Pub Date : 2025-02-01DOI: 10.1016/j.copbio.2024.103251
Friederike Dehli, Oscar O'Dwyer Lancaster-Jones, Daniela Duarte Campos
In vivo bioprinting strategies aim at facilitating immediate integration of engineered tissues with the host’s biological system. As integral parts of current bioprinting technologies, bioinks and robotics should be holistically considered for new biomedical applications. This implies that chosen bioinks should exhibit rheological properties that are compatible with the fabrication method and vice versa, bioprinting tools might need to be redesigned and reconstructed to fit the characteristics of the needed bioinks that after solidification act as supporting matrices for living cells. In this piece, we identify current challenges in merging the best of these two principles, we highlight relevant studies that have addressed this need, and we propose ideas how to approach this challenge in the next years.
{"title":"Optimizing the value of bioinks and robotics to advance in vivo bioprinting","authors":"Friederike Dehli, Oscar O'Dwyer Lancaster-Jones, Daniela Duarte Campos","doi":"10.1016/j.copbio.2024.103251","DOIUrl":"10.1016/j.copbio.2024.103251","url":null,"abstract":"<div><div><em>In vivo</em> bioprinting strategies aim at facilitating immediate integration of engineered tissues with the host’s biological system. As integral parts of current bioprinting technologies, bioinks and robotics should be holistically considered for new biomedical applications. This implies that chosen bioinks should exhibit rheological properties that are compatible with the fabrication method and <em>vice versa</em>, bioprinting tools might need to be redesigned and reconstructed to fit the characteristics of the needed bioinks that after solidification act as supporting matrices for living cells. In this piece, we identify current challenges in merging the best of these two principles, we highlight relevant studies that have addressed this need, and we propose ideas how to approach this challenge in the next years.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103251"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.copbio.2024.103246
Annie Gai , Yvonne Yamanaka
{"title":"Editorial overview: Nanobiotechnology for immunoengineering","authors":"Annie Gai , Yvonne Yamanaka","doi":"10.1016/j.copbio.2024.103246","DOIUrl":"10.1016/j.copbio.2024.103246","url":null,"abstract":"","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103246"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.copbio.2024.103243
Sudeep Agarwala , Michelle A. O’Malley , Thomas Eng
{"title":"Editorial Reflections on BioEnergy: Perspectives from 2024","authors":"Sudeep Agarwala , Michelle A. O’Malley , Thomas Eng","doi":"10.1016/j.copbio.2024.103243","DOIUrl":"10.1016/j.copbio.2024.103243","url":null,"abstract":"","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103243"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-02-01DOI: 10.1016/j.copbio.2024.103241
Mohammad B Belaffif , Morgan C Brown , Brenda Marcial , Can Baysal , Kankshita Swaminathan
Plants are an important source of food, energy, and bioproducts. Advances in genetics, genomics-assisted breeding, and biotechnology have facilitated the combining of desirable traits into elite cultivars. To ensure sustainable crop production in the face of climate challenges and population growth, it is essential to develop and implement techniques that increase crop yield and resilience in environments facing water scarcity, nutrient deficiencies, and other abiotic and biotic stressors. Plant transformation and genome editing are critical tools in the development of new cultivars. Here, we discuss recent advances in plant transformation technologies aimed at enhancing efficiency, throughput, and the number of transformable genotypes. These advancements include the use of morphogenic regulators, virus-mediated genetic modifications, and in planta transformation with Rhizobium rhizogenes.
{"title":"New strategies to advance plant transformation","authors":"Mohammad B Belaffif , Morgan C Brown , Brenda Marcial , Can Baysal , Kankshita Swaminathan","doi":"10.1016/j.copbio.2024.103241","DOIUrl":"10.1016/j.copbio.2024.103241","url":null,"abstract":"<div><div>Plants are an important source of food, energy, and bioproducts. Advances in genetics, genomics-assisted breeding, and biotechnology have facilitated the combining of desirable traits into elite cultivars. To ensure sustainable crop production in the face of climate challenges and population growth, it is essential to develop and implement techniques that increase crop yield and resilience in environments facing water scarcity, nutrient deficiencies, and other abiotic and biotic stressors. Plant transformation and genome editing are critical tools in the development of new cultivars. Here, we discuss recent advances in plant transformation technologies aimed at enhancing efficiency, throughput, and the number of transformable genotypes. These advancements include the use of morphogenic regulators, virus-mediated genetic modifications, and <em>in planta</em> transformation with <em>Rhizobium rhizogenes</em>.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"91 ","pages":"Article 103241"},"PeriodicalIF":7.1,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142892283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-27DOI: 10.1016/j.copbio.2025.103263
Sebastian Palacios , James J Collins , Domitilla Del Vecchio
Synthetic biology leverages engineering principles to program biology with new functions for applications in medicine, energy, food, and the environment. A central aspect of synthetic biology is the creation of synthetic gene circuits — engineered biological circuits capable of performing operations, detecting signals, and regulating cellular functions. Their development involves large design spaces with intricate interactions among circuit components and the host cellular machinery. Here, we discuss the emerging role of machine learning in addressing these challenges. We articulate how machine learning may enhance synthetic gene circuit engineering, from individual components to circuit-level aspects, while highlighting associated challenges. We discuss potential hybrid approaches that combine machine learning with mechanistic modeling to leverage the advantages of data-driven models with the prescriptive ability of mechanism-based models. Machine learning and its integration with mechanistic modeling are poised to advance synthetic biology, but challenges need to be overcome for such efforts to realize their potential.
{"title":"Machine learning for synthetic gene circuit engineering","authors":"Sebastian Palacios , James J Collins , Domitilla Del Vecchio","doi":"10.1016/j.copbio.2025.103263","DOIUrl":"10.1016/j.copbio.2025.103263","url":null,"abstract":"<div><div>Synthetic biology leverages engineering principles to program biology with new functions for applications in medicine, energy, food, and the environment. A central aspect of synthetic biology is the creation of synthetic gene circuits — engineered biological circuits capable of performing operations, detecting signals, and regulating cellular functions. Their development involves large design spaces with intricate interactions among circuit components and the host cellular machinery. Here, we discuss the emerging role of machine learning in addressing these challenges. We articulate how machine learning may enhance synthetic gene circuit engineering, from individual components to circuit-level aspects, while highlighting associated challenges. We discuss potential hybrid approaches that combine machine learning with mechanistic modeling to leverage the advantages of data-driven models with the prescriptive ability of mechanism-based models. Machine learning and its integration with mechanistic modeling are poised to advance synthetic biology, but challenges need to be overcome for such efforts to realize their potential.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103263"},"PeriodicalIF":7.1,"publicationDate":"2025-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143058236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1016/j.copbio.2024.103252
Anna Burgstaller , Sara Madureira , Oskar Staufer
Tissue functions rely on complex structural, biochemical, and biomechanical cues that guide cellular behavior and organization. Synthetic cells, a promising new class of biomaterials, hold significant potential for mimicking these tissue properties using simplified, nonliving building blocks. Advanced synthetic cell models have already shown utility in biotechnology and immunology, including applications in cancer targeting and antigen presentation. Recent bottom-up approaches have also enabled synthetic cells to assemble into 3D structures with controlled intercellular interactions, creating tissue-like architectures. Despite these advancements, challenges remain in replicating multicellular behaviors and dynamic mechanical environments. Here, we review recent advancements in synthetic cell-based tissue formation and introduce a three-pillar framework to streamline the development of synthetic tissues. This approach, focusing on synthetic extracellular matrix integration, synthetic cell self-organization, and adaptive biomechanics, could enable scalable synthetic tissues engineering for regenerative medicine and drug development.
{"title":"Synthetic cells in tissue engineering","authors":"Anna Burgstaller , Sara Madureira , Oskar Staufer","doi":"10.1016/j.copbio.2024.103252","DOIUrl":"10.1016/j.copbio.2024.103252","url":null,"abstract":"<div><div>Tissue functions rely on complex structural, biochemical, and biomechanical cues that guide cellular behavior and organization. Synthetic cells, a promising new class of biomaterials, hold significant potential for mimicking these tissue properties using simplified, nonliving building blocks. Advanced synthetic cell models have already shown utility in biotechnology and immunology, including applications in cancer targeting and antigen presentation. Recent bottom-up approaches have also enabled synthetic cells to assemble into 3D structures with controlled intercellular interactions, creating tissue-like architectures. Despite these advancements, challenges remain in replicating multicellular behaviors and dynamic mechanical environments. Here, we review recent advancements in synthetic cell-based tissue formation and introduce a three-pillar framework to streamline the development of synthetic tissues. This approach, focusing on synthetic extracellular matrix integration, synthetic cell self-organization, and adaptive biomechanics, could enable scalable synthetic tissues engineering for regenerative medicine and drug development.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103252"},"PeriodicalIF":7.1,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143028145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1016/j.copbio.2025.103261
Chris Pratt , Ana Soares
Biologically mediated adsorption and precipitation of phosphorus (P) from waste streams can restrict environmental P discharges. Here, we appraise progress in this field over the past decade. The research discipline has grown considerably in recent years. Industry ‘wastes’, including steel slags, continue to show promise as adsorbents with exceptionally high P retention capacities (>500 mg P g−1). Hydrotalcite, a nanomineral, offers prospects as a P removal technology with imbedded climate change mitigation capacity. Biomineral struvite formation, driven by microbial processes, offers an exciting P removal and recovery approach that can be applied to diverse wastewater types due to its feedstock-independent mechanisms, emerging immobilisation techniques and adaptability to mixed cultures. All of these factors facilitate efficient nutrient recycling and scalable application to the wastewater industry. Adsorbed and precipitated P can be applied to cropland to offset dependence on conventional fertiliser inputs. Therefore, in addition to water treatment, these biologically mediated processes also offer opportunities to support food production. Moreover, as many of the input materials covered in this review are industry byproducts and common organic materials, the removal of P from waste streams by adsorption and precipitation offers strong circularity potential that aligns with the UN’s Sustainable Development Goals. We call for future work to focus on long-term full-scale trials involving community, government and industry partners.
{"title":"New opportunities for biologically and chemically mediated adsorption and precipitation of phosphorus from wastewater","authors":"Chris Pratt , Ana Soares","doi":"10.1016/j.copbio.2025.103261","DOIUrl":"10.1016/j.copbio.2025.103261","url":null,"abstract":"<div><div>Biologically mediated adsorption and precipitation of phosphorus (P) from waste streams can restrict environmental P discharges. Here, we appraise progress in this field over the past decade. The research discipline has grown considerably in recent years. Industry ‘wastes’, including steel slags, continue to show promise as adsorbents with exceptionally high P retention capacities (>500 mg P g<sup>−1</sup>). Hydrotalcite, a nanomineral, offers prospects as a P removal technology with imbedded climate change mitigation capacity. Biomineral struvite formation, driven by microbial processes, offers an exciting P removal and recovery approach that can be applied to diverse wastewater types due to its feedstock-independent mechanisms, emerging immobilisation techniques and adaptability to mixed cultures. All of these factors facilitate efficient nutrient recycling and scalable application to the wastewater industry. Adsorbed and precipitated P can be applied to cropland to offset dependence on conventional fertiliser inputs. Therefore, in addition to water treatment, these biologically mediated processes also offer opportunities to support food production. Moreover, as many of the input materials covered in this review are industry byproducts and common organic materials, the removal of P from waste streams by adsorption and precipitation offers strong circularity potential that aligns with the UN’s Sustainable Development Goals. We call for future work to focus on long-term full-scale trials involving community, government and industry partners.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103261"},"PeriodicalIF":7.1,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-22DOI: 10.1016/j.copbio.2025.103262
Yang Zhou , Yu Wei , Lei Li , Tao Yan , Haifeng Ye
Optogenetics, an innovative approach integrating photonics and genetic engineering, enables precise control over molecular and cellular processes, opening up exciting new opportunities for precision-guided medicine. In this review, we highlight recent advances in optogenetic tools and their applications across a range of medical conditions, including vision restoration in retinitis pigmentosa via light-activated ion channels, precise immune response modulation in cancer immunotherapy, and blood glucose management in diabetes through controllable drug release. Optogenetics also plays a critical role in bioelectronic medicine, enabling seamless communication between electronic systems and biological tissues to enhance therapeutic precision. Finally, we discuss the challenges and potential transition of optogenetics from experimental models to clinical therapies, emphasizing its immense potential to transform future medical treatments.
{"title":"Optogenetics in medicine: innovations and therapeutic applications","authors":"Yang Zhou , Yu Wei , Lei Li , Tao Yan , Haifeng Ye","doi":"10.1016/j.copbio.2025.103262","DOIUrl":"10.1016/j.copbio.2025.103262","url":null,"abstract":"<div><div>Optogenetics, an innovative approach integrating photonics and genetic engineering, enables precise control over molecular and cellular processes, opening up exciting new opportunities for precision-guided medicine. In this review, we highlight recent advances in optogenetic tools and their applications across a range of medical conditions, including vision restoration in retinitis pigmentosa via light-activated ion channels, precise immune response modulation in cancer immunotherapy, and blood glucose management in diabetes through controllable drug release. Optogenetics also plays a critical role in bioelectronic medicine, enabling seamless communication between electronic systems and biological tissues to enhance therapeutic precision. Finally, we discuss the challenges and potential transition of optogenetics from experimental models to clinical therapies, emphasizing its immense potential to transform future medical treatments.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103262"},"PeriodicalIF":7.1,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143022601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-01-21DOI: 10.1016/j.copbio.2025.103257
Emma C Boismier , Elhussiny A Aboulnaga , Michaela A TerAvest
Zymomonas mobilis is an ethanologenic bacterium that has been used for over 1500 years to produce alcoholic beverages. Recently, this microbe has become a top candidate for biofuel production due to its efficient metabolism. Z. mobilis is being developed to utilize lignocellulosic biomass as a feedstock and synthesize a range of valuable chemicals and fuels. Genetic and metabolic engineering strategies are crucial to reach these goals. Recent advances include genome engineering, CRISPR editing, and CRISPRi knockdown of genes. Metabolic engineering has enabled redirection of carbon from the natural product ethanol to chemicals such as 2,3-butanediol and polyhydroxybutyrate. The approaches summarized here will streamline the development of Z. mobilis as an industrial chassis for sustainable liquid fuels and chemicals.
{"title":"Zymomonas mobilis: bringing an ancient human tool into the genomic era","authors":"Emma C Boismier , Elhussiny A Aboulnaga , Michaela A TerAvest","doi":"10.1016/j.copbio.2025.103257","DOIUrl":"10.1016/j.copbio.2025.103257","url":null,"abstract":"<div><div><em>Zymomonas mobilis</em> is an ethanologenic bacterium that has been used for over 1500 years to produce alcoholic beverages. Recently, this microbe has become a top candidate for biofuel production due to its efficient metabolism. <em>Z. mobilis</em> is being developed to utilize lignocellulosic biomass as a feedstock and synthesize a range of valuable chemicals and fuels. Genetic and metabolic engineering strategies are crucial to reach these goals. Recent advances include genome engineering, CRISPR editing, and CRISPRi knockdown of genes. Metabolic engineering has enabled redirection of carbon from the natural product ethanol to chemicals such as 2,3-butanediol and polyhydroxybutyrate. The approaches summarized here will streamline the development of <em>Z. mobilis</em> as an industrial chassis for sustainable liquid fuels and chemicals.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103257"},"PeriodicalIF":7.1,"publicationDate":"2025-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nonmodel microbes with unique advantages are emerging as industrial platforms, driven by advances in genetic engineering and omics technologies. Notable examples include the versatile soil bacterium Pseudomonas putida KT2440, the halophilic Halomonas bluephagenesis TD01, and the ethanologenic Zymomonas mobilis ZM4. While all three primarily use the Entner–Doudoroff pathway for glucose metabolism, they differ in various metabolic pathways and product synthesis. This review summarizes and compares their central carbon metabolism, advancements in genome engineering tools, and progress in scaling industrial applications from lab scale, to pilot scale, to full-scale commercial production. Understanding their similarities and differences informs future research on optimizing industrial applications and may guide the development of new microbial hosts.
{"title":"Comparing three emerging industrial cell factories: Pseudomonas putida KT2440, Halomonas bluephagenesis TD01, and Zymomonas mobilis ZM4","authors":"Yu-Hang Zhang , Chen-Ming Xue , Bai-Tao Chen , Pengfei Ouyang , Chen Ling","doi":"10.1016/j.copbio.2024.103255","DOIUrl":"10.1016/j.copbio.2024.103255","url":null,"abstract":"<div><div>Nonmodel microbes with unique advantages are emerging as industrial platforms, driven by advances in genetic engineering and omics technologies. Notable examples include the versatile soil bacterium <em>Pseudomonas putida</em> KT2440, the halophilic <em>Halomonas bluephagenesis</em> TD01, and the ethanologenic <em>Zymomonas mobilis</em> ZM4. While all three primarily use the Entner–Doudoroff pathway for glucose metabolism, they differ in various metabolic pathways and product synthesis. This review summarizes and compares their central carbon metabolism, advancements in genome engineering tools, and progress in scaling industrial applications from lab scale, to pilot scale, to full-scale commercial production. Understanding their similarities and differences informs future research on optimizing industrial applications and may guide the development of new microbial hosts.</div></div>","PeriodicalId":10833,"journal":{"name":"Current opinion in biotechnology","volume":"92 ","pages":"Article 103255"},"PeriodicalIF":7.1,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143001197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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