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Genome editing of epigenetic transgene silencing in Chlamydomonas reinhardtii. 莱茵衣藻表观遗传转基因沉默的基因组编辑。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-05-30 DOI: 10.1016/j.tibtech.2025.04.019
Alexander Einhaus, Arno Krieger, Laurenz Köhne, Bjarne Rautengarten, Nick Jacobebbinghaus, Merve Saudhof, Thomas Baier, Olaf Kruse
{"title":"Genome editing of epigenetic transgene silencing in Chlamydomonas reinhardtii.","authors":"Alexander Einhaus, Arno Krieger, Laurenz Köhne, Bjarne Rautengarten, Nick Jacobebbinghaus, Merve Saudhof, Thomas Baier, Olaf Kruse","doi":"10.1016/j.tibtech.2025.04.019","DOIUrl":"10.1016/j.tibtech.2025.04.019","url":null,"abstract":"<p><p>Eukaryotic microalgae are steadily advancing as promising green cell factories for sustainable modern biotechnology. However, one of the greatest hurdles to such use are the efficient transgene silencing mechanisms that drastically limit transgene expression levels and stability in engineered microalgal strains. Here, we used CRISPR/Cas9 to target multiple genes involved in epigenetic regulation in the model green microalga Chlamydomonas reinhardtii to identify key factors in epigenetic transgene silencing. Disruption of 11 candidate genes and subsequent systematic combination in double and triple knockout (KO) mutants, enabled a distinct reduction in transgene silencing and improved the stability of transgene expression compared with previously established strains. In addition, a split selectable marker system utilizing the Nostoc punctiforme DnaE split intein for dual-targeted genome editing was established. In summary, this work distinctly advances the biotechnological potential of C. reinhardtii and establishes a valuable mutant collection for further investigation of epigenetic regulation in green microalgae and potentially other eukaryotes.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1961-1981"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144226854","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}
引用次数: 0
Microbial cellulose production using ocean water: sustainable and cost-effective? 利用海水生产微生物纤维素：可持续和具有成本效益？
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-07-18 DOI: 10.1016/j.tibtech.2025.07.009
Rohan Karande
{"title":"Microbial cellulose production using ocean water: sustainable and cost-effective?","authors":"Rohan Karande","doi":"10.1016/j.tibtech.2025.07.009","DOIUrl":"10.1016/j.tibtech.2025.07.009","url":null,"abstract":"<p><p>In a recent paper, Shankar et al. present a promising proof-of-concept for bacterial cellulose (BC) production, exhibiting competitive material properties, utilizing ocean water (OW) despite the challenges posed by high salinity. By reducing dependence on freshwater resources, the work highlights both ecological and economic benefits related to current BC production methods.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1823-1824"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144668600","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}
引用次数: 0
C1 photochemotrophy - rethinking one-carbon metabolism in phototrophs. C1光化学营养——对光养生物单碳代谢的再思考。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-02-08 DOI: 10.1016/j.tibtech.2025.01.003
Maurycy Daroch, Dawei You, Faiz Rasul, Xiangjian Liu, Ying Jiang
{"title":"C1 photochemotrophy - rethinking one-carbon metabolism in phototrophs.","authors":"Maurycy Daroch, Dawei You, Faiz Rasul, Xiangjian Liu, Ying Jiang","doi":"10.1016/j.tibtech.2025.01.003","DOIUrl":"10.1016/j.tibtech.2025.01.003","url":null,"abstract":"<p><p>Excessive CO<sub>2</sub> emissions, caused by an imbalance between carbon oxidation and reduction, drive climate change. To address this, we propose photochemotrophic metabolism as an alternative to both canonical photosynthesis and synthetic one-carbon (C1) metabolism in heterotrophs. In photochemotrophy, naturally phototrophic microorganisms such as cyanobacteria serve as the chassis to assimilate chemically reduced and soluble C1 compounds such as formate or methanol by using carbon fixation cycles that are more efficient than the native Calvin cycle. Key potential advantages of photochemotrophy include enhanced carbon fixation efficiency, utilization of storable carbon compounds, retention of energy from the original CO<sub>2</sub> reduction, and decoupling of carbon delivery and electron source. This proposed strategy positions photochemotrophic cyanobacteria as a promising tool for advancing the bioeconomy.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1836-1848"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143383002","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}
引用次数: 0
Emerging supramolecular and living materials in oral medicine. 口腔医学中新兴的超分子和活性材料。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-04-07 DOI: 10.1016/j.tibtech.2025.03.006
Nicholas G Fischer, Tsung-Yi Lin, Yuanhui Xiang, Ting Sang, Zhou Ye
{"title":"Emerging supramolecular and living materials in oral medicine.","authors":"Nicholas G Fischer, Tsung-Yi Lin, Yuanhui Xiang, Ting Sang, Zhou Ye","doi":"10.1016/j.tibtech.2025.03.006","DOIUrl":"10.1016/j.tibtech.2025.03.006","url":null,"abstract":"<p><p>Conventional dental materials lack the ability to promote regeneration, necessitating innovative approaches for repairing dental, oral, and craniofacial (DOC) tissues. Supramolecular materials with reversible, tunable interactions, and engineered living materials (ELMs) that mimic natural tissue dynamics, present a promising pathway towards regenerative solutions in oral medicine. This review introduces the potential of these biomaterials, focusing on their applications in oral bioprinting, therapeutic delivery, and organ-on-a-chip (OOC) systems. We discuss the integration of these technologies into clinical applications, and offer insights into future developments that may redefine oral healthcare by enabling the regeneration of complex, dynamic tissue structures and improving therapeutic outcomes in oral diseases.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1876-1891"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812607","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}
引用次数: 0
Engineered transcription factor-binding arrays for DNA-based gene expression control in mammalian cells. 用于哺乳动物细胞dna基因表达控制的工程转录因子结合阵列。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-06-09 DOI: 10.1016/j.tibtech.2025.05.006
Annalise Zouein, Brittany Lende-Dorn, Kate E Galloway, Tom Ellis, Francesca Ceroni
{"title":"Engineered transcription factor-binding arrays for DNA-based gene expression control in mammalian cells.","authors":"Annalise Zouein, Brittany Lende-Dorn, Kate E Galloway, Tom Ellis, Francesca Ceroni","doi":"10.1016/j.tibtech.2025.05.006","DOIUrl":"10.1016/j.tibtech.2025.05.006","url":null,"abstract":"<p><p>Tools that manipulate gene expression in mammalian cells without any additional expression are critical for cell engineering applications. Here, we demonstrate the use of arrays of transcription factor (TF) recognition elements (REs) as DNA tools for controlling gene expression. We first demonstrate that TetR-based RE arrays can alter synthetic gene circuit performance. We then open the approach to any TF with a known binding site by developing a new technique called Cloning Troublesome Repeats in Loops (CTRL), which can assemble plasmids with up to 256 RE repeats. Transfection of custom RE array plasmids assembled by CTRL into mammalian cells modifies host cell gene regulation by sequestration of TFs of interest and can sequester both synthetic and native TFs, offering applications in the control of gene circuits and for directing cell fate. This work advances our ability to assemble repetitive DNA arrays and shows how TF-binding RE arrays expand possibilities in mammalian cell engineering.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2029-2048"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267301","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}
引用次数: 0
Glass fiber-interfaced CRISPR/Cas biosensing adaptable for diverse biomarker detection. 玻璃纤维接口CRISPR/Cas生物传感适用于多种生物标志物检测。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-05-29 DOI: 10.1016/j.tibtech.2025.05.001
Tian Yu, Siyi Zou, Yingxi Long, Yourong Ou, Shixian Liu, Tongjia Kang, Libing Song, Congcong Sun, Guozhen Liu
{"title":"Glass fiber-interfaced CRISPR/Cas biosensing adaptable for diverse biomarker detection.","authors":"Tian Yu, Siyi Zou, Yingxi Long, Yourong Ou, Shixian Liu, Tongjia Kang, Libing Song, Congcong Sun, Guozhen Liu","doi":"10.1016/j.tibtech.2025.05.001","DOIUrl":"10.1016/j.tibtech.2025.05.001","url":null,"abstract":"<p><p>Developing a generic sensitive platform for detecting diverse biomarkers is essential for a comprehensive understanding of disease states, guiding precision medicine. Herein, we introduce a versatile platform based on glass fiber interfaced CRISPR/Cas with a universal reagent setting (g-CURS), which used a fixed pair of CRISPR RNA (crRNA) and a single-stranded DNA (ssDNA) activator to enable detection of multiple nucleic acids or proteins with ultrahigh sensitivity. The fixed ssDNA activator was labeled on multiple specific ligation products or detection antibodies conjugated on glass fiber to initiate CRISPR/Cas12a-assisted rapid and exponential cascade amplification through circular reporters (CRs), generating fluorescence signals readable by a portable detector. g-CURS was able to detect viral nucleic acids with attomolar sensitivity within 30 min and multiple low-abundance proteins in extracellular vesicles of Parkinson's disease (PD) serum with subpicomolar sensitivity within 80 min. g-CURS simplifies CRISPR/Cas biosensing using a standard reagent setting, holding promise for biomarker discovery free from bulky instruments.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2003-2028"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144187999","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}
引用次数: 0
An in vivo target mutagenesis system for multiple hosts. 多宿主体内靶点诱变系统。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-05-08 DOI: 10.1016/j.tibtech.2025.04.005
Dong Yin, Qingxiao Pang, Yingbo Yuan, Tianyuan Su, Mengmeng Liu, Qian Wang, Jin Hou, Qingsheng Qi
{"title":"An in vivo target mutagenesis system for multiple hosts.","authors":"Dong Yin, Qingxiao Pang, Yingbo Yuan, Tianyuan Su, Mengmeng Liu, Qian Wang, Jin Hou, Qingsheng Qi","doi":"10.1016/j.tibtech.2025.04.005","DOIUrl":"10.1016/j.tibtech.2025.04.005","url":null,"abstract":"<p><p>In vivo target mutagenesis is a powerful approach to accelerate protein evolution. However, current approaches have been primarily developed in conventional organisms, limiting their capacity to evolve proteins with subtle variations across non-conventional host species. Here, we design an in vivo target mutagenesis system for multiple hosts (ITMU) utilizing the broad host-range plasmid RSF1010 replication element. The ITMU, which is based on a deaminase-helicase fusion and a primase error-prone DNA polymerase I fusion, induces all types of mutation in the target plasmid harboring the RSF1010 replicon, at a mutation rate 1.18 × 10<sup>5</sup>-fold higher than that of the host genome. We show that ITMU-based in vivo continuous evolution is effective in Escherichia coli, Pseudomonas putida, Corynebacterium glutamicum, and Yarrowia lipolytica. This demonstrates that the ITMU is applicable to multiple microbial chassis and provides a viable alternative to in vivo continuous evolution systems.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"2049-2072"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034111","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}
引用次数: 0
Process and quality considerations for recombinant adeno-associated virus manufacturing platforms. 重组腺相关病毒制造平台的工艺和质量考虑。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-03-27 DOI: 10.1016/j.tibtech.2025.02.016
Min Tae Park, Amrisha Verma, Clifford A Froelich, Seyed Pouria Motevalian
{"title":"Process and quality considerations for recombinant adeno-associated virus manufacturing platforms.","authors":"Min Tae Park, Amrisha Verma, Clifford A Froelich, Seyed Pouria Motevalian","doi":"10.1016/j.tibtech.2025.02.016","DOIUrl":"10.1016/j.tibtech.2025.02.016","url":null,"abstract":"<p><p>Recombinant adeno-associated virus (AAV) is a prominent gene therapy vector, offering a strong safety profile and sustained gene expression. Scaling up AAV manufacturing remains challenging due to its complex processes, high development costs, and the need for rigorous quality control. This review examines the most common AAV suspension production platforms, specifically transfection, infection, and stable producer cell lines (PCLs). For each platform, a list of common unit operations and typical ranges for critical operating parameters is provided, along with high-level product quality specifications. This review aims to offer insights into the advantages and challenges of each manufacturing platform, providing a framework for accelerated process development and informed selection of suitable production platform based on intended clinical use and target product profile.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1921-1937"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143731653","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}
引用次数: 0
Engineering advanced in vitro models of endothelial dysfunction. 内皮功能障碍的体外模型的工程进展。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-04-04 DOI: 10.1016/j.tibtech.2025.03.004
Jasneil Singh, Alexander M Ruhoff, Deepu Ashok, Steven G Wise, Anna Waterhouse
{"title":"Engineering advanced in vitro models of endothelial dysfunction.","authors":"Jasneil Singh, Alexander M Ruhoff, Deepu Ashok, Steven G Wise, Anna Waterhouse","doi":"10.1016/j.tibtech.2025.03.004","DOIUrl":"10.1016/j.tibtech.2025.03.004","url":null,"abstract":"<p><p>Endothelial dysfunction is an important initiator of cardiovascular disease, the leading cause of death globally, and often manifests in arterial regions with disturbed blood flow. Experimental model advances have crucially helped unravel physiological mechanisms. While in vivo models provide a dynamic environment, they often fail to mimic human physiology precisely and face significant ethical barriers. Advanced in vitro models, including organs-on-chips and bioreactors, combine human cells and blood flow to accurately replicate endothelial dysfunction. Newer models have enhanced scalability and accuracy, with organs-on-chips commonly outperforming standard preclinical methods. Importantly, recent endothelial dysfunction discoveries leverage dynamic models to identify and evaluate clinically promising therapeutics. Here, we examine these developments and explore opportunities to develop next-generation in vitro models of endothelial dysfunction.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1892-1903"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143789236","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}
引用次数: 0
Large language model for knowledge synthesis and AI-enhanced biomanufacturing. 用于知识合成和人工智能增强生物制造的大型语言模型。
IF 14.9 1区 工程技术
Trends in biotechnology Pub Date : 2025-08-01 Epub Date: 2025-03-05 DOI: 10.1016/j.tibtech.2025.02.008
Wenyu Li, Zhitao Mao, Zhengyang Xiao, Xiaoping Liao, Mattheos Koffas, Yixin Chen, Hongwu Ma, Yinjie J Tang
{"title":"Large language model for knowledge synthesis and AI-enhanced biomanufacturing.","authors":"Wenyu Li, Zhitao Mao, Zhengyang Xiao, Xiaoping Liao, Mattheos Koffas, Yixin Chen, Hongwu Ma, Yinjie J Tang","doi":"10.1016/j.tibtech.2025.02.008","DOIUrl":"10.1016/j.tibtech.2025.02.008","url":null,"abstract":"<p><p>Large language models (LLMs) are transforming synthetic biology (SynBio) education and research. In this review we cover the advancements and potential impacts of LLMs in biomanufacturing. First, we summarize recent developments and compare the capabilities of US and Chinese language models in addressing fundamental SynBio questions. Second, we discuss the application of LLMs in extracting SynBio information from unstructured data, constructing knowledge graphs, and enabling retrieval-augmented generation. Third, we anticipate that LLMs will not only revolutionize the design-build-test-learn (DBTL) cycle in metabolic modeling and engineering but also enable self-driving laboratories in future biomanufacturing. Finally, we emphasize the need for establishing benchmarks for LLMs, fostering trustworthy knowledge synthesis, developing biosecurity frameworks to prevent misuse, and encouraging collaboration among artificial intelligence (AI) scientists, SynBio researchers, and bioprocess engineers.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"1864-1875"},"PeriodicalIF":14.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574143","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}
引用次数: 0
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