Pub Date : 2025-12-18DOI: 10.1186/s13036-025-00598-6
Sajad Rahimi, Kamyar Khoshnevisan, Amir Hossein Izadi Nazar, Maryam Doostan, Hassan Maleki
{"title":"Exploring of therapeutic potential of indirubin-loaded nanofibrous scaffolds for localized melanoma treatment.","authors":"Sajad Rahimi, Kamyar Khoshnevisan, Amir Hossein Izadi Nazar, Maryam Doostan, Hassan Maleki","doi":"10.1186/s13036-025-00598-6","DOIUrl":"https://doi.org/10.1186/s13036-025-00598-6","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145781266","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}
Pub Date : 2025-12-16DOI: 10.1186/s13036-025-00601-0
Michihito Sasaki, Eri Fujii, Satoko Sasaki, Takuma Ariizumi, Kei Konishi, Akihiko Sato, William W Hall, Hirofumi Sawa, Yasuko Orba
Background: Infections with various RNA viruses and certain DNA viruses may produce double-stranded RNA (dsRNA) during replication, which trigger host innate immune responses. Immunoassays using anti-dsRNA antibodies have been widely employed to detect viral dsRNA. In this study, we used a luciferase-based dsRNA biosensor for viral dsRNA detection, which consists of protein kinase R (PKR)-derived dsRNA binding domains fused to split luciferase subunits and is available as part of a commercial system.
Results: We demonstrate the use of the dsRNA biosensor to measure viral dsRNA in RNA specimens extracted from cells infected with Japanese encephalitis virus (JEV). Moreover, the biosensor reacts to a broad-spectrum of dsRNAs from infection with representatives of various viral families including positive- and negative-sense single-stranded RNA (ssRNA) viruses, dsRNA viruses, and DNA viruses. We validated the specific interaction between the dsRNA biosensor and viral RNA including subgenomic flavivirus RNA (sfRNA) through RNA immunoprecipitation. Additionally, we observed luminescence signals directly from lysates of JEV-infected cells after cell lysis and phase separation with Triton X-114. Finally, we used the biosensor to assess the activity of antiviral compounds.
Conclusions: Our results demonstrate that the luciferase-based dsRNA biosensor offers a simple, homogeneous, and high-throughput platform for quantifying viral replication, presenting a promising alternative to antibody-based dsRNA detection methods.
{"title":"Universal and quantitative detection of double-stranded RNAs as a signature of pan-virus infections using a luciferase-based biosensor.","authors":"Michihito Sasaki, Eri Fujii, Satoko Sasaki, Takuma Ariizumi, Kei Konishi, Akihiko Sato, William W Hall, Hirofumi Sawa, Yasuko Orba","doi":"10.1186/s13036-025-00601-0","DOIUrl":"https://doi.org/10.1186/s13036-025-00601-0","url":null,"abstract":"<p><strong>Background: </strong>Infections with various RNA viruses and certain DNA viruses may produce double-stranded RNA (dsRNA) during replication, which trigger host innate immune responses. Immunoassays using anti-dsRNA antibodies have been widely employed to detect viral dsRNA. In this study, we used a luciferase-based dsRNA biosensor for viral dsRNA detection, which consists of protein kinase R (PKR)-derived dsRNA binding domains fused to split luciferase subunits and is available as part of a commercial system.</p><p><strong>Results: </strong>We demonstrate the use of the dsRNA biosensor to measure viral dsRNA in RNA specimens extracted from cells infected with Japanese encephalitis virus (JEV). Moreover, the biosensor reacts to a broad-spectrum of dsRNAs from infection with representatives of various viral families including positive- and negative-sense single-stranded RNA (ssRNA) viruses, dsRNA viruses, and DNA viruses. We validated the specific interaction between the dsRNA biosensor and viral RNA including subgenomic flavivirus RNA (sfRNA) through RNA immunoprecipitation. Additionally, we observed luminescence signals directly from lysates of JEV-infected cells after cell lysis and phase separation with Triton X-114. Finally, we used the biosensor to assess the activity of antiviral compounds.</p><p><strong>Conclusions: </strong>Our results demonstrate that the luciferase-based dsRNA biosensor offers a simple, homogeneous, and high-throughput platform for quantifying viral replication, presenting a promising alternative to antibody-based dsRNA detection methods.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145767980","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}
Pub Date : 2025-12-16DOI: 10.1186/s13036-025-00600-1
SangKu Yi, Beom Seok Kim, Eunna Choi, Eun-Jin Lee, Juhyun Kim
<p><strong>Background: </strong>The type III secretion system (T3SS) is a syringe-like machine that pathogenic bacteria use to inject effector proteins into host cells. Its ability to mediate targeted protein delivery has prompted efforts to adapt it for diverse biotechnological applications. However, the influence of bacterial host culture conditions on the performance of the T3SS-based circuits, which has never been systematically studied, is addressed in this study.</p><p><strong>Results: </strong>In this study, we developed and characterized an IPTG-inducible, refactored T3SS circuit (iT3SS) in Salmonella enterica, in which the prgH gene, encoding a protein of the basal body complex, was fused to the coding sequence of GFP in order to monitor the expression of the secretion system. The engineered system was shown to secrete efficiently the effector protein SptP. The dynamics of expression of the PrgH-GFP fusion was assessed in rich LB medium and in glucose minimal medium under various IPTG concentrations. Interestingly, secretion efficiency was maintained across IPTG concentrations in cells grown in glucose minimal medium, but not in cells grown in rich LB medium. In cells grown in LB medium, secretion and invasion efficiencies did not increase proportionally with increasing IPTG concentrations. Both PrgH abundance and SptP secretion efficiency were lower at high IPTG concentration than at low and medium IPTG concentrations. Since RNA-seq analysis of cells grown in LB medium revealed that the transcription of iT3SS genes increased proportionally to inducer level, this indicated that transcription was not the limiting factor for iT3SS expression. This suggested that the limiting factor might be due to a translational and/or post-translational burden of iT3SS component mRNAs. Indeed, uneven (not stoichiometric) translation of the iT3SS components and/or their imperfect folding might impair their assembly and insertion in the membrane. Consequently, one cannot exclude that the iT3SS components not properly assembled or integrated are being degraded, giving the wrong impression of a low translation level. Interestingly, RNA-seq revealed that in LB cultures at high IPTG concentration, stress-response genes were up-regulated whereas ribosomal protein-coding genes were down-regulated. This feature might contribute to limiting iT3SS translation. Several hypotheses are proposed in the discussion to explain how culture conditions could influence the functionality of iT3SS.</p><p><strong>Conclusions: </strong>Our findings demonstrate that the nature of the growth medium has an impact on the performance of programmable secretion systems that might be due to host's resource-allocation strategy that would have a negative impact on the translational efficiency of the iT3SS components, compromising their correct assembly and thus their membrane insertion. This insight provides a medium-aware framework for optimizing engineered secretion platforms for synthet
{"title":"Medium dependent factors govern the functionality of engineered type III secretion systems.","authors":"SangKu Yi, Beom Seok Kim, Eunna Choi, Eun-Jin Lee, Juhyun Kim","doi":"10.1186/s13036-025-00600-1","DOIUrl":"https://doi.org/10.1186/s13036-025-00600-1","url":null,"abstract":"<p><strong>Background: </strong>The type III secretion system (T3SS) is a syringe-like machine that pathogenic bacteria use to inject effector proteins into host cells. Its ability to mediate targeted protein delivery has prompted efforts to adapt it for diverse biotechnological applications. However, the influence of bacterial host culture conditions on the performance of the T3SS-based circuits, which has never been systematically studied, is addressed in this study.</p><p><strong>Results: </strong>In this study, we developed and characterized an IPTG-inducible, refactored T3SS circuit (iT3SS) in Salmonella enterica, in which the prgH gene, encoding a protein of the basal body complex, was fused to the coding sequence of GFP in order to monitor the expression of the secretion system. The engineered system was shown to secrete efficiently the effector protein SptP. The dynamics of expression of the PrgH-GFP fusion was assessed in rich LB medium and in glucose minimal medium under various IPTG concentrations. Interestingly, secretion efficiency was maintained across IPTG concentrations in cells grown in glucose minimal medium, but not in cells grown in rich LB medium. In cells grown in LB medium, secretion and invasion efficiencies did not increase proportionally with increasing IPTG concentrations. Both PrgH abundance and SptP secretion efficiency were lower at high IPTG concentration than at low and medium IPTG concentrations. Since RNA-seq analysis of cells grown in LB medium revealed that the transcription of iT3SS genes increased proportionally to inducer level, this indicated that transcription was not the limiting factor for iT3SS expression. This suggested that the limiting factor might be due to a translational and/or post-translational burden of iT3SS component mRNAs. Indeed, uneven (not stoichiometric) translation of the iT3SS components and/or their imperfect folding might impair their assembly and insertion in the membrane. Consequently, one cannot exclude that the iT3SS components not properly assembled or integrated are being degraded, giving the wrong impression of a low translation level. Interestingly, RNA-seq revealed that in LB cultures at high IPTG concentration, stress-response genes were up-regulated whereas ribosomal protein-coding genes were down-regulated. This feature might contribute to limiting iT3SS translation. Several hypotheses are proposed in the discussion to explain how culture conditions could influence the functionality of iT3SS.</p><p><strong>Conclusions: </strong>Our findings demonstrate that the nature of the growth medium has an impact on the performance of programmable secretion systems that might be due to host's resource-allocation strategy that would have a negative impact on the translational efficiency of the iT3SS components, compromising their correct assembly and thus their membrane insertion. This insight provides a medium-aware framework for optimizing engineered secretion platforms for synthet","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145767975","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":"Design and performance analysis of bionic trabecular bone scaffold structure based on Voronoi.","authors":"Linlin Liu, Xin Wang, Shuxian Wang, Juncai Liu, Jinghong Yang, Chen Zhou","doi":"10.1186/s13036-025-00596-8","DOIUrl":"https://doi.org/10.1186/s13036-025-00596-8","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145762909","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}
Pub Date : 2025-12-15DOI: 10.1186/s13036-025-00589-7
Somyong Lee, Soeon Ahn, Jin Ho Zong, Chulhong Oh, Sangwon Suh, Dong Soo Hwang
{"title":"Correction: Sustainable valorization of fish head wastes into nitrogen-based nutrients: a comparative life cycle assessment.","authors":"Somyong Lee, Soeon Ahn, Jin Ho Zong, Chulhong Oh, Sangwon Suh, Dong Soo Hwang","doi":"10.1186/s13036-025-00589-7","DOIUrl":"10.1186/s13036-025-00589-7","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":"19 1","pages":"110"},"PeriodicalIF":6.5,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12706940/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145762840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-13DOI: 10.1186/s13036-025-00587-9
Karla Machado-Torres, Alejandra Romero-Montero, Lorena Duarte-Peña, Gerardo Leyva-Gómez
The treatment of chronic and infected wounds remains a constant challenge; therefore, there is a need to develop multifunctional dressings that integrate mechanical resilience and antimicrobial activity via alternative drugs to prevent bacterial resistance. This study presents, for the first time, the design of self-healing hydrogels based on polyvinyl alcohol and polyvinylpyrrolidone, which were obtained by the freeze‒thaw method; these hydrogels enable physical crosslink formation without the use of toxic agents and serve as carriers for phenytoin repositioning, an antiepileptic drug recognized for its wound-healing properties. Phenytoin was incorporated via micelle-assisted solubilization, ensuring uniform distribution without damaging the hydrogel structure. The optimal formulation exhibited high swelling capacity (~ 450%), gradual disintegration (55% in 14 days), pseudoplastic behavior, and excellent self-healing ability even after multiple deformation cycles. Structural analyses (FTIR, DSC, TGA, SEM) confirmed dynamic hydrogen bonding interactions and an interconnected porous network conducive to tissue regeneration. Phenytoin release followed a diffusion mechanism, with a rapid initial phase followed by sustained release driven by chain relaxation and erosion, reaching 55% release in 4 days. The inclusion of phenytoin imparted antimicrobial activity, with 52% inhibition against Staphylococcus aureus and 30% against Pseudomonas aeruginosa. The results position this system as a groundbreaking alternative for phenytoin repurposing in wound treatment.
{"title":"Self-healing PVA/PVP micelle-hydrogel composite system for potential phenytoin repositioning in wound healing.","authors":"Karla Machado-Torres, Alejandra Romero-Montero, Lorena Duarte-Peña, Gerardo Leyva-Gómez","doi":"10.1186/s13036-025-00587-9","DOIUrl":"https://doi.org/10.1186/s13036-025-00587-9","url":null,"abstract":"<p><p>The treatment of chronic and infected wounds remains a constant challenge; therefore, there is a need to develop multifunctional dressings that integrate mechanical resilience and antimicrobial activity via alternative drugs to prevent bacterial resistance. This study presents, for the first time, the design of self-healing hydrogels based on polyvinyl alcohol and polyvinylpyrrolidone, which were obtained by the freeze‒thaw method; these hydrogels enable physical crosslink formation without the use of toxic agents and serve as carriers for phenytoin repositioning, an antiepileptic drug recognized for its wound-healing properties. Phenytoin was incorporated via micelle-assisted solubilization, ensuring uniform distribution without damaging the hydrogel structure. The optimal formulation exhibited high swelling capacity (~ 450%), gradual disintegration (55% in 14 days), pseudoplastic behavior, and excellent self-healing ability even after multiple deformation cycles. Structural analyses (FTIR, DSC, TGA, SEM) confirmed dynamic hydrogen bonding interactions and an interconnected porous network conducive to tissue regeneration. Phenytoin release followed a diffusion mechanism, with a rapid initial phase followed by sustained release driven by chain relaxation and erosion, reaching 55% release in 4 days. The inclusion of phenytoin imparted antimicrobial activity, with 52% inhibition against Staphylococcus aureus and 30% against Pseudomonas aeruginosa. The results position this system as a groundbreaking alternative for phenytoin repurposing in wound treatment.</p>","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145751955","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}
Pub Date : 2025-12-13DOI: 10.1186/s13036-025-00595-9
Arslan Sarwar, Linh Thanh Nguyen, Eun Yeol Lee
{"title":"Development of an ethanol-based microbial platform for 3-hydroxypropionic acid production using engineered Pseudomonas putida KT2440.","authors":"Arslan Sarwar, Linh Thanh Nguyen, Eun Yeol Lee","doi":"10.1186/s13036-025-00595-9","DOIUrl":"https://doi.org/10.1186/s13036-025-00595-9","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145751867","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}
Pub Date : 2025-12-13DOI: 10.1186/s13036-025-00592-y
Khoi Nhat Pham, Eun Yeol Lee
{"title":"Development of a semi-endogenous PRT-based expression system for Methylotuvimicrobium alcaliphilum and its application to enhance 3-hydroxybutyric acid production from methanol.","authors":"Khoi Nhat Pham, Eun Yeol Lee","doi":"10.1186/s13036-025-00592-y","DOIUrl":"https://doi.org/10.1186/s13036-025-00592-y","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145751836","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}
Pub Date : 2025-12-10DOI: 10.1186/s13036-025-00586-w
Junyeob Kim, Sang Woo Seo
{"title":"Enhanced methanol tolerance and utilization in Pichia pastoris revealed by adaptive laboratory evolution.","authors":"Junyeob Kim, Sang Woo Seo","doi":"10.1186/s13036-025-00586-w","DOIUrl":"https://doi.org/10.1186/s13036-025-00586-w","url":null,"abstract":"","PeriodicalId":15053,"journal":{"name":"Journal of Biological Engineering","volume":" ","pages":""},"PeriodicalIF":6.5,"publicationDate":"2025-12-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145723301","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}
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