Progress in molecular biology and translational science最新文献

{"title":"High-throughput screening of biomolecules using cell-free systems.","authors":"Brahmjot Singh, Jyoti, Suhail Kapta, Sandeep Kaur, Ajay Kumar, Gholamreza Abdi","doi":"10.1016/bs.pmbts.2025.11.001","DOIUrl":"10.1016/bs.pmbts.2025.11.001","url":null,"abstract":"<p><p>High-throughput screening (HTS) has revolutionized the identification and evaluation of biomolecules by enabling the parallel testing of large libraries of compounds, nucleic acids, and proteins against biological targets. Traditionally conducted in live cells, HTS faces limitations such as cellular toxicity, metabolic interference, and regulatory constraints. Cell-free systems (CFS), which operate in vitro using reconstituted transcription-translation machinery, have emerged as powerful alternatives. These systems circumvent the constraints of cellular physiology, allowing for rapid and tunable expression of biomolecules directly from DNA or RNA templates. This chapter explores the principles, platforms, and applications of CFS-based HTS, highlighting its transformative impact on synthetic biology, drug discovery, diagnostics, and protein engineering. Several cell-free systems are detailed, including those derived from E. coli, wheat germ, rabbit reticulocytes, and the defined PURE system. The integration of CFS with high-throughput platforms such as microplates, droplet microfluidics, and paper-based devices enables cost-effective, scalable, and multiplexed assays. Analytical readouts, including fluorescence, luminescence, mass spectrometry, and digital PCR, provide real-time, sensitive detection of biochemical outputs. Furthermore, automation and machine learning are increasingly incorporated through robotic liquid handling and data-driven DBTL cycles, accelerating discovery and design processes. Despite challenges such as high reagent costs and limited post-translational modifications, innovations such as lyophilized CFS kits, artificial cells, and AI-integrated closed-loop platforms are expanding the frontiers of HTS. Altogether, CFS-based HTS offers a flexible, rapid, and accessible approach for next-generation biomolecular screening and therapeutic development.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"187-217"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047250","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}

{"title":"Cell-free systems for development of biosensors.","authors":"Stuti Ganatra, Alok Pandya","doi":"10.1016/bs.pmbts.2025.09.003","DOIUrl":"10.1016/bs.pmbts.2025.09.003","url":null,"abstract":"<p><p>Cell-free systems (CFSs) have become powerful tools in synthetic biology, enabling the creation of fast, modular, and customizable biosensors without relying on living cells. By utilizing in vitro transcription and translation, these systems offer a finely controlled biochemical environment suitable for sensing applications in fields such as healthcare, environmental science, agriculture, and food quality assurance. This chapter provides an in-depth look at the design and functionality of CFS-based biosensors, highlighting the construction of genetic circuits, signal output strategies, and device formats including paper-based platforms, microfluidic systems, and wearable technologies. With use cases ranging from pathogen detection to monitoring environmental contaminants, cell-free biosensors are proving especially valuable in point-of-care (POC) and low-resource settings. The chapter also addresses current limitations such as shelf-life, sensitivity, and scalability and explores engineering solutions including AI-assisted design, molecular optimization, and advanced material integration. Looking ahead, the convergence of CFS biosensing with smart technologies such as IoT and distributed fabrication promises a new era of accessible, intelligent diagnostics.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"129-156"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047204","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}

{"title":"Cell-free systems for automation and robotics.","authors":"Juveriya Israr, Shabroz Alam, Ajay Kumar","doi":"10.1016/bs.pmbts.2025.08.008","DOIUrl":"10.1016/bs.pmbts.2025.08.008","url":null,"abstract":"<p><p>The amalgamation of cell-free systems with automation and robotics is transforming the domains of biotechnology and bioengineering. This chapter examines the swiftly advancing domain of robotic platforms utilizing cell-free protein synthesis (CFPS) and other programmable cell-free biological mechanisms. Cell-free systems have substantial benefits compared to conventional cell-based approaches, such as less contamination risk, improved control over reaction variables, and expedited response times. These attributes render them exceptionally appropriate for high-throughput screening, expedited prototyping of synthetic biology circuits, on-demand biomanufacturing, and point-of-care diagnostics. This chapter offers a detailed examination of the design, functionalities, and constraints of automated cell-free systems, emphasizing technologies such as microfluidic devices, liquid handling robots, and integrated analytical platforms. Principal difficulties addressed encompass standardization, the creation of more resilient and economical cell-free extracts, and the incorporation of artificial intelligence and machine learning for enhanced experimental design and process optimization. The integration of cell-free system programmability with the accuracy and scalability of automation and robotics is set to expedite discovery, facilitate the development of innovative biomaterials, and broaden access to advanced biotechnological tools and applications.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"218 ","pages":"109-127"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146047221","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}

{"title":"Computational approaches for protein complex modeling for intermediate resolution cryo-EM maps.","authors":"Joon Hong Park, Genki Terashi, Daisuke Kihara","doi":"10.1016/bs.pmbts.2026.03.003","DOIUrl":"10.1016/bs.pmbts.2026.03.003","url":null,"abstract":"<p><p>Cryogenic electron microscopy (cryo-EM) has become a central technology for determining macromolecular structures in structural biology. However, interpreting density maps by structure modeling from intermediate (∼5-10Å) to low resolution (over 10Å) cryo-EM maps often remains challenging. To meet the demand for accurate modeling tools in cryo-EM, we developed the EMSuite server (https://em.kiharalab.org/), a freely accessible platform that provides 14 computational tools for structure modeling and validation. In this chapter, we focus on three methods developed for intermediate resolution maps, DiffModeler, DMcloud, and VESPER, presenting their usages through the web server. DiffModeler builds full protein complexes by enhancing backbone positions with a diffusion-based generative model and using AlphaFold to predict structural models. Similarly, DMcloud performs local structure fitting instead of global structure fitting to eliminate incompatible regions in structure models to the map. Finally, VESPER is a general-use structure fitting method, which performs global structure-map and map-map fitting.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"223 ","pages":"147-168"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148472526","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}

{"title":"Innovations in cell-free synthetic biology via microfluidic approaches.","authors":"Samar Damiati","doi":"10.1016/bs.pmbts.2025.08.004","DOIUrl":"10.1016/bs.pmbts.2025.08.004","url":null,"abstract":"<p><p>Cell-free synthetic biology is a powerful technology that is gaining increasing popularity due to its ability to perform complex biochemical reactions in a well-controlled environment, isolated from the intricacies of living cells. Although it has demonstrated significant success in genetic part characterization and high-throughput protein production without the constraints of cellular membranes, cell-free systems still face several challenges. These include the limited volume available for transcription-translation machinery, the difficulty in standardizing cell lysis procedures, and the variability in cell extract performance across different laboratories. Microfluidic technology has become a powerful tool to address these challenges by supporting the miniaturization and automation of complex, multi-step workflows. Integrating cell-free gene and protein synthesis with microfluidic platforms has redefined bioprocessing, making it more compact and accessible. This synergy has unlocked a wide range of applications across diverse areas of synthetic biology in recent years. This book chapter reviews microfluidic-based methods for synthetic biology in cell-free environments. It highlights the fundamental principles of both cell-free systems and microfluidic technologies, and presents various examples of their integration. The chapter proposes this convergence as a pioneering approach to developing innovative platforms for synthetic biology, with potential applications in biomedical, therapeutic, diagnostic, and environmental contexts.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"219 ","pages":"211-235"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146194672","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}

{"title":"Artificial intelligence in wearable biosensing: Enhancing data analysis and decision-making.","authors":"Zenghui Ding, Wenhui Fang, Jixue Zhang, Changguo Fang, Yining Sun","doi":"10.1016/bs.pmbts.2025.06.012","DOIUrl":"10.1016/bs.pmbts.2025.06.012","url":null,"abstract":"<p><p>The convergence of artificial intelligence (AI) and wearable biosensors is revolutionizing personalized healthcare, enabling continuous monitoring, early detection of health issues, which enhances the efficiency of data processing and real-time decision-making. Multimodal Large Language Models (MLLMs) play a pivotal role in this ecosystem by offering advanced capabilities in analyzing complex health data, understanding nuanced health contexts, and generating tailored health recommendations instantaneously. This study provides insights into how machine learning, deep learning algorithms, and MLLM can work together to facilitate the analysis of physiologic data for real-time monitoring and early warning systems as well as complex decision support mechanisms. In addition, the emergence of clinical decision support systems (CDSS) driven by AI and MLLM provides comprehensive recommendations. Looking ahead, the potential convergence of digital people, meta-universes and world models with wearable biosensors presents an innovative vision for personalized health management.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"216 ","pages":"1-26"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024159","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}

{"title":"An introduction to non-coding RNAs.","authors":"Charan Psvv, Adithya Joseph, Praveen Ebenezer, Vandana Sankar, Renuka Suravajhala, R Shyama Prasad Rao, Prashanth Suravajhala","doi":"10.1016/bs.pmbts.2025.01.006","DOIUrl":"10.1016/bs.pmbts.2025.01.006","url":null,"abstract":"<p><p>Non-coding RNAs (ncRNAs) are a group of RNAs that do not encode proteins but play key roles in diverse biological functions such as gene regulation, chromatin remodeling, and other cellular processes. Two major types are small ncRNAs (sncRNAs, with a size of ∼21-34 nucleotides) and long ncRNAs (lncRNAs, size of>200 nucleotides), and each has multiple subtypes. Notably, ncRNAs constitute over 90 % of the RNAs from the human genome. Exploring ncRNAs is important to understand the complexities of cellular regulations and for potential therapeutic applications as biomarkers or therapies in various diseases such as cancer. In this chapter, we provide a gist of ncRNAs, their role in regulation.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"214 ","pages":"1-17"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144340378","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}

{"title":"Wearable biosensors: A comprehensive overview.","authors":"Kevin Y Wu, Meihua E Su, Yeonsu Kim, Louis Nguyen, Michael Marchand, Simon D Tran","doi":"10.1016/bs.pmbts.2025.05.011","DOIUrl":"10.1016/bs.pmbts.2025.05.011","url":null,"abstract":"<p><p>Wearable biosensors are revolutionizing the landscape of modern healthcare by enabling continuous, non-invasive monitoring and real-time diagnostics across a myriad of medical applications. This chapter provides a comprehensive overview of wearable biosensors, beginning with an exploration of their fundamental components, including biological elements, transducers, and electronic interfaces. It categorizes these devices based on the types of biological matrices they utilize, such as tears and saliva, and the nanomaterials and transduction mechanisms that underpin their functionality. Highlighting state-of-the-art advancements, the chapter delves into specific applications in ophthalmology and oral health, showcasing innovative tear-based sensors for monitoring intraocular pressure and glucose levels, as well as saliva-based devices for detecting oral diseases and systemic biomarkers. Through detailed examples, such as multifunctional contact lenses and smart mouthguards, the chapter illustrates the potential of these technologies to transform disease detection, health monitoring, and personalized treatment strategies. Additionally, it addresses the current challenges in wearable biosensor development, including issues of sensor accuracy, durability, and user comfort, while outlining future directions for research and integration into everyday healthcare practices. This chapter aims to provide readers with a thorough understanding of wearable biosensors' current state, innovations, and future potential in enhancing health and wellness monitoring.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"215 ","pages":"101-154"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668261","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}

{"title":"Oral delivery of protein and peptide therapeutics.","authors":"Vivek P Chavda, Pankti C Balar","doi":"10.1016/bs.pmbts.2024.11.003","DOIUrl":"10.1016/bs.pmbts.2024.11.003","url":null,"abstract":"<p><p>Oral administration of proteins and peptides has gained significant attention recently due to its potential to transform therapeutic strategies, providing a non-invasive and patient-friendly method for delivering biopharmaceuticals. The primary hurdle in oral delivery stems from the harsh conditions of the gastrointestinal (GI) tract, characterized by acidic pH, enzymatic degradation, and limited permeability across the intestinal epithelium. Various innovative approaches have emerged to overcome these challenges, including nanoparticle-based delivery systems, mucoadhesive formulations, and chemical modifications of peptides aimed at improving stability and absorption rates. Nanoparticle-based delivery systems, such as liposomes, polymeric nanoparticles, and solid lipid nanoparticles, hold promise in protecting proteins and peptides from enzymatic degradation while enhancing their bioavailability. These nanoparticles can be tailored to target specific areas within the GI tract, extending drug release and enhancing therapeutic effectiveness. Mucoadhesive formulations utilize polymers like chitosan, alginate, and polyethylene glycol (PEG) derivatives to adhere to GI mucosal surfaces, prolonging residence time and facilitating drug absorption. Chemical modifications, such as PEGylation, glycosylation, and lipidation have been employed to enhance the stability and permeability of proteins and peptides in the GI tract. PEGylation, in particular, has been widely used to extend the circulation half-life and reduce the immunogenicity of therapeutic proteins. Advancements in nanotechnology, especially the development of smart nanocarriers capable of responsive drug release triggered by pH or enzymatic stimuli, show promise in further improving oral delivery of proteins and peptides. The integration of bioinformatics and computational modeling techniques has facilitated the design of novel drug delivery systems with optimized pharmacokinetic profiles. This chapter focuses on the advancements and challenges in the oral delivery of protein and peptide-based drugs, highlighting the innovative strategies being explored to enhance therapeutic outcomes.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"212 ","pages":"355-387"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143693151","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}

{"title":"Technologies and emerging trends in wearable biosensing.","authors":"Stuti Ganatra, Nishita Bhanushali, Sumit Kosare, Hemangi Barot, Alok Pandya","doi":"10.1016/bs.pmbts.2025.06.011","DOIUrl":"10.1016/bs.pmbts.2025.06.011","url":null,"abstract":"<p><p>This chapter examines advancements and future trajectories in wearable biosensing technologies, a multidisciplinary field encompassing healthcare, materials science, and information technology. Wearable biosensors are revolutionizing real-time physiological and biochemical monitoring with applications in personalized health monitoring, disease diagnosis, fitness, and therapeutic interventions. In addition to Internet of Things (IoT) and wireless connectivity technologies such as Bluetooth Low Energy (BLE) and 5G, which facilitate transparent remote monitoring and data exchange, other notable innovations such as machine learning and artificial intelligence enhance real-time processing of data, predictive analytics, and personalized healthcare solutions. While lab-on-skin technologies support non-invasive continuous diagnostics, nanomaterials such as graphene and quantum dots have significantly enhanced the sensitivity and efficiency of sensors. Future developments will address multimodal sensor systems for comprehensive health monitoring, augmented reality/virtual reality (AR/VR) integration, and sustainable and self-healing biosensors. However, challenges related to scalability, commercialization, and environmentally conscious design persist. Significant case studies on diabetic management through continuous glucose monitoring and workplace stress monitoring conclude the chapter, highlighting the transformative potential of wearable biosensors in occupational health and healthcare.</p>","PeriodicalId":21157,"journal":{"name":"Progress in molecular biology and translational science","volume":"216 ","pages":"255-278"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145024150","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}