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Advances in induced anhydrobiosis for cell and gamete storage.
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-05 DOI: 10.1016/j.tibtech.2025.02.010
Pasqualino Loi, Luca Palazzese, Margherita Moncada, Martina Lo Sterzo, Domenico Iuso, Marta Czernik, Teruhiko Wakayama, Takahiro Kikawada
{"title":"Advances in induced anhydrobiosis for cell and gamete storage.","authors":"Pasqualino Loi, Luca Palazzese, Margherita Moncada, Martina Lo Sterzo, Domenico Iuso, Marta Czernik, Teruhiko Wakayama, Takahiro Kikawada","doi":"10.1016/j.tibtech.2025.02.010","DOIUrl":"https://doi.org/10.1016/j.tibtech.2025.02.010","url":null,"abstract":"<p><p>It will appear strange to most readers, but lyophilization of spermatozoa was described by Chris Polge's first article that demonstrated the viability of spermatozoa stored in liquid nitrogen (LN<sub>2)</sub>. Since then, cryopreservation has become the only biobanking choice. The demonstration that lyophilized spermatozoa remain fertile has rekindled interest in noncryogenic biobanking. This perspective has recently been embraced by engineers, physicists, and anhydrobiotic physiologists, and their synergy has remarkably advanced the field. Progress in water subtraction procedures and dehydration medium formulated by biomimicking anhydrobiotic organisms has brought spermatozoa drying close to practical application for biodiversity preservation and human-assisted reproduction, allowing at the same time easy and safe transport of genetic resources on Earth and eventually space travel.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":14.3,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143574193","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.
IF 14.3 1区 工程技术
Trends in biotechnology Pub 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":"https://doi.org/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":""},"PeriodicalIF":14.3,"publicationDate":"2025-03-05","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
CarveAdornCurate: a versatile cloud-based platform for constructing multiscale metabolic models.
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-04 DOI: 10.1016/j.tibtech.2025.01.011
Yang Cheng, Wenwen Yu, Xinyu Bi, Yanfeng Liu, Jianghua Li, Guocheng Du, Jian Chen, Xueqin Lv, Long Liu
{"title":"CarveAdornCurate: a versatile cloud-based platform for constructing multiscale metabolic models.","authors":"Yang Cheng, Wenwen Yu, Xinyu Bi, Yanfeng Liu, Jianghua Li, Guocheng Du, Jian Chen, Xueqin Lv, Long Liu","doi":"10.1016/j.tibtech.2025.01.011","DOIUrl":"https://doi.org/10.1016/j.tibtech.2025.01.011","url":null,"abstract":"<p><p>Multiscale modeling is a promising approach for understanding cellular behaviors. However, existing multiscale modeling tools require meticulously curated genome-scale metabolic models (GEMs) as inputs, limiting the broad applications of multiscale models due to complex and time-consuming construction processes. To this end, we developed a novel workflow named CarveAdornCurate (CAC) for de novo multiscale modeling. The Carve module generates an ensemble of GEMs with strong genetic evidence, which is then upgraded to multiscale models using Adorn module. The Curate module was designed to find features important to the generated models. These three modules are integrated into a cloud-based platform to promote broad accessibility. As proof of concept, we constructed CAC-based multiscale models for Corynebacterium glutamicum and Yarrowia lipolytica, demonstrating their potential in guiding metabolic engineering. Overall, CAC is demonstrated to be an efficient and user-friendly tool for constructing multiscale models. It is available online at www.carveadorncurate.com/.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":""},"PeriodicalIF":14.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568399","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
Regulation of animal and plant agricultural biotechnology.
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 DOI: 10.1016/j.tibtech.2024.11.003
Simona A Lubieniechi, Alison L Van Eenennaam, Stuart J Smyth
{"title":"Regulation of animal and plant agricultural biotechnology.","authors":"Simona A Lubieniechi, Alison L Van Eenennaam, Stuart J Smyth","doi":"10.1016/j.tibtech.2024.11.003","DOIUrl":"https://doi.org/10.1016/j.tibtech.2024.11.003","url":null,"abstract":"<p><p>Fifty years ago, scientists developed a regulatory framework for the safe use of recombinant DNA that focused on potential biosafety risks associated with the products of genetic engineering (GE). This morphed into an expensive and lengthy premarket risk assessment requirement for GE agricultural biotechnology products triggered solely by the fact that modern molecular technologies were involved in the development of those products. This has limited the commercialization of GE crop products primarily to multinational enterprises and precluded the development of GE animals at scale. Gene editing offers an opportunity to rethink the regulation of agricultural biotechnologies, and several countries have determined that gene-edited products lacking any 'foreign' DNA will be treated in the same way as products of conventional breeding.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":"43 3","pages":"511-521"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143524545","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 next-generation oxygen-generating scaffolds to enhance bone regeneration. 设计新一代氧气生成支架，促进骨再生。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-09-28 DOI: 10.1016/j.tibtech.2024.09.006
Jingtong Zhao, Naboneeta Sarkar, Yunke Ren, Arvind P Pathak, Warren L Grayson
{"title":"Engineering next-generation oxygen-generating scaffolds to enhance bone regeneration.","authors":"Jingtong Zhao, Naboneeta Sarkar, Yunke Ren, Arvind P Pathak, Warren L Grayson","doi":"10.1016/j.tibtech.2024.09.006","DOIUrl":"10.1016/j.tibtech.2024.09.006","url":null,"abstract":"<p><p>In bone, an adequate oxygen (O<sub>2</sub>) supply is crucial during development, homeostasis, and healing. Oxygen-generating scaffolds (OGS) have demonstrated significant potential to enhance bone regeneration. However, the complexity of O<sub>2</sub> delivery and signaling in vivo makes it challenging to tailor the design of OGS to precisely meet this biological requirement. We review recent advances in OGS and analyze persisting engineering and translational hurdles. We also discuss the potential of computational and machine learning (ML) models to facilitate the integration of novel imaging data with biological readouts and advanced biomanufacturing technologies. By elucidating how to tackle current challenges using cutting-edge technologies, we provide insights for transitioning from traditional to next-generation OGS to improve bone regeneration in patients.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"540-554"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11867879/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354601","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}
引用次数: 0
Phage-guided nanocarriers: a precision strategy against bacterial pathogens. 噬菌体引导的纳米载体：对抗细菌病原体的精准策略。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-09-27 DOI: 10.1016/j.tibtech.2024.09.002
Temoor Ahmed, Xinyan Xu, Muhammad Noman, Qi Wang, Bin Li
{"title":"Phage-guided nanocarriers: a precision strategy against bacterial pathogens.","authors":"Temoor Ahmed, Xinyan Xu, Muhammad Noman, Qi Wang, Bin Li","doi":"10.1016/j.tibtech.2024.09.002","DOIUrl":"10.1016/j.tibtech.2024.09.002","url":null,"abstract":"<p><p>Bacterial infections pose a major threat to human health. Here, we describe the recent development of phage-guided therapeutic agent-loaded engineered nanomaterials for precise elimination of bacterial pathogens. This forum highlights the underexplored potential of bioinspired nano-enabled strategies for managing bacterial infections in a precise and safe manner.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"494-497"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142354603","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
Evaluating neuroprivacy concerns in human brain organoid research. 评估人脑类器官研究中的神经隐私问题。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-09-20 DOI: 10.1016/j.tibtech.2024.09.001
Masanori Kataoka, Shu Ishida, Chie Kobayashi, Tsung-Ling Lee, Tsutomu Sawai
{"title":"Evaluating neuroprivacy concerns in human brain organoid research.","authors":"Masanori Kataoka, Shu Ishida, Chie Kobayashi, Tsung-Ling Lee, Tsutomu Sawai","doi":"10.1016/j.tibtech.2024.09.001","DOIUrl":"10.1016/j.tibtech.2024.09.001","url":null,"abstract":"<p><p>Neuroprivacy, or the privacy of neural data, has attracted considerable interest. Here, we explore the implications of neuroprivacy in human brain organoid research, detailing different interpretations of this right. Findings suggest a limited connection between neuroprivacy and brain organoid research, underscoring the importance of further examination of this critical issue.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"491-493"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142296436","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
Enhancing intestinal absorption of a macromolecule through engineered probiotic yeast in the murine gastrointestinal tract. 在小鼠胃肠道中通过工程益生菌酵母增强肠道对大分子的吸收。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-12-09 DOI: 10.1016/j.tibtech.2024.10.019
Hitesh P Gelli, Karl Alex Hedin, Martin F Laursen, Ruben-Vazquez Uribe, Morten Otto Alexander Sommer
{"title":"Enhancing intestinal absorption of a macromolecule through engineered probiotic yeast in the murine gastrointestinal tract.","authors":"Hitesh P Gelli, Karl Alex Hedin, Martin F Laursen, Ruben-Vazquez Uribe, Morten Otto Alexander Sommer","doi":"10.1016/j.tibtech.2024.10.019","DOIUrl":"10.1016/j.tibtech.2024.10.019","url":null,"abstract":"<p><p>Oral administration of therapeutic peptides is limited by poor intestinal absorption. Use of engineered microorganisms as drug delivery vehicles can overcome the challenges faced by conventional delivery methods. The potential of engineered microorganisms to act synergistically with the therapeutics they deliver opens new horizons for noninvasive treatment modalities. This study engineered a probiotic yeast, Saccharomyces boulardii, to produce cell-penetrating peptides (CPPs) in situ for enhanced intestinal permeability. Four CPPs were integrated into the yeast chromosome: RRL helix, Shuffle, Penetramax, and PN159. In vitro tests on a Caco-2 cell model showed that three CPP-producing strains increased permeability without causing permanent damage. In vivo experiments on mice revealed that Sb PN159 administration over 10 days significantly increased FITC-dextran translocation into the bloodstream without causing inflammation. This study demonstrates, for the first time, the ability of an engineered microorganism to modulate host permeability for improved intestinal absorption of a macromolecule.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"715-731"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142808148","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
Complex waste stream valorization through combined enzymatic hydrolysis and catabolic assimilation by Pseudomonas putida. 腐臭假单胞菌联合酶解和分解代谢同化的复杂废物流增值。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-12-04 DOI: 10.1016/j.tibtech.2024.10.020
Micaela Chacón, Guadalupe Alvarez-Gonzalez, Piya Gosalvitr, Adokiye Berepiki, Karl Fisher, Rosa Cuéllar-Franca, Neil Dixon
{"title":"Complex waste stream valorization through combined enzymatic hydrolysis and catabolic assimilation by Pseudomonas putida.","authors":"Micaela Chacón, Guadalupe Alvarez-Gonzalez, Piya Gosalvitr, Adokiye Berepiki, Karl Fisher, Rosa Cuéllar-Franca, Neil Dixon","doi":"10.1016/j.tibtech.2024.10.020","DOIUrl":"10.1016/j.tibtech.2024.10.020","url":null,"abstract":"<p><p>Biogenic waste-derived feedstocks for production of fuels, chemicals, and materials offer great potential supporting the transition to net-zero and greater circularity. However, such feedstocks are heterogeneous and subject to geographical and seasonal variability. Here, we show that, through careful strain selection and metabolic engineering, Pseudomonas putida can be employed to permit efficient co-utilization of highly heterogeneous substrate compositions derived from hydrolyzed mixed municipal-like waste fractions (food, plastic, organic, paper, cardboard, and textiles) for growth and synthesis of exemplar bioproducts. Design of experiments was employed to explore the combinatorial space of nine waste-derived monomers, displaying robust catabolic efficiency regardless of substrate composition. Prospective Life-Cycle Assessment (LCA) and Life-Cycle Costing (LCC) illustrated the climate change (CC) and economic advantages of biomanufacturing compared with conventional waste treatment options, demonstrating a 41-62% potential reduction in CC impact. This work demonstrates the potential for expanding treatment strategies for mixed waste to include engineered microbes.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"647-672"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787122","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
Efficiency and process development for microbial biomass production using oxic bioelectrosynthesis. 利用氧生物电合成生产微生物生物质的效率和工艺开发。
IF 14.3 1区 工程技术
Trends in biotechnology Pub Date : 2025-03-01 Epub Date: 2024-12-12 DOI: 10.1016/j.tibtech.2024.11.005
Leonie Rominger, Max Hackbarth, Tobias Jung, Marvin Scherzinger, Luis F M Rosa, Harald Horn, Martin Kaltschmitt, Cristian Picioreanu, Johannes Gescher
{"title":"Efficiency and process development for microbial biomass production using oxic bioelectrosynthesis.","authors":"Leonie Rominger, Max Hackbarth, Tobias Jung, Marvin Scherzinger, Luis F M Rosa, Harald Horn, Martin Kaltschmitt, Cristian Picioreanu, Johannes Gescher","doi":"10.1016/j.tibtech.2024.11.005","DOIUrl":"10.1016/j.tibtech.2024.11.005","url":null,"abstract":"<p><p>Autotrophic microbial electrosynthesis (MES) processes are mainly based on organisms that rely on carbon dioxide (CO<sub>2</sub>) as an electron acceptor and typically have low biomass yields. However, there are few data on the process and efficiencies of oxic MES (OMES). In this study, we used the knallgas bacterium Kyrpidia spormannii to investigate biomass formation and energy efficiency of cathode-dependent growth. The study revealed that the process can be carried out with the same electron efficiency as conventional gas fermentation, but overcomes disadvantages, such as the use of explosive gas mixtures. When accounting only for the electron input via electrical energy, a solar energy demand of 67.89 kWh kg<sup>-1</sup> dry biomass was determined. While anaerobic MES is ideally suited to produce methane, short-chain alcohols, and carboxylic acids, its aerobic counterpart could extend this important range of applications to not only protein for use in the food and feed sector, but also further complex products.</p>","PeriodicalId":23324,"journal":{"name":"Trends in biotechnology","volume":" ","pages":"673-695"},"PeriodicalIF":14.3,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142822714","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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