Xingyu Ye, Haoyang Wu, Jinghan Liu, Jiayi Xiang, Yan Feng, Qian Liu
{"title":"One-pot diagnostic methods based on CRISPR/Cas and Argonaute nucleases: strategies and perspectives.","authors":"Xingyu Ye, Haoyang Wu, Jinghan Liu, Jiayi Xiang, Yan Feng, Qian Liu","doi":"10.1016/j.tibtech.2024.06.009","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.009","url":null,"abstract":"<p><p>CRISPR/Cas and Argonaute (Ago) proteins, which target specific nucleic acid sequences, can be applied as diagnostic tools. Despite high specificity and efficiency, achieving sensitive detection often necessitates a preamplification step that involves opening the lid and multistep operation, which may elevate the risk of contamination and prove inadequate for point-of-care testing. Hence, various one-pot detection strategies have been developed that enable preamplification and sensing in a single operation. We outline the challenges of one-pot detection with Cas and Ago proteins, present several main implementation strategies, and discuss future prospects. This review offers comprehensive insights into this vital field and explores potential improvements to detection methods that will be beneficial for human health.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735072","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":"Bacillus methanolicus: an emerging chassis for low-carbon biomanufacturing.","authors":"Xueting Yang, Zhaojuan Zheng, Yu Wang","doi":"10.1016/j.tibtech.2024.06.013","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.013","url":null,"abstract":"<p><p>Bacillus methanolicus is a thermophilic methylotrophic bacterium that grows quickly on methanol in sea water-based media. It has been engineered for chemical bioproduction from methanol, but its efficiency needs improvement for industrialization. Synthetic biology approaches such as metabolic modeling and genome editing can reprogram B. methanolicus for low-carbon biomanufacturing.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141735071","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":"Engineered bacterial therapeutics with material solutions.","authors":"Sourik Dey, Shrikrishnan Sankaran","doi":"10.1016/j.tibtech.2024.06.011","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.011","url":null,"abstract":"<p><p>Recent advances in engineered bacterial therapeutics underscore their potential in treating diseases via targeted, live interventions. Despite their promising performance in early clinical phases, no engineered therapeutic bacteria have yet received approval, primarily due to challenges in proving efficacy while ensuring biosafety. Material science innovations, particularly the encapsulation of bacteria within hydrogels, present a promising avenue to enhance bacterial survival, efficacy, and safety in therapeutic applications. This review discusses this interdisciplinary approach to develop living therapeutic materials. Hydrogels not only safeguard the bacteria from harsh physiological conditions but also enable controlled therapeutic release and prevent unintended bacterial dissemination. The strategic use of encapsulation materials could redefine the delivery and functionality of engineered bacterial therapeutics, facilitating their clinical translation.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141727819","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}
Ileana L Co, Aleksandra Fomina, Michelle Nurse, Alison P McGuigan
{"title":"Applications and evolution of 3D cancer-immune cell models.","authors":"Ileana L Co, Aleksandra Fomina, Michelle Nurse, Alison P McGuigan","doi":"10.1016/j.tibtech.2024.06.008","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.008","url":null,"abstract":"<p><p>Understanding the highly complex tumor-immune landscape is an important goal for developing novel immune therapies for solid cancers. To this end, 3D cancer-immune models have emerged as patient-relevant in vitro tools for modeling the tumor-immune landscape and the cellular interactions within it. In this review, we provide an overview of the components and applications of 3D cancer-immune models and discuss their evolution from 2015 to 2023. Specifically, we observe trends in primary cell-sourced, T cell-based complex models used for therapy evaluation and biological discovery. Finally, we describe the challenges of implementing 3D cancer-immune models and the opportunities for maximizing their potential for deciphering the complex tumor-immune microenvironment and identifying novel, clinically relevant drug targets.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141724588","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}
Armand Bernard, Tristan Rossignol, Young-Kyoung Park
{"title":"Biotechnological approaches for producing natural pigments in yeasts.","authors":"Armand Bernard, Tristan Rossignol, Young-Kyoung Park","doi":"10.1016/j.tibtech.2024.06.012","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.012","url":null,"abstract":"<p><p>Pigments are widely used in the food, cosmetic, textile, pharmaceutical, and materials industries. Demand for natural pigments has been increasing due to concerns regarding potential health problems and environmental pollution from synthetic pigments. Microbial production of natural pigments is a promising alternative to chemical synthesis or extraction from natural sources. Here, we discuss yeasts as promising chassis for producing natural pigments with their advantageous traits such as genetic amenability, safety, rapid growth, metabolic diversity, and tolerance. Metabolic engineering strategies and optimizing strategies in downstream process to enhance production of natural pigments are thoroughly reviewed. We discuss the challenges, including expanding the range of natural pigments and improving their feasibility of industrial scale-up, as well as the potential strategies for future development.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141634658","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}
Maria Zolotareva, Francisco Cascalheira, Cátia Caneiras, Cristina Bárbara, Diogo Miguel Caetano, Miguel Cacho Teixeira
{"title":"In the flow of molecular miniaturized fungal diagnosis.","authors":"Maria Zolotareva, Francisco Cascalheira, Cátia Caneiras, Cristina Bárbara, Diogo Miguel Caetano, Miguel Cacho Teixeira","doi":"10.1016/j.tibtech.2024.06.010","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.010","url":null,"abstract":"<p><p>The diagnosis of fungal infections presents several challenges and limitations, stemming from the similarities in symptomatology, diversity of underlying pathogenic species, complexity of fungal biology, and scarcity of rapid, affordable, and point-of-care approaches. In this review, we assess technological advances enabling the conversion of cutting-edge laboratory molecular diagnostic methods to cost-effective microfluidic devices. The most promising strategies toward the design of DNA sequence-based fungal diagnostic systems, capable of capturing and deciphering the highly informative DNA of the pathogen and adapted for resource-limited settings, are discussed, bridging fungal biology, molecular genetics, microfluidics, and biosensors.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141580933","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}
Long Ma, Minghui Lu, Jingyu Jia, Nan Wang, Yaru Li, Weipan Peng, Shuli Man
{"title":"Engineered crRNA for CRISPR/Cas-assisted biosensing.","authors":"Long Ma, Minghui Lu, Jingyu Jia, Nan Wang, Yaru Li, Weipan Peng, Shuli Man","doi":"10.1016/j.tibtech.2024.06.006","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.06.006","url":null,"abstract":"<p><p>CRISPR/Cas-based diagnostics (CRISPR-Dx) face challenges, including difficulty in detecting ultrashort nucleotides, preamplification dependency, cross-contamination, insufficiency in on-pot detection paradigms, and inconvenience in detecting non-nucleic acid targets. This forum outlines the advances in engineered CRISPR RNA (crRNA) that address the aforementioned problems, highlighting challenges, opportunities, and future directions.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141564488","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}
Trends in biotechnologyPub Date : 2024-07-01Epub Date: 2024-03-15DOI: 10.1016/j.tibtech.2024.01.004
Maria Gabriella Fois, Martijn van Griensven, Stefan Giselbrecht, Pamela Habibović, Roman K Truckenmüller, Zeinab Niloofar Tahmasebi Birgani
{"title":"Mini-bones: miniaturized bone in vitro models.","authors":"Maria Gabriella Fois, Martijn van Griensven, Stefan Giselbrecht, Pamela Habibović, Roman K Truckenmüller, Zeinab Niloofar Tahmasebi Birgani","doi":"10.1016/j.tibtech.2024.01.004","DOIUrl":"10.1016/j.tibtech.2024.01.004","url":null,"abstract":"<p><p>In bone tissue engineering (TE) and regeneration, miniaturized, (sub)millimeter-sized bone models have become a popular trend since they bring about physiological biomimicry, precise orchestration of concurrent stimuli, and compatibility with high-throughput setups and high-content imaging. They also allow efficient use of cells, reagents, materials, and energy. In this review, we describe the state of the art of miniaturized in vitro bone models, or 'mini-bones', describing these models based on their characteristics of (multi)cellularity and engineered extracellular matrix (ECM), and elaborating on miniaturization approaches and fabrication techniques. We analyze the performance of 'mini-bone' models according to their applications for studying basic bone biology or as regeneration models, disease models, and screening platforms, and provide an outlook on future trends, challenges, and opportunities.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140870","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}
Trends in biotechnologyPub Date : 2024-07-01Epub Date: 2024-02-05DOI: 10.1016/j.tibtech.2024.01.003
Austin Stone, Abdelrahaman Youssef, Sadikshya Rijal, Rong Zhang, Xiao-Jun Tian
{"title":"Context-dependent redesign of robust synthetic gene circuits.","authors":"Austin Stone, Abdelrahaman Youssef, Sadikshya Rijal, Rong Zhang, Xiao-Jun Tian","doi":"10.1016/j.tibtech.2024.01.003","DOIUrl":"10.1016/j.tibtech.2024.01.003","url":null,"abstract":"<p><p>Cells provide dynamic platforms for executing exogenous genetic programs in synthetic biology, resulting in highly context-dependent circuit performance. Recent years have seen an increasing interest in understanding the intricacies of circuit-host relationships, their influence on the synthetic bioengineering workflow, and in devising strategies to alleviate undesired effects. We provide an overview of how emerging circuit-host interactions, such as growth feedback and resource competition, impact both deterministic and stochastic circuit behaviors. We also emphasize control strategies for mitigating these unwanted effects. This review summarizes the latest advances and the current state of host-aware and resource-aware design of synthetic gene circuits.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11223972/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698401","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Trends in biotechnologyPub Date : 2024-07-01Epub Date: 2024-02-05DOI: 10.1016/j.tibtech.2024.01.001
Gretel S Major, Vinh K Doan, Alessia Longoni, Marcela M M Bilek, Steven G Wise, Jelena Rnjak-Kovacina, Giselle C Yeo, Khoon S Lim
{"title":"Mapping the microcarrier design pathway to modernise clinical mesenchymal stromal cell expansion.","authors":"Gretel S Major, Vinh K Doan, Alessia Longoni, Marcela M M Bilek, Steven G Wise, Jelena Rnjak-Kovacina, Giselle C Yeo, Khoon S Lim","doi":"10.1016/j.tibtech.2024.01.001","DOIUrl":"10.1016/j.tibtech.2024.01.001","url":null,"abstract":"<p><p>Microcarrier expansion systems show exciting potential to revolutionise mesenchymal stromal cell (MSC)-based clinical therapies by providing an opportunity for economical large-scale expansion of donor- and patient-derived cells. The poor reproducibility and efficiency of cell expansion on commercial polystyrene microcarriers have driven the development of novel microcarriers with tuneable physical, mechanical, and cell-instructive properties. These new microcarriers show innovation toward improving cell expansion outcomes, although their limited biological characterisation and compatibility with dynamic culture systems suggest the need to realign the microcarrier design pathway. Clear headway has been made toward developing infrastructure necessary for scaling up these technologies; however, key challenges remain in characterising the wholistic effects of microcarrier properties on the biological fate and function of expanded MSCs.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":null,"pages":null},"PeriodicalIF":14.3,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139698402","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}