Recent advances in the chemical synthesis and modification of messenger RNA (mRNA) have generated growing interest in mRNA-based therapeutics. However, the inherent instability of mRNA in vivo and during storage remains a major challenge, requiring the development of safe and effective delivery systems. Lipid nanoparticles (LNPs) currently serve as the primary vehicle for mRNA delivery, with well-documented clinical success. Nevertheless, immunogenicity associated with certain components underscores the need for biocompatible alternatives. To address these stability and safety concerns, we developed an mRNA-loaded DNA hydrogel based on self-gelatinizable nucleic acid technology. The hydrogel is formed through the self-assembly of designed DNA units and provides an inherently biocompatible framework. mRNA loaded into the hydrogel exhibited sustained protein expression in myofibroblasts due to controlled mRNA release, while inducing negligible proinflammatory cytokine production or cytotoxicity in antigen-presenting cells. Additionally, the hydrogel markedly enhanced mRNA resistance to both nuclease degradation and storage-induced degradation. These findings demonstrate that mRNA-loaded DNA hydrogels can serve as a promising, biocompatible platform for next-generation mRNA therapeutics, achieving both enhanced stability and reduced immunogenicity.
{"title":"Improved Messenger RNA Stability and Biocompatibility Through Self-Gelatinizable Nucleic Acids.","authors":"Takumi Tanifuji,Kosuke Kusamori,Chihiro Tanaka,Hideki Sakai,Shoko Itakura,Makiya Nishikawa","doi":"10.1002/bit.70158","DOIUrl":"https://doi.org/10.1002/bit.70158","url":null,"abstract":"Recent advances in the chemical synthesis and modification of messenger RNA (mRNA) have generated growing interest in mRNA-based therapeutics. However, the inherent instability of mRNA in vivo and during storage remains a major challenge, requiring the development of safe and effective delivery systems. Lipid nanoparticles (LNPs) currently serve as the primary vehicle for mRNA delivery, with well-documented clinical success. Nevertheless, immunogenicity associated with certain components underscores the need for biocompatible alternatives. To address these stability and safety concerns, we developed an mRNA-loaded DNA hydrogel based on self-gelatinizable nucleic acid technology. The hydrogel is formed through the self-assembly of designed DNA units and provides an inherently biocompatible framework. mRNA loaded into the hydrogel exhibited sustained protein expression in myofibroblasts due to controlled mRNA release, while inducing negligible proinflammatory cytokine production or cytotoxicity in antigen-presenting cells. Additionally, the hydrogel markedly enhanced mRNA resistance to both nuclease degradation and storage-induced degradation. These findings demonstrate that mRNA-loaded DNA hydrogels can serve as a promising, biocompatible platform for next-generation mRNA therapeutics, achieving both enhanced stability and reduced immunogenicity.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"107 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145961332","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
l-Pipecolic acid (l-PA) and its hydroxylated derivatives (hydroxypipecolic acids, HPAs) are non-proteinogenic amino acids that serve as valuable chiral building blocks for pharmaceuticals, antibiotics, and natural products. Conventional chemical synthesis of these compounds often suffers from operational complexity, poor environmental compatibility, and insufficient stereochemical control, driving a shift toward biosynthetic approaches. This review covers recent advances in enzyme engineering and synthetic biology aimed at enabling sustainable and efficient production of l-PA and HPAs. For l-PA biosynthesis, various metabolic engineering strategies to enhance its production in microbes are introduced, and enzyme cascades, single enzyme strategy, and immobilized enzyme strategy involved in l-PA production are discussed. Regarding HPAs biosynthesis, which involves the regioselective hydroxylation of l-PA, their structural features, catalytic mechanisms, and recent progress in the biosynthesis of diverse HPAs, the protein engineering of proline hydroxylase is emphasized. Finally, we present future perspectives to accelerate the biosynthetic production of l-PA and HPAs.
{"title":"Biosynthesis of L-Pipecolic Acid and Its Hydroxylated Derivatives: Enzyme, Engineering, and Synthesis Method.","authors":"Shu-Fang Li,Xiao-Xia Zhu,Yu-Sheng Hu,Ru-Hao Li,Ya-Ping Xue,Yu-Guo Zheng","doi":"10.1002/bit.70156","DOIUrl":"https://doi.org/10.1002/bit.70156","url":null,"abstract":"l-Pipecolic acid (l-PA) and its hydroxylated derivatives (hydroxypipecolic acids, HPAs) are non-proteinogenic amino acids that serve as valuable chiral building blocks for pharmaceuticals, antibiotics, and natural products. Conventional chemical synthesis of these compounds often suffers from operational complexity, poor environmental compatibility, and insufficient stereochemical control, driving a shift toward biosynthetic approaches. This review covers recent advances in enzyme engineering and synthetic biology aimed at enabling sustainable and efficient production of l-PA and HPAs. For l-PA biosynthesis, various metabolic engineering strategies to enhance its production in microbes are introduced, and enzyme cascades, single enzyme strategy, and immobilized enzyme strategy involved in l-PA production are discussed. Regarding HPAs biosynthesis, which involves the regioselective hydroxylation of l-PA, their structural features, catalytic mechanisms, and recent progress in the biosynthesis of diverse HPAs, the protein engineering of proline hydroxylase is emphasized. Finally, we present future perspectives to accelerate the biosynthetic production of l-PA and HPAs.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"2 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145961331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rebecca S. Pereles, Jyotirmoy Roy, Michael D. Brooks, Max S. Wicha, Jacqueline S. Jeruss, Lonnie D. Shea, Sophia M. Orbach
In breast cancer patients, metastasis is the stage of disease where prognosis significantly worsens. However, the timing at which metastasis initiates and the location of metastatic lesions in an organ are stochastic, limiting the timely identification of disease and the administration of treatments. Herein, we employ a synthetic metastatic niche comprised of a microporous scaffold to investigate the dynamic immune processes associated with metastatic progression. Upon implantation, the porous scaffold is infiltrated with immune cells and recruits tumor cells. We have previously reported stable tumor cell numbers in the scaffold, suggesting a state of metastatic dormancy. Towards understanding dormancy, we investigated the immune cell dynamics at the scaffold, including neutrophils, monocytes, and dendritic cells, and compared these changes to the lungs, the native metastatic niche in this model. The cell phenotypes within the scaffold microenvironment are initially polarized toward an anti‐tumor phenotype and become progressively more pro‐tumor with disease progression, similar to the lung microenvironment. However, the phenotypes at the scaffold are consistently less pro‐tumor than the phenotypes in the lung, consistent with the lung supporting tumor cell expansion and the scaffold exhibiting dormancy. Signaling pathways identified from the analysis are consistent with the changing innate cell phenotypes, with macrophages having a significant role during the early responses and neutrophils dominating the latter stages of disease. Collectively, the scaffold captures the immune dynamics during disease progression and the signaling that underlies stable tumor cell numbers, providing a tool for investigating the mechanisms of disease progression.
{"title":"Dynamic Immune Cell Composition, Phenotypes, and Signaling in an Engineered Metastatic Niche","authors":"Rebecca S. Pereles, Jyotirmoy Roy, Michael D. Brooks, Max S. Wicha, Jacqueline S. Jeruss, Lonnie D. Shea, Sophia M. Orbach","doi":"10.1002/bit.70140","DOIUrl":"https://doi.org/10.1002/bit.70140","url":null,"abstract":"In breast cancer patients, metastasis is the stage of disease where prognosis significantly worsens. However, the timing at which metastasis initiates and the location of metastatic lesions in an organ are stochastic, limiting the timely identification of disease and the administration of treatments. Herein, we employ a synthetic metastatic niche comprised of a microporous scaffold to investigate the dynamic immune processes associated with metastatic progression. Upon implantation, the porous scaffold is infiltrated with immune cells and recruits tumor cells. We have previously reported stable tumor cell numbers in the scaffold, suggesting a state of metastatic dormancy. Towards understanding dormancy, we investigated the immune cell dynamics at the scaffold, including neutrophils, monocytes, and dendritic cells, and compared these changes to the lungs, the native metastatic niche in this model. The cell phenotypes within the scaffold microenvironment are initially polarized toward an anti‐tumor phenotype and become progressively more pro‐tumor with disease progression, similar to the lung microenvironment. However, the phenotypes at the scaffold are consistently less pro‐tumor than the phenotypes in the lung, consistent with the lung supporting tumor cell expansion and the scaffold exhibiting dormancy. Signaling pathways identified from the analysis are consistent with the changing innate cell phenotypes, with macrophages having a significant role during the early responses and neutrophils dominating the latter stages of disease. Collectively, the scaffold captures the immune dynamics during disease progression and the signaling that underlies stable tumor cell numbers, providing a tool for investigating the mechanisms of disease progression.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"253 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145947446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shake flasks are widely used in early-stage bioprocess development but are limited by their inability to monitor and control key gas-transfer variables such as dissolved oxygen and carbon dioxide. In this study, we present a jacketed breathable flask system that enables real-time gas control in a standard shaking environment. Across multiple media formulations and fill volumes, this system consistently deferred oxygen limitation and enhanced culture performance, achieving > 150% higher biomass and 140% greater recombinant protein yield compared to conventional flasks. Time-resolved analysis of pH and extracellular metabolites revealed reduced accumulation of oxygen-sensitive byproducts, including acetate, pyruvate, and succinate, indicating a shift toward more efficient respiratory metabolism. The jacketed breathable flask also enabled continuous monitoring and regulation of critical process parameters, creating a bioreactor-like environment in a high-throughput, low-cost format. The biomass accumulation and specific growth rate observed in jacketed breathable flask are comparable to those reported for Escherichia coli cultures in stirred tank bioreactor application notes for Eppendorf BioBLU 3f. These findings establish breathable flasks as a scalable and accessible platform with bioreactor-like performance for upstream process optimization and accelerate biomanufacturing development at the lab scale.
{"title":"Development of a Jacketed Breathable Shake Flask With Process Monitoring, Control, and Bioreactor-Like Performance.","authors":"Vikash Kumar,Chad Sundberg,Venkatesh Srinivasan,Aaron Thole,Michael Tolosa,Govind Rao","doi":"10.1002/bit.70157","DOIUrl":"https://doi.org/10.1002/bit.70157","url":null,"abstract":"Shake flasks are widely used in early-stage bioprocess development but are limited by their inability to monitor and control key gas-transfer variables such as dissolved oxygen and carbon dioxide. In this study, we present a jacketed breathable flask system that enables real-time gas control in a standard shaking environment. Across multiple media formulations and fill volumes, this system consistently deferred oxygen limitation and enhanced culture performance, achieving > 150% higher biomass and 140% greater recombinant protein yield compared to conventional flasks. Time-resolved analysis of pH and extracellular metabolites revealed reduced accumulation of oxygen-sensitive byproducts, including acetate, pyruvate, and succinate, indicating a shift toward more efficient respiratory metabolism. The jacketed breathable flask also enabled continuous monitoring and regulation of critical process parameters, creating a bioreactor-like environment in a high-throughput, low-cost format. The biomass accumulation and specific growth rate observed in jacketed breathable flask are comparable to those reported for Escherichia coli cultures in stirred tank bioreactor application notes for Eppendorf BioBLU 3f. These findings establish breathable flasks as a scalable and accessible platform with bioreactor-like performance for upstream process optimization and accelerate biomanufacturing development at the lab scale.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"15 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Isobutanol is a fusel alcohol that can be produced microbially for use as a biofuel or upgraded into sustainable aviation fuel (SAF). A key enzyme in the isobutanol biosynthetic pathway is 2-ketoacid decarboxylase (KDC), which irreversibly decarboxylates 2-ketoisovalerate (KIV) to yield isobutyraldehyde. However, many previously characterized KDC enzymes also act promiscuously on other 2-ketoacids, (e.g., pyruvate) to produce a related aldehyde (e.g., acetaldehyde). This unwanted side reaction is especially important when isobutanol is produced in Saccharomyces cerevisiae (S. cerevisiae) because it leads to pyruvate being diverted to ethanol. In order to make S. cerevisiae a strict isobutanologen, a KDC enzyme that is specific for KIV must be deployed. In this study, we used a combination of cell-based and in vitro enzyme assays to investigate KDC substrate specificity, characterizing a large set of homologs for KIV, pyruvate, and phenylpyruvate (PPV) activity. A diverse range of substrate specificities was discovered, and some previously uncharacterized KDCs were revealed to have high KIV activity and low pyruvate activity. Multi-site saturation mutagenesis (SSM) of one of these KDCs identified mutants with increased KIV activity, while maintaining low levels of pyruvate activity. In a KIV bioconversion experiment, bioprospected and engineered KDCs allowed similar KIV consumption to when using the previously characterized Lactococcus lactis KdcA, though with some ethanol also produced. The KDCs identified here show promise for production of isobutanol and other alcohols derived from 2-ketoacids, and the dataset of newly characterized KDCs can inform future efforts to understand and engineer substrate specificity in KDCs.
{"title":"Engineering of 2-ketoacid Decarboxylases for Production of Isobutanol and Other Fusel Alcohols in Saccharomyces cerevisiae.","authors":"Joshua J Dietrich,Maelia Dziedzic,Jia Sun,Sri Harsha Adusumilli,Carla Gonçalves,Chris Todd Hittinger,Brian F Pfleger","doi":"10.1002/bit.70150","DOIUrl":"https://doi.org/10.1002/bit.70150","url":null,"abstract":"Isobutanol is a fusel alcohol that can be produced microbially for use as a biofuel or upgraded into sustainable aviation fuel (SAF). A key enzyme in the isobutanol biosynthetic pathway is 2-ketoacid decarboxylase (KDC), which irreversibly decarboxylates 2-ketoisovalerate (KIV) to yield isobutyraldehyde. However, many previously characterized KDC enzymes also act promiscuously on other 2-ketoacids, (e.g., pyruvate) to produce a related aldehyde (e.g., acetaldehyde). This unwanted side reaction is especially important when isobutanol is produced in Saccharomyces cerevisiae (S. cerevisiae) because it leads to pyruvate being diverted to ethanol. In order to make S. cerevisiae a strict isobutanologen, a KDC enzyme that is specific for KIV must be deployed. In this study, we used a combination of cell-based and in vitro enzyme assays to investigate KDC substrate specificity, characterizing a large set of homologs for KIV, pyruvate, and phenylpyruvate (PPV) activity. A diverse range of substrate specificities was discovered, and some previously uncharacterized KDCs were revealed to have high KIV activity and low pyruvate activity. Multi-site saturation mutagenesis (SSM) of one of these KDCs identified mutants with increased KIV activity, while maintaining low levels of pyruvate activity. In a KIV bioconversion experiment, bioprospected and engineered KDCs allowed similar KIV consumption to when using the previously characterized Lactococcus lactis KdcA, though with some ethanol also produced. The KDCs identified here show promise for production of isobutanol and other alcohols derived from 2-ketoacids, and the dataset of newly characterized KDCs can inform future efforts to understand and engineer substrate specificity in KDCs.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"265 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jessica Graham,Sathanandam S Anand,Joel Bercu,Lauren Besenhofer,Christina de Zafra,Yu Feng,Susanne Glowienke,Jedd Hillegass,Richard Hutchinson,Robert Jolly,Melisa Masuda-Herrera,Tyler Nicholas,Daniela Olszova,Matthew Schmitz,Florian Semmelmann,Eric Tien
Host cell proteins (HCPs) are important process-related impurities produced by the host organism during the manufacturing of biotherapeutics. Even trace amounts of these contaminants can be considered significant during drug development due to their potential impact on the quality, safety, and/or efficacy of the therapeutic. This article summarizes the findings of a survey conducted by the IQ DruSafe Impurities Safety Working Group (Biologics Impurities Subteam) concerning industry practices and challenges related to HCPs in biologic therapeutics. The survey addressed four key areas: the scope of HCP control challenges, practices for HCP control and monitoring, methods for qualification of HCP levels, and regulatory interactions. Results revealed both perceived risks and experienced impact from HCP impurities as well as analytical strategies for their identification and quantification. The article also presents current default limits being employed for total and individual HCP impurities, approaches for assessing the safety and immunogenicity risk of HCPs, and a summary of feedback from global health authorities. Overall, the survey results illustrate progress in HCP management across biologic drug development while underscoring persistent challenges. The findings point to emerging best practices informed by historical knowledge and also reveal areas where a harmonized approach may be justified. Identifying and addressing challenges will require sustained industry collaboration and ongoing engagement with regulatory authorities to ensure the continued advancement of safe, effective biologic therapeutics.
{"title":"Assessment and Control of Host Cell Proteins in Biologics: Survey of Industry Practices and a Vision for Harmonization.","authors":"Jessica Graham,Sathanandam S Anand,Joel Bercu,Lauren Besenhofer,Christina de Zafra,Yu Feng,Susanne Glowienke,Jedd Hillegass,Richard Hutchinson,Robert Jolly,Melisa Masuda-Herrera,Tyler Nicholas,Daniela Olszova,Matthew Schmitz,Florian Semmelmann,Eric Tien","doi":"10.1002/bit.70154","DOIUrl":"https://doi.org/10.1002/bit.70154","url":null,"abstract":"Host cell proteins (HCPs) are important process-related impurities produced by the host organism during the manufacturing of biotherapeutics. Even trace amounts of these contaminants can be considered significant during drug development due to their potential impact on the quality, safety, and/or efficacy of the therapeutic. This article summarizes the findings of a survey conducted by the IQ DruSafe Impurities Safety Working Group (Biologics Impurities Subteam) concerning industry practices and challenges related to HCPs in biologic therapeutics. The survey addressed four key areas: the scope of HCP control challenges, practices for HCP control and monitoring, methods for qualification of HCP levels, and regulatory interactions. Results revealed both perceived risks and experienced impact from HCP impurities as well as analytical strategies for their identification and quantification. The article also presents current default limits being employed for total and individual HCP impurities, approaches for assessing the safety and immunogenicity risk of HCPs, and a summary of feedback from global health authorities. Overall, the survey results illustrate progress in HCP management across biologic drug development while underscoring persistent challenges. The findings point to emerging best practices informed by historical knowledge and also reveal areas where a harmonized approach may be justified. Identifying and addressing challenges will require sustained industry collaboration and ongoing engagement with regulatory authorities to ensure the continued advancement of safe, effective biologic therapeutics.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"397 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145937762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Salidroside, a major bioactive component of Rhodiola rosea, exhibits diverse pharmacological activities and broad applications, but faces biosynthesis challenges. Herein, we developed a synergistic strategy to construct a high-level plasmid-free salidroside production strain W6U4. First, multi-copy genomic integration of the phenylpyruvate decarboxylase mutant ARO10D331C and glycosyltransferase UGT85A1 was performed to enhance precursor tyrosol synthesis and glycosylation efficiency. Subsequently, systematic metabolic engineering was applied to redirect metabolic flux: reinforcing the pentose phosphate and shikimate pathways and eliminating competing pathways, which boosted salidroside titer to 2.63 g/L in shake flasks. Finally, optimized fed-batch fermentation in a 5-L bioreactor with two-stage temperature control (37°C for growth, 30°C for induction) and early log-phase induction (OD600 = 15) resulted in 33.68 g/L salidroside, the highest reported titer to date, with only 0.40 g/L residual tyrosol. This integrated strategy establishes an efficient, stable microbial platform for salidroside production, highlighting the synergistic effect in advancing industrial-scale biosynthesis.
{"title":"Engineering Plasmid-Free Escherichia coli via Synergistic Metabolic Tuning and Fermentation Optimization for High-Titer Salidroside Biosynthesis","authors":"Man Zhao, Kerui Liu, Xingyu Chen, Guofei Zheng, Zhiqiang Liu, Yuguo Zheng","doi":"10.1002/bit.70153","DOIUrl":"https://doi.org/10.1002/bit.70153","url":null,"abstract":"Salidroside, a major bioactive component of <i>Rhodiola rosea</i>, exhibits diverse pharmacological activities and broad applications, but faces biosynthesis challenges. Herein, we developed a synergistic strategy to construct a high-level plasmid-free salidroside production strain W6U4. First, multi-copy genomic integration of the phenylpyruvate decarboxylase mutant <i>ARO10</i><sup><i>D331C</i></sup> and glycosyltransferase <i>UGT85A1</i> was performed to enhance precursor tyrosol synthesis and glycosylation efficiency. Subsequently, systematic metabolic engineering was applied to redirect metabolic flux: reinforcing the pentose phosphate and shikimate pathways and eliminating competing pathways, which boosted salidroside titer to 2.63 g/L in shake flasks. Finally, optimized fed-batch fermentation in a 5-L bioreactor with two-stage temperature control (37°C for growth, 30°C for induction) and early log-phase induction (OD<sub>600</sub> = 15) resulted in 33.68 g/L salidroside, the highest reported titer to date, with only 0.40 g/L residual tyrosol. This integrated strategy establishes an efficient, stable microbial platform for salidroside production, highlighting the synergistic effect in advancing industrial-scale biosynthesis.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"131 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919883","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Maximilian Siska, Emma Pajak, Katrin Rosenthal, Antonio del Rio Chanona, Eric von Lieres, Laura M. Helleckes
Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small data sets, and provide adaptive suggestions for sequential experimentation. While still in its infancy, Bayesian optimization has recently gained traction in bioprocess engineering. However, experimentation with biological systems is highly complex and the resulting experimental uncertainty requires specific extensions to classical Bayesian optimization. Moreover, current literature often targets readers with a strong statistical background, limiting its accessibility for practitioners. In light of these developments, this review has two aims: first, to provide an intuitive and practical introduction to Bayesian optimization; and second, to outline promising application areas and open algorithmic challenges, thereby highlighting opportunities for future research in machine learning.
{"title":"A Guide to Bayesian Optimization in Bioprocess Engineering","authors":"Maximilian Siska, Emma Pajak, Katrin Rosenthal, Antonio del Rio Chanona, Eric von Lieres, Laura M. Helleckes","doi":"10.1002/bit.70129","DOIUrl":"https://doi.org/10.1002/bit.70129","url":null,"abstract":"Bayesian optimization has become widely popular across various experimental sciences due to its favorable attributes: it can handle noisy data, perform well with relatively small data sets, and provide adaptive suggestions for sequential experimentation. While still in its infancy, Bayesian optimization has recently gained traction in bioprocess engineering. However, experimentation with biological systems is highly complex and the resulting experimental uncertainty requires specific extensions to classical Bayesian optimization. Moreover, current literature often targets readers with a strong statistical background, limiting its accessibility for practitioners. In light of these developments, this review has two aims: first, to provide an intuitive and practical introduction to Bayesian optimization; and second, to outline promising application areas and open algorithmic challenges, thereby highlighting opportunities for future research in machine learning.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"43 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145919809","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biotechnology and Bioengineering: Volume 123, Number 2, February 2026","authors":"","doi":"10.1002/bit.70152","DOIUrl":"10.1002/bit.70152","url":null,"abstract":"","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"123 2","pages":"269-272"},"PeriodicalIF":3.6,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/epdf/10.1002/bit.70152","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145920295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ting Huang,Hongmei Ge,Zhenbing Wu,Yibo Zhang,Lifeng Wang,Chenyuan Dang,Jie Fu
Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 +-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.
{"title":"Resistance of Microbial Community in Activated Sludge to Nano-Ag Stress Through Regulation of N-Acyl Homoserine Lactones-Mediated Quorum Sensing.","authors":"Ting Huang,Hongmei Ge,Zhenbing Wu,Yibo Zhang,Lifeng Wang,Chenyuan Dang,Jie Fu","doi":"10.1002/bit.70155","DOIUrl":"https://doi.org/10.1002/bit.70155","url":null,"abstract":"Nano-Ag is increasingly detected in WWTP due to its widespread application, posing a significant threat to microbial communities responsible for wastewater treatment efficiency. Prior studies have demonstrated that quorum sensing (QS) can modulate bacterial tolerance to various environmental stressors in sludge systems. However, the feasibility and mechanisms of N-acyl homoserine lactones (AHLs)-mediated QS regulation to improve the resistance of microorganisms in WWTPs to nano-Ag shocks have been unexplored. Hence, we conducted sequencing batch reactor experiments, and as expected, nano-Ag significantly reduced the treatment performance of bioreactors. However, with the addition of AHLs (C6-HSL, C10-HSL, and C14-HSL) in the bioreactors, the microbial resistance in activated sludge to nano-Ag stress had been evidently enhanced, including the restoration of the sludge morphology, settleability, biomass and extracellular polymeric substances (EPS), as well as the treatment performance of bioreactors on removals of ammonium nitrogen (NH4 +-N), chemical oxygen demand (COD), and suspended solids. The joint analysis of metagenomics, metatranscriptomics, and metametabolomics indicated the multifunctional bacteria (e.g., Amaricoccus, Hydrogenophaga, and Brevundimonas) played a very important role during the regulation of AHLs-mediated QS, which harbored functional genes associated with nitrogen metabolism, carbon metabolism, silver resistance, and AHLs response. The upregulation on glutathione-dependent metabolisms (e.g., glutathione-oxidized glutathione redox cycle) and biosynthesis of EPS (e.g., poly-N-acetylglucosamine) were beneficial for the enhancement of microbial resistance to nano-Ag. This study provided a potentially feasible strategy and important theoretical basis to enhance the robustness and restore the function of microorganisms in wastewater treatment systems by using AHLs-mediated QS regulation.","PeriodicalId":9168,"journal":{"name":"Biotechnology and Bioengineering","volume":"23 1","pages":""},"PeriodicalIF":3.8,"publicationDate":"2026-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145907709","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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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