Bioprocess and Biosystems Engineering最新文献

{"title":"Decoding the distribution, structure-function-redox potential relationship and recent advances in fungal laccases: a systematic approach.","authors":"Rhydum Sharma, Richa Salwan, Nirlap Kour, Kartik Sharma, Vivek Sharma","doi":"10.1007/s00449-025-03260-z","DOIUrl":"10.1007/s00449-025-03260-z","url":null,"abstract":"<p><p>Laccases, categorized as multicopper oxidases, are recognized for their multifaceted roles in ecosystems and their utility in diverse industrial applications. Laccases from higher fungi, specifically Ascomycota and Basidiomycota, have garnered significant research interest due to their elevated redox potentials and their capacity to degrade lignin in decaying wood, alongside other industrial uses. Here, we have conducted a comprehensive and systematic analysis on fungal laccases using Web of Science, Scopus, PubMed, and ScienceDirect. The genomic distribution, phylogenetic affiliation, and structural organization of laccase-encoding genes in higher fungal species were investigated, as were the catalytic mechanisms of the corresponding enzymes. Additionally, the study explores the correlation between structural domains and redox potential, as well as the impact of post-translational modifications like glycosylation on enzyme activity. Furthermore, the recent advancements in laccase engineering, employing strategies such as rational design, directed evolution, and heterologous expression are discussed. The review also explores the scope of \"artificial intelligence and machine learning\" in deducing the structure-function relationships, optimizing codon usage, predicting signal peptides, enhancing enzymatic performance, and developing host-specific genetic engineering techniques is also discussed for tailoring fungal laccases to meet the demands of industrial biocatalysis for improved activity and stability.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2369-2392"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145629137","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":"40 years of bioprocess and biosystems engineering: a retroperspective and an outlook.","authors":"Kathrin Castiglione, Dirk Weuster-Botz","doi":"10.1007/s00449-026-03413-8","DOIUrl":"10.1007/s00449-026-03413-8","url":null,"abstract":"","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2317-2319"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148766188","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":"Managing complexity in research data management for heterogeneous biotechnological data: a perspective on interacting as data steward.","authors":"Martina Rehnert, Ralf Takors","doi":"10.1007/s00449-026-03380-0","DOIUrl":"10.1007/s00449-026-03380-0","url":null,"abstract":"<p><p>Biotechnology is an interconnected and globally significant field with expanding impact on industries, bioeconomy and healthcare. The associated rapid increase in data generation requires effective research data management (RDM) that ensures compliance with the FAIR principles (findable, accessible, interoperable and reusable) while addressing challenges related to heterogeneous data formats, metadata complexity, data protection, and governance requirements. Furthermore, archiving and storage of heterogeneous, often proprietary data formats, and subject-specific ontologies in cross-domains can pose challenges for RDM. In a use case involving 50 international, cross-discipline biotechnology researchers, an institutional repository was used for RDM and to manage heterogeneous data formats such as experimental, computer-aided modeling and process engineering data in accordance with the FAIR principles. The RDM built on the repository's existing centralized infrastructure, but this did not entirely meet user expectations for their practical research applications. While centralized top-down infrastructures of repositories provided the technical foundation for FAIR data handling, our observation showed that generic repository frameworks and standardized workflows required continuous, discipline-specific, and human mediated support integrated into everyday research workflows. As intermediaries between institutional requirements and research practice, data stewards can provide valuable insights into the challenges of implementing sustainable RDM helping to optimize repository support structures and align them with researchers' evolving needs in complex real-world biotechnology research environments.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2321-2331"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582134/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148519749","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}

{"title":"Integrated one-pot ultrasound-assisted method for carotenoid extraction from Rhodosporidium toruloides.","authors":"Lachi Wankhede, Gaurav Bhardwaj, Carlos Saul Osorio-González, Satinder Kaur Brar","doi":"10.1007/s00449-026-03299-6","DOIUrl":"10.1007/s00449-026-03299-6","url":null,"abstract":"","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2551-2560"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147353903","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":"Is faster always better? A critical assessment of Vibrio natriegens as microbial host for recombinant protein production.","authors":"Stefanie Brückner, Maike Scherer, Matthias Tobler, Bastian Blombach, Kathrin Castiglione","doi":"10.1007/s00449-026-03352-4","DOIUrl":"10.1007/s00449-026-03352-4","url":null,"abstract":"<p><p>The marine bacterium Vibrio natriegens has emerged as a promising candidate for recombinant protein production, primarily due to its rapid growth rate combined with its high protein synthesis capacity. These attributes have the potential to shorten production processes while achieving high yields of heterologously produced proteins. This review provides a concise overview of the substantial progress that has been made in the development of genetic tools and expression systems for V. natriegens, highlighting their successful application to the production of a wide range of proteins, including challenging targets such as membrane proteins. In addition, it critically examines the advantages and limitations of this organism as a production host, with a particular focus on whether its rapid growth translates into a tangible benefit for recombinant protein production. By contrasting the current status of V. natriegens with established Escherichia coli-based systems, key technological and biological developments required for its broader adoption are identified. In particular, the scale-up of protein production for potential industrial implementation remains underexplored and may present significant challenges due to the physiological demands of V. natriegens, including high oxygen requirements and the need for salt-supplemented media. Ultimately, whether fast growth equates to superior productivity, and whether V. natriegens can establish itself as a robust and broadly applicable protein production host, will depend on continued strain development and process intensification.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2353-2368"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148026980","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}

{"title":"Automated high-throughput screening combined with model-assisted analysis enables quantitative identification of process drivers and trade-offs during extracellular Fab production in Escherichia coli.","authors":"Fabian Schröder-Kleeberg, Lucas Kaspersetz, Sanchir Anar Neff, Markus Zoellkau, Markus Glaser, Markus Brunner, Christian Bosch, Mariano Nicolas Cruz Bournazou, Peter Neubauer","doi":"10.1007/s00449-026-03379-7","DOIUrl":"10.1007/s00449-026-03379-7","url":null,"abstract":"<p><p>Production of Fab antibody fragments with Escherichia coli strains engineered for extracellular product release can reduce downstream processing requirements but often compromises cellular integrity, resulting in increased cell lysis. To investigate the balance between product formation, product release, and cellular robustness, 32 fed-batch cultivation conditions spanning six process parameters were systematically evaluated in automated high-throughput bioreactors. In total, 100 cultivations were performed, and mechanistic modeling was applied to estimate cell lysis, product formation, and product release kinetics. The combined experimental and model-based analysis revealed a pronounced trade-off between productivity and robustness. Conditions yielding high Fab titers showed minimal cell lysis rates but also slow product release, whereas elevated release kinetics were consistently associated with substantial lysis and reduced Fab titers. Induction strength emerged as the primary driver for maximizing Fab titer, while production temperature governed the balance between product release and cell lysis. Compared to the reference condition, Fab titers increased approximately twofold to 730 mg L[Formula: see text] while reducing the cell lysis rate by up to eightfold to near-negligible levels, albeit at the expense of a 2.2-fold lower product release rate. Robustness studies under large-scale-relevant conditions identified moderate substrate heterogeneities as an additional factor enhancing productivity while reducing cell lysis. Furthermore, the extensive dataset enabled refinement of a previously developed product model by introducing an induction-strength-dependent production load and provided mechanistic insight into the relationship between product release and cell lysis. Overall, the study demonstrates how mechanistic modeling enhances the interpretation of automated high-throughput screening experiments by linking observable process responses to underlying physiological behavior and enabling quantitative analysis of complex production trade-offs.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2409-2428"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582191/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148760805","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}

{"title":"Nanocarrier-mediated delivery of polyphenols: an emerging strategy for overcoming biological barriers in gastrointestinal cancer therapy.","authors":"Sekar Vijayakumar, Anbu Malar Michael, Zaira I González-Sánchez, Mani Divya, Esteban F Durán-Lara, Yonggang Peng, Ying Yu, Mingchun Li","doi":"10.1007/s00449-026-03322-w","DOIUrl":"10.1007/s00449-026-03322-w","url":null,"abstract":"","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2393-2408"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147508769","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":"The optimization of thermostable recombinant α-amylase for efficient fabric desizing using response surface methodology and surface morphology analysis.","authors":"Krishnendu Mondal, Prayatna Sharma, Ishfaq Nabi Najar, Tanmoy Jana, Sudipta Samanta, Subhas Giri, Arijit Jana, Nagendra Thakur, Keshab Chandra Mondal","doi":"10.1007/s00449-026-03345-3","DOIUrl":"10.1007/s00449-026-03345-3","url":null,"abstract":"<p><p>A thermostable α-amylase gene (Amyk4) from Bacillus licheniformis k4cm (or similar thermophilic Bacillus), isolated from a Himalayan hot spring in Sikkim, India, was successfully cloned and expressed in Escherichia coli BL21(DE3). The purified recombinant α-amylase (Amyk4) exhibited maximal activity (153.2 ± 1.05 U/mL) at 80 °C and pH 6.0, with a half-life of 30.39 h and enhanced stability in the presence of Ca²⁺, indicating its suitability for high-temperature industrial applications. The cotton fabric desizing was optimized using Response Surface Methodology (Box-Behnken design). Optimal conditions (pH 6.9, 80 °C, enzyme dosage of 190 U/g, and treatment time of 95 min) achieved a TEGEWA rating of 8 and a weight loss of 6.6%. The quadratic model showed strong statistical validity (R² = 0.9205 for TEGEWA and 0.9168 for weight loss). Among the evaluated variables, pH, enzyme concentration, and reaction time significantly influenced desizing efficiency. Non-ionic surfactants slightly improved desizing efficiency compared to ionic surfactants. Scanning electron microscopy (SEM) analysis confirmed effective starch removal without fibre damage. These findings demonstrate the potential of recombinant Amyk4 as a thermostable, eco-friendly candidate for sustainable textile desizing applications.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2487-2505"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147970109","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":"Mechanistic model for HEK293 viral vector processes and its application in a digital shadow framework.","authors":"Kim B Kuchemüller, Jonas Austerjost, Rafael Machleid, Alena Roßkamp, Julia Niemann, Chris McCready","doi":"10.1007/s00449-026-03362-2","DOIUrl":"10.1007/s00449-026-03362-2","url":null,"abstract":"<p><p>A mechanistic model describing HEK293 cell growth and viral vector production was developed and calibrated for adenoviral processes and subsequently transferred to adeno‑associated and lentiviral cultures. The model represents key cellular states-viable, dead, and lysed cells-linked through substrate consumption, metabolic inhibition, and virus‑specific toxicity terms. By adjusting a limited set of parameters, the same mechanistic structure, combined with vector specific parameter sets, could accurately reproduce distinct infection and transfection dynamics, demonstrating cross‑platform applicability. As a demonstrator for real‑time deployment, the mechanistic framework was combined with an orthogonal projections to latent structures model based on dielectric spectroscopy data to form a Digital Shadow. The soft‑sensor layer provided real‑time viable cell density values that continuously updated the mechanistic simulation, yielding online predictions of culture growth and infection timing. Validation with adenoviral perfusion datasets confirmed high agreement between simulated and measured viable cell concentrations. This study demonstrates that transferable mechanistic models can serve as a robust foundation for hybrid digital systems in bioprocessing. The proposed Digital Shadow exemplifies how such models can be connected to inline monitoring tools for enhanced process understanding and decision support, paving the way toward closed‑loop Digital Twin applications in viral vector manufacturing.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2459-2470"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148257251","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}

{"title":"Simulating large-scale biotech bubble columns: challenges and insights from the parcel approach.","authors":"Carolin Link, Lars Puiman, Ralf Takors","doi":"10.1007/s00449-026-03397-5","DOIUrl":"10.1007/s00449-026-03397-5","url":null,"abstract":"<p><p>The growing industrial demand for economically attractive large-scale bioprocesses has increased the need for reliable and computationally feasible modelling approaches. Gas fermentation plays a particular role as the targeted commodities ask for large-scale solutions using bubble-column type bioreactors that allow them to benefit from the economy-of-scale. To reduce development efforts, large-scale designs increasingly build on computational fluid dynamics (CFD) simulations. State-of-the-art approaches employ finite-volume Reynolds-averaged Navier-Stokes (FV-RANS) methods that require enormous computational efforts. In contrast, Euler-Lagrange (E-L) approaches offer detailed local resolution as a prerequisite for optimum bioreactor design. By tracking individual bubbles, they predict bubble population dynamics while computations are parallelized. However, to cope with realistic bubble numbers, large-scale simulations typically make use of the so-called 'parcel size' approach, i.e. multiple bubbles are represented by a single computational particle. This study applies Lattice Boltzmann large eddy simulations (LB-LES) to illustrate the observed consequences: Swarm-like bubble behavior is found that results in inhomogeneous bubble distributions. As a consequence, the volumetric mass transfer coefficient k_La, a key criterion for design, may be biased. Comparing results with state-of-the-art FV-RANS simulations revealed similarities of transient flow structures and averaged velocity values. However, local deviations are found that mirror handling differences of turbulence representation and the impact of the parcel approach. The findings demonstrate the potential and current limitations of parcel-based modelling for large-scale bioreactors.</p>","PeriodicalId":9024,"journal":{"name":"Bioprocess and Biosystems Engineering","volume":" ","pages":"2441-2457"},"PeriodicalIF":4.3,"publicationDate":"2026-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13582231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148696925","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}