026.108804","DOIUrl":"10.1016/j.biotechadv.2026.108804","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108804"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145987937","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}

{"title":"Vanadium-dependent haloperoxidases: Recent advances and perspectives","authors":"Bishuang Chen ,&nbsp;Yongyi Zeng ,&nbsp;Jiangtao Sha ,&nbsp;Huanhuan Li ,&nbsp;Yunhan Zhang ,&nbsp;Lan Liu ,&nbsp;Wuyuan Zhang","doi":"10.1016/j.biotechadv.2026.108797","DOIUrl":"10.1016/j.biotechadv.2026.108797","url":null,"abstract":"<div><div>Vanadium-dependent haloperoxidases (VHPOs) represent a distinct class of halogenating enzymes that catalyze the oxidation of halide ions into hypohalous acids using hydrogen peroxide and a redox-stable vanadate cofactor. In recent years, VHPOs have gained considerable attention in synthetic community due to their exceptional operational robustness, broad substrate tolerance, and particularly, the potential in driving green halo-compound synthesis. The rapid progress using VHPOs in organic synthesis inspires this review covering VHPOs discovery, structure-function insights, mechanistic elucidation, and various synthetic applications. Special attention is given to recent breakthroughs in understanding the halide and substrate specificity of VHPOs, including the identification of substrate-access tunnels and enzyme-bound halogenation mechanisms. These findings not only challenge the long-standing diffusible HOX model but also enable rational enzyme engineering. VHPOs are emerging as powerful tools for selective halogenation and sustainable synthesis, with promising prospects in synthetic biology, materials science, and environmental biotechnology.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108797"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145921095","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}

{"title":"Integrating multi-omics and artificial intelligence fuels advanced target identification and drug discovery","authors":"Hang Chen ,&nbsp;Ying Shi ,&nbsp;Meiling Yuan ,&nbsp;Huihui Li ,&nbsp;Xiaowei Liu","doi":"10.1016/j.biotechadv.2025.108785","DOIUrl":"10.1016/j.biotechadv.2025.108785","url":null,"abstract":"<div><div>Target identification is pivotal for developing novel therapeutics in cancer and other diseases. Traditional experiment screening methods are constrained by low throughput and the complexity of biological systems. Multi-omics technologies offer a transformative solution by providing comprehensive, multi-dimensional insights into molecular mechanisms. However, the exponential growth of multi-omics data necessitates efficient computational algorithms for dimensionality reduction and unravel the intricate biological processes. Artificial intelligence (AI) has emerged as a powerful tool capable of analyzing complementary multi-modal data streams. The integration of multi-omics technologies and AI algorithms has revolutionized target identification and drug discovery. This review highlights prevalent omics techniques and their role in target identification and drug discovery, outlines key machine learning (ML) classifications, and describes the integration of multi-omics with AI. We explore the applications of AI-driven multi-omics in various stages of drug discovery, including target identification, target validation, lead optimization, as well as clinical evaluation, underscoring the transformative potential of this approach. Additionally, we discuss the challenges associated with this integrative strategy and future trends in the field. As the integration of multi-omics and AI continues to expand, we anticipate a paradigm shift in target identification and drug discovery, paving the way for more precise and effective therapies.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108785"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145845089","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}

{"title":"Designing prokaryotic gene expression regulatory elements: From genomic mining to artificial intelligence-driven generation","authors":"Xuan Zhou,&nbsp;Wenyan Cao,&nbsp;Chao Huang,&nbsp;Xiaojuan Zhang,&nbsp;Shenghu Zhou,&nbsp;Yu Deng","doi":"10.1016/j.biotechadv.2025.108781","DOIUrl":"10.1016/j.biotechadv.2025.108781","url":null,"abstract":"<div><div>Gene expression regulatory elements (GEREs) play a pivotal role in the control of gene transcription and translation. The design of GEREs with precise and tunable activity remains a major challenge in synthetic biology. Over the past decades, engineering strategies have evolved from empirical sequence mining and random mutagenesis to increasingly rational approaches guided by biophysical models and artificial intelligence. In this review, we systematically examine the design principles, representative studies, and implementation strategies for each GERE class, highlighting how mining, modular recombination, targeted mutagenesis, and deep generative modeling contribute to the development of functional regulatory elements. We further discuss the strengths and limitations of these strategies, offering practical guidance for optimizing microbial cell factory bioproduction through the fine-tuning of gene expression.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108781"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145784804","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}

{"title":"Biosynthesis of functional carbohydrates from glycolytic node precursors glucose-6-phosphate and fructose-6-phosphate: Advances and prospects","authors":"Ran You ,&nbsp;Xueqin Lv ,&nbsp;Yan Zhang ,&nbsp;Jian Chen ,&nbsp;Long Liu","doi":"10.1016/j.biotechadv.2026.108808","DOIUrl":"10.1016/j.biotechadv.2026.108808","url":null,"abstract":"<div><div>Glucose-6-phosphate (G-6-P) and fructose-6-phosphate (F-6-P), which are located upstream of glycolysis, are crucial node compounds that provide carbon skeletons and supply energy for cell growth. <em>De novo</em> microbial synthesis of functional carbohydrates involves the derivatization of G-6-P and F-6-P. It is often associated with negative growth effects, creating challenges for efficient production. In this review, the main derivatization reactions with G-6-P and F-6-P as precursors were divided into three categories: the IAD (<strong>I</strong>somerization <strong>A</strong>nd <strong>D</strong>ephosphorylation) module, the FGF (<strong>F</strong>-6-P to <strong>G</strong>DP-<strong>F</strong>ucose) module, and the FAA (<strong>F</strong>-6-P trans<strong>A</strong>cetylation and trans<strong>A</strong>mination) module. The representative functional carbohydrates of these pathways were briefly introduced, and pathway reconstruction and optimization for these carbohydrates were summarized. In addition, advances in central carbon metabolism regulation for G-6-P and F-6-P redirection were classified and summarized. Finally, the synthesis of functional carbohydrates by microbial redirection of G-6-P and F-6-P was investigated. This review facilitates the understanding of strategies and core principles involved in glycolytic node G-6-P and F-6-P redirection and the <em>de novo</em> biosynthesis of functional carbohydrate derivatives. It has significant implications for constructing efficient microbial cell factories that redirect G-6-P and F-6-P to derivatives and enable their industrial production.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108808"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146001550","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}

{"title":"Sensing for early-stage plant disease: From pathogenesis to sensor design","authors":"Junfeng Xie,&nbsp;Wenxuan Xu,&nbsp;Ranhua Xiong,&nbsp;Chaobo Huang,&nbsp;Miaomiao Zhu","doi":"10.1016/j.biotechadv.2026.108798","DOIUrl":"10.1016/j.biotechadv.2026.108798","url":null,"abstract":"<div><div>Pathogenic plant diseases pose a serious risk to global food supplies and to the sustainable development of agriculture and forestry. Conventional control strategies, which rely heavily on chemical treatments, can disrupt ecological balance and may also affect human health. There is therefore a strong need for environmentally benign and efficient technologies that can detect disease at an early stage. This review surveys recent advances and remaining challenges in sensor based early detection of plant diseases, following the path from basic concepts to practical deployment. It first considers the biological traits and infection processes of major pathogens and identifies characteristic signaling molecules released by infected plants, which serve as design cues for sensing platforms. Existing detection strategies are then grouped into two broad categories. Direct approaches aim at the pathogen itself and use optical or electrochemical biosensors that incorporate antibodies or DNA probes. Indirect approaches focus on plant responses to stress and monitor indicators such as trace volatile organic compounds (VOCs), low frequency acoustic signals and changes in plant phenotype. Finally, the review summarizes the main classes of sensors, discusses their current limitations and outlines possible routes for technological translation and future development. Grounded in plant pathology and early disease monitoring, the review aims to provide researchers and practitioners with both an overview of the field and practical guidance for further work.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108798"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145902703","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}

{"title":"Capitalizing on mechanistic insights to power design of future-ready intracellular optogenetics tools","authors":"Si Bin Chew,&nbsp;Emily Harjabrata,&nbsp;Cameron Jing Han Goh,&nbsp;Qunxiang Ong","doi":"10.1016/j.biotechadv.2025.108761","DOIUrl":"10.1016/j.biotechadv.2025.108761","url":null,"abstract":"<div><div>Intracellular optogenetics represents a rapidly advancing biotechnology that enables precise, reversible control of protein activity, signaling dynamics, and cellular behaviours using genetically encoded, light-responsive systems. Originally pioneered in neuroscience through channelrhodopsins to manipulate neuronal excitability, the field has since expanded into diverse intracellular applications with broad implications for medicine, agriculture, and biomanufacturing. Key to these advances are photoreceptors such as cryptochrome 2 (CRY2), light–oxygen–voltage (LOV) domains, and phytochromes, which undergo conformational changes upon illumination to trigger conditional protein–protein interactions, localization shifts, or phase transitions. Recent engineering breakthroughs—including the creation of red-light responsive systems such as MagRed that exploit endogenous biliverdin—have enhanced tissue penetration, minimized phototoxicity, and expanded applicability to complex biological systems.</div><div>This review provides an overarching synthesis of the molecular principles underlying intracellular optogenetic actuators, including the photophysical basis of light-induced conformational changes, oligomerization, and signaling control. We highlight strategies that employ domain fusions, rational mutagenesis, and synthetic circuits to extend their utility across biological and industrial contexts. We also critically assess current limitations, such as chromophore dependence, light delivery challenges, and safety considerations, so as to frame realistic paths towards translation. Looking ahead, future opportunities include multi-colour and multiplexed systems, integration with high-throughput omics and artificial intelligence, and development of non-invasive modalities suited for <em>in vivo</em> and industrial applications.</div><div>Intracellular optogenetics is thus emerging as a versatile platform technology, with the potential to reshape how we interrogate biology and engineer cells for therapeutic, agricultural, and environmental solutions.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108761"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145554410","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}

{"title":"UGT708 glycosyltransferases: Nature's architects of C-glycosides","authors":"Bhawna Verma ,&nbsp;Palak Arora ,&nbsp;Shahnawaz Hussain ,&nbsp;Ritu Devi ,&nbsp;Suphla Gupta","doi":"10.1016/j.biotechadv.2025.108787","DOIUrl":"10.1016/j.biotechadv.2025.108787","url":null,"abstract":"<div><div>Uridine Diphosphate glycosyltransferases (UGTs) catalyze the transfer of glycosyl moieties from donors to acceptors, a modification critical for plant growth, development, and metabolic homeostasis. These enzymes are ubiquitous across all life domains, playing key roles in the biosynthesis of diverse glycosides. This review focuses on the plant UGT708 family, which is uniquely characterized by its ability to form stable <em>C</em>-glycosidic bonds on flavonoid backbones, enhancing metabolic stability and bioactivity. We conducted a comprehensive analysis of UGT distribution and functional evolution across life forms, highlighting their evolutionary significance and diversification. Emphasizing plant-specific adaptations, UGT708 enzymes specialize in <em>C</em>-glycosylation of flavonoid, polyphenolic compounds, diketones and aromatic hydrocarbons, particularly 2-hydroxyflavanones and polyhydroxy ketones, facilitating the production of defense metabolites such as schaftosides and isoschaftosides which enhance plant resilience to environmental stresses. Clade-specific variations in the conserved PSPG motif, notably in monocots, correlate with differences in sugar-donor specificity and substrate promiscuity, reflecting structural and functional diversity within the family. Structural analyses reveal key active site residues responsible for selective <em>C</em>-glycosylation, resulting in a broad spectrum of glycosides with ecological and therapeutic importance. While UGT708s hold great promise as biocatalysts for generating bioactive compounds, more detailed studies on their molecular interactions and catalytic mechanisms are essential to fully exploit their potential in agriculture, medicine, and industry.</div></div>","PeriodicalId":8946,"journal":{"name":"Biotechnology advances","volume":"87 ","pages":"Article 108787"},"PeriodicalIF":12.5,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145822890","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}